[SCM] The Molecular Modelling Toolkit packaging branch, master, updated. debian/2.7.8-1-5-g8a6e929
Picca Frédéric-Emmanuel
picca at debian.org
Sun Jun 16 12:38:35 UTC 2013
The following commit has been merged in the master branch:
commit cb69b215504b5cf2bc40035cf76407a54b33efa6
Author: Picca Frédéric-Emmanuel <picca at debian.org>
Date: Sun Jun 16 12:40:22 2013 +0200
Imported Upstream version 2.7.9
diff --git a/Doc/CHANGELOG b/Doc/CHANGELOG
index 790c246..52e8c78 100644
--- a/Doc/CHANGELOG
+++ b/Doc/CHANGELOG
@@ -1,3 +1,23 @@
+2.7.8 --> 2.7.9
+===============
+
+Improvements:
+
+- Allow a Collection to be constructed from a generator
+
+- Make Amber file parser more tolerant to accept more mod_files
+
+- More pdb_alternative atom names: GROMACS-style OC1/OC2 in
+ C-terminal peptide group
+
+- Compile C versions of extension modules if Cython is not installed
+
+Bug fixes:
+
+- Remove long delays when deallocating thread-based
+ energy evaluators
+
+
2.7.7 --> 2.7.8
===============
diff --git a/MMTK/Collections.py b/MMTK/Collections.py
index 318c9ef..a5f1b05 100644
--- a/MMTK/Collections.py
+++ b/MMTK/Collections.py
@@ -14,7 +14,7 @@ from MMTK.Geometry import superpositionFit
from Scientific.Geometry import Vector, Tensor, Objects3D
from Scientific.Geometry import Transformation
from Scientific import N
-import copy, itertools
+import copy, itertools, types
#
# This class defines groups of atoms. It is used as a base class
@@ -605,11 +605,16 @@ class Collection(GroupOfAtoms, Visualization.Viewable):
def __init__(self, *objects):
"""
- :param objects: a chemical object or a sequence of chemical objects that
- define the initial content of the collection.
+ :param objects: a chemical object or a sequence of or a generator
+ yielding chemical objects that define the initial
+ content of the collection.
"""
self.objects = []
- self.addObject(objects)
+ if len(objects) == 1 and isinstance(objects[0], types.GeneratorType):
+ for obj in objects[0]:
+ self.addObject(obj)
+ else:
+ self.addObject(objects)
is_collection = 1
diff --git a/MMTK/Database/Groups/peptide_ct b/MMTK/Database/Groups/peptide_ct
index 7bc1756..765cc34 100644
--- a/MMTK/Database/Groups/peptide_ct
+++ b/MMTK/Database/Groups/peptide_ct
@@ -9,5 +9,5 @@ bonds = [Bond(N, H), Bond(N, C_alpha), Bond(C_alpha, H_alpha), Bond(C_alpha, C),
pdbmap = [('', {'N': N, 'O': O, 'HA': H_alpha, 'CA': C_alpha, 'H': H, 'OXT': O_2, 'C': C, }, ), ]
amber_atom_type = {C: 'C', H: 'H', H_alpha: 'H1', O: 'O2', C_alpha: 'CT', O_2: 'O2', N: 'N', }
amber12_atom_type = {C: 'C', H: 'H', H_alpha: 'H1', O: 'O2', C_alpha: 'CX', O_2: 'O2', N: 'N', }
-pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', "O'": 'O', "O''": 'OXT', 'HA2': 'HA', '2HA': 'HA'}
+pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'OC1': 'O', 'OC2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', "O'": 'O', "O''": 'OXT', 'HA2': 'HA', '2HA': 'HA'}
name = 'peptide C terminus'
diff --git a/MMTK/Database/Groups/peptide_ct_noh b/MMTK/Database/Groups/peptide_ct_noh
index 64e5ac8..4aab58d 100644
--- a/MMTK/Database/Groups/peptide_ct_noh
+++ b/MMTK/Database/Groups/peptide_ct_noh
@@ -6,5 +6,5 @@ O_2 = Atom('O')
bonds = [Bond(N, C_alpha), Bond(C_alpha, C), Bond(C, O), Bond(C, O_2), ]
pdbmap = [('', {'C': C, 'O': O, 'CA': C_alpha, 'N': N, 'OXT': O_2, }, ), ]
amber_atom_type = {C: 'C', N: 'N', O: 'O2', C_alpha: 'CT', O_2: 'O2', }
-pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', }
+pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', 'OC2': 'OXT', 'OC1': 'O', }
name = 'peptide C terminus'
diff --git a/MMTK/Database/Groups/peptide_ct_uni b/MMTK/Database/Groups/peptide_ct_uni
index e805289..03b3461 100644
--- a/MMTK/Database/Groups/peptide_ct_uni
+++ b/MMTK/Database/Groups/peptide_ct_uni
@@ -9,5 +9,5 @@ pdbmap = [('', {'N': N, 'O': O, 'CA': C_alpha, 'C': C, 'H': H, 'OXT': O_2, }, ),
amber91_atom_type = {C_alpha: 'CH', O: 'O2', N: 'N', C: 'C', O_2: 'O2', H: 'H', }
opls_atom_type = {C_alpha: 'CH', O: 'O2', N: 'N', C: 'C', O_2: 'O2', H: 'H', }
opls_charge = {C_alpha: .1, O: -.8, N: -.57, C: .7, O_2: -.8, H: .37, }
-pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', }
+pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', 'OC2': 'OXT', 'OC1': 'O', }
name = 'peptide C terminus'
diff --git a/MMTK/Database/Groups/peptide_ct_uni2 b/MMTK/Database/Groups/peptide_ct_uni2
index c740777..9a091ec 100644
--- a/MMTK/Database/Groups/peptide_ct_uni2
+++ b/MMTK/Database/Groups/peptide_ct_uni2
@@ -7,5 +7,5 @@ O_2 = Atom('O')
bonds = [Bond(N, H), Bond(N, C_alpha), Bond(C_alpha, C), Bond(C, O), Bond(C, O_2), ]
pdbmap = [('', {'N': N, 'O': O, 'CA': C_alpha, 'C': C, 'H': H, 'OXT': O_2, }, ), ]
amber91_atom_type = {C_alpha: 'CH', O: 'O2', N: 'N', O_2: 'O2', C: 'C', H: 'H', }
-pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', }
+pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', 'OC2': 'OXT', 'OC1': 'O', }
name = 'peptide C terminus'
diff --git a/MMTK/Database/Groups/peptide_ct_uni3 b/MMTK/Database/Groups/peptide_ct_uni3
index e805289..03b3461 100644
--- a/MMTK/Database/Groups/peptide_ct_uni3
+++ b/MMTK/Database/Groups/peptide_ct_uni3
@@ -9,5 +9,5 @@ pdbmap = [('', {'N': N, 'O': O, 'CA': C_alpha, 'C': C, 'H': H, 'OXT': O_2, }, ),
amber91_atom_type = {C_alpha: 'CH', O: 'O2', N: 'N', C: 'C', O_2: 'O2', H: 'H', }
opls_atom_type = {C_alpha: 'CH', O: 'O2', N: 'N', C: 'C', O_2: 'O2', H: 'H', }
opls_charge = {C_alpha: .1, O: -.8, N: -.57, C: .7, O_2: -.8, H: .37, }
-pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', }
+pdb_alternative = {'O1': 'O', 'O2': 'OXT', 'HN': 'H', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', 'OC2': 'OXT', 'OC1': 'O', }
name = 'peptide C terminus'
diff --git a/MMTK/Database/Groups/peptide_nt_ct b/MMTK/Database/Groups/peptide_nt_ct
index 81c8b41..f89dabc 100644
--- a/MMTK/Database/Groups/peptide_nt_ct
+++ b/MMTK/Database/Groups/peptide_nt_ct
@@ -12,4 +12,4 @@ pdbmap = [('', {'N': N, 'O': O, '2HT': H_2, 'HA': H_alpha, 'CA': C_alpha, '1HT':
name = 'peptide N terminus/C terminus'
amber_atom_type = {H_3: 'H', C: 'C', O: 'O', H_alpha: 'HP', H_1: 'H', C_alpha: 'CT', H_2: 'H', N: 'N3', O_2: 'O2',}
amber12_atom_type = {H_3: 'H', C: 'C', O: 'O', H_alpha: 'HP', H_1: 'H', C_alpha: 'CX', H_2: 'H', N: 'N3', O_2: 'O2',}
-pdb_alternative = {'HT1': '1HT', 'HT2': '2HT', 'HT3': '3HT', 'H1': '1HT', 'H3': '3HT', 'H2': '2HT', '2HA': 'HA', 'HA2': 'HA', 'O2': 'OXT', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', "O'": 'O', "O''": 'OXT'}
+pdb_alternative = {'HT1': '1HT', 'HT2': '2HT', 'HT3': '3HT', 'H1': '1HT', 'H3': '3HT', 'H2': '2HT', '2HA': 'HA', 'HA2': 'HA', 'O2': 'OXT', 'OT': 'OXT', 'OT2': 'OXT', 'OT1': 'O', 'OC2': 'OXT', 'OC1': 'O', "O'": 'O', "O''": 'OXT'}
diff --git a/MMTK/ForceFields/Amber/AmberData.py b/MMTK/ForceFields/Amber/AmberData.py
index c17fb8f..71e7577 100644
--- a/MMTK/ForceFields/Amber/AmberData.py
+++ b/MMTK/ForceFields/Amber/AmberData.py
@@ -146,9 +146,6 @@ class AmberParameters(object):
line = file.readline().rstrip()
if not line: break
names, params = line[:11], line[11:]
- name1, name2, name3, name4 = [_normalizeName(n)
- for n in names.split('-')]
- name1, name2, name3, name4 = _sort4(name1, name2, name3, name4)
params = params.strip().split()[:4]
divf = int(params[0])
k = float(params[1])
@@ -158,6 +155,9 @@ class AmberParameters(object):
append.addTerm(divf, k, delta, n)
if n >= 0: append = None
else:
+ name1, name2, name3, name4 = [_normalizeName(name)
+ for name in names.split('-')]
+ name1, name2, name3, name4 = _sort4(name1, name2, name3, name4)
p = AmberDihedralParameters(self.atom_types[name1],
self.atom_types[name2],
self.atom_types[name3],
diff --git a/MMTK/Geometry.py b/MMTK/Geometry.py
index bac9c4d..cfcbed5 100644
--- a/MMTK/Geometry.py
+++ b/MMTK/Geometry.py
@@ -750,8 +750,8 @@ def superpositionFit(confs):
position for each atom
:type confs: sequence of (float, Vector, Vector)
:returns: the quaternion representing the rotation,
- the center of mass in the alternate configuraton,
the center of mass in the reference configuration,
+ the center of mass in the alternate configuraton,
and the RMS distance after the optimal superposition
"""
w_sum = 0.
diff --git a/MMTK/__pkginfo__.py b/MMTK/__pkginfo__.py
index a6a919c..cdda1d6 100644
--- a/MMTK/__pkginfo__.py
+++ b/MMTK/__pkginfo__.py
@@ -1,3 +1,3 @@
# Data used both in the package and by setup.py
-__version__ = '2.7.8'
+__version__ = '2.7.9'
diff --git a/Src/MMTK_forcefield.c b/Src/MMTK_forcefield.c
index c73e726..f5e2f61 100644
--- a/Src/MMTK_forcefield.c
+++ b/Src/MMTK_forcefield.c
@@ -502,12 +502,24 @@ evaluator_dealloc(PyFFEvaluatorObject *self)
for (i = 1; i < self->nthreads; i++) {
int j = 50;
tinfo->exit = 1;
+#if THREAD_DEBUG
+ printf("Releasing thread %d\n", tinfo->input.thread_id);
+#endif
PyThread_release_lock(tinfo->lock);
while (!tinfo->stop && j--) {
+#if THREAD_DEBUG
+ printf("evaluator_dealloc: Waiting for thread %d to stop (tinfo->stop is %d)\n",
+ tinfo->input.thread_id, tinfo->stop);
+#endif
#ifdef MS_WINDOWS
- Sleep(10);
+ Sleep(10); /* 10 ms */
#else
- sleep(10);
+ {
+ struct timeval tv;
+ tv.tv_sec = 0;
+ tv.tv_usec = 10000; /* 10 ms */
+ select(0, NULL, NULL, NULL, &tv);
+ }
#endif
}
Py_XDECREF(tinfo->energy.gradients);
diff --git a/Src/MMTK_restraints.c b/Src/MMTK_restraints.c
index 00adaa7..9cdc0e5 100644
--- a/Src/MMTK_restraints.c
+++ b/Src/MMTK_restraints.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Mon Jul 9 09:47:32 2012 */
+/* Generated by Cython 0.16 on Tue Oct 23 15:24:45 2012 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
diff --git a/Src/MMTK_trajectory_generator.c b/Src/MMTK_trajectory_generator.c
index 0d5c6ff..e84e34e 100644
--- a/Src/MMTK_trajectory_generator.c
+++ b/Src/MMTK_trajectory_generator.c
@@ -1,16 +1,16 @@
-/* Generated by Cython 0.15 on Wed Dec 14 16:44:42 2011 */
+/* Generated by Cython 0.17.3 on Thu May 23 17:58:18 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -22,36 +22,47 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
-#if PY_VERSION_HEX < 0x02040000
- #define METH_COEXIST 0
- #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
- #define PyDict_Contains(d,o) PySequence_Contains(d,o)
+#ifndef Py_HUGE_VAL
+ #define Py_HUGE_VAL HUGE_VAL
+#endif
+#ifdef PYPY_VERSION
+#define CYTHON_COMPILING_IN_PYPY 1
+#define CYTHON_COMPILING_IN_CPYTHON 0
+#else
+#define CYTHON_COMPILING_IN_PYPY 0
+#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -59,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -73,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -83,24 +92,44 @@
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
-
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#endif
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -108,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -127,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -135,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -154,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -167,16 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -195,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -209,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -218,6 +228,15 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
@@ -271,7 +290,7 @@
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
@@ -295,8 +314,12 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
-
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
/* Test for GCC > 2.95 */
@@ -321,7 +344,6 @@ static int __pyx_clineno = 0;
static const char * __pyx_cfilenm= __FILE__;
static const char *__pyx_filename;
-
#if !defined(CYTHON_CCOMPLEX)
#if defined(__cplusplus)
#define CYTHON_CCOMPLEX 1
@@ -331,7 +353,6 @@ static const char *__pyx_filename;
#define CYTHON_CCOMPLEX 0
#endif
#endif
-
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#include <complex>
@@ -339,27 +360,56 @@ static const char *__pyx_filename;
#include <complex.h>
#endif
#endif
-
#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
#undef _Complex_I
#define _Complex_I 1.0fj
#endif
+
static const char *__pyx_f[] = {
"MMTK_trajectory_generator.pyx",
"numpy.pxd",
"numeric.pxi",
"forcefield.pxi",
+ "type.pxd",
};
+#define IS_UNSIGNED(type) (((type) -1) > 0)
+struct __Pyx_StructField_;
+#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
+typedef struct {
+ const char* name; /* for error messages only */
+ struct __Pyx_StructField_* fields;
+ size_t size; /* sizeof(type) */
+ size_t arraysize[8]; /* length of array in each dimension */
+ int ndim;
+ char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */
+ char is_unsigned;
+ int flags;
+} __Pyx_TypeInfo;
+typedef struct __Pyx_StructField_ {
+ __Pyx_TypeInfo* type;
+ const char* name;
+ size_t offset;
+} __Pyx_StructField;
+typedef struct {
+ __Pyx_StructField* field;
+ size_t parent_offset;
+} __Pyx_BufFmt_StackElem;
+typedef struct {
+ __Pyx_StructField root;
+ __Pyx_BufFmt_StackElem* head;
+ size_t fmt_offset;
+ size_t new_count, enc_count;
+ size_t struct_alignment;
+ int is_complex;
+ char enc_type;
+ char new_packmode;
+ char enc_packmode;
+ char is_valid_array;
+} __Pyx_BufFmt_Context;
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds);
-
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-/* "numpy.pxd":719
+/* "numpy.pxd":723
* # in Cython to enable them only on the right systems.
*
* ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
@@ -368,7 +418,7 @@ typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
*/
typedef npy_int8 __pyx_t_5numpy_int8_t;
-/* "numpy.pxd":720
+/* "numpy.pxd":724
*
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
@@ -377,7 +427,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t;
*/
typedef npy_int16 __pyx_t_5numpy_int16_t;
-/* "numpy.pxd":721
+/* "numpy.pxd":725
* ctypedef npy_int8 int8_t
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
@@ -386,7 +436,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t;
*/
typedef npy_int32 __pyx_t_5numpy_int32_t;
-/* "numpy.pxd":722
+/* "numpy.pxd":726
* ctypedef npy_int16 int16_t
* ctypedef npy_int32 int32_t
* ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
@@ -395,7 +445,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t;
*/
typedef npy_int64 __pyx_t_5numpy_int64_t;
-/* "numpy.pxd":726
+/* "numpy.pxd":730
* #ctypedef npy_int128 int128_t
*
* ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
@@ -404,7 +454,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t;
*/
typedef npy_uint8 __pyx_t_5numpy_uint8_t;
-/* "numpy.pxd":727
+/* "numpy.pxd":731
*
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
@@ -413,7 +463,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t;
*/
typedef npy_uint16 __pyx_t_5numpy_uint16_t;
-/* "numpy.pxd":728
+/* "numpy.pxd":732
* ctypedef npy_uint8 uint8_t
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
@@ -422,7 +472,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t;
*/
typedef npy_uint32 __pyx_t_5numpy_uint32_t;
-/* "numpy.pxd":729
+/* "numpy.pxd":733
* ctypedef npy_uint16 uint16_t
* ctypedef npy_uint32 uint32_t
* ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
@@ -431,7 +481,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t;
*/
typedef npy_uint64 __pyx_t_5numpy_uint64_t;
-/* "numpy.pxd":733
+/* "numpy.pxd":737
* #ctypedef npy_uint128 uint128_t
*
* ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
@@ -440,7 +490,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t;
*/
typedef npy_float32 __pyx_t_5numpy_float32_t;
-/* "numpy.pxd":734
+/* "numpy.pxd":738
*
* ctypedef npy_float32 float32_t
* ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
@@ -449,7 +499,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t;
*/
typedef npy_float64 __pyx_t_5numpy_float64_t;
-/* "numpy.pxd":743
+/* "numpy.pxd":747
* # The int types are mapped a bit surprising --
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t # <<<<<<<<<<<<<<
@@ -458,7 +508,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t;
*/
typedef npy_long __pyx_t_5numpy_int_t;
-/* "numpy.pxd":744
+/* "numpy.pxd":748
* # numpy.int corresponds to 'l' and numpy.long to 'q'
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
@@ -467,7 +517,7 @@ typedef npy_long __pyx_t_5numpy_int_t;
*/
typedef npy_longlong __pyx_t_5numpy_long_t;
-/* "numpy.pxd":745
+/* "numpy.pxd":749
* ctypedef npy_long int_t
* ctypedef npy_longlong long_t
* ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
@@ -476,7 +526,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t;
*/
typedef npy_longlong __pyx_t_5numpy_longlong_t;
-/* "numpy.pxd":747
+/* "numpy.pxd":751
* ctypedef npy_longlong longlong_t
*
* ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
@@ -485,7 +535,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t;
*/
typedef npy_ulong __pyx_t_5numpy_uint_t;
-/* "numpy.pxd":748
+/* "numpy.pxd":752
*
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
@@ -494,7 +544,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
-/* "numpy.pxd":749
+/* "numpy.pxd":753
* ctypedef npy_ulong uint_t
* ctypedef npy_ulonglong ulong_t
* ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
@@ -503,7 +553,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
*/
typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
-/* "numpy.pxd":751
+/* "numpy.pxd":755
* ctypedef npy_ulonglong ulonglong_t
*
* ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
@@ -512,7 +562,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
*/
typedef npy_intp __pyx_t_5numpy_intp_t;
-/* "numpy.pxd":752
+/* "numpy.pxd":756
*
* ctypedef npy_intp intp_t
* ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
@@ -521,7 +571,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t;
*/
typedef npy_uintp __pyx_t_5numpy_uintp_t;
-/* "numpy.pxd":754
+/* "numpy.pxd":758
* ctypedef npy_uintp uintp_t
*
* ctypedef npy_double float_t # <<<<<<<<<<<<<<
@@ -530,7 +580,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t;
*/
typedef npy_double __pyx_t_5numpy_float_t;
-/* "numpy.pxd":755
+/* "numpy.pxd":759
*
* ctypedef npy_double float_t
* ctypedef npy_double double_t # <<<<<<<<<<<<<<
@@ -539,7 +589,7 @@ typedef npy_double __pyx_t_5numpy_float_t;
*/
typedef npy_double __pyx_t_5numpy_double_t;
-/* "numpy.pxd":756
+/* "numpy.pxd":760
* ctypedef npy_double float_t
* ctypedef npy_double double_t
* ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
@@ -547,7 +597,6 @@ typedef npy_double __pyx_t_5numpy_double_t;
* ctypedef npy_cfloat cfloat_t
*/
typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
-
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
typedef ::std::complex< float > __pyx_t_float_complex;
@@ -568,14 +617,14 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
typedef struct { double real, imag; } __pyx_t_double_complex;
#endif
+
/*--- Type declarations ---*/
struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator;
struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator;
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString;
-struct __pyx_Generator_object;
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr;
-/* "numpy.pxd":758
+/* "numpy.pxd":762
* ctypedef npy_longdouble longdouble_t
*
* ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
@@ -584,7 +633,7 @@ struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr;
*/
typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
-/* "numpy.pxd":759
+/* "numpy.pxd":763
*
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
@@ -593,7 +642,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
*/
typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
-/* "numpy.pxd":760
+/* "numpy.pxd":764
* ctypedef npy_cfloat cfloat_t
* ctypedef npy_cdouble cdouble_t
* ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
@@ -602,7 +651,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
*/
typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
-/* "numpy.pxd":762
+/* "numpy.pxd":766
* ctypedef npy_clongdouble clongdouble_t
*
* ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<<
@@ -702,7 +751,7 @@ struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString {
PyObject_HEAD
PyObject *__pyx_v_options;
- PyObject *__pyx_v_self;
+ struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self;
};
@@ -713,18 +762,8 @@ struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString {
* '')[:-2]
*
*/
-struct __pyx_Generator_object {
- PyObject_HEAD
- __pyx_generator_body_t body;
- int is_running;
- int resume_label;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
-};
-
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr {
- struct __pyx_Generator_object __pyx_base;
+ PyObject_HEAD
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *__pyx_outer_scope;
PyObject *__pyx_v_o;
PyObject *__pyx_t_0;
@@ -774,12 +813,9 @@ struct __pyx_vtabstruct_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerat
void (*calculateEnergies)(struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *, PyArrayObject *, energy_data *, struct __pyx_opt_args_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_calculateEnergies *__pyx_optional_args);
};
static struct __pyx_vtabstruct_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *__pyx_vtabptr_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator;
-
-
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
-
#if CYTHON_REFNANNY
typedef struct {
void (*INCREF)(void*, PyObject*, int);
@@ -792,8 +828,21 @@ static struct __pyx_vtabstruct_25MMTK_trajectory_generator_EnergyBasedTrajectory
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
- #define __Pyx_RefNannySetupContext(name) __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
- #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+#ifdef WITH_THREAD
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ if (acquire_gil) { \
+ PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ PyGILState_Release(__pyx_gilstate_save); \
+ } else { \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ }
+#else
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+#endif
+ #define __Pyx_RefNannyFinishContext() \
+ __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
#define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
@@ -804,7 +853,7 @@ static struct __pyx_vtabstruct_25MMTK_trajectory_generator_EnergyBasedTrajectory
#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
#define __Pyx_RefNannyDeclarations
- #define __Pyx_RefNannySetupContext(name)
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)
#define __Pyx_RefNannyFinishContext()
#define __Pyx_INCREF(r) Py_INCREF(r)
#define __Pyx_DECREF(r) Py_DECREF(r)
@@ -815,19 +864,38 @@ static struct __pyx_vtabstruct_25MMTK_trajectory_generator_EnergyBasedTrajectory
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -835,16 +903,14 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname);
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
- const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (PyList_Append(L, x) < 0) return NULL;
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- }
- else {
+ } else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -856,54 +922,52 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-/* Run-time type information about structs used with buffers */
-struct __Pyx_StructField_;
-
-typedef struct {
- const char* name; /* for error messages only */
- struct __Pyx_StructField_* fields;
- size_t size; /* sizeof(type) */
- char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject */
-} __Pyx_TypeInfo;
-
-typedef struct __Pyx_StructField_ {
- __Pyx_TypeInfo* type;
- const char* name;
- size_t offset;
-} __Pyx_StructField;
-
-typedef struct {
- __Pyx_StructField* field;
- size_t parent_offset;
-} __Pyx_BufFmt_StackElem;
-
-
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
+static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj,
+ __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-
static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
-static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
+
+typedef struct {
+ Py_ssize_t shape, strides, suboffsets;
+} __Pyx_Buf_DimInfo;
+typedef struct {
+ size_t refcount;
+ Py_buffer pybuffer;
+} __Pyx_Buffer;
+typedef struct {
+ __Pyx_Buffer *rcbuffer;
+ char *data;
+ __Pyx_Buf_DimInfo diminfo[8];
+} __Pyx_LocalBuf_ND;
+
#if PY_MAJOR_VERSION < 3
-static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
-static void __Pyx_ReleaseBuffer(Py_buffer *view);
+ static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+ static void __Pyx_ReleaseBuffer(Py_buffer *view);
#else
-#define __Pyx_GetBuffer PyObject_GetBuffer
-#define __Pyx_ReleaseBuffer PyBuffer_Release
+ #define __Pyx_GetBuffer PyObject_GetBuffer
+ #define __Pyx_ReleaseBuffer PyBuffer_Release
#endif
-Py_ssize_t __Pyx_zeros[] = {0, 0};
-Py_ssize_t __Pyx_minusones[] = {-1, -1};
+
+static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
+static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
+
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
#define __Pyx_CREAL(z) ((z).real())
@@ -916,7 +980,6 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level);
#define __Pyx_CREAL(z) ((z).real)
#define __Pyx_CIMAG(z) ((z).imag)
#endif
-
#if defined(_WIN32) && defined(__cplusplus) && CYTHON_CCOMPLEX
#define __Pyx_SET_CREAL(z,x) ((z).real(x))
#define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
@@ -1037,19 +1100,69 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+#define __Pyx_Generator_USED
+#include <structmember.h>
+#include <frameobject.h>
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+typedef struct {
+ PyObject_HEAD
+ __pyx_generator_body_t body;
+ PyObject *closure;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+ PyObject *gi_weakreflist;
+ PyObject *classobj;
+ PyObject *yieldfrom;
+ int resume_label;
+ char is_running; // using T_BOOL for property below requires char value
+} __pyx_GeneratorObject;
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure);
+static int __pyx_Generator_init(void);
+static int __Pyx_Generator_clear(PyObject* self);
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
+#else
+#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
+#endif
+
static int __Pyx_check_binary_version(void);
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
- int __pyx_lineno, const char *__pyx_filename); /*proto*/
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+
/* Module declarations from 'cpython.buffer' */
/* Module declarations from 'cpython.ref' */
@@ -1058,6 +1171,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.object' */
+/* Module declarations from '__builtin__' */
+
+/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
+
/* Module declarations from 'libc.stdlib' */
/* Module declarations from 'numpy' */
@@ -1068,21 +1186,12 @@ static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *, PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *, PyObject *, PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *, PyObject *, PyObject *, PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *, PyObject *, PyObject *, PyObject *, PyObject *); /*proto*/
static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
-static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *, PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *); /*proto*/
/* Module declarations from 'Scientific.N' */
/* Module declarations from 'MMTK_forcefield' */
-/* Module declarations from 'cython.cython.view' */
-
/* Module declarations from 'cython' */
/* Module declarations from 'MMTK_trajectory_generator' */
@@ -1091,9 +1200,8 @@ static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator_EnergyTerm = 0;
static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator_TrajectoryGenerator = 0;
static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator = 0;
static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct__optionString = 0;
-static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator___pyx_Generator = 0;
static PyTypeObject *__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr = 0;
-static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), 'R' };
+static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 };
#define __Pyx_MODULE_NAME "MMTK_trajectory_generator"
int __pyx_module_is_main_MMTK_trajectory_generator = 0;
@@ -1104,6 +1212,27 @@ static PyObject *__pyx_builtin_sum;
static PyObject *__pyx_builtin_MemoryError;
static PyObject *__pyx_builtin_range;
static PyObject *__pyx_builtin_RuntimeError;
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_universe, PyObject *__pyx_v_options, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2setCallOptions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getActions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6cleanupActions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8getOption(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_option); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_10optionString(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12__call__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14start_py(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__set__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_4__del__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self); /* proto */
+static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__(struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_universe, PyObject *__pyx_v_options, PyObject *__pyx_v_name); /* proto */
+static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
static char __pyx_k_2[] = "getSpecificationList";
static char __pyx_k_3[] = "undefined option: ";
static char __pyx_k_4[] = "=";
@@ -1243,67 +1372,57 @@ static PyObject *__pyx_k_tuple_26;
static PyObject *__pyx_k_tuple_27;
static PyObject *__pyx_k_tuple_29;
-/* "MMTK_trajectory_generator.pyx":33
- * """
- *
- * def __init__(self, universe, options, name): # <<<<<<<<<<<<<<
- * self.universe = universe
- * self.options = options
- */
-
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_universe = 0;
PyObject *__pyx_v_options = 0;
PyObject *__pyx_v_name = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__universe,&__pyx_n_s__options,&__pyx_n_s__name,0};
- __Pyx_RefNannySetupContext("__init__");
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ {
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__universe,&__pyx_n_s__options,&__pyx_n_s__name,0};
PyObject* values[3] = {0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__universe);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__options);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
}
- case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name);
- if (likely(values[2])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__universe)) != 0)) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__options)) != 0)) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 2:
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name)) != 0)) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
}
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 33; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
}
__pyx_v_universe = values[0];
__pyx_v_options = values[1];
__pyx_v_name = values[2];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_universe = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_options = PyTuple_GET_ITEM(__pyx_args, 1);
- __pyx_v_name = PyTuple_GET_ITEM(__pyx_args, 2);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
@@ -1313,6 +1432,27 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), __pyx_v_universe, __pyx_v_options, __pyx_v_name);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "MMTK_trajectory_generator.pyx":33
+ * """
+ *
+ * def __init__(self, universe, options, name): # <<<<<<<<<<<<<<
+ * self.universe = universe
+ * self.options = options
+ */
+
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_universe, PyObject *__pyx_v_options, PyObject *__pyx_v_name) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_RefNannySetupContext("__init__", 0);
/* "MMTK_trajectory_generator.pyx":34
*
@@ -1323,9 +1463,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
*/
__Pyx_INCREF(__pyx_v_universe);
__Pyx_GIVEREF(__pyx_v_universe);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe = __pyx_v_universe;
+ __Pyx_GOTREF(__pyx_v_self->universe);
+ __Pyx_DECREF(__pyx_v_self->universe);
+ __pyx_v_self->universe = __pyx_v_universe;
/* "MMTK_trajectory_generator.pyx":35
* def __init__(self, universe, options, name):
@@ -1336,9 +1476,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
*/
__Pyx_INCREF(__pyx_v_options);
__Pyx_GIVEREF(__pyx_v_options);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options = __pyx_v_options;
+ __Pyx_GOTREF(__pyx_v_self->options);
+ __Pyx_DECREF(__pyx_v_self->options);
+ __pyx_v_self->options = __pyx_v_options;
/* "MMTK_trajectory_generator.pyx":36
* self.universe = universe
@@ -1349,9 +1489,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
*/
__Pyx_INCREF(__pyx_v_name);
__Pyx_GIVEREF(__pyx_v_name);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->name);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->name);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->name = __pyx_v_name;
+ __Pyx_GOTREF(__pyx_v_self->name);
+ __Pyx_DECREF(__pyx_v_self->name);
+ __pyx_v_self->name = __pyx_v_name;
/* "MMTK_trajectory_generator.pyx":37
* self.options = options
@@ -1363,9 +1503,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options = ((PyObject *)__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_self->call_options);
+ __Pyx_DECREF(__pyx_v_self->call_options);
+ __pyx_v_self->call_options = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":38
@@ -1376,11 +1516,11 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
* self.tspec = NULL
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->features);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->features);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->features = ((PyObject *)__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_self->features);
+ __Pyx_DECREF(__pyx_v_self->features);
+ __pyx_v_self->features = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":39
@@ -1390,7 +1530,7 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
* self.tspec = NULL
*
*/
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->tvars = NULL;
+ __pyx_v_self->tvars = NULL;
/* "MMTK_trajectory_generator.pyx":40
* self.features = []
@@ -1399,7 +1539,7 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
*
* def setCallOptions(self, options):
*/
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->tspec = NULL;
+ __pyx_v_self->tspec = NULL;
__pyx_r = 0;
goto __pyx_L0;
@@ -1412,6 +1552,17 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_3setCallOptions(PyObject *__pyx_v_self, PyObject *__pyx_v_options); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_3setCallOptions(PyObject *__pyx_v_self, PyObject *__pyx_v_options) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("setCallOptions (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2setCallOptions(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyObject *)__pyx_v_options));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":42
* self.tspec = NULL
*
@@ -1420,11 +1571,10 @@ static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__(P
*
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1setCallOptions(PyObject *__pyx_v_self, PyObject *__pyx_v_options); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1setCallOptions(PyObject *__pyx_v_self, PyObject *__pyx_v_options) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2setCallOptions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("setCallOptions");
+ __Pyx_RefNannySetupContext("setCallOptions", 0);
/* "MMTK_trajectory_generator.pyx":43
*
@@ -1435,9 +1585,9 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1set
*/
__Pyx_INCREF(__pyx_v_options);
__Pyx_GIVEREF(__pyx_v_options);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options = __pyx_v_options;
+ __Pyx_GOTREF(__pyx_v_self->call_options);
+ __Pyx_DECREF(__pyx_v_self->call_options);
+ __pyx_v_self->call_options = __pyx_v_options;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -1445,6 +1595,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1set
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_5getActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_5getActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("getActions (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getActions(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":45
* self.call_options = options
*
@@ -1453,8 +1614,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1set
* steps = self.getOption('steps')
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2getActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2getActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getActions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_v_steps = NULL;
PyObject *__pyx_v_a = NULL;
PyObject *__pyx_r = NULL;
@@ -1473,7 +1633,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("getActions");
+ __Pyx_RefNannySetupContext("getActions", 0);
/* "MMTK_trajectory_generator.pyx":46
*
@@ -1496,9 +1656,9 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
* except ValueError:
* steps = None
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__getOption); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__getOption); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_k_tuple_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_k_tuple_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_steps = __pyx_t_5;
@@ -1507,8 +1667,8 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L12_try_end;
- __pyx_L5_error:;
+ goto __pyx_L10_try_end;
+ __pyx_L3_error:;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -1522,7 +1682,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
__pyx_t_6 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_6) {
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.getActions", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_4, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_4, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_7);
@@ -1540,20 +1700,20 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- goto __pyx_L6_exception_handled;
+ goto __pyx_L4_exception_handled;
}
- __pyx_L7_except_error:;
+ __pyx_L5_except_error:;
__Pyx_XGIVEREF(__pyx_t_1);
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
goto __pyx_L1_error;
- __pyx_L6_exception_handled:;
+ __pyx_L4_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_1);
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
- __pyx_L12_try_end:;
+ __pyx_L10_try_end:;
}
/* "MMTK_trajectory_generator.pyx":50
@@ -1565,22 +1725,30 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyList_CheckExact(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions) || PyTuple_CheckExact(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions)) {
- __pyx_t_4 = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions; __Pyx_INCREF(__pyx_t_4); __pyx_t_8 = 0;
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyList_CheckExact(__pyx_v_self->actions) || PyTuple_CheckExact(__pyx_v_self->actions)) {
+ __pyx_t_4 = __pyx_v_self->actions; __Pyx_INCREF(__pyx_t_4); __pyx_t_8 = 0;
__pyx_t_9 = NULL;
} else {
- __pyx_t_8 = -1; __pyx_t_4 = PyObject_GetIter(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_self->actions); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_9 = Py_TYPE(__pyx_t_4)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_4)) {
+ if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++;
- } else if (PyTuple_CheckExact(__pyx_t_4)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_4, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_5 = __pyx_t_9(__pyx_t_4);
if (unlikely(!__pyx_t_5)) {
@@ -1598,10 +1766,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
__pyx_t_5 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s_2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
__Pyx_INCREF(__pyx_v_steps);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_steps);
__Pyx_GIVEREF(__pyx_v_steps);
@@ -1609,7 +1777,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- if (unlikely(PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_11))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_11))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
@@ -1636,6 +1804,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7cleanupActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7cleanupActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("cleanupActions (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6cleanupActions(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":52
* return [a.getSpecificationList(self, steps) for a in self.actions]
*
@@ -1644,8 +1823,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2get
* a.cleanup()
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cleanupActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cleanupActions(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6cleanupActions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_v_a = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -1657,7 +1835,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cle
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("cleanupActions");
+ __Pyx_RefNannySetupContext("cleanupActions", 0);
/* "MMTK_trajectory_generator.pyx":53
*
@@ -1666,21 +1844,29 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cle
* a.cleanup()
*
*/
- if (PyList_CheckExact(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions) || PyTuple_CheckExact(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions)) {
- __pyx_t_1 = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
+ if (PyList_CheckExact(__pyx_v_self->actions) || PyTuple_CheckExact(__pyx_v_self->actions)) {
+ __pyx_t_1 = __pyx_v_self->actions; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
__pyx_t_3 = NULL;
} else {
- __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_self->actions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
@@ -1727,6 +1913,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cle
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_9getOption(PyObject *__pyx_v_self, PyObject *__pyx_v_option); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_9getOption(PyObject *__pyx_v_self, PyObject *__pyx_v_option) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("getOption (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8getOption(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyObject *)__pyx_v_option));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":56
* a.cleanup()
*
@@ -1735,8 +1932,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cle
* value = self.call_options[option]
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getOption(PyObject *__pyx_v_self, PyObject *__pyx_v_option); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getOption(PyObject *__pyx_v_self, PyObject *__pyx_v_option) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8getOption(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_option) {
PyObject *__pyx_v_value = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -1764,7 +1960,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("getOption");
+ __Pyx_RefNannySetupContext("getOption", 0);
/* "MMTK_trajectory_generator.pyx":57
*
@@ -1787,7 +1983,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
* except KeyError:
* try:
*/
- __pyx_t_4 = PyObject_GetItem(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options, __pyx_v_option); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_4 = PyObject_GetItem(__pyx_v_self->call_options, __pyx_v_option); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_v_value = __pyx_t_4;
__pyx_t_4 = 0;
@@ -1795,8 +1991,8 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L12_try_end;
- __pyx_L5_error:;
+ goto __pyx_L10_try_end;
+ __pyx_L3_error:;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
/* "MMTK_trajectory_generator.pyx":59
@@ -1809,7 +2005,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__pyx_t_5 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_5) {
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.getOption", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_6, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_6, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_7);
@@ -1835,7 +2031,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
* except KeyError:
* try:
*/
- __pyx_t_11 = PyObject_GetItem(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options, __pyx_v_option); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_11 = PyObject_GetItem(__pyx_v_self->options, __pyx_v_option); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_11;
@@ -1844,8 +2040,8 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L22_try_end;
- __pyx_L15_error:;
+ goto __pyx_L20_try_end;
+ __pyx_L13_error:;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
/* "MMTK_trajectory_generator.pyx":62
@@ -1858,7 +2054,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__pyx_t_5 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_5) {
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.getOption", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ if (__Pyx_GetException(&__pyx_t_11, &__pyx_t_12, &__pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_GOTREF(__pyx_t_12);
__Pyx_GOTREF(__pyx_t_13);
@@ -1884,9 +2080,9 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
* except KeyError:
* raise ValueError('undefined option: ' + option)
*/
- __pyx_t_17 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__default_options); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L25_error;}
+ __pyx_t_17 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__default_options); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L23_error;}
__Pyx_GOTREF(__pyx_t_17);
- __pyx_t_18 = PyObject_GetItem(__pyx_t_17, __pyx_v_option); if (!__pyx_t_18) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L25_error;}
+ __pyx_t_18 = PyObject_GetItem(__pyx_t_17, __pyx_v_option); if (!__pyx_t_18) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L23_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_v_value);
@@ -1896,8 +2092,8 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_XDECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- goto __pyx_L32_try_end;
- __pyx_L25_error:;
+ goto __pyx_L30_try_end;
+ __pyx_L23_error:;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
@@ -1911,7 +2107,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__pyx_t_5 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_5) {
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.getOption", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_18, &__pyx_t_17, &__pyx_t_19) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L27_except_error;}
+ if (__Pyx_GetException(&__pyx_t_18, &__pyx_t_17, &__pyx_t_19) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L25_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_GOTREF(__pyx_t_17);
__Pyx_GOTREF(__pyx_t_19);
@@ -1923,72 +2119,72 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
* return value
*
*/
- __pyx_t_20 = PyNumber_Add(((PyObject *)__pyx_kp_s_3), __pyx_v_option); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L27_except_error;}
+ __pyx_t_20 = PyNumber_Add(((PyObject *)__pyx_kp_s_3), __pyx_v_option); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L25_except_error;}
__Pyx_GOTREF(__pyx_t_20);
- __pyx_t_21 = PyTuple_New(1); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L27_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_21));
+ __pyx_t_21 = PyTuple_New(1); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L25_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_20);
__Pyx_GIVEREF(__pyx_t_20);
__pyx_t_20 = 0;
- __pyx_t_20 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L27_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L25_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
__Pyx_Raise(__pyx_t_20, 0, 0, 0);
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L27_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L25_except_error;}
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- goto __pyx_L26_exception_handled;
+ goto __pyx_L24_exception_handled;
}
- __pyx_L27_except_error:;
+ __pyx_L25_except_error:;
__Pyx_XGIVEREF(__pyx_t_14);
__Pyx_XGIVEREF(__pyx_t_15);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16);
- goto __pyx_L17_except_error;
- __pyx_L26_exception_handled:;
+ goto __pyx_L15_except_error;
+ __pyx_L24_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_14);
__Pyx_XGIVEREF(__pyx_t_15);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_14, __pyx_t_15, __pyx_t_16);
- __pyx_L32_try_end:;
+ __pyx_L30_try_end:;
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- goto __pyx_L16_exception_handled;
+ goto __pyx_L14_exception_handled;
}
- __pyx_L17_except_error:;
+ __pyx_L15_except_error:;
__Pyx_XGIVEREF(__pyx_t_8);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10);
- goto __pyx_L7_except_error;
- __pyx_L16_exception_handled:;
+ goto __pyx_L5_except_error;
+ __pyx_L14_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_8);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_ExceptionReset(__pyx_t_8, __pyx_t_9, __pyx_t_10);
- __pyx_L22_try_end:;
+ __pyx_L20_try_end:;
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- goto __pyx_L6_exception_handled;
+ goto __pyx_L4_exception_handled;
}
- __pyx_L7_except_error:;
+ __pyx_L5_except_error:;
__Pyx_XGIVEREF(__pyx_t_1);
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
goto __pyx_L1_error;
- __pyx_L6_exception_handled:;
+ __pyx_L4_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_1);
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_1, __pyx_t_2, __pyx_t_3);
- __pyx_L12_try_end:;
+ __pyx_L10_try_end:;
}
/* "MMTK_trajectory_generator.pyx":67
@@ -2025,7 +2221,18 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4get
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
+
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_11optionString(PyObject *__pyx_v_self, PyObject *__pyx_v_options); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_11optionString(PyObject *__pyx_v_self, PyObject *__pyx_v_options) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("optionString (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_10optionString(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyObject *)__pyx_v_options));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+static PyObject *__pyx_gb_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
/* "MMTK_trajectory_generator.pyx":70
*
@@ -2035,37 +2242,45 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
*
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_12optionString_genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_12optionString_genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_genexpr(PyObject *__pyx_self) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("genexpr");
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_RefNannySetupContext("genexpr", 0);
__pyx_cur_scope = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
- __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *)__pyx_self;
+ __pyx_cur_scope->__pyx_outer_scope = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *) __pyx_self;
__Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope));
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope);
- __pyx_self = __pyx_self;
- __pyx_cur_scope->__pyx_base.resume_label = 0;
- __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_25MMTK_trajectory_generator_12optionString_1generator;
- __Pyx_GIVEREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) __pyx_cur_scope;
+ {
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_2generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) gen;
+ }
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.optionString.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_2generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
{
+ struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
Py_ssize_t __pyx_t_2;
@@ -2075,8 +2290,8 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
PyObject *__pyx_t_6 = NULL;
PyObject *__pyx_t_7 = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("25MMTK_trajectory_generator_12optionString_1generator");
- switch (__pyx_cur_scope->__pyx_base.resume_label) {
+ __Pyx_RefNannySetupContext("None", 0);
+ switch (__pyx_generator->resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
@@ -2085,7 +2300,8 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
}
__pyx_L3_first_run:;
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options)) { __Pyx_RaiseClosureNameError("options"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }if (PyList_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options)) {
+ if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options)) { __Pyx_RaiseClosureNameError("options"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (PyList_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_options)) {
__pyx_t_1 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_options; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
__pyx_t_3 = NULL;
} else {
@@ -2094,12 +2310,20 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
__pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
@@ -2118,10 +2342,11 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
__pyx_t_4 = 0;
__pyx_t_4 = PyNumber_Add(__pyx_cur_scope->__pyx_v_o, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_self)) { __Pyx_RaiseClosureNameError("self"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_5 = PyObject_GetAttr(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_self, __pyx_n_s__getOption); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_self)) { __Pyx_RaiseClosureNameError("self"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_cur_scope->__pyx_outer_scope->__pyx_v_self), __pyx_n_s__getOption); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_o);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_cur_scope->__pyx_v_o);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_o);
@@ -2148,7 +2373,7 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_cur_scope->__pyx_base.resume_label = 1;
+ __pyx_generator->resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
@@ -2159,7 +2384,7 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetNone(PyExc_StopIteration);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
@@ -2170,7 +2395,8 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_cur_scope->__pyx_base.resume_label = -1;
+ __pyx_generator->resume_label = -1;
+ __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
@@ -2183,8 +2409,7 @@ static PyObject *__pyx_gb_25MMTK_trajectory_generator_12optionString_1generator(
* '')[:-2]
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5optionString(PyObject *__pyx_v_self, PyObject *__pyx_v_options); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5optionString(PyObject *__pyx_v_self, PyObject *__pyx_v_options) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_10optionString(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -2193,18 +2418,18 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5opt
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("optionString");
+ __Pyx_RefNannySetupContext("optionString", 0);
__pyx_cur_scope = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *)__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct__optionString->tp_new(__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct__optionString, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
- __Pyx_INCREF(__pyx_v_self);
__pyx_cur_scope->__pyx_v_self = __pyx_v_self;
- __Pyx_INCREF(__pyx_v_options);
- __pyx_cur_scope->__pyx_v_options = __pyx_v_options;
+ __Pyx_INCREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
__Pyx_GIVEREF((PyObject *)__pyx_cur_scope->__pyx_v_self);
+ __pyx_cur_scope->__pyx_v_options = __pyx_v_options;
+ __Pyx_INCREF(__pyx_cur_scope->__pyx_v_options);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_options);
/* "MMTK_trajectory_generator.pyx":70
@@ -2223,10 +2448,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5opt
*
* def __call__(self, **options):
*/
- __pyx_t_1 = __pyx_pf_25MMTK_trajectory_generator_12optionString_genexpr(((PyObject*)__pyx_cur_scope), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12optionString_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
@@ -2257,6 +2482,25 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5opt
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_13__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_13__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_options = 0;
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__call__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return NULL;}
+ if (__pyx_kwds && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__call__", 1))) return NULL;
+ __pyx_v_options = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_options)) return NULL;
+ __Pyx_GOTREF(__pyx_v_options);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12__call__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), __pyx_v_options);
+ __Pyx_XDECREF(__pyx_v_options);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":73
* '')[:-2]
*
@@ -2265,9 +2509,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5opt
* try:
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_options = 0;
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12__call__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_options) {
PyObject *__pyx_v_MMTK_state_accessor = NULL;
PyObject *__pyx_v_configuration = NULL;
PyObject *__pyx_v_masses = NULL;
@@ -2286,13 +2528,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("__call__");
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__call__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return NULL;}
- if (__pyx_kwds && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__call__", 1))) return NULL;
- __pyx_v_options = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_options)) return NULL;
- __Pyx_GOTREF(__pyx_v_options);
+ __Pyx_RefNannySetupContext("__call__", 0);
/* "MMTK_trajectory_generator.pyx":74
*
@@ -2301,10 +2537,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* try:
* self.actions = self.getOption('actions')
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setCallOptions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__setCallOptions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_options));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_options));
__Pyx_GIVEREF(((PyObject *)__pyx_v_options));
@@ -2335,22 +2571,22 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* except ValueError:
* self.actions = []
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__getOption); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__getOption); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions = __pyx_t_2;
+ __Pyx_GOTREF(__pyx_v_self->actions);
+ __Pyx_DECREF(__pyx_v_self->actions);
+ __pyx_v_self->actions = __pyx_t_2;
__pyx_t_2 = 0;
}
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L12_try_end;
- __pyx_L5_error:;
+ goto __pyx_L10_try_end;
+ __pyx_L3_error:;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2365,7 +2601,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_7) {
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_t_1);
@@ -2377,30 +2613,30 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* try:
* if self.getOption('background'):
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions = ((PyObject *)__pyx_t_8);
+ __Pyx_GOTREF(__pyx_v_self->actions);
+ __Pyx_DECREF(__pyx_v_self->actions);
+ __pyx_v_self->actions = ((PyObject *)__pyx_t_8);
__pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L6_exception_handled;
+ goto __pyx_L4_exception_handled;
}
- __pyx_L7_except_error:;
+ __pyx_L5_except_error:;
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_ExceptionReset(__pyx_t_4, __pyx_t_5, __pyx_t_6);
goto __pyx_L1_error;
- __pyx_L6_exception_handled:;
+ __pyx_L4_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_ExceptionReset(__pyx_t_4, __pyx_t_5, __pyx_t_6);
- __pyx_L12_try_end:;
+ __pyx_L10_try_end:;
}
/* "MMTK_trajectory_generator.pyx":79
@@ -2424,12 +2660,12 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* import MMTK_state_accessor
* self.state_accessor = MMTK_state_accessor.StateAccessor()
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__getOption); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__getOption); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_9) {
@@ -2440,7 +2676,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.state_accessor = MMTK_state_accessor.StateAccessor()
* self.actions.append(self.state_accessor)
*/
- __pyx_t_3 = __Pyx_Import(((PyObject *)__pyx_n_s__MMTK_state_accessor), 0, -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_3 = __Pyx_Import(((PyObject *)__pyx_n_s__MMTK_state_accessor), 0, -1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_MMTK_state_accessor = __pyx_t_3;
__pyx_t_3 = 0;
@@ -2452,15 +2688,15 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.actions.append(self.state_accessor)
* except ValueError:
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_MMTK_state_accessor, __pyx_n_s__StateAccessor); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_MMTK_state_accessor, __pyx_n_s__StateAccessor); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor = __pyx_t_1;
+ __Pyx_GOTREF(__pyx_v_self->state_accessor);
+ __Pyx_DECREF(__pyx_v_self->state_accessor);
+ __pyx_v_self->state_accessor = __pyx_t_1;
__pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":83
@@ -2470,18 +2706,18 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* except ValueError:
* pass
*/
- __pyx_t_1 = __Pyx_PyObject_Append(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions, ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
+ __pyx_t_1 = __Pyx_PyObject_Append(__pyx_v_self->actions, __pyx_v_self->state_accessor); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L23;
+ goto __pyx_L21;
}
- __pyx_L23:;
+ __pyx_L21:;
}
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L22_try_end;
- __pyx_L15_error:;
+ goto __pyx_L20_try_end;
+ __pyx_L13_error:;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -2497,19 +2733,19 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_7) {
PyErr_Restore(0,0,0);
- goto __pyx_L16_exception_handled;
+ goto __pyx_L14_exception_handled;
}
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_6, __pyx_t_5, __pyx_t_4);
goto __pyx_L1_error;
- __pyx_L16_exception_handled:;
+ __pyx_L14_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_6);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_6, __pyx_t_5, __pyx_t_4);
- __pyx_L22_try_end:;
+ __pyx_L20_try_end:;
}
/* "MMTK_trajectory_generator.pyx":86
@@ -2525,13 +2761,13 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- PyTuple_SET_ITEM(__pyx_t_1, 1, ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- __Pyx_GIVEREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __Pyx_INCREF(__pyx_v_self->universe);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_self->universe);
+ __Pyx_GIVEREF(__pyx_v_self->universe);
__pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -2545,7 +2781,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* free(self.tvars)
* self.tvars = NULL
*/
- __pyx_t_9 = (((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->tvars != NULL);
+ __pyx_t_9 = (__pyx_v_self->tvars != NULL);
if (__pyx_t_9) {
/* "MMTK_trajectory_generator.pyx":88
@@ -2555,7 +2791,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.tvars = NULL
* configuration = self.universe.configuration()
*/
- free(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->tvars);
+ free(__pyx_v_self->tvars);
/* "MMTK_trajectory_generator.pyx":89
* if self.tvars != NULL:
@@ -2564,10 +2800,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* configuration = self.universe.configuration()
* self.conf_array = configuration.array
*/
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->tvars = NULL;
- goto __pyx_L24;
+ __pyx_v_self->tvars = NULL;
+ goto __pyx_L22;
}
- __pyx_L24:;
+ __pyx_L22:;
/* "MMTK_trajectory_generator.pyx":90
* free(self.tvars)
@@ -2576,7 +2812,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.conf_array = configuration.array
* self.declareTrajectoryVariable_array(self.conf_array,
*/
- __pyx_t_2 = PyObject_GetAttr(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe, __pyx_n_s__configuration); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->universe, __pyx_n_s__configuration); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -2595,9 +2831,9 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__Pyx_GOTREF(__pyx_t_1);
if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 91; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->conf_array);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->conf_array));
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->conf_array = ((PyArrayObject *)__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_self->conf_array);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->conf_array));
+ __pyx_v_self->conf_array = ((PyArrayObject *)__pyx_t_1);
__pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":92
@@ -2607,7 +2843,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* "configuration",
* "Configuration:\n",
*/
- __pyx_t_1 = ((PyObject *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->conf_array);
+ __pyx_t_1 = ((PyObject *)__pyx_v_self->conf_array);
__Pyx_INCREF(__pyx_t_1);
/* "MMTK_trajectory_generator.pyx":96
@@ -2617,7 +2853,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.universe_spec = <PyUniverseSpecObject *>self.universe._spec
* if self.universe_spec.geometry_data_length > 0:
*/
- ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->declareTrajectoryVariable_array(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyArrayObject *)__pyx_t_1), __pyx_k__configuration, __pyx_k_9, length_unit_name, PyTrajectory_Configuration); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->declareTrajectoryVariable_array(__pyx_v_self, ((PyArrayObject *)__pyx_t_1), __pyx_k__configuration, __pyx_k_9, length_unit_name, PyTrajectory_Configuration); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 92; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":97
@@ -2627,9 +2863,9 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* if self.universe_spec.geometry_data_length > 0:
* self.declareTrajectoryVariable_box(
*/
- __pyx_t_1 = PyObject_GetAttr(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe, __pyx_n_s___spec); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->universe, __pyx_n_s___spec); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 97; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe_spec = ((PyUniverseSpecObject *)__pyx_t_1);
+ __pyx_v_self->universe_spec = ((PyUniverseSpecObject *)__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/* "MMTK_trajectory_generator.pyx":98
@@ -2639,7 +2875,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.declareTrajectoryVariable_box(
* self.universe_spec.geometry_data,
*/
- __pyx_t_9 = (((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe_spec->geometry_data_length > 0);
+ __pyx_t_9 = (__pyx_v_self->universe_spec->geometry_data_length > 0);
if (__pyx_t_9) {
/* "MMTK_trajectory_generator.pyx":101
@@ -2649,10 +2885,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* masses = self.universe.masses()
* self.declareTrajectoryVariable_array(masses.array,
*/
- ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->declareTrajectoryVariable_box(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe_spec->geometry_data, ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe_spec->geometry_data_length); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L25;
+ ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->declareTrajectoryVariable_box(__pyx_v_self, __pyx_v_self->universe_spec->geometry_data, __pyx_v_self->universe_spec->geometry_data_length); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 99; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L23;
}
- __pyx_L25:;
+ __pyx_L23:;
/* "MMTK_trajectory_generator.pyx":102
* self.universe_spec.geometry_data,
@@ -2661,7 +2897,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.declareTrajectoryVariable_array(masses.array,
* "masses",
*/
- __pyx_t_1 = PyObject_GetAttr(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe, __pyx_n_s__masses); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->universe, __pyx_n_s__masses); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -2687,7 +2923,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.natoms = self.universe.numberOfAtoms()
* self.df = self.universe.degreesOfFreedom()
*/
- ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->declareTrajectoryVariable_array(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyArrayObject *)__pyx_t_2), __pyx_k__masses, __pyx_k_10, mass_unit_name, PyTrajectory_Internal); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->declareTrajectoryVariable_array(__pyx_v_self, ((PyArrayObject *)__pyx_t_2), __pyx_k__masses, __pyx_k_10, mass_unit_name, PyTrajectory_Internal); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
/* "MMTK_trajectory_generator.pyx":108
@@ -2697,14 +2933,14 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.df = self.universe.degreesOfFreedom()
* self.declareTrajectoryVariable_int(&self.df,
*/
- __pyx_t_2 = PyObject_GetAttr(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe, __pyx_n_s__numberOfAtoms); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->universe, __pyx_n_s__numberOfAtoms); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_7 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->natoms = __pyx_t_7;
+ __pyx_v_self->natoms = __pyx_t_7;
/* "MMTK_trajectory_generator.pyx":109
* PyTrajectory_Internal)
@@ -2713,14 +2949,14 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.declareTrajectoryVariable_int(&self.df,
* "degrees_of_freedom",
*/
- __pyx_t_1 = PyObject_GetAttr(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe, __pyx_n_s__degreesOfFreedom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->universe, __pyx_n_s__degreesOfFreedom); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_7 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->df = __pyx_t_7;
+ __pyx_v_self->df = __pyx_t_7;
/* "MMTK_trajectory_generator.pyx":113
* "degrees_of_freedom",
@@ -2729,7 +2965,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* if self.getOption('background'):
* from MMTK import ThreadManager
*/
- ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->declareTrajectoryVariable_int(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), (&((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->df), __pyx_k__degrees_of_freedom, __pyx_k_11, __pyx_k_6, PyTrajectory_Internal); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->declareTrajectoryVariable_int(__pyx_v_self, (&__pyx_v_self->df), __pyx_k__degrees_of_freedom, __pyx_k_11, __pyx_k_6, PyTrajectory_Internal); if (unlikely(PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "MMTK_trajectory_generator.pyx":114
* "Degrees of freedom: %d\n",
@@ -2738,7 +2974,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* from MMTK import ThreadManager
* return ThreadManager.TrajectoryGeneratorThread(
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__getOption); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__getOption); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -2755,14 +2991,18 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* self.universe, self.start_py, (), self.state_accessor)
*/
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__ThreadManager));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__ThreadManager));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ThreadManager));
__pyx_t_2 = __Pyx_Import(((PyObject *)__pyx_n_s__MMTK), ((PyObject *)__pyx_t_1), -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__ThreadManager); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__ThreadManager);
+ if (__pyx_t_1 == NULL) {
+ if (PyErr_ExceptionMatches(PyExc_AttributeError)) __Pyx_RaiseImportError(__pyx_n_s__ThreadManager);
+ if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_1);
__pyx_v_ThreadManager = __pyx_t_1;
@@ -2787,21 +3027,21 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* else:
* self.start()
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__start_py); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start_py); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- __Pyx_GIVEREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_self->universe);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_self->universe);
+ __Pyx_GIVEREF(__pyx_v_self->universe);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_empty_tuple));
PyTuple_SET_ITEM(__pyx_t_3, 2, ((PyObject *)__pyx_empty_tuple));
__Pyx_GIVEREF(((PyObject *)__pyx_empty_tuple));
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- PyTuple_SET_ITEM(__pyx_t_3, 3, ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- __Pyx_GIVEREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
+ __Pyx_INCREF(__pyx_v_self->state_accessor);
+ PyTuple_SET_ITEM(__pyx_t_3, 3, __pyx_v_self->state_accessor);
+ __Pyx_GIVEREF(__pyx_v_self->state_accessor);
__pyx_t_1 = 0;
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -2810,7 +3050,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L26;
+ goto __pyx_L24;
}
/*else*/ {
@@ -2821,7 +3061,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
* return None
*
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->start(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->start(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -2837,7 +3077,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__pyx_r = Py_None;
goto __pyx_L0;
}
- __pyx_L26:;
+ __pyx_L24:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -2849,7 +3089,6 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
__Pyx_AddTraceback("MMTK_trajectory_generator.TrajectoryGenerator.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_options);
__Pyx_XDECREF(__pyx_v_MMTK_state_accessor);
__Pyx_XDECREF(__pyx_v_configuration);
__Pyx_XDECREF(__pyx_v_masses);
@@ -2859,6 +3098,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_15start_py(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_15start_py(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("start_py (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14start_py(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pyx":122
* return None
*
@@ -2867,15 +3117,14 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__c
*
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7start_py(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7start_py(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14start_py(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("start_py");
+ __Pyx_RefNannySetupContext("start_py", 0);
/* "MMTK_trajectory_generator.pyx":123
*
@@ -2884,7 +3133,7 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7sta
*
* cdef start(self):
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->__pyx_vtab)->start(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self->__pyx_vtab)->start(__pyx_v_self); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -2908,10 +3157,10 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7sta
*
*/
-static PyObject *__pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_start(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
+static PyObject *__pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_start(CYTHON_UNUSED struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("start");
+ __Pyx_RefNannySetupContext("start", 0);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -2933,12 +3182,13 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator__addTrajec
int __pyx_v_n;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- int __pyx_t_2;
+ PyTrajectoryVariable *__pyx_t_2;
int __pyx_t_3;
+ int __pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("_addTrajectoryVariable");
+ __Pyx_RefNannySetupContext("_addTrajectoryVariable", 0);
/* "MMTK_trajectory_generator.pyx":131
* cdef PyTrajectoryVariable *tv
@@ -3018,7 +3268,8 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator__addTrajec
* while tv.name != NULL:
* n += 1
*/
- __pyx_v_tv = __pyx_v_self->tvars;
+ __pyx_t_2 = __pyx_v_self->tvars;
+ __pyx_v_tv = __pyx_t_2;
/* "MMTK_trajectory_generator.pyx":141
* n = 0
@@ -3088,9 +3339,9 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator__addTrajec
* tv[i] = self.tvars[i]
* tv[n] = v
*/
- __pyx_t_2 = __pyx_v_n;
- for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
- __pyx_v_i = __pyx_t_3;
+ __pyx_t_3 = __pyx_v_n;
+ for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
+ __pyx_v_i = __pyx_t_4;
/* "MMTK_trajectory_generator.pyx":149
* raise MemoryError
@@ -3161,7 +3412,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_declareTra
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("declareTrajectoryVariable_double");
+ __Pyx_RefNannySetupContext("declareTrajectoryVariable_double", 0);
/* "MMTK_trajectory_generator.pyx":159
* int data_class) except *:
@@ -3247,7 +3498,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_declareTra
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("declareTrajectoryVariable_int");
+ __Pyx_RefNannySetupContext("declareTrajectoryVariable_int", 0);
/* "MMTK_trajectory_generator.pyx":171
* int data_class) except *:
@@ -3335,7 +3586,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_declareTra
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("declareTrajectoryVariable_array");
+ __Pyx_RefNannySetupContext("declareTrajectoryVariable_array", 0);
/* "MMTK_trajectory_generator.pyx":183
* int data_class) except *:
@@ -3490,7 +3741,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_declareTra
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("declareTrajectoryVariable_box");
+ __Pyx_RefNannySetupContext("declareTrajectoryVariable_box", 0);
/* "MMTK_trajectory_generator.pyx":199
* cdef void declareTrajectoryVariable_box(self, double * var, int l) except *:
@@ -3589,7 +3840,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_initialize
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("initializeTrajectoryActions");
+ __Pyx_RefNannySetupContext("initializeTrajectoryActions", 0);
/* "MMTK_trajectory_generator.pyx":209
*
@@ -3686,7 +3937,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_finalizeTr
*/
int __pyx_v_error = ((int)0);
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("finalizeTrajectoryActions");
+ __Pyx_RefNannySetupContext("finalizeTrajectoryActions", 0);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
__pyx_v_error = __pyx_optional_args->error;
@@ -3739,7 +3990,7 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_finalizeTr
static int __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_trajectoryActions(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, int __pyx_v_step) {
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("trajectoryActions");
+ __Pyx_RefNannySetupContext("trajectoryActions", 0);
/* "MMTK_trajectory_generator.pyx":224
*
@@ -3898,6 +4149,17 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_releaseWri
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pxd":23
* cdef class TrajectoryGenerator(object):
*
@@ -3906,14 +4168,13 @@ static void __pyx_f_25MMTK_trajectory_generator_19TrajectoryGenerator_releaseWri
* cdef readonly features
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->universe;
+ __Pyx_INCREF(__pyx_v_self->universe);
+ __pyx_r = __pyx_v_self->universe;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -3923,14 +4184,24 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8uni
return __pyx_r;
}
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(PyObject *__pyx_v_self) {
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7options_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7options_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->options;
+ __Pyx_INCREF(__pyx_v_self->options);
+ __pyx_r = __pyx_v_self->options;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -3940,14 +4211,24 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7opt
return __pyx_r;
}
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(PyObject *__pyx_v_self) {
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_4name_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_4name_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->name);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->name;
+ __Pyx_INCREF(__pyx_v_self->name);
+ __pyx_r = __pyx_v_self->name;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -3957,6 +4238,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4nam
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pxd":24
*
* cdef readonly universe, options, name
@@ -3965,14 +4257,13 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4nam
* cdef readonly actions
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->call_options;
+ __Pyx_INCREF(__pyx_v_self->call_options);
+ __pyx_r = __pyx_v_self->call_options;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -3982,6 +4273,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12ca
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8features_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8features_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pxd":25
* cdef readonly universe, options, name
* cdef readonly call_options
@@ -3990,14 +4292,13 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12ca
* cdef public state_accessor
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->features);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->features;
+ __Pyx_INCREF(__pyx_v_self->features);
+ __pyx_r = __pyx_v_self->features;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -4007,6 +4308,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8fea
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pxd":26
* cdef readonly call_options
* cdef readonly features
@@ -4015,14 +4327,13 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8fea
* cdef PyTrajectoryVariable *tvars
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->actions;
+ __Pyx_INCREF(__pyx_v_self->actions);
+ __pyx_r = __pyx_v_self->actions;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -4032,6 +4343,17 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7act
return __pyx_r;
}
+/* Python wrapper */
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
/* "MMTK_trajectory_generator.pxd":27
* cdef readonly features
* cdef readonly actions
@@ -4040,14 +4362,13 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7act
* cdef PyTrajectoryOutputSpec *tspec
*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- __pyx_r = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor;
+ __Pyx_INCREF(__pyx_v_self->state_accessor);
+ __pyx_r = __pyx_v_self->state_accessor;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -4057,101 +4378,109 @@ static PyObject *__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14st
return __pyx_r;
}
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+/* Python wrapper */
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__set__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__set__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__set__");
+ __Pyx_RefNannySetupContext("__set__", 0);
__Pyx_INCREF(__pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor = __pyx_v_value;
+ __Pyx_GOTREF(__pyx_v_self->state_accessor);
+ __Pyx_DECREF(__pyx_v_self->state_accessor);
+ __pyx_v_self->state_accessor = __pyx_v_value;
__pyx_r = 0;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__del__(PyObject *__pyx_v_self); /*proto*/
-static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__del__(PyObject *__pyx_v_self) {
+/* Python wrapper */
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_5__del__(PyObject *__pyx_v_self); /*proto*/
+static int __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_5__del__(PyObject *__pyx_v_self) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_4__del__(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_4__del__(struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__del__");
+ __Pyx_RefNannySetupContext("__del__", 0);
__Pyx_INCREF(Py_None);
__Pyx_GIVEREF(Py_None);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor);
- ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)__pyx_v_self)->state_accessor = Py_None;
+ __Pyx_GOTREF(__pyx_v_self->state_accessor);
+ __Pyx_DECREF(__pyx_v_self->state_accessor);
+ __pyx_v_self->state_accessor = Py_None;
__pyx_r = 0;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "MMTK_trajectory_generator.pyx":254
- * cdef class EnergyBasedTrajectoryGenerator(TrajectoryGenerator):
- *
- * def __init__(self, universe, options, name): # <<<<<<<<<<<<<<
- * TrajectoryGenerator.__init__(self, universe, options, name)
- * self.evaluator_object = None
- */
-
-static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static int __pyx_pw_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_universe = 0;
PyObject *__pyx_v_options = 0;
PyObject *__pyx_v_name = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__universe,&__pyx_n_s__options,&__pyx_n_s__name,0};
- __Pyx_RefNannySetupContext("__init__");
- if (unlikely(__pyx_kwds)) {
- Py_ssize_t kw_args = PyDict_Size(__pyx_kwds);
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ {
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__universe,&__pyx_n_s__options,&__pyx_n_s__name,0};
PyObject* values[3] = {0,0,0};
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
- case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
- case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
- case 0: break;
- default: goto __pyx_L5_argtuple_error;
- }
- switch (PyTuple_GET_SIZE(__pyx_args)) {
- case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__universe);
- if (likely(values[0])) kw_args--;
- else goto __pyx_L5_argtuple_error;
- case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__options);
- if (likely(values[1])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__pyx_kwds)) {
+ Py_ssize_t kw_args;
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
+ case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
+ case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ case 0: break;
+ default: goto __pyx_L5_argtuple_error;
+ }
+ kw_args = PyDict_Size(__pyx_kwds);
+ switch (pos_args) {
+ case 0:
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__universe)) != 0)) kw_args--;
+ else goto __pyx_L5_argtuple_error;
+ case 1:
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__options)) != 0)) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
+ case 2:
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name)) != 0)) kw_args--;
+ else {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ }
}
- case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name);
- if (likely(values[2])) kw_args--;
- else {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(kw_args > 0)) {
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
- }
- if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 254; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
+ goto __pyx_L5_argtuple_error;
+ } else {
+ values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
+ values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
+ values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
}
__pyx_v_universe = values[0];
__pyx_v_options = values[1];
__pyx_v_name = values[2];
- } else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
- goto __pyx_L5_argtuple_error;
- } else {
- __pyx_v_universe = PyTuple_GET_ITEM(__pyx_args, 0);
- __pyx_v_options = PyTuple_GET_ITEM(__pyx_args, 1);
- __pyx_v_name = PyTuple_GET_ITEM(__pyx_args, 2);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
@@ -4161,6 +4490,29 @@ static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__(((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self), __pyx_v_universe, __pyx_v_options, __pyx_v_name);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "MMTK_trajectory_generator.pyx":254
+ * cdef class EnergyBasedTrajectoryGenerator(TrajectoryGenerator):
+ *
+ * def __init__(self, universe, options, name): # <<<<<<<<<<<<<<
+ * TrajectoryGenerator.__init__(self, universe, options, name)
+ * self.evaluator_object = None
+ */
+
+static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__(struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *__pyx_v_self, PyObject *__pyx_v_universe, PyObject *__pyx_v_options, PyObject *__pyx_v_name) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_RefNannySetupContext("__init__", 0);
/* "MMTK_trajectory_generator.pyx":255
*
@@ -4172,10 +4524,10 @@ static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
__pyx_t_1 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_25MMTK_trajectory_generator_TrajectoryGenerator)), __pyx_n_s____init__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
__Pyx_INCREF(__pyx_v_universe);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_universe);
__Pyx_GIVEREF(__pyx_v_universe);
@@ -4200,9 +4552,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
*/
__Pyx_INCREF(Py_None);
__Pyx_GIVEREF(Py_None);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->evaluator_object);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->evaluator_object);
- ((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->evaluator_object = Py_None;
+ __Pyx_GOTREF(__pyx_v_self->evaluator_object);
+ __Pyx_DECREF(__pyx_v_self->evaluator_object);
+ __pyx_v_self->evaluator_object = Py_None;
/* "MMTK_trajectory_generator.pyx":257
* TrajectoryGenerator.__init__(self, universe, options, name)
@@ -4213,9 +4565,9 @@ static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
*/
__Pyx_INCREF(Py_None);
__Pyx_GIVEREF(Py_None);
- __Pyx_GOTREF(((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->c_evaluator_object);
- __Pyx_DECREF(((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->c_evaluator_object);
- ((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->c_evaluator_object = Py_None;
+ __Pyx_GOTREF(__pyx_v_self->c_evaluator_object);
+ __Pyx_DECREF(__pyx_v_self->c_evaluator_object);
+ __pyx_v_self->c_evaluator_object = Py_None;
/* "MMTK_trajectory_generator.pyx":258
* self.evaluator_object = None
@@ -4224,7 +4576,7 @@ static int __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
*
* cdef void initializeTrajectoryActions(self) except *:
*/
- ((struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)__pyx_v_self)->evaluator = NULL;
+ __pyx_v_self->evaluator = NULL;
__pyx_r = 0;
goto __pyx_L0;
@@ -4256,7 +4608,7 @@ static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("initializeTrajectoryActions");
+ __Pyx_RefNannySetupContext("initializeTrajectoryActions", 0);
/* "MMTK_trajectory_generator.pyx":261
*
@@ -4294,7 +4646,7 @@ static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__threads), __pyx_v_nt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -4365,7 +4717,7 @@ static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("finalizeTrajectoryActions");
+ __Pyx_RefNannySetupContext("finalizeTrajectoryActions", 0);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
__pyx_v_error = __pyx_optional_args->error;
@@ -4438,7 +4790,7 @@ static int __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- __Pyx_RefNannySetupContext("trajectoryActions");
+ __Pyx_RefNannySetupContext("trajectoryActions", 0);
/* "MMTK_trajectory_generator.pyx":278
* cdef int trajectoryActions(self, int step) except -1:
@@ -4537,29 +4889,28 @@ static int __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_
static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_calculateEnergies(struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *__pyx_v_self, PyArrayObject *__pyx_v_conf_array, energy_data *__pyx_v_energy, struct __pyx_opt_args_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_calculateEnergies *__pyx_optional_args) {
int __pyx_v_small_change = ((int)0);
- Py_buffer __pyx_bstruct_conf_array;
- Py_ssize_t __pyx_bstride_0_conf_array = 0;
- Py_ssize_t __pyx_bstride_1_conf_array = 0;
- Py_ssize_t __pyx_bshape_0_conf_array = 0;
- Py_ssize_t __pyx_bshape_1_conf_array = 0;
+ __Pyx_LocalBuf_ND __pyx_pybuffernd_conf_array;
+ __Pyx_Buffer __pyx_pybuffer_conf_array;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("calculateEnergies");
+ __Pyx_RefNannySetupContext("calculateEnergies", 0);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
__pyx_v_small_change = __pyx_optional_args->small_change;
}
}
- __pyx_bstruct_conf_array.buf = NULL;
+ __pyx_pybuffer_conf_array.pybuffer.buf = NULL;
+ __pyx_pybuffer_conf_array.refcount = 0;
+ __pyx_pybuffernd_conf_array.data = NULL;
+ __pyx_pybuffernd_conf_array.rcbuffer = &__pyx_pybuffer_conf_array;
{
__Pyx_BufFmt_StackElem __pyx_stack[1];
- if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_bstruct_conf_array, (PyObject*)__pyx_v_conf_array, &__Pyx_TypeInfo_double, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_conf_array.rcbuffer->pybuffer, (PyObject*)__pyx_v_conf_array, &__Pyx_TypeInfo_double, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_bstride_0_conf_array = __pyx_bstruct_conf_array.strides[0]; __pyx_bstride_1_conf_array = __pyx_bstruct_conf_array.strides[1];
- __pyx_bshape_0_conf_array = __pyx_bstruct_conf_array.shape[0]; __pyx_bshape_1_conf_array = __pyx_bstruct_conf_array.shape[1];
+ __pyx_pybuffernd_conf_array.diminfo[0].strides = __pyx_pybuffernd_conf_array.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_conf_array.diminfo[0].shape = __pyx_pybuffernd_conf_array.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_conf_array.diminfo[1].strides = __pyx_pybuffernd_conf_array.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_conf_array.diminfo[1].shape = __pyx_pybuffernd_conf_array.rcbuffer->pybuffer.shape[1];
/* "MMTK_trajectory_generator.pyx":291
* energy_data *energy, int small_change=0) \
@@ -4677,17 +5028,28 @@ static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
__pyx_L1_error:;
{ PyObject *__pyx_type, *__pyx_value, *__pyx_tb;
__Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb);
- __Pyx_SafeReleaseBuffer(&__pyx_bstruct_conf_array);
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_conf_array.rcbuffer->pybuffer);
__Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);}
__Pyx_AddTraceback("MMTK_trajectory_generator.EnergyBasedTrajectoryGenerator.calculateEnergies", __pyx_clineno, __pyx_lineno, __pyx_filename);
goto __pyx_L2;
__pyx_L0:;
- __Pyx_SafeReleaseBuffer(&__pyx_bstruct_conf_array);
+ __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_conf_array.rcbuffer->pybuffer);
__pyx_L2:;
__Pyx_RefNannyFinishContext();
}
-/* "numpy.pxd":190
+/* Python wrapper */
+static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
+static CYTHON_UNUSED int __pyx_pw_5numpy_7ndarray_1__getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__getbuffer__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5numpy_7ndarray___getbuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info), ((int)__pyx_v_flags));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "numpy.pxd":194
* # experimental exception made for __getbuffer__ and __releasebuffer__
* # -- the details of this may change.
* def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<<
@@ -4695,8 +5057,7 @@ static void __pyx_f_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator
* # requirements, and does not yet fullfill the PEP.
*/
-static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
-static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
+static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags) {
int __pyx_v_copy_shape;
int __pyx_v_i;
int __pyx_v_ndim;
@@ -4721,13 +5082,13 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("__getbuffer__");
+ __Pyx_RefNannySetupContext("__getbuffer__", 0);
if (__pyx_v_info != NULL) {
__pyx_v_info->obj = Py_None; __Pyx_INCREF(Py_None);
__Pyx_GIVEREF(__pyx_v_info->obj);
}
- /* "numpy.pxd":196
+ /* "numpy.pxd":200
* # of flags
*
* if info == NULL: return # <<<<<<<<<<<<<<
@@ -4738,11 +5099,11 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
if (__pyx_t_1) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "numpy.pxd":199
+ /* "numpy.pxd":203
*
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -4751,7 +5112,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_endian_detector = 1;
- /* "numpy.pxd":200
+ /* "numpy.pxd":204
* cdef int copy_shape, i, ndim
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -4760,16 +5121,16 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "numpy.pxd":202
+ /* "numpy.pxd":206
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0)
*
* ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<<
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
*/
- __pyx_v_ndim = PyArray_NDIM(((PyArrayObject *)__pyx_v_self));
+ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self);
- /* "numpy.pxd":204
+ /* "numpy.pxd":208
* ndim = PyArray_NDIM(self)
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -4779,7 +5140,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = ((sizeof(npy_intp)) != (sizeof(Py_ssize_t)));
if (__pyx_t_1) {
- /* "numpy.pxd":205
+ /* "numpy.pxd":209
*
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* copy_shape = 1 # <<<<<<<<<<<<<<
@@ -4787,11 +5148,11 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
* copy_shape = 0
*/
__pyx_v_copy_shape = 1;
- goto __pyx_L6;
+ goto __pyx_L4;
}
/*else*/ {
- /* "numpy.pxd":207
+ /* "numpy.pxd":211
* copy_shape = 1
* else:
* copy_shape = 0 # <<<<<<<<<<<<<<
@@ -4800,9 +5161,9 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_copy_shape = 0;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "numpy.pxd":209
+ /* "numpy.pxd":213
* copy_shape = 0
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -4812,37 +5173,37 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = ((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS);
if (__pyx_t_1) {
- /* "numpy.pxd":210
+ /* "numpy.pxd":214
*
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<<
* raise ValueError(u"ndarray is not C contiguous")
*
*/
- __pyx_t_2 = (!PyArray_CHKFLAGS(((PyArrayObject *)__pyx_v_self), NPY_C_CONTIGUOUS));
+ __pyx_t_2 = (!PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS));
__pyx_t_3 = __pyx_t_2;
} else {
__pyx_t_3 = __pyx_t_1;
}
if (__pyx_t_3) {
- /* "numpy.pxd":211
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_19), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_19), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "numpy.pxd":213
+ /* "numpy.pxd":217
* raise ValueError(u"ndarray is not C contiguous")
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<<
@@ -4852,46 +5213,46 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_3 = ((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS);
if (__pyx_t_3) {
- /* "numpy.pxd":214
+ /* "numpy.pxd":218
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<<
* raise ValueError(u"ndarray is not Fortran contiguous")
*
*/
- __pyx_t_1 = (!PyArray_CHKFLAGS(((PyArrayObject *)__pyx_v_self), NPY_F_CONTIGUOUS));
+ __pyx_t_1 = (!PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS));
__pyx_t_2 = __pyx_t_1;
} else {
__pyx_t_2 = __pyx_t_3;
}
if (__pyx_t_2) {
- /* "numpy.pxd":215
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_21), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_21), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
}
- __pyx_L8:;
+ __pyx_L6:;
- /* "numpy.pxd":217
+ /* "numpy.pxd":221
* raise ValueError(u"ndarray is not Fortran contiguous")
*
* info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<<
* info.ndim = ndim
* if copy_shape:
*/
- __pyx_v_info->buf = PyArray_DATA(((PyArrayObject *)__pyx_v_self));
+ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self);
- /* "numpy.pxd":218
+ /* "numpy.pxd":222
*
* info.buf = PyArray_DATA(self)
* info.ndim = ndim # <<<<<<<<<<<<<<
@@ -4900,7 +5261,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_info->ndim = __pyx_v_ndim;
- /* "numpy.pxd":219
+ /* "numpy.pxd":223
* info.buf = PyArray_DATA(self)
* info.ndim = ndim
* if copy_shape: # <<<<<<<<<<<<<<
@@ -4909,7 +5270,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
if (__pyx_v_copy_shape) {
- /* "numpy.pxd":222
+ /* "numpy.pxd":226
* # Allocate new buffer for strides and shape info.
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2) # <<<<<<<<<<<<<<
@@ -4918,7 +5279,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2)));
- /* "numpy.pxd":223
+ /* "numpy.pxd":227
* # This is allocated as one block, strides first.
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim # <<<<<<<<<<<<<<
@@ -4927,7 +5288,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim);
- /* "numpy.pxd":224
+ /* "numpy.pxd":228
* info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2)
* info.shape = info.strides + ndim
* for i in range(ndim): # <<<<<<<<<<<<<<
@@ -4938,49 +5299,49 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) {
__pyx_v_i = __pyx_t_6;
- /* "numpy.pxd":225
+ /* "numpy.pxd":229
* info.shape = info.strides + ndim
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<<
* info.shape[i] = PyArray_DIMS(self)[i]
* else:
*/
- (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(((PyArrayObject *)__pyx_v_self))[__pyx_v_i]);
+ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]);
- /* "numpy.pxd":226
+ /* "numpy.pxd":230
* for i in range(ndim):
* info.strides[i] = PyArray_STRIDES(self)[i]
* info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<<
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
*/
- (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(((PyArrayObject *)__pyx_v_self))[__pyx_v_i]);
+ (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]);
}
- goto __pyx_L9;
+ goto __pyx_L7;
}
/*else*/ {
- /* "numpy.pxd":228
+ /* "numpy.pxd":232
* info.shape[i] = PyArray_DIMS(self)[i]
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<<
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
*/
- __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(((PyArrayObject *)__pyx_v_self)));
+ __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self));
- /* "numpy.pxd":229
+ /* "numpy.pxd":233
* else:
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<<
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
*/
- __pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(((PyArrayObject *)__pyx_v_self)));
+ __pyx_v_info->shape = ((Py_ssize_t *)PyArray_DIMS(__pyx_v_self));
}
- __pyx_L9:;
+ __pyx_L7:;
- /* "numpy.pxd":230
+ /* "numpy.pxd":234
* info.strides = <Py_ssize_t*>PyArray_STRIDES(self)
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL # <<<<<<<<<<<<<<
@@ -4989,25 +5350,25 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_info->suboffsets = NULL;
- /* "numpy.pxd":231
+ /* "numpy.pxd":235
* info.shape = <Py_ssize_t*>PyArray_DIMS(self)
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<<
* info.readonly = not PyArray_ISWRITEABLE(self)
*
*/
- __pyx_v_info->itemsize = PyArray_ITEMSIZE(((PyArrayObject *)__pyx_v_self));
+ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self);
- /* "numpy.pxd":232
+ /* "numpy.pxd":236
* info.suboffsets = NULL
* info.itemsize = PyArray_ITEMSIZE(self)
* info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<<
*
* cdef int t
*/
- __pyx_v_info->readonly = (!PyArray_ISWRITEABLE(((PyArrayObject *)__pyx_v_self)));
+ __pyx_v_info->readonly = (!PyArray_ISWRITEABLE(__pyx_v_self));
- /* "numpy.pxd":235
+ /* "numpy.pxd":239
*
* cdef int t
* cdef char* f = NULL # <<<<<<<<<<<<<<
@@ -5016,17 +5377,19 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_f = NULL;
- /* "numpy.pxd":236
+ /* "numpy.pxd":240
* cdef int t
* cdef char* f = NULL
* cdef dtype descr = self.descr # <<<<<<<<<<<<<<
* cdef list stack
* cdef int offset
*/
- __Pyx_INCREF(((PyObject *)((PyArrayObject *)__pyx_v_self)->descr));
- __pyx_v_descr = ((PyArrayObject *)__pyx_v_self)->descr;
+ __pyx_t_4 = ((PyObject *)__pyx_v_self->descr);
+ __Pyx_INCREF(__pyx_t_4);
+ __pyx_v_descr = ((PyArray_Descr *)__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "numpy.pxd":240
+ /* "numpy.pxd":244
* cdef int offset
*
* cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<<
@@ -5035,7 +5398,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr);
- /* "numpy.pxd":242
+ /* "numpy.pxd":246
* cdef bint hasfields = PyDataType_HASFIELDS(descr)
*
* if not hasfields and not copy_shape: # <<<<<<<<<<<<<<
@@ -5051,7 +5414,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
}
if (__pyx_t_1) {
- /* "numpy.pxd":244
+ /* "numpy.pxd":248
* if not hasfields and not copy_shape:
* # do not call releasebuffer
* info.obj = None # <<<<<<<<<<<<<<
@@ -5063,49 +5426,50 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__Pyx_GOTREF(__pyx_v_info->obj);
__Pyx_DECREF(__pyx_v_info->obj);
__pyx_v_info->obj = Py_None;
- goto __pyx_L12;
+ goto __pyx_L10;
}
/*else*/ {
- /* "numpy.pxd":247
+ /* "numpy.pxd":251
* else:
* # need to call releasebuffer
* info.obj = self # <<<<<<<<<<<<<<
*
* if not hasfields:
*/
- __Pyx_INCREF(__pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
__Pyx_GOTREF(__pyx_v_info->obj);
__Pyx_DECREF(__pyx_v_info->obj);
- __pyx_v_info->obj = __pyx_v_self;
+ __pyx_v_info->obj = ((PyObject *)__pyx_v_self);
}
- __pyx_L12:;
+ __pyx_L10:;
- /* "numpy.pxd":249
+ /* "numpy.pxd":253
* info.obj = self
*
* if not hasfields: # <<<<<<<<<<<<<<
* t = descr.type_num
- * if ((descr.byteorder == '>' and little_endian) or
+ * if ((descr.byteorder == c'>' and little_endian) or
*/
__pyx_t_1 = (!__pyx_v_hasfields);
if (__pyx_t_1) {
- /* "numpy.pxd":250
+ /* "numpy.pxd":254
*
* if not hasfields:
* t = descr.type_num # <<<<<<<<<<<<<<
- * if ((descr.byteorder == '>' and little_endian) or
- * (descr.byteorder == '<' and not little_endian)):
+ * if ((descr.byteorder == c'>' and little_endian) or
+ * (descr.byteorder == c'<' and not little_endian)):
*/
- __pyx_v_t = __pyx_v_descr->type_num;
+ __pyx_t_5 = __pyx_v_descr->type_num;
+ __pyx_v_t = __pyx_t_5;
- /* "numpy.pxd":251
+ /* "numpy.pxd":255
* if not hasfields:
* t = descr.type_num
- * if ((descr.byteorder == '>' and little_endian) or # <<<<<<<<<<<<<<
- * (descr.byteorder == '<' and not little_endian)):
+ * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
+ * (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
*/
__pyx_t_1 = (__pyx_v_descr->byteorder == '>');
@@ -5116,10 +5480,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
}
if (!__pyx_t_2) {
- /* "numpy.pxd":252
+ /* "numpy.pxd":256
* t = descr.type_num
- * if ((descr.byteorder == '>' and little_endian) or
- * (descr.byteorder == '<' and not little_endian)): # <<<<<<<<<<<<<<
+ * if ((descr.byteorder == c'>' and little_endian) or
+ * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
*/
@@ -5136,24 +5500,24 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
}
if (__pyx_t_1) {
- /* "numpy.pxd":253
- * if ((descr.byteorder == '>' and little_endian) or
- * (descr.byteorder == '<' and not little_endian)):
+ /* "numpy.pxd":257
+ * if ((descr.byteorder == c'>' and little_endian) or
+ * (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_23), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_23), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L12;
}
- __pyx_L14:;
+ __pyx_L12:;
- /* "numpy.pxd":254
- * (descr.byteorder == '<' and not little_endian)):
+ /* "numpy.pxd":258
+ * (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<<
* elif t == NPY_UBYTE: f = "B"
@@ -5162,10 +5526,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_BYTE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__b;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":255
+ /* "numpy.pxd":259
* raise ValueError(u"Non-native byte order not supported")
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<<
@@ -5175,10 +5539,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_UBYTE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__B;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":256
+ /* "numpy.pxd":260
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<<
@@ -5188,10 +5552,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_SHORT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__h;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":257
+ /* "numpy.pxd":261
* elif t == NPY_UBYTE: f = "B"
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<<
@@ -5201,10 +5565,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_USHORT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__H;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":258
+ /* "numpy.pxd":262
* elif t == NPY_SHORT: f = "h"
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<<
@@ -5214,10 +5578,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_INT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__i;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":259
+ /* "numpy.pxd":263
* elif t == NPY_USHORT: f = "H"
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<<
@@ -5227,10 +5591,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_UINT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__I;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":260
+ /* "numpy.pxd":264
* elif t == NPY_INT: f = "i"
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<<
@@ -5240,10 +5604,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_LONG);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__l;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":261
+ /* "numpy.pxd":265
* elif t == NPY_UINT: f = "I"
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<<
@@ -5253,10 +5617,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_ULONG);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__L;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":262
+ /* "numpy.pxd":266
* elif t == NPY_LONG: f = "l"
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<<
@@ -5266,10 +5630,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_LONGLONG);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__q;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":263
+ /* "numpy.pxd":267
* elif t == NPY_ULONG: f = "L"
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<<
@@ -5279,10 +5643,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_ULONGLONG);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__Q;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":264
+ /* "numpy.pxd":268
* elif t == NPY_LONGLONG: f = "q"
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<<
@@ -5292,10 +5656,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_FLOAT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__f;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":265
+ /* "numpy.pxd":269
* elif t == NPY_ULONGLONG: f = "Q"
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<<
@@ -5305,10 +5669,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_DOUBLE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__d;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":266
+ /* "numpy.pxd":270
* elif t == NPY_FLOAT: f = "f"
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<<
@@ -5318,10 +5682,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_LONGDOUBLE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__g;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":267
+ /* "numpy.pxd":271
* elif t == NPY_DOUBLE: f = "d"
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<<
@@ -5331,10 +5695,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_CFLOAT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__Zf;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":268
+ /* "numpy.pxd":272
* elif t == NPY_LONGDOUBLE: f = "g"
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<<
@@ -5344,10 +5708,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_CDOUBLE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__Zd;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":269
+ /* "numpy.pxd":273
* elif t == NPY_CFLOAT: f = "Zf"
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<<
@@ -5357,10 +5721,10 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_CLONGDOUBLE);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__Zg;
- goto __pyx_L15;
+ goto __pyx_L13;
}
- /* "numpy.pxd":270
+ /* "numpy.pxd":274
* elif t == NPY_CDOUBLE: f = "Zd"
* elif t == NPY_CLONGDOUBLE: f = "Zg"
* elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<<
@@ -5370,37 +5734,37 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_t == NPY_OBJECT);
if (__pyx_t_1) {
__pyx_v_f = __pyx_k__O;
- goto __pyx_L15;
+ goto __pyx_L13;
}
/*else*/ {
- /* "numpy.pxd":272
+ /* "numpy.pxd":276
* elif t == NPY_OBJECT: f = "O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* info.format = f
* return
*/
- __pyx_t_4 = PyInt_FromLong(__pyx_v_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_24), __pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_24), __pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L15:;
+ __pyx_L13:;
- /* "numpy.pxd":273
+ /* "numpy.pxd":277
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f # <<<<<<<<<<<<<<
@@ -5409,7 +5773,7 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_v_info->format = __pyx_v_f;
- /* "numpy.pxd":274
+ /* "numpy.pxd":278
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* info.format = f
* return # <<<<<<<<<<<<<<
@@ -5418,57 +5782,57 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
*/
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L11;
}
/*else*/ {
- /* "numpy.pxd":276
+ /* "numpy.pxd":280
* return
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<<
- * info.format[0] = '^' # Native data types, manual alignment
+ * info.format[0] = c'^' # Native data types, manual alignment
* offset = 0
*/
__pyx_v_info->format = ((char *)malloc(255));
- /* "numpy.pxd":277
+ /* "numpy.pxd":281
* else:
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
- * info.format[0] = '^' # Native data types, manual alignment # <<<<<<<<<<<<<<
+ * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<<
* offset = 0
* f = _util_dtypestring(descr, info.format + 1,
*/
(__pyx_v_info->format[0]) = '^';
- /* "numpy.pxd":278
+ /* "numpy.pxd":282
* info.format = <char*>stdlib.malloc(_buffer_format_string_len)
- * info.format[0] = '^' # Native data types, manual alignment
+ * info.format[0] = c'^' # Native data types, manual alignment
* offset = 0 # <<<<<<<<<<<<<<
* f = _util_dtypestring(descr, info.format + 1,
* info.format + _buffer_format_string_len,
*/
__pyx_v_offset = 0;
- /* "numpy.pxd":281
+ /* "numpy.pxd":285
* f = _util_dtypestring(descr, info.format + 1,
* info.format + _buffer_format_string_len,
* &offset) # <<<<<<<<<<<<<<
- * f[0] = 0 # Terminate format string
+ * f[0] = c'\0' # Terminate format string
*
*/
- __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_f = __pyx_t_9;
- /* "numpy.pxd":282
+ /* "numpy.pxd":286
* info.format + _buffer_format_string_len,
* &offset)
- * f[0] = 0 # Terminate format string # <<<<<<<<<<<<<<
+ * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<<
*
* def __releasebuffer__(ndarray self, Py_buffer* info):
*/
- (__pyx_v_f[0]) = 0;
+ (__pyx_v_f[0]) = '\x00';
}
- __pyx_L13:;
+ __pyx_L11:;
__pyx_r = 0;
goto __pyx_L0;
@@ -5493,31 +5857,39 @@ static CYTHON_UNUSED int __pyx_pf_5numpy_7ndarray___getbuffer__(PyObject *__pyx_
return __pyx_r;
}
-/* "numpy.pxd":284
- * f[0] = 0 # Terminate format string
+/* Python wrapper */
+static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/
+static CYTHON_UNUSED void __pyx_pw_5numpy_7ndarray_3__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__releasebuffer__ (wrapper)", 0);
+ __pyx_pf_5numpy_7ndarray_2__releasebuffer__(((PyArrayObject *)__pyx_v_self), ((Py_buffer *)__pyx_v_info));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "numpy.pxd":288
+ * f[0] = c'\0' # Terminate format string
*
* def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<<
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format)
*/
-static CYTHON_UNUSED void __pyx_pf_5numpy_7ndarray_1__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info); /*proto*/
-static CYTHON_UNUSED void __pyx_pf_5numpy_7ndarray_1__releasebuffer__(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
+static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info) {
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- __Pyx_RefNannySetupContext("__releasebuffer__");
+ __Pyx_RefNannySetupContext("__releasebuffer__", 0);
- /* "numpy.pxd":285
+ /* "numpy.pxd":289
*
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<<
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
*/
- __pyx_t_1 = PyArray_HASFIELDS(((PyArrayObject *)__pyx_v_self));
+ __pyx_t_1 = PyArray_HASFIELDS(__pyx_v_self);
if (__pyx_t_1) {
- /* "numpy.pxd":286
+ /* "numpy.pxd":290
* def __releasebuffer__(ndarray self, Py_buffer* info):
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format) # <<<<<<<<<<<<<<
@@ -5525,11 +5897,11 @@ static CYTHON_UNUSED void __pyx_pf_5numpy_7ndarray_1__releasebuffer__(PyObject *
* stdlib.free(info.strides)
*/
free(__pyx_v_info->format);
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "numpy.pxd":287
+ /* "numpy.pxd":291
* if PyArray_HASFIELDS(self):
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<<
@@ -5539,7 +5911,7 @@ static CYTHON_UNUSED void __pyx_pf_5numpy_7ndarray_1__releasebuffer__(PyObject *
__pyx_t_1 = ((sizeof(npy_intp)) != (sizeof(Py_ssize_t)));
if (__pyx_t_1) {
- /* "numpy.pxd":288
+ /* "numpy.pxd":292
* stdlib.free(info.format)
* if sizeof(npy_intp) != sizeof(Py_ssize_t):
* stdlib.free(info.strides) # <<<<<<<<<<<<<<
@@ -5547,14 +5919,14 @@ static CYTHON_UNUSED void __pyx_pf_5numpy_7ndarray_1__releasebuffer__(PyObject *
*
*/
free(__pyx_v_info->strides);
- goto __pyx_L6;
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
__Pyx_RefNannyFinishContext();
}
-/* "numpy.pxd":764
+/* "numpy.pxd":768
* ctypedef npy_cdouble complex_t
*
* cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<<
@@ -5569,9 +5941,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("PyArray_MultiIterNew1");
+ __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0);
- /* "numpy.pxd":765
+ /* "numpy.pxd":769
*
* cdef inline object PyArray_MultiIterNew1(a):
* return PyArray_MultiIterNew(1, <void*>a) # <<<<<<<<<<<<<<
@@ -5579,7 +5951,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
* cdef inline object PyArray_MultiIterNew2(a, b):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 765; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(1, ((void *)__pyx_v_a)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5597,7 +5969,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__
return __pyx_r;
}
-/* "numpy.pxd":767
+/* "numpy.pxd":771
* return PyArray_MultiIterNew(1, <void*>a)
*
* cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<<
@@ -5612,9 +5984,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("PyArray_MultiIterNew2");
+ __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0);
- /* "numpy.pxd":768
+ /* "numpy.pxd":772
*
* cdef inline object PyArray_MultiIterNew2(a, b):
* return PyArray_MultiIterNew(2, <void*>a, <void*>b) # <<<<<<<<<<<<<<
@@ -5622,7 +5994,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
* cdef inline object PyArray_MultiIterNew3(a, b, c):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(2, ((void *)__pyx_v_a), ((void *)__pyx_v_b)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5640,7 +6012,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__
return __pyx_r;
}
-/* "numpy.pxd":770
+/* "numpy.pxd":774
* return PyArray_MultiIterNew(2, <void*>a, <void*>b)
*
* cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<<
@@ -5655,9 +6027,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("PyArray_MultiIterNew3");
+ __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0);
- /* "numpy.pxd":771
+ /* "numpy.pxd":775
*
* cdef inline object PyArray_MultiIterNew3(a, b, c):
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c) # <<<<<<<<<<<<<<
@@ -5665,7 +6037,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(3, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5683,7 +6055,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__
return __pyx_r;
}
-/* "numpy.pxd":773
+/* "numpy.pxd":777
* return PyArray_MultiIterNew(3, <void*>a, <void*>b, <void*> c)
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<<
@@ -5698,9 +6070,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("PyArray_MultiIterNew4");
+ __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0);
- /* "numpy.pxd":774
+ /* "numpy.pxd":778
*
* cdef inline object PyArray_MultiIterNew4(a, b, c, d):
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d) # <<<<<<<<<<<<<<
@@ -5708,7 +6080,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(4, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5726,7 +6098,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__
return __pyx_r;
}
-/* "numpy.pxd":776
+/* "numpy.pxd":780
* return PyArray_MultiIterNew(4, <void*>a, <void*>b, <void*>c, <void*> d)
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<<
@@ -5741,9 +6113,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("PyArray_MultiIterNew5");
+ __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0);
- /* "numpy.pxd":777
+ /* "numpy.pxd":781
*
* cdef inline object PyArray_MultiIterNew5(a, b, c, d, e):
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e) # <<<<<<<<<<<<<<
@@ -5751,7 +6123,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyArray_MultiIterNew(5, ((void *)__pyx_v_a), ((void *)__pyx_v_b), ((void *)__pyx_v_c), ((void *)__pyx_v_d), ((void *)__pyx_v_e)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -5769,7 +6141,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__
return __pyx_r;
}
-/* "numpy.pxd":779
+/* "numpy.pxd":783
* return PyArray_MultiIterNew(5, <void*>a, <void*>b, <void*>c, <void*> d, <void*> e)
*
* cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<<
@@ -5792,18 +6164,19 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
+ PyObject *(*__pyx_t_6)(PyObject *);
int __pyx_t_7;
int __pyx_t_8;
int __pyx_t_9;
- long __pyx_t_10;
- char *__pyx_t_11;
+ int __pyx_t_10;
+ long __pyx_t_11;
+ char *__pyx_t_12;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
- __Pyx_RefNannySetupContext("_util_dtypestring");
+ __Pyx_RefNannySetupContext("_util_dtypestring", 0);
- /* "numpy.pxd":786
+ /* "numpy.pxd":790
* cdef int delta_offset
* cdef tuple i
* cdef int endian_detector = 1 # <<<<<<<<<<<<<<
@@ -5812,7 +6185,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_endian_detector = 1;
- /* "numpy.pxd":787
+ /* "numpy.pxd":791
* cdef tuple i
* cdef int endian_detector = 1
* cdef bint little_endian = ((<char*>&endian_detector)[0] != 0) # <<<<<<<<<<<<<<
@@ -5821,7 +6194,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0);
- /* "numpy.pxd":790
+ /* "numpy.pxd":794
* cdef tuple fields
*
* for childname in descr.names: # <<<<<<<<<<<<<<
@@ -5829,31 +6202,36 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* child, new_offset = fields
*/
if (unlikely(((PyObject *)__pyx_v_descr->names) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_t_1 = ((PyObject *)__pyx_v_descr->names); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_childname);
__pyx_v_childname = __pyx_t_3;
__pyx_t_3 = 0;
- /* "numpy.pxd":791
+ /* "numpy.pxd":795
*
* for childname in descr.names:
* fields = descr.fields[childname] # <<<<<<<<<<<<<<
* child, new_offset = fields
*
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected tuple, got %.200s", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyTuple_CheckExact(__pyx_t_3))||((__pyx_t_3) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected tuple, got %.200s", Py_TYPE(__pyx_t_3)->tp_name), 0))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF(((PyObject *)__pyx_v_fields));
__pyx_v_fields = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "numpy.pxd":792
+ /* "numpy.pxd":796
* for childname in descr.names:
* fields = descr.fields[childname]
* child, new_offset = fields # <<<<<<<<<<<<<<
@@ -5862,20 +6240,49 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
if (likely(PyTuple_CheckExact(((PyObject *)__pyx_v_fields)))) {
PyObject* sequence = ((PyObject *)__pyx_v_fields);
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
+ #if CYTHON_COMPILING_IN_CPYTHON
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_4 = PyTuple_GET_ITEM(sequence, 1);
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_4);
- } else {
- __Pyx_UnpackTupleError(((PyObject *)__pyx_v_fields), 2);
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (1) {
+ __Pyx_RaiseNoneNotIterableError(); {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ } else
+ {
+ Py_ssize_t index = -1;
+ __pyx_t_5 = PyObject_GetIter(((PyObject *)__pyx_v_fields)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = Py_TYPE(__pyx_t_5)->tp_iternext;
+ index = 0; __pyx_t_3 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_3);
+ index = 1; __pyx_t_4 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_4);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = NULL;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ goto __pyx_L6_unpacking_done;
+ __pyx_L5_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_unpacking_done:;
}
- if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5numpy_dtype))))) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF(((PyObject *)__pyx_v_child));
__pyx_v_child = ((PyArray_Descr *)__pyx_t_3);
__pyx_t_3 = 0;
@@ -5883,99 +6290,98 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
__pyx_v_new_offset = __pyx_t_4;
__pyx_t_4 = 0;
- /* "numpy.pxd":794
+ /* "numpy.pxd":798
* child, new_offset = fields
*
* if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<<
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
*/
- __pyx_t_4 = PyInt_FromLong((__pyx_v_end - __pyx_v_f)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong((__pyx_v_end - __pyx_v_f)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Subtract(__pyx_v_new_offset, __pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Subtract(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Subtract(__pyx_t_4, __pyx_t_5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_int_15, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_3, __pyx_int_15, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
- /* "numpy.pxd":795
+ /* "numpy.pxd":799
*
* if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
- * if ((child.byteorder == '>' and little_endian) or
+ * if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_t_5 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_26), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_26), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L7;
}
- __pyx_L5:;
+ __pyx_L7:;
- /* "numpy.pxd":797
+ /* "numpy.pxd":801
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd")
*
- * if ((child.byteorder == '>' and little_endian) or # <<<<<<<<<<<<<<
- * (child.byteorder == '<' and not little_endian)):
+ * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<<
+ * (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported")
*/
- __pyx_t_6 = (__pyx_v_child->byteorder == '>');
- if (__pyx_t_6) {
- __pyx_t_7 = __pyx_v_little_endian;
+ __pyx_t_7 = (__pyx_v_child->byteorder == '>');
+ if (__pyx_t_7) {
+ __pyx_t_8 = __pyx_v_little_endian;
} else {
- __pyx_t_7 = __pyx_t_6;
+ __pyx_t_8 = __pyx_t_7;
}
- if (!__pyx_t_7) {
+ if (!__pyx_t_8) {
- /* "numpy.pxd":798
+ /* "numpy.pxd":802
*
- * if ((child.byteorder == '>' and little_endian) or
- * (child.byteorder == '<' and not little_endian)): # <<<<<<<<<<<<<<
+ * if ((child.byteorder == c'>' and little_endian) or
+ * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<<
* raise ValueError(u"Non-native byte order not supported")
* # One could encode it in the format string and have Cython
*/
- __pyx_t_6 = (__pyx_v_child->byteorder == '<');
- if (__pyx_t_6) {
- __pyx_t_8 = (!__pyx_v_little_endian);
- __pyx_t_9 = __pyx_t_8;
+ __pyx_t_7 = (__pyx_v_child->byteorder == '<');
+ if (__pyx_t_7) {
+ __pyx_t_9 = (!__pyx_v_little_endian);
+ __pyx_t_10 = __pyx_t_9;
} else {
- __pyx_t_9 = __pyx_t_6;
+ __pyx_t_10 = __pyx_t_7;
}
- __pyx_t_6 = __pyx_t_9;
+ __pyx_t_7 = __pyx_t_10;
} else {
- __pyx_t_6 = __pyx_t_7;
+ __pyx_t_7 = __pyx_t_8;
}
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
- /* "numpy.pxd":799
- * if ((child.byteorder == '>' and little_endian) or
- * (child.byteorder == '<' and not little_endian)):
+ /* "numpy.pxd":803
+ * if ((child.byteorder == c'>' and little_endian) or
+ * (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_27), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_27), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
}
- __pyx_L6:;
+ __pyx_L8:;
- /* "numpy.pxd":809
+ /* "numpy.pxd":813
*
* # Output padding bytes
* while offset[0] < new_offset: # <<<<<<<<<<<<<<
@@ -5983,16 +6389,15 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* f += 1
*/
while (1) {
- __pyx_t_5 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong((__pyx_v_offset[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_new_offset, Py_LT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_5, __pyx_v_new_offset, Py_LT); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (!__pyx_t_6) break;
+ if (!__pyx_t_7) break;
- /* "numpy.pxd":810
+ /* "numpy.pxd":814
* # Output padding bytes
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<<
@@ -6001,7 +6406,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
(__pyx_v_f[0]) = 120;
- /* "numpy.pxd":811
+ /* "numpy.pxd":815
* while offset[0] < new_offset:
* f[0] = 120 # "x"; pad byte
* f += 1 # <<<<<<<<<<<<<<
@@ -6010,430 +6415,413 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
*/
__pyx_v_f = (__pyx_v_f + 1);
- /* "numpy.pxd":812
+ /* "numpy.pxd":816
* f[0] = 120 # "x"; pad byte
* f += 1
* offset[0] += 1 # <<<<<<<<<<<<<<
*
* offset[0] += child.itemsize
*/
- __pyx_t_10 = 0;
- (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + 1);
+ __pyx_t_11 = 0;
+ (__pyx_v_offset[__pyx_t_11]) = ((__pyx_v_offset[__pyx_t_11]) + 1);
}
- /* "numpy.pxd":814
+ /* "numpy.pxd":818
* offset[0] += 1
*
* offset[0] += child.itemsize # <<<<<<<<<<<<<<
*
* if not PyDataType_HASFIELDS(child):
*/
- __pyx_t_10 = 0;
- (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + __pyx_v_child->elsize);
+ __pyx_t_11 = 0;
+ (__pyx_v_offset[__pyx_t_11]) = ((__pyx_v_offset[__pyx_t_11]) + __pyx_v_child->elsize);
- /* "numpy.pxd":816
+ /* "numpy.pxd":820
* offset[0] += child.itemsize
*
* if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<<
* t = child.type_num
* if end - f < 5:
*/
- __pyx_t_6 = (!PyDataType_HASFIELDS(__pyx_v_child));
- if (__pyx_t_6) {
+ __pyx_t_7 = (!PyDataType_HASFIELDS(__pyx_v_child));
+ if (__pyx_t_7) {
- /* "numpy.pxd":817
+ /* "numpy.pxd":821
*
* if not PyDataType_HASFIELDS(child):
* t = child.type_num # <<<<<<<<<<<<<<
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.")
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_child->type_num); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_child->type_num); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_t);
__pyx_v_t = __pyx_t_3;
__pyx_t_3 = 0;
- /* "numpy.pxd":818
+ /* "numpy.pxd":822
* if not PyDataType_HASFIELDS(child):
* t = child.type_num
* if end - f < 5: # <<<<<<<<<<<<<<
* raise RuntimeError(u"Format string allocated too short.")
*
*/
- __pyx_t_6 = ((__pyx_v_end - __pyx_v_f) < 5);
- if (__pyx_t_6) {
+ __pyx_t_7 = ((__pyx_v_end - __pyx_v_f) < 5);
+ if (__pyx_t_7) {
- /* "numpy.pxd":819
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_t_3 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_29), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_RuntimeError, ((PyObject *)__pyx_k_tuple_29), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L12;
}
- __pyx_L10:;
+ __pyx_L12:;
- /* "numpy.pxd":822
+ /* "numpy.pxd":826
*
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<<
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 98;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":823
+ /* "numpy.pxd":827
* # Until ticket #99 is fixed, use integers to avoid warnings
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<<
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
*/
- __pyx_t_5 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 66;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":824
+ /* "numpy.pxd":828
* if t == NPY_BYTE: f[0] = 98 #"b"
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<<
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 104;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":825
+ /* "numpy.pxd":829
* elif t == NPY_UBYTE: f[0] = 66 #"B"
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<<
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
*/
- __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 72;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":826
+ /* "numpy.pxd":830
* elif t == NPY_SHORT: f[0] = 104 #"h"
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<<
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 105;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":827
+ /* "numpy.pxd":831
* elif t == NPY_USHORT: f[0] = 72 #"H"
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<<
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
*/
- __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 73;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":828
+ /* "numpy.pxd":832
* elif t == NPY_INT: f[0] = 105 #"i"
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<<
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 108;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":829
+ /* "numpy.pxd":833
* elif t == NPY_UINT: f[0] = 73 #"I"
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<<
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
*/
- __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 76;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":830
+ /* "numpy.pxd":834
* elif t == NPY_LONG: f[0] = 108 #"l"
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<<
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGLONG); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 113;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":831
+ /* "numpy.pxd":835
* elif t == NPY_ULONG: f[0] = 76 #"L"
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<<
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
*/
- __pyx_t_5 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_ULONGLONG); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 81;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":832
+ /* "numpy.pxd":836
* elif t == NPY_LONGLONG: f[0] = 113 #"q"
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<<
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_FLOAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 102;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":833
+ /* "numpy.pxd":837
* elif t == NPY_ULONGLONG: f[0] = 81 #"Q"
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<<
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
*/
- __pyx_t_5 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_DOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 100;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":834
+ /* "numpy.pxd":838
* elif t == NPY_FLOAT: f[0] = 102 #"f"
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<<
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
*/
- __pyx_t_3 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_LONGDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 103;
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":835
+ /* "numpy.pxd":839
* elif t == NPY_DOUBLE: f[0] = 100 #"d"
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<<
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
*/
- __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CFLOAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 102;
__pyx_v_f = (__pyx_v_f + 1);
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":836
+ /* "numpy.pxd":840
* elif t == NPY_LONGDOUBLE: f[0] = 103 #"g"
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<<
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O"
*/
- __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_CDOUBLE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 100;
__pyx_v_f = (__pyx_v_f + 1);
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":837
+ /* "numpy.pxd":841
* elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<<
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
*/
- __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(NPY_CLONGDOUBLE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 90;
(__pyx_v_f[1]) = 103;
__pyx_v_f = (__pyx_v_f + 1);
- goto __pyx_L11;
+ goto __pyx_L13;
}
- /* "numpy.pxd":838
+ /* "numpy.pxd":842
* elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd
* elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg
* elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<<
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
*/
- __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(NPY_OBJECT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
(__pyx_v_f[0]) = 79;
- goto __pyx_L11;
+ goto __pyx_L13;
}
/*else*/ {
- /* "numpy.pxd":840
+ /* "numpy.pxd":844
* elif t == NPY_OBJECT: f[0] = 79 #"O"
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<<
* f += 1
* else:
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_24), __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_u_24), __pyx_v_t); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[1]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[1]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L11:;
+ __pyx_L13:;
- /* "numpy.pxd":841
+ /* "numpy.pxd":845
* else:
* raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t)
* f += 1 # <<<<<<<<<<<<<<
@@ -6441,25 +6829,25 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
* # Cython ignores struct boundary information ("T{...}"),
*/
__pyx_v_f = (__pyx_v_f + 1);
- goto __pyx_L9;
+ goto __pyx_L11;
}
/*else*/ {
- /* "numpy.pxd":845
+ /* "numpy.pxd":849
* # Cython ignores struct boundary information ("T{...}"),
* # so don't output it
* f = _util_dtypestring(child, f, end, offset) # <<<<<<<<<<<<<<
* return f
*
*/
- __pyx_t_11 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_11 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_f = __pyx_t_11;
+ __pyx_t_12 = __pyx_f_5numpy__util_dtypestring(__pyx_v_child, __pyx_v_f, __pyx_v_end, __pyx_v_offset); if (unlikely(__pyx_t_12 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_f = __pyx_t_12;
}
- __pyx_L9:;
+ __pyx_L11:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "numpy.pxd":846
+ /* "numpy.pxd":850
* # so don't output it
* f = _util_dtypestring(child, f, end, offset)
* return f # <<<<<<<<<<<<<<
@@ -6488,7 +6876,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx
return __pyx_r;
}
-/* "numpy.pxd":961
+/* "numpy.pxd":965
*
*
* cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<<
@@ -6500,9 +6888,9 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
PyObject *__pyx_v_baseptr;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- __Pyx_RefNannySetupContext("set_array_base");
+ __Pyx_RefNannySetupContext("set_array_base", 0);
- /* "numpy.pxd":963
+ /* "numpy.pxd":967
* cdef inline void set_array_base(ndarray arr, object base):
* cdef PyObject* baseptr
* if base is None: # <<<<<<<<<<<<<<
@@ -6512,7 +6900,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__pyx_t_1 = (__pyx_v_base == Py_None);
if (__pyx_t_1) {
- /* "numpy.pxd":964
+ /* "numpy.pxd":968
* cdef PyObject* baseptr
* if base is None:
* baseptr = NULL # <<<<<<<<<<<<<<
@@ -6524,7 +6912,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
/*else*/ {
- /* "numpy.pxd":966
+ /* "numpy.pxd":970
* baseptr = NULL
* else:
* Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<<
@@ -6533,7 +6921,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_INCREF(__pyx_v_base);
- /* "numpy.pxd":967
+ /* "numpy.pxd":971
* else:
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base # <<<<<<<<<<<<<<
@@ -6544,7 +6932,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
}
__pyx_L3:;
- /* "numpy.pxd":968
+ /* "numpy.pxd":972
* Py_INCREF(base) # important to do this before decref below!
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base) # <<<<<<<<<<<<<<
@@ -6553,7 +6941,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
*/
Py_XDECREF(__pyx_v_arr->base);
- /* "numpy.pxd":969
+ /* "numpy.pxd":973
* baseptr = <PyObject*>base
* Py_XDECREF(arr.base)
* arr.base = baseptr # <<<<<<<<<<<<<<
@@ -6565,7 +6953,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
__Pyx_RefNannyFinishContext();
}
-/* "numpy.pxd":971
+/* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -6577,9 +6965,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- __Pyx_RefNannySetupContext("get_array_base");
+ __Pyx_RefNannySetupContext("get_array_base", 0);
- /* "numpy.pxd":972
+ /* "numpy.pxd":976
*
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL: # <<<<<<<<<<<<<<
@@ -6589,7 +6977,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
__pyx_t_1 = (__pyx_v_arr->base == NULL);
if (__pyx_t_1) {
- /* "numpy.pxd":973
+ /* "numpy.pxd":977
* cdef inline object get_array_base(ndarray arr):
* if arr.base is NULL:
* return None # <<<<<<<<<<<<<<
@@ -6604,7 +6992,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
}
/*else*/ {
- /* "numpy.pxd":975
+ /* "numpy.pxd":979
* return None
* else:
* return <object>arr.base # <<<<<<<<<<<<<<
@@ -6624,7 +7012,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_get_array_base(PyArrayObject *__py
}
static struct __pyx_vtabstruct_25MMTK_trajectory_generator_TrajectoryGenerator __pyx_vtable_25MMTK_trajectory_generator_TrajectoryGenerator;
-static PyObject *__pyx_tp_new_25MMTK_trajectory_generator_TrajectoryGenerator(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_25MMTK_trajectory_generator_TrajectoryGenerator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -6643,14 +7031,14 @@ static PyObject *__pyx_tp_new_25MMTK_trajectory_generator_TrajectoryGenerator(Py
static void __pyx_tp_dealloc_25MMTK_trajectory_generator_TrajectoryGenerator(PyObject *o) {
struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *p = (struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)o;
- Py_XDECREF(p->universe);
- Py_XDECREF(p->options);
- Py_XDECREF(p->name);
- Py_XDECREF(p->call_options);
- Py_XDECREF(p->features);
- Py_XDECREF(p->actions);
- Py_XDECREF(p->state_accessor);
- Py_XDECREF(((PyObject *)p->conf_array));
+ Py_CLEAR(p->universe);
+ Py_CLEAR(p->options);
+ Py_CLEAR(p->name);
+ Py_CLEAR(p->call_options);
+ Py_CLEAR(p->features);
+ Py_CLEAR(p->actions);
+ Py_CLEAR(p->state_accessor);
+ Py_CLEAR(p->conf_array);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -6714,50 +7102,50 @@ static int __pyx_tp_clear_25MMTK_trajectory_generator_TrajectoryGenerator(PyObje
return 0;
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_universe(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_universe(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8universe_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_options(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7options___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_options(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7options_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_name(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4name___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_name(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_4name_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_call_options(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_call_options(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_12call_options_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_features(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_8features___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_features(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_8features_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_actions(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_actions(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7actions_1__get__(o);
}
-static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_state_accessor(PyObject *o, void *x) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor___get__(o);
+static PyObject *__pyx_getprop_25MMTK_trajectory_generator_19TrajectoryGenerator_state_accessor(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__get__(o);
}
-static int __pyx_setprop_25MMTK_trajectory_generator_19TrajectoryGenerator_state_accessor(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_25MMTK_trajectory_generator_19TrajectoryGenerator_state_accessor(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_1__set__(o, v);
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_3__set__(o, v);
}
else {
- return __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_2__del__(o);
+ return __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_14state_accessor_5__del__(o);
}
}
static PyMethodDef __pyx_methods_25MMTK_trajectory_generator_TrajectoryGenerator[] = {
- {__Pyx_NAMESTR("setCallOptions"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_1setCallOptions, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("getActions"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_2getActions, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("cleanupActions"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_3cleanupActions, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("getOption"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_4getOption, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("optionString"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_5optionString, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("start_py"), (PyCFunction)__pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_7start_py, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("setCallOptions"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_3setCallOptions, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("getActions"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_5getActions, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("cleanupActions"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_7cleanupActions, METH_NOARGS, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("getOption"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_9getOption, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("optionString"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_11optionString, METH_O, __Pyx_DOCSTR(0)},
+ {__Pyx_NAMESTR("start_py"), (PyCFunction)__pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_15start_py, METH_NOARGS, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
@@ -6889,7 +7277,7 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator_TrajectoryGenerator =
&__pyx_tp_as_sequence_TrajectoryGenerator, /*tp_as_sequence*/
&__pyx_tp_as_mapping_TrajectoryGenerator, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator_6__call__, /*tp_call*/
+ __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_13__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -6910,7 +7298,7 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator_TrajectoryGenerator =
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_25MMTK_trajectory_generator_19TrajectoryGenerator___init__, /*tp_init*/
+ __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_1__init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_25MMTK_trajectory_generator_TrajectoryGenerator, /*tp_new*/
0, /*tp_free*/
@@ -6940,8 +7328,8 @@ static PyObject *__pyx_tp_new_25MMTK_trajectory_generator_EnergyBasedTrajectoryG
static void __pyx_tp_dealloc_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator(PyObject *o) {
struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *p = (struct __pyx_obj_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator *)o;
- Py_XDECREF(p->evaluator_object);
- Py_XDECREF(p->c_evaluator_object);
+ Py_CLEAR(p->evaluator_object);
+ Py_CLEAR(p->c_evaluator_object);
__pyx_tp_dealloc_25MMTK_trajectory_generator_TrajectoryGenerator(o);
}
@@ -7092,7 +7480,11 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator_EnergyBasedTrajectory
&__pyx_tp_as_sequence_EnergyBasedTrajectoryGenerator, /*tp_as_sequence*/
&__pyx_tp_as_mapping_EnergyBasedTrajectoryGenerator, /*tp_as_mapping*/
0, /*tp_hash*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_25MMTK_trajectory_generator_19TrajectoryGenerator_13__call__, /*tp_call*/
+ #else
0, /*tp_call*/
+ #endif
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -7113,7 +7505,7 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator_EnergyBasedTrajectory
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator___init__, /*tp_init*/
+ __pyx_pw_25MMTK_trajectory_generator_30EnergyBasedTrajectoryGenerator_1__init__, /*tp_init*/
0, /*tp_alloc*/
__pyx_tp_new_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator, /*tp_new*/
0, /*tp_free*/
@@ -7129,7 +7521,7 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator_EnergyBasedTrajectory
#endif
};
-static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct__optionString(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct__optionString(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -7141,8 +7533,8 @@ static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct__op
static void __pyx_tp_dealloc_25MMTK_trajectory_generator___pyx_scope_struct__optionString(PyObject *o) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *p = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *)o;
- Py_XDECREF(p->__pyx_v_options);
- Py_XDECREF(((PyObject *)p->__pyx_v_self));
+ Py_CLEAR(p->__pyx_v_options);
+ Py_CLEAR(p->__pyx_v_self);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -7165,7 +7557,7 @@ static int __pyx_tp_clear_25MMTK_trajectory_generator___pyx_scope_struct__option
p->__pyx_v_options = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->__pyx_v_self);
- p->__pyx_v_self = Py_None; Py_INCREF(Py_None);
+ p->__pyx_v_self = ((struct __pyx_obj_25MMTK_trajectory_generator_TrajectoryGenerator *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
@@ -7328,219 +7720,9 @@ static PyTypeObject __pyx_type_25MMTK_trajectory_generator___pyx_scope_struct__o
#endif
};
-static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_Generator_object *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- p = ((struct __pyx_Generator_object *)o);
- p->exc_type = 0;
- p->exc_value = 0;
- p->exc_traceback = 0;
- return o;
-}
-
-static void __pyx_tp_dealloc_25MMTK_trajectory_generator___pyx_Generator(PyObject *o) {
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- Py_XDECREF(p->exc_type);
- Py_XDECREF(p->exc_value);
- Py_XDECREF(p->exc_traceback);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_25MMTK_trajectory_generator___pyx_Generator(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- if (p->exc_type) {
- e = (*v)(p->exc_type, a); if (e) return e;
- }
- if (p->exc_value) {
- e = (*v)(p->exc_value, a); if (e) return e;
- }
- if (p->exc_traceback) {
- e = (*v)(p->exc_traceback, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_25MMTK_trajectory_generator___pyx_Generator(PyObject *o) {
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->exc_type);
- p->exc_type = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->exc_value);
- p->exc_value = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->exc_traceback);
- p->exc_traceback = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_25MMTK_trajectory_generator___pyx_Generator[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
- {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence___pyx_Generator = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping___pyx_Generator = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_Generator_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("MMTK_trajectory_generator.__pyx_Generator"), /*tp_name*/
- sizeof(struct __pyx_Generator_object), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_25MMTK_trajectory_generator___pyx_Generator, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number___pyx_Generator, /*tp_as_number*/
- &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- 0, /*tp_doc*/
- __pyx_tp_traverse_25MMTK_trajectory_generator___pyx_Generator, /*tp_traverse*/
- __pyx_tp_clear_25MMTK_trajectory_generator___pyx_Generator, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- PyObject_SelfIter, /*tp_iter*/
- __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_methods_25MMTK_trajectory_generator___pyx_Generator, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_25MMTK_trajectory_generator___pyx_Generator, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *p;
- PyObject *o = __pyx_tp_new_25MMTK_trajectory_generator___pyx_Generator(t, a, k);
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
p = ((struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)o);
p->__pyx_outer_scope = 0;
@@ -7551,16 +7733,15 @@ static PyObject *__pyx_tp_new_25MMTK_trajectory_generator___pyx_scope_struct_1_g
static void __pyx_tp_dealloc_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)o;
- Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
- Py_XDECREF(p->__pyx_v_o);
- Py_XDECREF(p->__pyx_t_0);
- __pyx_tp_dealloc_25MMTK_trajectory_generator___pyx_Generator(o);
+ Py_CLEAR(p->__pyx_outer_scope);
+ Py_CLEAR(p->__pyx_v_o);
+ Py_CLEAR(p->__pyx_t_0);
+ (*Py_TYPE(o)->tp_free)(o);
}
static int __pyx_tp_traverse_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)o;
- e = __pyx_tp_traverse_25MMTK_trajectory_generator___pyx_Generator(o, v, a); if (e) return e;
if (p->__pyx_outer_scope) {
e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
}
@@ -7576,7 +7757,6 @@ static int __pyx_tp_traverse_25MMTK_trajectory_generator___pyx_scope_struct_1_ge
static int __pyx_tp_clear_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr *)o;
PyObject* tmp;
- __pyx_tp_clear_25MMTK_trajectory_generator___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_outer_scope);
p->__pyx_outer_scope = ((struct __pyx_obj_25MMTK_trajectory_generator___pyx_scope_struct__optionString *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -7825,7 +8005,7 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_sum = __Pyx_GetName(__pyx_b, __pyx_n_s__sum); if (!__pyx_builtin_sum) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_MemoryError = __Pyx_GetName(__pyx_b, __pyx_n_s__MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_n_s__RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_RuntimeError = __Pyx_GetName(__pyx_b, __pyx_n_s__RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -7833,7 +8013,7 @@ static int __Pyx_InitCachedBuiltins(void) {
static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants");
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
/* "MMTK_trajectory_generator.pyx":47
* def getActions(self):
@@ -7843,7 +8023,7 @@ static int __Pyx_InitCachedConstants(void) {
* steps = None
*/
__pyx_k_tuple_1 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_1));
+ __Pyx_GOTREF(__pyx_k_tuple_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__steps));
PyTuple_SET_ITEM(__pyx_k_tuple_1, 0, ((PyObject *)__pyx_n_s__steps));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__steps));
@@ -7857,7 +8037,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.actions = []
*/
__pyx_k_tuple_7 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_7));
+ __Pyx_GOTREF(__pyx_k_tuple_7);
__Pyx_INCREF(((PyObject *)__pyx_n_s__actions));
PyTuple_SET_ITEM(__pyx_k_tuple_7, 0, ((PyObject *)__pyx_n_s__actions));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__actions));
@@ -7871,7 +8051,7 @@ static int __Pyx_InitCachedConstants(void) {
* self.state_accessor = MMTK_state_accessor.StateAccessor()
*/
__pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_8));
+ __Pyx_GOTREF(__pyx_k_tuple_8);
__Pyx_INCREF(((PyObject *)__pyx_n_s__background));
PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_n_s__background));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__background));
@@ -7885,7 +8065,7 @@ static int __Pyx_InitCachedConstants(void) {
* return ThreadManager.TrajectoryGeneratorThread(
*/
__pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_12));
+ __Pyx_GOTREF(__pyx_k_tuple_12);
__Pyx_INCREF(((PyObject *)__pyx_n_s__background));
PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_n_s__background));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__background));
@@ -7899,7 +8079,7 @@ static int __Pyx_InitCachedConstants(void) {
*
*/
__pyx_k_tuple_15 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_15));
+ __Pyx_GOTREF(__pyx_k_tuple_15);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
PyTuple_SET_ITEM(__pyx_k_tuple_15, 0, ((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
@@ -7913,91 +8093,91 @@ static int __Pyx_InitCachedConstants(void) {
* self.c_evaluator_object = self.evaluator_object.CEvaluator()
*/
__pyx_k_tuple_17 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_17));
+ __Pyx_GOTREF(__pyx_k_tuple_17);
__Pyx_INCREF(((PyObject *)__pyx_n_s__threads));
PyTuple_SET_ITEM(__pyx_k_tuple_17, 0, ((PyObject *)__pyx_n_s__threads));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__threads));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
- /* "numpy.pxd":211
+ /* "numpy.pxd":215
* if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)):
* raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<<
*
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
*/
- __pyx_k_tuple_19 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_19)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_19));
+ __pyx_k_tuple_19 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_19)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_19);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_18));
PyTuple_SET_ITEM(__pyx_k_tuple_19, 0, ((PyObject *)__pyx_kp_u_18));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_18));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
- /* "numpy.pxd":215
+ /* "numpy.pxd":219
* if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS)
* and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)):
* raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<<
*
* info.buf = PyArray_DATA(self)
*/
- __pyx_k_tuple_21 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_21)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_21));
+ __pyx_k_tuple_21 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_21)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_21);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_20));
PyTuple_SET_ITEM(__pyx_k_tuple_21, 0, ((PyObject *)__pyx_kp_u_20));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_20));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_21));
- /* "numpy.pxd":253
- * if ((descr.byteorder == '>' and little_endian) or
- * (descr.byteorder == '<' and not little_endian)):
+ /* "numpy.pxd":257
+ * if ((descr.byteorder == c'>' and little_endian) or
+ * (descr.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* if t == NPY_BYTE: f = "b"
* elif t == NPY_UBYTE: f = "B"
*/
- __pyx_k_tuple_23 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_23));
+ __pyx_k_tuple_23 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_23);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_22));
PyTuple_SET_ITEM(__pyx_k_tuple_23, 0, ((PyObject *)__pyx_kp_u_22));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_22));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
- /* "numpy.pxd":795
+ /* "numpy.pxd":799
*
* if (end - f) - (new_offset - offset[0]) < 15:
* raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<<
*
- * if ((child.byteorder == '>' and little_endian) or
+ * if ((child.byteorder == c'>' and little_endian) or
*/
- __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_26));
+ __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_26);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_25));
PyTuple_SET_ITEM(__pyx_k_tuple_26, 0, ((PyObject *)__pyx_kp_u_25));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_25));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
- /* "numpy.pxd":799
- * if ((child.byteorder == '>' and little_endian) or
- * (child.byteorder == '<' and not little_endian)):
+ /* "numpy.pxd":803
+ * if ((child.byteorder == c'>' and little_endian) or
+ * (child.byteorder == c'<' and not little_endian)):
* raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<<
* # One could encode it in the format string and have Cython
* # complain instead, BUT: < and > in format strings also imply
*/
- __pyx_k_tuple_27 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_27)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_27));
+ __pyx_k_tuple_27 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_27)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_27);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_22));
PyTuple_SET_ITEM(__pyx_k_tuple_27, 0, ((PyObject *)__pyx_kp_u_22));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_22));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_27));
- /* "numpy.pxd":819
+ /* "numpy.pxd":823
* t = child.type_num
* if end - f < 5:
* raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<<
*
* # Until ticket #99 is fixed, use integers to avoid warnings
*/
- __pyx_k_tuple_29 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_29));
+ __pyx_k_tuple_29 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_29);
__Pyx_INCREF(((PyObject *)__pyx_kp_u_28));
PyTuple_SET_ITEM(__pyx_k_tuple_29, 0, ((PyObject *)__pyx_kp_u_28));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_u_28));
@@ -8037,12 +8217,18 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
Py_FatalError("failed to import 'refnanny' module");
}
#endif
- __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)");
+ __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)", 0);
if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #ifdef __pyx_binding_PyCFunctionType_USED
- if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __Pyx_CyFunction_USED
+ if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_FusedFunction_USED
+ if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_Generator_USED
+ if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
@@ -8053,16 +8239,23 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("MMTK_trajectory_generator"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("MMTK_trajectory_generator"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ {
+ PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyDict_GetItemString(modules, "MMTK_trajectory_generator")) {
+ if (unlikely(PyDict_SetItemString(modules, "MMTK_trajectory_generator", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -8111,17 +8304,21 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
__pyx_ptype_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator = &__pyx_type_25MMTK_trajectory_generator_EnergyBasedTrajectoryGenerator;
if (PyType_Ready(&__pyx_type_25MMTK_trajectory_generator___pyx_scope_struct__optionString) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct__optionString = &__pyx_type_25MMTK_trajectory_generator___pyx_scope_struct__optionString;
- if (PyType_Ready(&__pyx_Generator_type) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_25MMTK_trajectory_generator___pyx_Generator = &__pyx_Generator_type;
- __pyx_type_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr.tp_base = __pyx_ptype_25MMTK_trajectory_generator___pyx_Generator;
if (PyType_Ready(&__pyx_type_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr = &__pyx_type_25MMTK_trajectory_generator___pyx_scope_struct_1_genexpr;
/*--- Type import code ---*/
- __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
+ #if CYTHON_COMPILING_IN_PYPY
+ sizeof(PyTypeObject),
+ #else
+ sizeof(PyHeapTypeObject),
+ #endif
+ 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
@@ -8161,14 +8358,18 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
* cimport numpy as N
*/
__pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Features));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Features));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Features));
__pyx_t_2 = __Pyx_Import(((PyObject *)__pyx_n_s__MMTK), ((PyObject *)__pyx_t_1), -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__Features); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__Features);
+ if (__pyx_t_1 == NULL) {
+ if (PyErr_ExceptionMatches(PyExc_AttributeError)) __Pyx_RaiseImportError(__pyx_n_s__Features);
+ if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Features, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -8196,7 +8397,7 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "numpy.pxd":971
+ /* "numpy.pxd":975
* arr.base = baseptr
*
* cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<<
@@ -8223,7 +8424,6 @@ PyMODINIT_FUNC PyInit_MMTK_trajectory_generator(void)
}
/* Runtime support code */
-
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
@@ -8264,7 +8464,6 @@ static void __Pyx_RaiseArgtupleInvalid(
{
Py_ssize_t num_expected;
const char *more_or_less;
-
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
@@ -8276,7 +8475,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -8290,7 +8489,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -8306,55 +8505,77 @@ static int __Pyx_ParseOptionalKeywords(
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
-
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- /* unexpected keyword found */
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
}
+ name++;
}
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
+ }
+ }
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -8375,6 +8596,7 @@ bad:
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -8383,19 +8605,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -8403,10 +8633,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -8418,11 +8651,10 @@ bad:
return -1;
}
-
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
-
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
@@ -8432,55 +8664,60 @@ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyOb
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_Restore(type, value, tb);
+#endif
}
-
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
-
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(type, value, tb);
+#endif
}
-
#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- /* cause is unused */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -8503,7 +8740,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
#endif
}
-
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
@@ -8512,10 +8748,9 @@ raise_error:
Py_XDECREF(tb);
return;
}
-
#else /* Python 3+ */
-
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -8525,7 +8760,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
if (value == Py_None)
value = 0;
-
if (PyExceptionInstance_Check(type)) {
if (value) {
PyErr_SetString(PyExc_TypeError,
@@ -8534,13 +8768,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -8557,14 +8814,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
-
PyErr_SetObject(type, value);
-
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
@@ -8574,8 +8826,8 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
Py_XDECREF(tmp_tb);
}
}
-
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
@@ -8591,13 +8843,17 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
{
PyObject* key = 0;
Py_ssize_t pos = 0;
+#if CPYTHON_COMPILING_IN_PYPY
+ if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
+ goto invalid_keyword;
+ return 1;
+#else
while (PyDict_Next(kwdict, &pos, &key, 0)) {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
- goto invalid_keyword_type;
+ if (unlikely(!PyUnicode_Check(key)))
+ goto invalid_keyword_type;
}
if ((!kw_allowed) && unlikely(key))
goto invalid_keyword;
@@ -8606,6 +8862,7 @@ invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
return 0;
+#endif
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
@@ -8634,18 +8891,6 @@ static CYTHON_INLINE int __Pyx_IsLittleEndian(void) {
unsigned int n = 1;
return *(unsigned char*)(&n) != 0;
}
-
-typedef struct {
- __Pyx_StructField root;
- __Pyx_BufFmt_StackElem* head;
- size_t fmt_offset;
- size_t new_count, enc_count;
- int is_complex;
- char enc_type;
- char new_packmode;
- char enc_packmode;
-} __Pyx_BufFmt_Context;
-
static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
__Pyx_BufFmt_StackElem* stack,
__Pyx_TypeInfo* type) {
@@ -8664,6 +8909,8 @@ static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
ctx->enc_count = 0;
ctx->enc_type = 0;
ctx->is_complex = 0;
+ ctx->is_valid_array = 0;
+ ctx->struct_alignment = 0;
while (type->typegroup == 'S') {
++ctx->head;
ctx->head->field = type->fields;
@@ -8671,7 +8918,6 @@ static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
type = type->fields->type;
}
}
-
static int __Pyx_BufFmt_ParseNumber(const char** ts) {
int count;
const char* t = *ts;
@@ -8687,15 +8933,21 @@ static int __Pyx_BufFmt_ParseNumber(const char** ts) {
*ts = t;
return count;
}
-
+static int __Pyx_BufFmt_ExpectNumber(const char **ts) {
+ int number = __Pyx_BufFmt_ParseNumber(ts);
+ if (number == -1) /* First char was not a digit */
+ PyErr_Format(PyExc_ValueError,\
+ "Does not understand character buffer dtype format string ('%c')", **ts);
+ return number;
+}
static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) {
PyErr_Format(PyExc_ValueError,
"Unexpected format string character: '%c'", ch);
}
-
static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
switch (ch) {
- case 'b': return "'char'";
+ case 'c': return "'char'";
+ case 'b': return "'signed char'";
case 'B': return "'unsigned char'";
case 'h': return "'short'";
case 'H': return "'unsigned short'";
@@ -8711,14 +8963,14 @@ static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) {
case 'T': return "a struct";
case 'O': return "Python object";
case 'P': return "a pointer";
+ case 's': case 'p': return "a string";
case 0: return "end";
default: return "unparseable format string";
}
}
-
static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
switch (ch) {
- case '?': case 'c': case 'b': case 'B': return 1;
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
case 'h': case 'H': return 2;
case 'i': case 'I': case 'l': case 'L': return 4;
case 'q': case 'Q': return 8;
@@ -8734,10 +8986,9 @@ static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) {
return 0;
}
}
-
static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
switch (ch) {
- case 'c': case 'b': case 'B': return 1;
+ case 'c': case 'b': case 'B': case 's': case 'p': return 1;
case 'h': case 'H': return sizeof(short);
case 'i': case 'I': return sizeof(int);
case 'l': case 'L': return sizeof(long);
@@ -8754,7 +9005,6 @@ static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) {
}
}
}
-
typedef struct { char c; short x; } __Pyx_st_short;
typedef struct { char c; int x; } __Pyx_st_int;
typedef struct { char c; long x; } __Pyx_st_long;
@@ -8765,10 +9015,9 @@ typedef struct { char c; void *x; } __Pyx_st_void_p;
#ifdef HAVE_LONG_LONG
typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong;
#endif
-
-static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, int is_complex) {
+static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
switch (ch) {
- case '?': case 'c': case 'b': case 'B': return 1;
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
@@ -8784,21 +9033,59 @@ static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, int is_complex) {
return 0;
}
}
-
+/* These are for computing the padding at the end of the struct to align
+ on the first member of the struct. This will probably the same as above,
+ but we don't have any guarantees.
+ */
+typedef struct { short x; char c; } __Pyx_pad_short;
+typedef struct { int x; char c; } __Pyx_pad_int;
+typedef struct { long x; char c; } __Pyx_pad_long;
+typedef struct { float x; char c; } __Pyx_pad_float;
+typedef struct { double x; char c; } __Pyx_pad_double;
+typedef struct { long double x; char c; } __Pyx_pad_longdouble;
+typedef struct { void *x; char c; } __Pyx_pad_void_p;
+#ifdef HAVE_LONG_LONG
+typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
+#endif
+static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
switch (ch) {
- case 'c': case 'b': case 'h': case 'i': case 'l': case 'q': return 'I';
- case 'B': case 'H': case 'I': case 'L': case 'Q': return 'U';
- case 'f': case 'd': case 'g': return (is_complex ? 'C' : 'R');
- case 'O': return 'O';
- case 'P': return 'P';
+ case 'c':
+ return 'H';
+ case 'b': case 'h': case 'i':
+ case 'l': case 'q': case 's': case 'p':
+ return 'I';
+ case 'B': case 'H': case 'I': case 'L': case 'Q':
+ return 'U';
+ case 'f': case 'd': case 'g':
+ return (is_complex ? 'C' : 'R');
+ case 'O':
+ return 'O';
+ case 'P':
+ return 'P';
default: {
__Pyx_BufFmt_RaiseUnexpectedChar(ch);
return 0;
}
}
}
-
static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
if (ctx->head == NULL || ctx->head->field == &ctx->root) {
const char* expected;
@@ -8823,16 +9110,37 @@ static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
parent->type->name, field->name);
}
}
-
static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
char group;
- size_t size, offset;
+ size_t size, offset, arraysize = 1;
if (ctx->enc_type == 0) return 0;
+ if (ctx->head->field->type->arraysize[0]) {
+ int i, ndim = 0;
+ if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
+ ctx->is_valid_array = ctx->head->field->type->ndim == 1;
+ ndim = 1;
+ if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %zu",
+ ctx->head->field->type->arraysize[0], ctx->enc_count);
+ return -1;
+ }
+ }
+ if (!ctx->is_valid_array) {
+ PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
+ ctx->head->field->type->ndim, ndim);
+ return -1;
+ }
+ for (i = 0; i < ctx->head->field->type->ndim; i++) {
+ arraysize *= ctx->head->field->type->arraysize[i];
+ }
+ ctx->is_valid_array = 0;
+ ctx->enc_count = 1;
+ }
group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
do {
__Pyx_StructField* field = ctx->head->field;
__Pyx_TypeInfo* type = field->type;
-
if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
} else {
@@ -8844,35 +9152,35 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
if (align_at == 0) return -1;
align_mod_offset = ctx->fmt_offset % align_at;
if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
+ if (ctx->struct_alignment == 0)
+ ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
+ ctx->is_complex);
}
-
if (type->size != size || type->typegroup != group) {
if (type->typegroup == 'C' && type->fields != NULL) {
- /* special case -- treat as struct rather than complex number */
size_t parent_offset = ctx->head->parent_offset + field->offset;
++ctx->head;
ctx->head->field = type->fields;
ctx->head->parent_offset = parent_offset;
continue;
}
-
- __Pyx_BufFmt_RaiseExpected(ctx);
- return -1;
+ if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
+ } else {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
}
-
offset = ctx->head->parent_offset + field->offset;
if (ctx->fmt_offset != offset) {
PyErr_Format(PyExc_ValueError,
- "Buffer dtype mismatch; next field is at offset %"PY_FORMAT_SIZE_T"d but %"PY_FORMAT_SIZE_T"d expected",
+ "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
(Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
return -1;
}
-
ctx->fmt_offset += size;
-
+ if (arraysize)
+ ctx->fmt_offset += (arraysize - 1) * size;
--ctx->enc_count; /* Consume from buffer string */
-
- /* Done checking, move to next field, pushing or popping struct stack if needed */
while (1) {
if (field == &ctx->root) {
ctx->head = NULL;
@@ -8904,7 +9212,48 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
ctx->is_complex = 0;
return 0;
}
-
+static CYTHON_INLINE PyObject *
+__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
+{
+ const char *ts = *tsp;
+ int i = 0, number;
+ int ndim = ctx->head->field->type->ndim;
+;
+ ++ts;
+ if (ctx->new_count != 1) {
+ PyErr_SetString(PyExc_ValueError,
+ "Cannot handle repeated arrays in format string");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ while (*ts && *ts != ')') {
+ if (isspace(*ts))
+ continue;
+ number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %d",
+ ctx->head->field->type->arraysize[i], number);
+ if (*ts != ',' && *ts != ')')
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a comma in format string, got '%c'", *ts);
+ if (*ts == ',') ts++;
+ i++;
+ }
+ if (i != ndim)
+ return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
+ ctx->head->field->type->ndim, i);
+ if (!*ts) {
+ PyErr_SetString(PyExc_ValueError,
+ "Unexpected end of format string, expected ')'");
+ return NULL;
+ }
+ ctx->is_valid_array = 1;
+ ctx->new_count = 1;
+ *tsp = ++ts;
+ return Py_None;
+}
static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
int got_Z = 0;
while (1) {
@@ -8919,7 +9268,7 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
__Pyx_BufFmt_RaiseExpected(ctx);
return NULL;
}
- return ts;
+ return ts;
case ' ':
case 10:
case 13:
@@ -8951,12 +9300,17 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
{
const char* ts_after_sub;
size_t i, struct_count = ctx->new_count;
+ size_t struct_alignment = ctx->struct_alignment;
ctx->new_count = 1;
++ts;
if (*ts != '{') {
PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
return NULL;
}
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0; /* Erase processed last struct element */
+ ctx->enc_count = 0;
+ ctx->struct_alignment = 0;
++ts;
ts_after_sub = ts;
for (i = 0; i != struct_count; ++i) {
@@ -8964,10 +9318,19 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
if (!ts_after_sub) return NULL;
}
ts = ts_after_sub;
+ if (struct_alignment) ctx->struct_alignment = struct_alignment;
}
break;
case '}': /* end of substruct; either repeat or move on */
- ++ts;
+ {
+ size_t alignment = ctx->struct_alignment;
+ ++ts;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0; /* Erase processed last struct element */
+ if (alignment && ctx->fmt_offset % alignment) {
+ ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
+ }
+ }
return ts;
case 'x':
if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
@@ -8988,13 +9351,11 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
case 'l': case 'L': case 'q': case 'Q':
case 'f': case 'd': case 'g':
- case 'O':
+ case 'O': case 's': case 'p':
if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
ctx->enc_packmode == ctx->new_packmode) {
- /* Continue pooling same type */
ctx->enc_count += ctx->new_count;
} else {
- /* New type */
if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
ctx->enc_count = ctx->new_count;
ctx->enc_packmode = ctx->new_packmode;
@@ -9010,20 +9371,18 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha
while(*ts != ':') ++ts;
++ts;
break;
+ case '(':
+ if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
+ break;
default:
{
- int number = __Pyx_BufFmt_ParseNumber(&ts);
- if (number == -1) { /* First char was not a digit */
- PyErr_Format(PyExc_ValueError,
- "Does not understand character buffer dtype format string ('%c')", *ts);
- return NULL;
- }
- ctx->new_count = (size_t)number;
+ int number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ ctx->new_count = (size_t)number;
}
}
}
}
-
static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
buf->buf = NULL;
buf->obj = NULL;
@@ -9031,8 +9390,10 @@ static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
buf->shape = __Pyx_zeros;
buf->suboffsets = __Pyx_minusones;
}
-
-static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack) {
+static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
+ Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
+ int nd, int cast, __Pyx_BufFmt_StackElem* stack)
+{
if (obj == Py_None || obj == NULL) {
__Pyx_ZeroBuffer(buf);
return 0;
@@ -9052,7 +9413,7 @@ static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* ob
}
if ((unsigned)buf->itemsize != dtype->size) {
PyErr_Format(PyExc_ValueError,
- "Item size of buffer (%"PY_FORMAT_SIZE_T"d byte%s) does not match size of '%s' (%"PY_FORMAT_SIZE_T"d byte%s)",
+ "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
buf->itemsize, (buf->itemsize > 1) ? "s" : "",
dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
goto fail;
@@ -9063,39 +9424,74 @@ fail:;
__Pyx_ZeroBuffer(buf);
return -1;
}
-
static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
if (info->buf == NULL) return;
if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
__Pyx_ReleaseBuffer(info);
}
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
- index, (index == 1) ? "" : "s");
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ index, (index == 1) ? "" : "s");
}
static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
}
-static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
- if (t == Py_None) {
- __Pyx_RaiseNoneNotIterableError();
- } else if (PyTuple_GET_SIZE(t) < index) {
- __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
} else {
- __Pyx_RaiseTooManyValuesError(index);
+ return __Pyx_IterFinish();
}
+ return 0;
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -9103,9 +9499,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
-
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -9117,35 +9516,85 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
#if PY_MAJOR_VERSION < 3
static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ CYTHON_UNUSED PyObject *getbuffer_cobj;
#if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
+ if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
#endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pf_5numpy_7ndarray___getbuffer__(obj, view, flags);
- else {
- PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
- return -1;
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_getbuffer"))) {
+ getbufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (getbufferproc) PyCapsule_GetPointer(getbuffer_cobj, "getbuffer(obj, view, flags)");
+ #else
+ func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj);
+ #endif
+ Py_DECREF(getbuffer_cobj);
+ if (!func)
+ goto fail;
+ return func(obj, view, flags);
+ } else {
+ PyErr_Clear();
}
+ #endif
+ PyErr_Format(PyExc_TypeError, "'%100s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+#if PY_VERSION_HEX < 0x02060000
+fail:
+#endif
+ return -1;
}
-
static void __Pyx_ReleaseBuffer(Py_buffer *view) {
- PyObject* obj = view->obj;
- if (obj) {
- #if PY_VERSION_HEX >= 0x02060000
- if (PyObject_CheckBuffer(obj)) {PyBuffer_Release(view); return;}
- #endif
- if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) __pyx_pf_5numpy_7ndarray_1__releasebuffer__(obj, view);
+ PyObject *obj = view->obj;
+ CYTHON_UNUSED PyObject *releasebuffer_cobj;
+ if (!obj) return;
+ #if PY_VERSION_HEX >= 0x02060000
+ if (PyObject_CheckBuffer(obj)) {
+ PyBuffer_Release(view);
+ return;
+ }
+ #endif
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
+ #if PY_VERSION_HEX < 0x02060000
+ if (obj->ob_type->tp_dict &&
+ (releasebuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict,
+ "__pyx_releasebuffer"))) {
+ releasebufferproc func;
+ #if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0)
+ func = (releasebufferproc) PyCapsule_GetPointer(releasebuffer_cobj, "releasebuffer(obj, view)");
+ #else
+ func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj);
+ #endif
+ Py_DECREF(releasebuffer_cobj);
+ if (!func)
+ goto fail;
+ func(obj, view);
+ return;
+ } else {
+ PyErr_Clear();
+ }
+ #endif
+ goto nofail;
+#if PY_VERSION_HEX < 0x02060000
+fail:
+#endif
+ PyErr_WriteUnraisable(obj);
+nofail:
Py_DECREF(obj);
view->obj = NULL;
- }
}
+#endif /* PY_MAJOR_VERSION < 3 */
-#endif
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
PyObject *py_import = 0;
PyObject *empty_list = 0;
PyObject *module = 0;
@@ -9171,12 +9620,33 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
goto bad;
#if PY_VERSION_HEX >= 0x02050000
{
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ /* try package relative import first */
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0; /* try absolute import on failure */
+ }
+ #endif
+ if (!module) {
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ }
}
#else
if (level>0) {
@@ -9193,6 +9663,15 @@ bad:
return module;
}
+static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
+#if PY_MAJOR_VERSION < 3
+ PyErr_Format(PyExc_ImportError, "cannot import name %.230s",
+ PyString_AsString(name));
+#else
+ PyErr_Format(PyExc_ImportError, "cannot import name %S", name);
+#endif
+}
+
#if CYTHON_CCOMPLEX
#ifdef __cplusplus
static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
@@ -9835,125 +10314,522 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
-
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
-
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-
+#else
+ PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
+ PyErr_SetExcInfo(*type, *value, *tb);
+#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
-{
- Py_XDECREF(self->exc_type);
- Py_XDECREF(self->exc_value);
- Py_XDECREF(self->exc_traceback);
-
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
+static PyTypeObject *__pyx_GeneratorType = 0;
+#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
+#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
+ PyObject *et, *ev, *tb;
+ PyObject *value = NULL;
+ __Pyx_ErrFetch(&et, &ev, &tb);
+ if (!et) {
+ Py_XDECREF(tb);
+ Py_XDECREF(ev);
+ Py_INCREF(Py_None);
+ *pvalue = Py_None;
+ return 0;
+ }
+ if (unlikely(et != PyExc_StopIteration) &&
+ unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ if (likely(et == PyExc_StopIteration)) {
+ if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
+ if (!ev) {
+ Py_INCREF(Py_None);
+ ev = Py_None;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+ *pvalue = ev;
+ return 0;
+ }
+ }
+ PyErr_NormalizeException(&et, &ev, &tb);
+ if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+#if PY_VERSION_HEX >= 0x030300A0
+ value = ((PyStopIterationObject *)ev)->value;
+ Py_INCREF(value);
+ Py_DECREF(ev);
+#else
+ {
+ PyObject* args = PyObject_GetAttrString(ev, "args");
+ Py_DECREF(ev);
+ if (likely(args)) {
+ value = PyObject_GetItem(args, 0);
+ Py_DECREF(args);
+ }
+ if (unlikely(!value)) {
+ __Pyx_ErrRestore(NULL, NULL, NULL);
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+ }
+#endif
+ *pvalue = value;
+ return 0;
+}
+#endif
+static CYTHON_INLINE
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
+ PyObject *exc_type = self->exc_type;
+ PyObject *exc_value = self->exc_value;
+ PyObject *exc_traceback = self->exc_traceback;
self->exc_type = NULL;
self->exc_value = NULL;
self->exc_traceback = NULL;
+ Py_XDECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_traceback);
}
-
-static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
-{
- PyObject *retval;
-
- if (self->is_running) {
+static CYTHON_INLINE
+int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
+ if (unlikely(gen->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return NULL;
+ return 1;
}
-
- if (self->resume_label == 0) {
- if (value && value != Py_None) {
+ return 0;
+}
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
+ PyObject *retval;
+ assert(!self->is_running);
+ if (unlikely(self->resume_label == 0)) {
+ if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
"can't send non-None value to a "
"just-started generator");
return NULL;
}
}
-
- if (self->resume_label == -1) {
+ if (unlikely(self->resume_label == -1)) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
-
-
- if (value)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (value) {
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Generators always return to their most recent caller, not
+ * necessarily their creator. */
+ if (self->exc_traceback) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_XINCREF(tstate->frame);
+ assert(f->f_back == NULL);
+ f->f_back = tstate->frame;
+ }
+#endif
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+ } else {
__Pyx_Generator_ExceptionClear(self);
-
+ }
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
-
- if (retval)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (retval) {
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Don't keep the reference to f_back any longer than necessary. It
+ * may keep a chain of frames alive or it could create a reference
+ * cycle. */
+ if (self->exc_traceback) {
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_CLEAR(f->f_back);
+ }
+#endif
+ } else {
__Pyx_Generator_ExceptionClear(self);
-
+ }
return retval;
}
-
-static PyObject *__Pyx_Generator_Next(PyObject *self)
-{
- return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
+ PyObject *ret;
+ PyObject *val = NULL;
+ __Pyx_Generator_Undelegate(gen);
+ __Pyx_PyGen_FetchStopIterationValue(&val);
+ ret = __Pyx_Generator_SendEx(gen, val);
+ Py_XDECREF(val);
+ return ret;
+}
+static PyObject *__Pyx_Generator_Next(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ ret = Py_TYPE(yf)->tp_iternext(yf);
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, Py_None);
}
-
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
-{
- return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Send(yf, value);
+ } else {
+ if (value == Py_None)
+ ret = PyIter_Next(yf);
+ else
+ ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
+ }
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, value);
}
-
-static PyObject *__Pyx_Generator_Close(PyObject *self)
-{
- struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
- PyObject *retval;
+static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
+ PyObject *retval = NULL;
+ int err = 0;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ retval = __Pyx_Generator_Close(yf);
+ if (!retval)
+ return -1;
+ } else {
+ PyObject *meth;
+ gen->is_running = 1;
+ meth = PyObject_GetAttrString(yf, "close");
+ if (unlikely(!meth)) {
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_WriteUnraisable(yf);
+ }
+ PyErr_Clear();
+ } else {
+ retval = PyObject_CallFunction(meth, NULL);
+ Py_DECREF(meth);
+ if (!retval)
+ err = -1;
+ }
+ gen->is_running = 0;
+ }
+ Py_XDECREF(retval);
+ return err;
+}
+static PyObject *__Pyx_Generator_Close(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject *retval, *raised_exception;
+ PyObject *yf = gen->yieldfrom;
+ int err = 0;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ Py_INCREF(yf);
+ err = __Pyx_Generator_CloseIter(gen, yf);
+ __Pyx_Generator_Undelegate(gen);
+ Py_DECREF(yf);
+ }
+ if (err == 0)
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(generator, NULL);
+ retval = __Pyx_Generator_SendEx(gen, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
-#if PY_VERSION_HEX < 0x02050000
- if (PyErr_ExceptionMatches(PyExc_StopIteration))
-#else
- if (PyErr_ExceptionMatches(PyExc_StopIteration)
- || PyErr_ExceptionMatches(PyExc_GeneratorExit))
+ raised_exception = PyErr_Occurred();
+ if (!raised_exception
+ || raised_exception == PyExc_StopIteration
+#if PY_VERSION_HEX >= 0x02050000
+ || raised_exception == PyExc_GeneratorExit
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
#endif
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- PyErr_Clear(); /* ignore these errors */
+ if (raised_exception) PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
-{
- struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
-
+ PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ Py_INCREF(yf);
+#if PY_VERSION_HEX >= 0x02050000
+ if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
+ int err = __Pyx_Generator_CloseIter(gen, yf);
+ Py_DECREF(yf);
+ __Pyx_Generator_Undelegate(gen);
+ if (err < 0)
+ return __Pyx_Generator_SendEx(gen, NULL);
+ goto throw_here;
+ }
+#endif
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Throw(yf, args);
+ } else {
+ PyObject *meth = PyObject_GetAttrString(yf, "throw");
+ if (unlikely(!meth)) {
+ Py_DECREF(yf);
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ gen->is_running = 0;
+ return NULL;
+ }
+ PyErr_Clear();
+ __Pyx_Generator_Undelegate(gen);
+ gen->is_running = 0;
+ goto throw_here;
+ }
+ ret = PyObject_CallObject(meth, args);
+ Py_DECREF(meth);
+ }
+ gen->is_running = 0;
+ Py_DECREF(yf);
+ if (!ret) {
+ ret = __Pyx_Generator_FinishDelegation(gen);
+ }
+ return ret;
+ }
+throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(generator, NULL);
+ return __Pyx_Generator_SendEx(gen, NULL);
+}
+static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_VISIT(gen->closure);
+ Py_VISIT(gen->classobj);
+ Py_VISIT(gen->yieldfrom);
+ Py_VISIT(gen->exc_type);
+ Py_VISIT(gen->exc_value);
+ Py_VISIT(gen->exc_traceback);
+ return 0;
+}
+static int __Pyx_Generator_clear(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->yieldfrom);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
+ return 0;
+}
+static void __Pyx_Generator_dealloc(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject_GC_UnTrack(gen);
+ if (gen->gi_weakreflist != NULL)
+ PyObject_ClearWeakRefs(self);
+ PyObject_GC_Track(self);
+ if (gen->resume_label > 0) {
+ Py_TYPE(gen)->tp_del(self);
+ if (self->ob_refcnt > 0)
+ return; /* resurrected. :( */
+ }
+ PyObject_GC_UnTrack(self);
+ __Pyx_Generator_clear(self);
+ PyObject_GC_Del(gen);
+}
+static void __Pyx_Generator_del(PyObject *self) {
+ PyObject *res;
+ PyObject *error_type, *error_value, *error_traceback;
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ if (gen->resume_label <= 0)
+ return ;
+ assert(self->ob_refcnt == 0);
+ self->ob_refcnt = 1;
+ __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
+ res = __Pyx_Generator_Close(self);
+ if (res == NULL)
+ PyErr_WriteUnraisable(self);
+ else
+ Py_DECREF(res);
+ __Pyx_ErrRestore(error_type, error_value, error_traceback);
+ /* Undo the temporary resurrection; can't use DECREF here, it would
+ * cause a recursive call.
+ */
+ assert(self->ob_refcnt > 0);
+ if (--self->ob_refcnt == 0)
+ return; /* this is the normal path out */
+ /* close() resurrected it! Make it look like the original Py_DECREF
+ * never happened.
+ */
+ {
+ Py_ssize_t refcnt = self->ob_refcnt;
+ _Py_NewReference(self);
+ self->ob_refcnt = refcnt;
+ }
+#if CYTHON_COMPILING_FOR_CPYTHON
+ assert(PyType_IS_GC(self->ob_type) &&
+ _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
+ /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
+ * we need to undo that. */
+ _Py_DEC_REFTOTAL;
+#endif
+ /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
+ * chain, so no more to do there.
+ * If COUNT_ALLOCS, the original decref bumped tp_frees, and
+ * _Py_NewReference bumped tp_allocs: both of those need to be
+ * undone.
+ */
+#ifdef COUNT_ALLOCS
+ --Py_TYPE(self)->tp_frees;
+ --Py_TYPE(self)->tp_allocs;
+#endif
+}
+static PyMemberDef __pyx_Generator_memberlist[] = {
+ {(char *) "gi_running",
+#if PY_VERSION_HEX >= 0x02060000
+ T_BOOL,
+#else
+ T_BYTE,
+#endif
+ offsetof(__pyx_GeneratorObject, is_running),
+ READONLY,
+ NULL},
+ {0, 0, 0, 0, 0}
+};
+static PyMethodDef __pyx_Generator_methods[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
+ {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
+ {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyTypeObject __pyx_GeneratorType_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("generator"), /*tp_name*/
+ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+#else
+ 0, /*reserved*/
+#endif
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+ 0, /*tp_doc*/
+ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
+ 0, /*tp_iter*/
+ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
+ __pyx_Generator_methods, /*tp_methods*/
+ __pyx_Generator_memberlist, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ 0, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ __Pyx_Generator_del, /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+#endif
+};
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure) {
+ __pyx_GeneratorObject *gen =
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
+ if (gen == NULL)
+ return NULL;
+ gen->body = body;
+ gen->closure = closure;
+ Py_XINCREF(closure);
+ gen->is_running = 0;
+ gen->resume_label = 0;
+ gen->classobj = NULL;
+ gen->yieldfrom = NULL;
+ gen->exc_type = NULL;
+ gen->exc_value = NULL;
+ gen->exc_traceback = NULL;
+ gen->gi_weakreflist = NULL;
+ PyObject_GC_Track(gen);
+ return gen;
+}
+static int __pyx_Generator_init(void) {
+ __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
+ __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
+ if (PyType_Ready(&__pyx_GeneratorType_type)) {
+ return -1;
+ }
+ __pyx_GeneratorType = &__pyx_GeneratorType_type;
+ return 0;
}
static int __Pyx_check_binary_version(void) {
@@ -9975,6 +10851,23 @@ static int __Pyx_check_binary_version(void) {
return 0;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -9984,15 +10877,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
-
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(class_name);
- #else
- py_name = PyUnicode_FromString(class_name);
- #endif
+ py_name = __Pyx_PyIdentifier_FromString(class_name);
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
@@ -10008,7 +10896,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) {
+ if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -10018,7 +10906,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) {
+ else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -10032,28 +10920,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(name);
- #else
- py_name = PyUnicode_FromString(name);
- #endif
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
PyObject *ob = PyCapsule_New(vtable, 0, 0);
@@ -10071,29 +10937,105 @@ bad:
return -1;
}
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-
-static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
- int __pyx_lineno, const char *__pyx_filename) {
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
- PyObject *py_globals = 0;
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
-
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(__pyx_filename);
+ py_srcfile = PyString_FromString(filename);
#else
- py_srcfile = PyUnicode_FromString(__pyx_filename);
+ py_srcfile = PyUnicode_FromString(filename);
#endif
if (!py_srcfile) goto bad;
- if (__pyx_clineno) {
+ if (c_line) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#endif
}
else {
@@ -10104,28 +11046,45 @@ static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
#endif
}
if (!py_funcname) goto bad;
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_code = PyCode_New(
+ py_code = __Pyx_PyCode_New(
0, /*int argcount,*/
- #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
- #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- __pyx_lineno, /*int firstlineno,*/
+ py_line, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- if (!py_code) goto bad;
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
@@ -10133,11 +11092,9 @@ static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = __pyx_lineno;
+ py_frame->f_lineno = py_line;
PyTraceBack_Here(py_frame);
bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
@@ -10172,6 +11129,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
+
/* Type Conversion Functions */
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
diff --git a/Tools/add_amber12_atom_types.py b/Tools/add_amber12_atom_types.py
new file mode 100644
index 0000000..dc68c93
--- /dev/null
+++ b/Tools/add_amber12_atom_types.py
@@ -0,0 +1,181 @@
+import compiler
+import compiler.ast
+
+groups = ['ace_beginning_nt',
+ 'adenine',
+ 'ala_sidechain',
+ 'alanine',
+ 'alanine_ct',
+ 'alanine_nt',
+ 'arg_sidechain',
+ 'arginine',
+ 'arginine_ct',
+ 'arginine_nt',
+ 'asn_sidechain',
+ 'asp_sidechain',
+ 'asp_sidechain_neutral',
+ 'asparagine',
+ 'asparagine_ct',
+ 'asparagine_nt',
+ 'aspartic_acid',
+ 'aspartic_acid_ct',
+ 'aspartic_acid_neutral',
+ 'aspartic_acid_nt',
+ 'cym_sidechain',
+ 'cys_sidechain',
+ 'cysteine',
+ 'cysteine_ct',
+ 'cysteine_nt',
+ 'cysteine_with_negative_charge',
+ 'cystine_ss',
+ 'cystine_ss_ct',
+ 'cystine_ss_nt',
+ 'cytosine',
+ 'cyx_sidechain',
+ 'd-adenosine',
+ 'd-adenosine_3ter',
+ 'd-adenosine_5ter',
+ 'd-adenosine_5ter_3ter',
+ 'd-cytosine',
+ 'd-cytosine_3ter',
+ 'd-cytosine_5ter',
+ 'd-cytosine_5ter_3ter',
+ 'd-guanosine',
+ 'd-guanosine_3ter',
+ 'd-guanosine_5ter',
+ 'd-guanosine_5ter_3ter',
+ 'd-thymine',
+ 'd-thymine_3ter',
+ 'd-thymine_5ter',
+ 'd-thymine_5ter_3ter',
+ 'desoxyribose',
+ 'desoxyribose_3ter',
+ 'desoxyribose_5ter',
+ 'desoxyribose_5ter_3ter',
+ 'gln_sidechain',
+ 'glu_sidechain',
+ 'glu_sidechain_neutral',
+ 'glutamic_acid',
+ 'glutamic_acid_ct',
+ 'glutamic_acid_neutral',
+ 'glutamic_acid_nt',
+ 'glutamine',
+ 'glutamine_ct',
+ 'glutamine_nt',
+ 'gly_nt_sidechain',
+ 'gly_sidechain',
+ 'glycine',
+ 'glycine_ct',
+ 'glycine_nt',
+ 'guanine',
+ 'hid_sidechain',
+ 'hie_sidechain',
+ 'hip_sidechain',
+ 'histidine',
+ 'histidine_ct',
+ 'histidine_deltah',
+ 'histidine_deltah_ct',
+ 'histidine_deltah_nt',
+ 'histidine_epsilonh',
+ 'histidine_epsilonh_ct',
+ 'histidine_epsilonh_nt',
+ 'histidine_nt',
+ 'histidine_plus',
+ 'histidine_plus_ct',
+ 'histidine_plus_nt',
+ 'ile_sidechain',
+ 'isoleucine',
+ 'isoleucine_ct',
+ 'isoleucine_nt',
+ 'leu_sidechain',
+ 'leucine',
+ 'leucine_ct',
+ 'leucine_nt',
+ 'lys_sidechain',
+ 'lys_sidechain_neutral',
+ 'lysine',
+ 'lysine_ct',
+ 'lysine_neutral',
+ 'lysine_neutral_ct',
+ 'lysine_neutral_nt',
+ 'lysine_nt',
+ 'met_sidechain',
+ 'methionine',
+ 'methionine_ct',
+ 'methionine_nt',
+ 'na_phosphate',
+ 'nmethyl_ct',
+ 'peptide',
+ 'peptide_ct',
+ 'peptide_nt',
+ 'peptide_nt_ct',
+ 'peptide_proline',
+ 'peptide_proline_ct',
+ 'peptide_proline_nt',
+ 'phe_sidechain',
+ 'phenylalanine',
+ 'phenylalanine_ct',
+ 'phenylalanine_nt',
+ 'pro_sidechain',
+ 'pro_sidechain_nt',
+ 'proline',
+ 'proline_ct',
+ 'proline_nt',
+ 'r-adenosine',
+ 'r-adenosine_3ter',
+ 'r-adenosine_5ter',
+ 'r-adenosine_5ter_3ter',
+ 'r-cytosine',
+ 'r-cytosine_3ter',
+ 'r-cytosine_5ter',
+ 'r-cytosine_5ter_3ter',
+ 'r-guanosine',
+ 'r-guanosine_3ter',
+ 'r-guanosine_5ter',
+ 'r-guanosine_5ter_3ter',
+ 'r-uracil',
+ 'r-uracil_3ter',
+ 'r-uracil_5ter',
+ 'r-uracil_5ter_3ter',
+ 'ribose',
+ 'ribose_3ter',
+ 'ribose_5ter',
+ 'ribose_5ter_3ter',
+ 'ser_sidechain',
+ 'serine',
+ 'serine_ct',
+ 'serine_nt',
+ 'thr_sidechain',
+ 'threonine',
+ 'threonine_ct',
+ 'threonine_nt',
+ 'thymine',
+ 'trp_sidechain',
+ 'tryptophan',
+ 'tryptophan_ct',
+ 'tryptophan_nt',
+ 'tyr_sidechain',
+ 'tyrosine',
+ 'tyrosine_ct',
+ 'tyrosine_nt',
+ 'uracil',
+ 'val_sidechain',
+ 'valine',
+ 'valine_ct',
+ 'valine_nt']
+
+for filename in groups:
+
+ ast = compiler.parse(file(filename).read())
+ stmts = ast.getChildren()[1].getChildren()
+
+ vars = set()
+ for stmt in stmts:
+ if isinstance(stmt, compiler.ast.Assign):
+ var_name = stmt.getChildren()[0].getChildren()[0]
+ vars.add(var_name)
+ if 'amber_atom_type' in vars \
+ and 'amber12_atom_type' not in vars:
+ print filename
+ with file(filename, 'a') as f:
+ f.write("amber12_atom_type = amber_atom_type\n")
diff --git a/Tools/fix_amber12.py b/Tools/fix_amber12.py
deleted file mode 100644
index 68f173d..0000000
--- a/Tools/fix_amber12.py
+++ /dev/null
@@ -1,20 +0,0 @@
-import compiler
-import compiler.ast
-
-for filename in file('amber12_fix'):
-
- filename = filename.strip()
-
- ast = compiler.parse(file(filename).read())
- stmts = ast.getChildren()[1].getChildren()
-
- vars = set()
- for stmt in stmts:
- if isinstance(stmt, compiler.ast.Assign):
- var_name = stmt.getChildren()[0].getChildren()[0]
- vars.add(var_name)
- if 'amber_atom_type' in vars \
- and 'amber12_atom_type' not in vars:
- print filename
- with file(filename, 'a') as f:
- f.write("amber12_atom_type = amber_atom_type\n")
diff --git a/setup.py b/setup.py
index 85fc4e4..1a75e26 100644
--- a/setup.py
+++ b/setup.py
@@ -28,7 +28,7 @@ if use_cython:
from Cython.Distutils import build_ext
use_cython = True
except ImportError:
- pass
+ use_cython = False
if not use_cython:
from distutils.command.build_ext import build_ext
src_ext = 'pyx' if use_cython else 'c'
--
The Molecular Modelling Toolkit packaging
More information about the debian-science-commits
mailing list