[sagemath] 01/02: Add more dependencies for Sage 7.1
Ximin Luo
infinity0 at debian.org
Tue Jul 5 16:30:35 UTC 2016
This is an automated email from the git hooks/post-receive script.
infinity0 pushed a commit to branch master
in repository sagemath.
commit 1a0a458dd95473c8fcae0b1ccd6bf6b52920d0a8
Author: Ximin Luo <infinity0 at debian.org>
Date: Tue Jul 5 18:29:15 2016 +0200
Add more dependencies for Sage 7.1
---
debian/control | 21 +++++-
debian/patches/nauty-bin-rename.patch | 33 +++++++++
debian/patches/series | 1 +
debian/pruner/configure.ac | 127 ++++++++++++++++++++++++++++++++++
debian/pruner/pruner.py.in | 19 +++++
5 files changed, 200 insertions(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 02a33e0..910c86c 100644
--- a/debian/control
+++ b/debian/control
@@ -20,9 +20,12 @@ Build-Depends:
gap (>= 4r6p4),
gap-dev (>= 4r6p5-3),
gfan,
+ git,
gmp-ecm,
gnutls-dev,
- ipython,
+ ipython (>= 4.1.2),
+ jupyter-client,
+ jupyter-core,
lcalc (>= 1.23+dfsg-5sage1),
libatlas-base-dev,
libblas-dev,
@@ -31,6 +34,7 @@ Build-Depends:
libcliquer-dev,
libec-dev (>= 20160101-1+sage1),
libecm-dev,
+ libflint-arb-dev,
libflint-dev (>= 2.3),
libfplll-dev,
libfreetype6-dev,
@@ -72,17 +76,24 @@ Build-Depends:
maxima (= 5.35.1-5sage2),
maxima-doc (= 5.35.1-5sage2),
maxima-share (= 5.35.1-5sage2),
+ nauty,
palp (>= 2.1-2),
pari-doc (>= 2.8-1564-gdeac36e-1),
pari-galdata,
pari-seadata,
python2.7-dev,
+ python-backports-abc,
python-backports.ssl-match-hostname,
python-crypto,
python-cvxopt,
+ python-cycler,
+ python-decorator,
python-docutils,
+ python-functools32,
python-gd,
python-gnutls,
+ python-ipykernel,
+ python-ipython-genutils,
python-jsonschema,
python-matplotlib,
python-mistune,
@@ -90,19 +101,27 @@ Build-Depends:
python-mpmath,
python-networkx,
python-numpy,
+ python-path,
python-pexpect,
+ python-pickleshare,
python-pil,
python-pip,
python-pkgconfig,
python-ply,
+ python-ptyprocess,
python-pygments,
python-rpy2,
python-scipy,
python-setuptools,
+ python-setuptools-scm,
+ python-simplegeneric,
+ python-singledispatch,
python-sphinx,
python-sympy,
python-tornado,
+ python-traitlets,
python-twisted,
+ python-vcversioner,
python-zmq,
python-zodb,
r-cran-lattice,
diff --git a/debian/patches/nauty-bin-rename.patch b/debian/patches/nauty-bin-rename.patch
new file mode 100644
index 0000000..95017ab
--- /dev/null
+++ b/debian/patches/nauty-bin-rename.patch
@@ -0,0 +1,33 @@
+--- a/sage/src/sage/graphs/digraph_generators.py
++++ b/sage/src/sage/graphs/digraph_generators.py
+@@ -484,7 +484,7 @@
+
+ nauty_input += " "+str(n) +" "
+
+- sp = subprocess.Popen("gentourng {0}".format(nauty_input), shell=True,
++ sp = subprocess.Popen("nauty-gentourng {0}".format(nauty_input), shell=True,
+ stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, close_fds=True)
+
+--- a/sage/src/sage/graphs/graph_generators.py
++++ b/sage/src/sage/graphs/graph_generators.py
+@@ -869,7 +869,7 @@
+ >A geng -d0D3 n=4 e=0-6
+ """
+ import subprocess
+- sp = subprocess.Popen("geng {0}".format(options), shell=True,
++ sp = subprocess.Popen("nauty-geng {0}".format(options), shell=True,
+ stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, close_fds=True)
+ if debug:
+--- a/sage/src/sage/graphs/hypergraph_generators.py
++++ b/sage/src/sage/graphs/hypergraph_generators.py
+@@ -136,7 +136,7 @@
+
+ nauty_input += " "+str(number_of_vertices) +" "+str(number_of_sets)+" "
+
+- sp = subprocess.Popen("genbg {0}".format(nauty_input), shell=True,
++ sp = subprocess.Popen("nauty-genbg {0}".format(nauty_input), shell=True,
+ stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE, close_fds=True)
+
diff --git a/debian/patches/series b/debian/patches/series
index d6a3ddb..6877831 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -11,3 +11,4 @@ rubiks_executables_renames.patch
python_installs_in_userdir.patch
pari.patch
spkg_ipython_fix.patch
+nauty-bin-rename.patch
diff --git a/debian/pruner/configure.ac b/debian/pruner/configure.ac
index f0c15d9..39d9476 100644
--- a/debian/pruner/configure.ac
+++ b/debian/pruner/configure.ac
@@ -14,6 +14,14 @@ PKG_PROG_PKG_CONFIG
AC_CHECK_HEADER(atlas/clapack.h, HAS_ATLAS="True", HAS_ATLAS="False")
AC_SUBST(HAS_ATLAS)
+AC_CHECK_PYTHON_MODULE(backports_abc)
+if test "x${PYTHON_backports_abc}" = "x1"; then
+ HAS_BACKPORTS_ABC="True"
+else
+ HAS_BACKPORTS_ABC="False"
+fi
+AC_SUBST(HAS_BACKPORTS_ABC)
+
# FIXME(backports_ssl_match_hostname): only needed for tornado, hence not needed
HAS_BACKPORTS_SSL_MATCH_HOSTNAME="True"
AC_SUBST(HAS_BACKPORTS_SSL_MATCH_HOSTNAME)
@@ -56,6 +64,14 @@ else
fi
AC_SUBST(HAS_CVXOPT)
+AC_CHECK_PYTHON_MODULE(cycler)
+if test "x${PYTHON_cycler}" = "x1"; then
+ HAS_CYCLER="True"
+else
+ HAS_CYCLER="False"
+fi
+AC_SUBST(HAS_CYCLER)
+
AC_CHECK_PROG(HAS_CYTHON, cython, "True", "False")
AC_SUBST(HAS_CYTHON)
@@ -67,6 +83,14 @@ else
fi
AC_SUBST(HAS_DATEUTIL)
+AC_CHECK_PYTHON_MODULE(decorator)
+if test "x${PYTHON_decorator}" = "x1"; then
+ HAS_DECORATOR="True"
+else
+ HAS_DECORATOR="False"
+fi
+AC_SUBST(HAS_DECORATOR)
+
AC_CHECK_PYTHON_MODULE(docutils)
if test "x${PYTHON_docutils}" = "x1"; then
HAS_DOCUTILS="True"
@@ -105,6 +129,12 @@ AC_SUBST(HAS_FFLAS_FFPACK)
AC_CHECK_HEADER(flint/config.h, HAS_FLINT="True", HAS_FLINT="False")
AC_SUBST(HAS_FLINT)
+old_CPPFLAGS=$CPPFLAGS
+CPPFLAGS="$old_CPPFLAGS -I/usr/include/flint"
+AC_CHECK_HEADER(arb.h, HAS_ARB="True", HAS_ARB="False")
+CPPFLAGS=$old_CPPFLAGS
+AC_SUBST(HAS_ARB)
+
AC_CHECK_PROG(HAS_FLINTQS, QuadraticSieve, "True", "False")
AC_SUBST(HAS_FLINTQS)
@@ -116,6 +146,14 @@ AC_SUBST(HAS_FPLLL)
AC_CHECK_PROG(HAS_FREETYPE, freetype-config, "True", "False")
AC_SUBST(HAS_FREETYPE)
+AC_CHECK_PYTHON_MODULE(functools32)
+if test "x${PYTHON_functools32}" = "x1"; then
+ HAS_FUNCTOOLS32="True"
+else
+ HAS_FUNCTOOLS32="False"
+fi
+AC_SUBST(HAS_FUNCTOOLS32)
+
AC_CHECK_FILE(/usr/include/gap/gap.h, HAS_GAP="True", HAS_GAP="False")
AC_SUBST(HAS_GAP)
@@ -153,9 +191,25 @@ AC_SUBST(HAS_ICONV)
AC_CHECK_HEADER(iml.h, HAS_IML="True", HAS_IML="False", [#include "gmp.h"])
AC_SUBST(HAS_IML)
+AC_CHECK_PYTHON_MODULE(ipykernel)
+if test "x${PYTHON_ipykernel}" = "x1"; then
+ HAS_IPYKERNEL="True"
+else
+ HAS_IPYKERNEL="False"
+fi
+AC_SUBST(HAS_IPYKERNEL)
+
AC_CHECK_PROG(HAS_IPYTHON, ipython, "True", "False")
AC_SUBST(HAS_IPYTHON)
+AC_CHECK_PYTHON_MODULE(ipython_genutils)
+if test "x${PYTHON_ipython_genutils}" = "x1"; then
+ HAS_IPYTHON_GENUTILS="True"
+else
+ HAS_IPYTHON_GENUTILS="False"
+fi
+AC_SUBST(HAS_IPYTHON_GENUTILS)
+
AC_CHECK_PYTHON_MODULE(jinja2)
if test "x${PYTHON_jinja2}" = "x1"; then
HAS_JINJA2="True"
@@ -176,6 +230,12 @@ else
fi
AC_SUBST(HAS_JSONSCHEMA)
+AC_CHECK_PROG(HAS_JUPYTER_CLIENT, jupyter-kernelspec, "True", "False")
+AC_SUBST(HAS_JUPYTER_CLIENT)
+
+AC_CHECK_PROG(HAS_JUPYTER_CORE, jupyter, "True", "False")
+AC_SUBST(HAS_JUPYTER_CORE)
+
AC_LANG_PUSH([C++])
AC_CHECK_HEADER(Lfunction/L.h, HAS_LCALC="True", HAS_LCALC="False")
AC_LANG_POP([C++])
@@ -264,6 +324,9 @@ else
fi
AC_SUBST(HAS_MPMATH)
+AC_CHECK_PROG(HAS_NAUTY, nauty-genbg, "True", "False")
+AC_SUBST(HAS_NAUTY)
+
AC_CHECK_HEADERS(ncurses.h, HAS_NCURSES="True", HAS_NCURSES="False")
AC_SUBST(HAS_NCURSES)
@@ -301,6 +364,14 @@ AC_SUBST(HAS_PARI_SEADATA)
AC_CHECK_PROG(HAS_PATCH, patch, "True", "False")
AC_SUBST(HAS_PATCH)
+AC_CHECK_PYTHON_MODULE(path)
+if test "x${PYTHON_path}" = "x1"; then
+ HAS_PATHPY="True"
+else
+ HAS_PATHPY="False"
+fi
+AC_SUBST(HAS_PATHPY)
+
AC_CHECK_PYTHON_MODULE(pexpect)
if test "x${PYTHON_pexpect}" = "x1"; then
HAS_PEXPECT="True"
@@ -309,6 +380,14 @@ else
fi
AC_SUBST(HAS_PEXPECT)
+AC_CHECK_PYTHON_MODULE(pickleshare)
+if test "x${PYTHON_pickleshare}" = "x1"; then
+ HAS_PICKLESHARE="True"
+else
+ HAS_PICKLESHARE="False"
+fi
+AC_SUBST(HAS_PICKLESHARE)
+
AC_CHECK_PYTHON_MODULE(PIL)
if test "x${PYTHON_PIL}" = "x1"; then
HAS_PIL="True"
@@ -378,6 +457,14 @@ else
fi
AC_SUBST(HAS_PYPARSING)
+AC_CHECK_PYTHON_MODULE(ptyprocess)
+if test "x${PYTHON_ptyprocess}" = "x1"; then
+ HAS_PTYPROCESS="True"
+else
+ HAS_PTYPROCESS="False"
+fi
+AC_SUBST(HAS_PTYPROCESS)
+
PKG_CHECK_MODULES(python, python-2.7, [HAS_PYTHON='True'], [HAS_PYTHON='False'])
AC_SUBST(HAS_PYTHON)
@@ -444,6 +531,30 @@ else
fi
AC_SUBST(HAS_SETUPTOOLS)
+AC_CHECK_PYTHON_MODULE(setuptools_scm)
+if test "x${PYTHON_setuptools_scm}" = "x1"; then
+ HAS_SETUPTOOLS_SCM="True"
+else
+ HAS_SETUPTOOLS_SCM="False"
+fi
+AC_SUBST(HAS_SETUPTOOLS_SCM)
+
+AC_CHECK_PYTHON_MODULE(simplegeneric)
+if test "x${PYTHON_simplegeneric}" = "x1"; then
+ HAS_SIMPLEGENERIC="True"
+else
+ HAS_SIMPLEGENERIC="False"
+fi
+AC_SUBST(HAS_SIMPLEGENERIC)
+
+AC_CHECK_PYTHON_MODULE(singledispatch)
+if test "x${PYTHON_singledispatch}" = "x1"; then
+ HAS_SINGLEDISPATCH="True"
+else
+ HAS_SINGLEDISPATCH="False"
+fi
+AC_SUBST(HAS_SINGLEDISPATCH)
+
# FIXME(singular): using the debian-science repository
AC_LANG_PUSH([C++])
old_CPPFLAGS=$CPPFLAGS
@@ -498,6 +609,22 @@ else
fi
AC_SUBST(HAS_TORNADO)
+AC_CHECK_PYTHON_MODULE(traitlets)
+if test "x${PYTHON_traitlets}" = "x1"; then
+ HAS_TRAITLETS="True"
+else
+ HAS_TRAITLETS="False"
+fi
+AC_SUBST(HAS_TRAITLETS)
+
+AC_CHECK_PYTHON_MODULE(vcversioner)
+if test "x${PYTHON_vcversioner}" = "x1"; then
+ HAS_VCVERSIONER="True"
+else
+ HAS_VCVERSIONER="False"
+fi
+AC_SUBST(HAS_VCVERSIONER)
+
# FIXME(zeromq): useful only for pyzmq
HAS_ZEROMQ="True"
AC_SUBST(HAS_ZEROMQ)
diff --git a/debian/pruner/pruner.py.in b/debian/pruner/pruner.py.in
index 03b8a6d..d25b9bc 100644
--- a/debian/pruner/pruner.py.in
+++ b/debian/pruner/pruner.py.in
@@ -39,7 +39,9 @@ mkdir_if_needed ('@SAGE_ROOT@/local')
mkdir_if_needed ('@SAGE_ROOT@/local/include')
dico = {
+ 'arb': @HAS_ARB@,
'atlas': @HAS_ATLAS@,
+ 'backports_abc': @HAS_BACKPORTS_ABC@,
'backports_ssl_match_hostname': @HAS_BACKPORTS_SSL_MATCH_HOSTNAME@,
'boost_cropped': @HAS_BOOST@,
'brial': @HAS_POLYBORI@,
@@ -51,8 +53,10 @@ dico = {
'combinatorial_designs': @HAS_COMBINATORIAL_DESIGNS@,
'conway_polynomials': @HAS_CONWAY_POLYNOMIALS@,
'cvxopt': @HAS_CVXOPT@,
+ 'cycler': @HAS_CYCLER@,
'cython': @HAS_CYTHON@,
'dateutil': @HAS_DATEUTIL@,
+ 'decorator': @HAS_DECORATOR@,
'docutils': @HAS_DOCUTILS@,
'ecl': @HAS_ECL@,
'eclib': @HAS_ECLIB@,
@@ -63,6 +67,7 @@ dico = {
'flintqs': @HAS_FLINTQS@,
'libfplll': @HAS_FPLLL@,
'freetype': @HAS_FREETYPE@,
+ 'functools32': @HAS_FUNCTOOLS32@,
'gap': @HAS_GAP@,
'gc': @HAS_BOEHM_GC@,
'libgd': @HAS_GD@,
@@ -76,10 +81,14 @@ dico = {
'gsl': @HAS_GSL@,
'iconv': @HAS_ICONV@,
'iml': @HAS_IML@,
+ 'ipykernel': @HAS_IPYKERNEL@,
'ipython': @HAS_IPYTHON@,
+ 'ipython_genutils': @HAS_IPYTHON_GENUTILS@,
'jinja2': @HAS_JINJA2@,
'jmol': @HAS_JMOL@,
'jsonschema': @HAS_JSONSCHEMA@,
+ 'jupyter_client': @HAS_JUPYTER_CLIENT@,
+ 'jupyter_core': @HAS_JUPYTER_CORE@,
'lcalc': @HAS_LCALC@,
'libgap': @HAS_LIBGAP@,
'libpng': @HAS_LIBPNG@,
@@ -97,6 +106,7 @@ dico = {
'mpfr': @HAS_MPFR@,
'mpir': @HAS_MPIR@,
'mpmath': @HAS_MPMATH@,
+ 'nauty': @HAS_NAUTY@,
'ncurses': @HAS_NCURSES@,
'networkx': @HAS_NETWORKX@,
'ntl': @HAS_NTL@,
@@ -106,7 +116,9 @@ dico = {
'pari_galdata': @HAS_PARI_GALDATA@,
'pari_seadata_small': @HAS_PARI_SEADATA@,
'patch': @HAS_PATCH@,
+ 'pathpy': @HAS_PATHPY@,
'pexpect': @HAS_PEXPECT@,
+ 'pickleshare': @HAS_PICKLESHARE@,
'pillow': @HAS_PIL@,
'pip': @HAS_PIP@,
'pkgconf': @HAS_PKGCONF@,
@@ -114,16 +126,19 @@ dico = {
'planarity': @HAS_PLANARITY@,
'polytopes_db': @HAS_POLYTOPES@,
'ppl': @HAS_PPL@,
+ 'ptyprocess': @HAS_PTYPROCESS@,
'pycrypto': @HAS_PYCRYPTO@,
'pygments': @HAS_PYGMENTS@,
'pynac': @HAS_PYNAC@,
'pyparsing': @HAS_PYPARSING@,
+ 'python2': @HAS_PYTHON@,
'pyzmq': @HAS_PYZMQ@,
'r': @HAS_R@,
'ratpoints': @HAS_RATPOINTS@,
# those two go together afaik:
'readline': @HAS_READLINE@,
'termcap': @HAS_READLINE@,
+ 'traitlets': @HAS_TRAITLETS@,
'rpy2': @HAS_RPY2@,
'rubiks': @HAS_RUBIKS@,
'rw': @HAS_RW@,
@@ -132,6 +147,9 @@ dico = {
'scipy': @HAS_SCIPY@,
'scons': @HAS_SCONS@,
'setuptools': @HAS_SETUPTOOLS@,
+ 'setuptools_scm': @HAS_SETUPTOOLS_SCM@,
+ 'simplegeneric': @HAS_SIMPLEGENERIC@,
+ 'singledispatch': @HAS_SINGLEDISPATCH@,
'singular': @HAS_SINGULAR@,
'six': @HAS_SIX@,
'sphinx': @HAS_SPHINX@,
@@ -141,6 +159,7 @@ dico = {
'sympy': @HAS_SYMPY@,
'tachyon': @HAS_TACHYON@,
'tornado': @HAS_TORNADO@,
+ 'vcversioner': @HAS_VCVERSIONER@,
'zeromq': @HAS_ZEROMQ@,
'zlib': @HAS_ZLIB@,
'zn_poly': @HAS_ZNPOLY@
--
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