[sagemath] 07/10: Refresh more patches.
Tobias Hansen
thansen at moszumanska.debian.org
Fri Jun 9 21:34:43 UTC 2017
This is an automated email from the git hooks/post-receive script.
thansen pushed a commit to branch master
in repository sagemath.
commit 204b626628d8837a558a1bcea0ebad891fb3c2fe
Author: Tobias Hansen <thansen at debian.org>
Date: Fri Jun 9 21:55:12 2017 +0100
Refresh more patches.
---
debian/changelog | 3 ++
debian/patches/d0-paths-sharedata.patch | 2 +-
debian/patches/d0-paths.patch | 36 ++---------------
debian/patches/d0-singular.patch | 15 ++-----
debian/patches/d1-install-paths.patch | 69 ++++++++-------------------------
debian/patches/d1-sage-cli.patch | 62 ++++++++++++++---------------
6 files changed, 58 insertions(+), 129 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index f30fbbd..7261ff5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -13,6 +13,9 @@ sagemath (8.0~beta9-1) UNRELEASED; urgency=medium
May need further modifications after https://trac.sagemath.org/ticket/21479
- d0-libgap-sage.patch
- d0-pari-stackwarn.patch
+ - d0-paths.patch
+ - d0-singular.patch
+ - d1-install-paths.patch
-- Tobias Hansen <thansen at debian.org> Thu, 08 Jun 2017 21:19:49 +0000
diff --git a/debian/patches/d0-paths-sharedata.patch b/debian/patches/d0-paths-sharedata.patch
index cf506fd..30e6043 100644
--- a/debian/patches/d0-paths-sharedata.patch
+++ b/debian/patches/d0-paths-sharedata.patch
@@ -49,7 +49,7 @@ Forwarded: TODO
global _db
--- a/sage/src/sage/graphs/strongly_regular_db.pyx
+++ b/sage/src/sage/graphs/strongly_regular_db.pyx
-@@ -3163,8 +3163,7 @@
+@@ -3213,8 +3213,7 @@
return
import json
diff --git a/debian/patches/d0-paths.patch b/debian/patches/d0-paths.patch
index a107694..d60087f 100644
--- a/debian/patches/d0-paths.patch
+++ b/debian/patches/d0-paths.patch
@@ -6,7 +6,7 @@ Forwarded: not-needed
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/sage/src/sage/interfaces/gap.py
+++ b/sage/src/sage/interfaces/gap.py
-@@ -193,7 +193,7 @@
+@@ -194,7 +194,7 @@
WORKSPACE = gap_workspace_file()
@@ -17,7 +17,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/sage/src/sage/misc/cython.py
+++ b/sage/src/sage/misc/cython.py
-@@ -414,7 +414,7 @@
+@@ -488,7 +488,7 @@
file_list = []
for fname in additional_source_files:
fname = fname.replace("$SAGE_SRC", SAGE_SRC)
@@ -50,7 +50,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
sage: from sage.interfaces.qepcad import _qepcad_atoms
--- a/sage/src/sage/tests/cmdline.py
+++ b/sage/src/sage/tests/cmdline.py
-@@ -561,12 +561,6 @@
+@@ -570,12 +570,6 @@
sage: ret
0
@@ -63,36 +63,6 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Test GP using the ``-f`` option which prevents the reading of a ``.gprc``
configuration file::
---- a/sage/src/sage/all.py
-+++ b/sage/src/sage/all.py
-@@ -15,27 +15,6 @@
- sage: from sage import *
- sage: frames = [x for x in gc.get_objects() if inspect.isframe(x)]
-
--We exclude the known files and check to see that there are no others::
--
-- sage: import os
-- sage: allowed = [os.path.join("lib","python","threading.py")]
-- sage: allowed.append(os.path.join("lib","python","multiprocessing"))
-- sage: allowed.append(os.path.join("sage","doctest"))
-- sage: allowed.append(os.path.join("bin","sage-runtests"))
-- sage: allowed.append(os.path.join("site-packages","IPython"))
-- sage: allowed.append(os.path.join("bin","sage-ipython"))
-- sage: allowed.append("<ipython console>")
-- sage: allowed.append("<doctest sage.all[3]>")
-- sage: allowed.append(os.path.join("sage","combinat","species","generating_series.py"))
-- sage: for i in frames:
-- ....: filename, lineno, funcname, linelist, indx = inspect.getframeinfo(i)
-- ....: for nm in allowed:
-- ....: if nm in filename:
-- ....: break
-- ....: else:
-- ....: print(filename)
-- ....:
--
- Check that the Sage Notebook is not imported at startup (see
- :trac:`15335`)::
-
--- a/sage/src/sage/interfaces/jmoldata.py
+++ b/sage/src/sage/interfaces/jmoldata.py
@@ -148,7 +148,7 @@
diff --git a/debian/patches/d0-singular.patch b/debian/patches/d0-singular.patch
index 3228d23..ced09f1 100644
--- a/debian/patches/d0-singular.patch
+++ b/debian/patches/d0-singular.patch
@@ -6,7 +6,7 @@ Forwarded: not-needed
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/sage/src/sage/interfaces/singular.py
+++ b/sage/src/sage/interfaces/singular.py
-@@ -650,7 +650,8 @@
+@@ -652,7 +652,8 @@
s = Expect.eval(self, x, **kwds)
@@ -16,7 +16,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
raise SingularError('Singular error:\n%s'%s)
if get_verbose() > 0:
-@@ -2291,7 +2292,7 @@
+@@ -2287,7 +2288,7 @@
nodes.clear()
node_names.clear()
@@ -27,7 +27,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
new_lookup = re.compile("\* ([^:]*):*([^.]*)\..*")
--- a/sage/src/sage/misc/cython.py
+++ b/sage/src/sage/misc/cython.py
-@@ -242,6 +242,11 @@
+@@ -278,6 +278,11 @@
args = ['-w','-O2'] + args
libdirs = cblas_library_dirs
@@ -39,12 +39,3 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
# Add cysignals directory to includes
for path in sys.path:
inc.append(path)
-@@ -311,7 +316,7 @@
-
- sage: code = [
- ....: "#clang C++",
-- ....: "#clib m readline Singular givaro ntl gmpxx gmp",
-+ ....: "#clib m readline singular-Singular givaro ntl gmpxx gmp",
- ....: "from sage.rings.polynomial.multi_polynomial_libsingular cimport MPolynomial_libsingular",
- ....: "from sage.libs.singular.polynomial cimport singular_polynomial_pow",
- ....: "def test(MPolynomial_libsingular p):",
diff --git a/debian/patches/d1-install-paths.patch b/debian/patches/d1-install-paths.patch
index 7d97037..ebd90b7 100644
--- a/debian/patches/d1-install-paths.patch
+++ b/debian/patches/d1-install-paths.patch
@@ -23,7 +23,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
from sage.misc.sageinspect import loadable_module_extension
--- a/sage/src/setup.py
+++ b/sage/src/setup.py
-@@ -174,9 +174,9 @@
+@@ -185,9 +185,9 @@
# (that are likely to change on an upgrade) here:
# [At least at the moment. Make sure the headers aren't copied with "-p",
# or explicitly touch them in the respective spkg's spkg-install.]
@@ -35,26 +35,17 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+ "ntl": [ os.path.join('/usr/include', 'NTL', 'config.h') ]
}
- import pkgconfig
-@@ -202,7 +202,7 @@
-
- m.extra_compile_args = m.extra_compile_args + extra_compile_args
- m.extra_link_args = m.extra_link_args + extra_link_args
-- m.library_dirs = m.library_dirs + libgap_library_dirs + [os.path.join(SAGE_LOCAL, "lib")]
-+ m.library_dirs = m.library_dirs + libgap_library_dirs + [os.path.join(SAGE_LOCAL, "lib"), '/usr/lib']
- m.include_dirs = m.include_dirs + libgap_include_dirs + include_dirs
-
--- a/sage/sage
+++ b/sage/sage
-@@ -22,6 +22,7 @@
- # automatically.
- #SAGE_ROOT=/path/to/sage-version
+@@ -16,6 +16,7 @@
+ # along with this program; if not, write to the Free Software
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+if test -n "$SAGE_LOCAL"; then export PATH="$SAGE_LOCAL/bin:$PATH"; fi
-
- # Resolve all symbolic links in a filename. This more or less behaves
+ # Set SAGE_ROOT to the location of the sage install, i.e. the directory
+ # containing this shell script. If unset, we will try to figure it out
--- a/sage/src/sage/env.py
+++ b/sage/src/sage/env.py
@@ -103,9 +103,9 @@
@@ -82,7 +73,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
import distutils.sysconfig
--- a/sage/configure.ac
+++ b/sage/configure.ac
-@@ -1006,8 +1006,7 @@
+@@ -1025,8 +1025,7 @@
AC_MSG_ERROR([[Cannot perform incremental update, run "make distclean && make"]])
fi
else
@@ -210,7 +201,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
file = filename
--- a/sage/src/sage_setup/docbuild/ext/multidocs.py
+++ b/sage/src/sage_setup/docbuild/ext/multidocs.py
-@@ -283,7 +283,7 @@
+@@ -285,7 +285,7 @@
"""
app.builder.info(bold('linking _static directory.'))
static_dir = os.path.join(app.builder.outdir, '_static')
@@ -221,38 +212,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
shutil.rmtree(static_dir)
--- a/sage/src/Makefile.in
+++ b/sage/src/Makefile.in
-@@ -40,7 +40,7 @@
- SAGE_BUILD_DIR=/doesnotexist \
- SAGE_PKGS=$(abs_top_srcdir)/build/pkgs \
- SAGE_CYTHONIZED=$(abs_builddir)/build/cythonized \
-- && python -u setup.py --no-user-cfg build install)
-+ && python -u setup.py --no-user-cfg build install --root ../../debian/build --install-layout deb -O2)
-
- clean:
- @echo "Deleting Sage library build artifacts..."
---- a/sage/src/sage/plot/plot3d/base.pyx
-+++ b/sage/src/sage/plot/plot3d/base.pyx
-@@ -386,19 +386,13 @@
- if isinstance(backend, BackendIPythonNotebook):
- scripts = ( """
- <script src="/nbextensions/threejs/three.min.js"></script>
--<script src="/nbextensions/threejs/OrbitControls.js"></script>
--<script>
-- if ( !window.THREE ) document.write('\
--<script src="https://cdn.rawgit.com/mrdoob/three.js/r80/build/three.min.js"><\/script>\
--<script src="https://cdn.rawgit.com/mrdoob/three.js/r80/examples/js/controls/OrbitControls.js"><\/script>');
--</script>
-+<script src="/nbextensions/threejs/examples/js/controls/OrbitControls.js"></script>
- """ )
- else:
-- from sage.env import SAGE_SHARE
- scripts = ( """
--<script src="{0}/threejs/three.min.js"></script>
--<script src="{0}/threejs/OrbitControls.js"></script>
-- """.format( SAGE_SHARE ) )
-+<script src="{0}/three.min.js"></script>
-+<script src="{0}/examples/js/controls/OrbitControls.js"></script>
-+ """.format( "file:///usr/share/javascript/three" ) )
-
- b = self.bounding_box()
- bounds = '[{{"x":{}, "y":{}, "z":{}}}, {{"x":{}, "y":{}, "z":{}}}]'.format(
+@@ -39,7 +39,7 @@
+ SAGE_BUILD_DIR=/doesnotexist \
+ SAGE_PKGS=$(abs_top_srcdir)/build/pkgs \
+ SAGE_CYTHONIZED=$(abs_builddir)/build/cythonized \
+- && sage-python23 -u setup.py --no-user-cfg build install
++ && sage-python23 -u setup.py --no-user-cfg build install --root ../../debian/build --install-layout deb -O2
+ if [ "$$UNAME" = "CYGWIN" ]; then \
+ sage-rebase.sh "$$SAGE_LOCAL" 2>/dev/null; \
+ fi
diff --git a/debian/patches/d1-sage-cli.patch b/debian/patches/d1-sage-cli.patch
index 345caf1..488b03b 100644
--- a/debian/patches/d1-sage-cli.patch
+++ b/debian/patches/d1-sage-cli.patch
@@ -25,10 +25,10 @@ Forwarded: not-needed
echo " 'default', 'sagenb', 'jupyter', and 'export')"
echo " -n, --notebook -- shortcut for --notebook=default"
- echo " -optional -- list all optional packages that can be installed"
- echo " -python [...] -- run the Python interpreter"
+ echo " -python [...] -- run the Python 2 interpreter"
+ echo " -python3 [...] -- run the Python 3 interpreter"
echo " -R [...] -- run Sage's R with given arguments"
- echo " -singular [...] -- run Sage's singular with given arguments"
-@@ -42,10 +37,6 @@
+@@ -43,10 +38,6 @@
echo " --optional - controls which optional tests are run"
echo " --sagenb - test all sagenb files"
echo " --help - show all testing options"
@@ -39,7 +39,7 @@ Forwarded: not-needed
echo " -v, -version -- display Sage version information"
exit 0
}
-@@ -68,7 +59,6 @@
+@@ -69,7 +60,6 @@
echo " -- pass the option through to ipython"
echo " -v, -version -- display Sage version information"
echo " -dumpversion -- print Sage version"
@@ -47,7 +47,7 @@ Forwarded: not-needed
echo
#### 1.......................26..................................................78
-@@ -79,8 +69,6 @@
+@@ -80,8 +70,6 @@
echo " See the output of sage --notebook --help"
echo " for more details and examples of how to pass"
echo " optional arguments"
@@ -56,7 +56,7 @@ Forwarded: not-needed
echo " -inotebook [...] -- start the *insecure* Sage notebook (deprecated)"
echo " -n, -notebook [...] -- start the default Sage notebook (options are the"
echo " same as for the notebook command in Sage). See the"
-@@ -94,7 +82,6 @@
+@@ -95,7 +83,6 @@
echo " -cython [...] -- run Cython with given arguments"
echo " -ecl [...] -- run Common Lisp"
echo " -gap [...] -- run Sage's Gap with given arguments"
@@ -64,7 +64,7 @@ Forwarded: not-needed
echo " -gdb -- run Sage under the control of gdb"
echo " -gp [...] -- run Sage's PARI/GP calculator with given arguments"
echo " -ipython [...] -- run Sage's IPython using the default environment (not"
-@@ -113,7 +100,6 @@
+@@ -114,7 +101,6 @@
echo " (not installed currently, run sage -i polymake)"
echo " -python [...] -- run the Python interpreter"
echo " -R [...] -- run Sage's R with given arguments"
@@ -72,7 +72,7 @@ Forwarded: not-needed
echo " -sh [...] -- run \$SHELL ($SHELL) with Sage environment variables"
echo " -singular [...] -- run Sage's singular with given arguments"
echo " -sqlite3 [...] -- run Sage's sqlite3 with given arguments"
-@@ -122,55 +108,7 @@
+@@ -123,55 +109,7 @@
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -129,7 +129,7 @@ Forwarded: not-needed
echo " -startuptime [module] -- display how long each component of Sage takes to"
echo " start up; optionally specify a module to get more"
echo " details about that particular module"
-@@ -179,9 +117,7 @@
+@@ -180,9 +118,7 @@
echo " selected options:"
echo " --long - include lines with the phrase 'long time'"
echo " --verbose - print debugging output during the test"
@@ -139,7 +139,7 @@ Forwarded: not-needed
echo " --initial - only show the first failure per block"
echo " --debug - drop into PDB after an unexpected error"
echo " --failed - only test files that failed last test"
-@@ -197,9 +133,6 @@
+@@ -198,9 +134,6 @@
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
echo "Documentation:"
@@ -149,7 +149,7 @@ Forwarded: not-needed
echo " -docbuild [lang/]<document> <html|pdf|...> -- Build the Sage documentation"
echo " -search_src <string> -- search through all the Sage library code for string"
echo " -search_doc <string> -- search through the Sage documentation for string"
-@@ -222,16 +155,6 @@
+@@ -223,16 +156,6 @@
echo
#### 1.......................26..................................................78
#### |.....................--.|...................................................|
@@ -166,7 +166,7 @@ Forwarded: not-needed
echo "Valgrind memory debugging:"
echo " -cachegrind -- run Sage using Valgrind's cachegrind tool. The log"
echo " files are named sage-cachegrind.PID can be found in"
-@@ -272,91 +195,6 @@
+@@ -273,91 +196,6 @@
exit $status
fi
@@ -258,12 +258,12 @@ Forwarded: not-needed
#####################################################################
# Source sage-env ($0 is the name of this "sage" script, so we can just
-@@ -382,47 +220,13 @@
+@@ -383,47 +221,14 @@
# Prepare for running Sage, either interactively or non-interactively.
sage_setup() {
- # Check that we're not in a source tarball which hasn't been built yet (#13561).
-- if [ ! -d "$SAGE_LOCAL/lib/python/site-packages/sage" ]; then
+- if [ ! -x "$SAGE_LOCAL/bin/sage" ]; then
- echo >&2 '************************************************************************'
- echo >&2 'It seems that you are attempting to run Sage from an unpacked source'
- echo >&2 'tarball, but you have not compiled it yet (or maybe the build has not'
@@ -290,7 +290,7 @@ Forwarded: not-needed
sage-cleaner &>/dev/null &
}
--
+
-# Check to see if the whole Sage install tree has moved. If so,
-# change various hardcoded paths. Skip this if we don't have write
-# access to $SAGE_LOCAL (e.g. when running as a different user) or
@@ -308,7 +308,7 @@ Forwarded: not-needed
# Start an interactive Sage session, this function never returns.
interactive_sage() {
sage_setup
-@@ -482,11 +286,6 @@
+@@ -483,11 +288,6 @@
exec gap "$@"
fi
@@ -320,7 +320,7 @@ Forwarded: not-needed
if [ "$1" = '-gp' -o "$1" = '--gp' ]; then
shift
exec gp "$@"
-@@ -532,11 +331,6 @@
+@@ -533,11 +333,6 @@
exec kash "$@"
fi
@@ -332,7 +332,7 @@ Forwarded: not-needed
if [ "$1" = '-maxima' -o "$1" = '--maxima' ]; then
shift
exec maxima-sage "$@"
-@@ -552,21 +346,6 @@
+@@ -553,21 +348,6 @@
exec M2 "$@"
fi
@@ -354,7 +354,7 @@ Forwarded: not-needed
if [ "$1" = '-python' -o "$1" = '--python' ]; then
shift
exec python "$@"
-@@ -587,11 +366,6 @@
+@@ -598,11 +378,6 @@
exec git "$@"
fi
@@ -366,7 +366,7 @@ Forwarded: not-needed
if [ "$1" = '-sh' -o "$1" = '--sh' ]; then
# AUTHORS:
# - Carl Witty and William Stein: initial version
-@@ -711,20 +485,6 @@
+@@ -722,20 +497,6 @@
fi
#####################################################################
@@ -387,7 +387,7 @@ Forwarded: not-needed
# File conversion
#####################################################################
-@@ -747,11 +507,6 @@
+@@ -758,11 +519,6 @@
# Run Sage's versions of the standard Algebra/Geometry etc. software
#####################################################################
@@ -399,7 +399,7 @@ Forwarded: not-needed
if [[ "$1" =~ ^--notebook=.* || "$1" =~ ^-n=.* || "$1" =~ ^-notebook=.* ]] ; then
sage-cleaner &>/dev/null &
exec sage-notebook "$@"
-@@ -762,13 +517,6 @@
+@@ -773,13 +529,6 @@
exec sage-notebook "$@"
fi
@@ -413,7 +413,7 @@ Forwarded: not-needed
if [ "$1" = "-inotebook" -o "$1" = '--inotebook' ]; then
shift
sage-cleaner &>/dev/null &
-@@ -787,38 +535,19 @@
+@@ -798,38 +547,19 @@
exit 0
fi
@@ -454,7 +454,7 @@ Forwarded: not-needed
shift
exec sage-runtests -p "$@"
else
-@@ -827,16 +556,6 @@
+@@ -838,16 +568,6 @@
fi
fi
@@ -471,7 +471,7 @@ Forwarded: not-needed
if [ "$1" = '-testall' -o "$1" = "--testall" ]; then
shift
SAGE_BANNER=no sage_setup
-@@ -851,114 +570,6 @@
+@@ -862,114 +582,6 @@
exec sage-eval "$@"
fi
@@ -586,7 +586,7 @@ Forwarded: not-needed
if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then
shift
exec python -m "sage_setup.docbuild" "$@"
-@@ -1030,10 +641,6 @@
+@@ -1041,10 +653,6 @@
fi
if [ $# -ge 1 ]; then
@@ -615,8 +615,8 @@ Forwarded: not-needed
---optional
--preparse
--python
- -q
-@@ -199,36 +196,6 @@
+ --python3
+@@ -200,36 +197,6 @@
sage: ret
0
@@ -653,7 +653,7 @@ Forwarded: not-needed
Test ``sage-run`` on a Python file, both with an absolute and with a relative path::
sage: dir = tmp_dir(); name = 'python_test_file.py'
-@@ -415,50 +382,6 @@
+@@ -416,50 +383,6 @@
...
RuntimeError: refusing to run doctests...
@@ -664,7 +664,7 @@ Forwarded: not-needed
- sage: test='r\"\"\"Add a doc-test for the fixdoctest command line option and, in particular, check that\n:trac:`10589` is fixed.\n\nEXAMPLES::\n\n sage: 1+1 # incorrect output\n 3\n sage: m=matrix(ZZ,3) # output when none is expected\n [0 0 0]\n [0 0 0]\n [1 0 0]\n sage: (2/3)*m # no output when it is expected\n sage: mu=PartitionTuple([[4,4],[3,3,2,1],[1,1]]) # output when none is expected\n [4, 4, 3, 3, 2, 1, 1]\n sage: m [...]
- sage: test_file = os.path.join(tmp_dir(), 'test_file.py')
- sage: F = open(test_file, 'w')
-- sage: F.write(test)
+- sage: _ = F.write(test)
- sage: F.close()
- sage: (out, err, ret) = test_executable(["sage", "--fixdoctests", test_file])
- sage: with open(test_file, 'r') as f:
@@ -704,7 +704,7 @@ Forwarded: not-needed
Test external programs being called by Sage::
sage: (out, err, ret) = test_executable(["sage", "--sh"], "echo Hello World\nexit 42\n")
-@@ -600,32 +523,6 @@
+@@ -609,32 +532,6 @@
sage: ret
0
--
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