Package: sagemath / 8.8-1

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Package Version Patches format
sagemath 8.8-1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
u0 version ecl 16.1.3.patch #22191 | (download)

sage/src/sage/libs/ecl.pyx | 18 16 + 2 - 0 !
sage/src/sage/libs/eclsig.h | 42 42 + 0 - 0 !
2 files changed, 58 insertions(+), 2 deletions(-)

 set ecl to not trap floating point exceptions, so that sigfpe will
 not occur


u1 pkgconfig extra link flags.patch #27205 | (download)

sage/src/sage/env.py | 6 6 + 0 - 0 !
sage/src/sage/libs/linbox/fflas.pxd | 1 1 + 0 - 0 !
sage/src/sage/libs/linbox/linbox.pxd | 1 1 + 0 - 0 !
sage/src/sage/libs/linbox/linbox_flint_interface.pxd | 1 1 + 0 - 0 !
4 files changed, 9 insertions(+)

 also use ldflags from pkg-config that are not -l or -l
 The concrete failure is that the flag -fopenmp is missing for linbox and fflas-ffpack.
 In principle these flags should be respected for all extensions that use
 pkg-config, also in module_list.py.
u1 fix atrocious symlink logic.patch #22444 | (download)

sage/src/sage/repl/ipython_kernel/install.py | 10 9 + 1 - 0 !
1 file changed, 9 insertions(+), 1 deletion(-)

 fix atrocious logic in symlink()
 If the desired result is already in effect, do nothing. Otherwise, proceed
 with the previous behaviour, but handle permissions errors correctly.
 We don't actually need any part of this file in Debian, but fixing this (so
 that post-install tests don't fail) was easier than trying to figure out if
 removing the file would have other consequences elsewhere.
u1 looser doctest basename.patch #22445 | (download)

sage/src/sage/doctest/sources.py | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 make sage.doctest.sources.get_basename work in more situations
 This lets you specify SAGE_SRC like /path/to/test/dir/../../src/dir, which
 avoids post-install test failures in sage/doctest/test.py
u1 scripts dir.patch #22731 | (download)

sage/src/bin/sage | 12 6 + 6 - 0 !
sage/src/bin/sage-cachegrind | 2 1 + 1 - 0 !
sage/src/bin/sage-callgrind | 2 1 + 1 - 0 !
sage/src/bin/sage-env | 2 1 + 1 - 0 !
sage/src/bin/sage-massif | 2 1 + 1 - 0 !
sage/src/bin/sage-omega | 2 1 + 1 - 0 !
sage/src/bin/sage-valgrind | 2 1 + 1 - 0 !
sage/src/sage/doctest/control.py | 12 6 + 6 - 0 !
sage/src/sage/env.py | 1 1 + 0 - 0 !
sage/src/sage/interfaces/maxima.py | 4 2 + 2 - 0 !
10 files changed, 21 insertions(+), 20 deletions(-)

 define and use sage_scripts_dir in more places
 So distros can install them somewhere other than /usr/bin
u1 ipywidgets repr.patch #https://github.com/jupyter widgets/ipywidgets/pull/1031 | (download)

sage/src/sage/repl/ipython_kernel/widgets.py | 32 31 + 1 - 0 !
1 file changed, 31 insertions(+), 1 deletion(-)

 money-patch ipywidgets in the way that sage upstream expects
 Sage upstream patches ipywidgets, but this is still being discussed
 upstream (see Bug below). In the meantime, we can have Sage monkey-patch
 ipywidgets at runtime, to prevent other users of ipywidgets being affected.
u1 workaround sympow malloc perturb.patch #https://salsa.debian.org/science team/sympow/merge_requests/1, reported to upstream by private email | (download)

sage/src/sage/lfunctions/sympow.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 work around sympow segfault due to malloc_perturb_
u1 fix trivial test cases.patch #25094, #25096, #25102, the interpreter bits do not seem necessary anymore | (download)

sage/src/sage/interfaces/tachyon.py | 2 1 + 1 - 0 !
sage/src/sage/tests/books/judson-abstract-algebra/sylow-sage.py | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 fix trivial test cases to work
 Includes cases of:
 - add more "..." wildcard patterns to the test
 - changing the value to an exactly-equivalent value. 
 These should probably be forwarded upstream.
 .
 Also includes cases of:
 - update an expected error message to some conceptually identical message
u2 fix sympow cachedir.patch | (download)

sage/src/sage/lfunctions/sympow.py | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 set sympow_cachedir to be inside dot_sage
 Otherwise tests fail in sbuild because sympow can't create HOME/.sympow
u2 allow override sage local.patch | (download)

sage/build/make/install | 4 2 + 2 - 0 !
sage/configure.ac | 2 1 + 1 - 0 !
sage/sage | 2 2 + 0 - 0 !
sage/src/bin/sage-env | 2 1 + 1 - 0 !
sage/src/sage/env.py | 2 1 + 1 - 0 !
5 files changed, 7 insertions(+), 5 deletions(-)

 allow sage_local to be overridden from outside the makefiles
 This makes it easier for package managers to create binary distributions.
 However, keep SAGE_SPKG_INST relative to SAGE_ROOT rather than SAGE_LOCAL
 since that would be a more intrusive change.
d0 arb.patch | (download)

sage/src/module_list.py | 4 2 + 2 - 0 !
sage/src/sage/libs/arb/acb.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/acb_calc.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/acb_elliptic.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/acb_hypgeom.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/acb_modular.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/acb_poly.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/arb.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/arf.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/bernoulli.pxd | 2 1 + 1 - 0 !
sage/src/sage/libs/arb/mag.pxd | 2 1 + 1 - 0 !
11 files changed, 12 insertions(+), 12 deletions(-)

 link with -lflint-arb instead of -larb
 The name of the arb library is libflint-arb in Debian.
d0 gsl cblas.patch | (download)

sage/src/module_list.py | 7 3 + 4 - 0 !
sage/src/sage/misc/cython.py | 7 3 + 4 - 0 !
2 files changed, 6 insertions(+), 8 deletions(-)

 hard-code gsl cblas paths and keep gslcblas in gsl_libs
 Debian does not provide a pkg-config file for libgslcblas,
 so just hard-code the paths here for Sage
 .
 Also, when gslcblas is removed from gsl_libs we currently get this error
 at the beginning of the doc build:
 ImportError: /usr/lib/x86_64-linux-gnu/libgsl.so.19: undefined symbol: cblas_ctrmv
 Does libgsl need to be linked against gslcblas?
d0 libgap path.patch | (download)

sage/src/sage/env.py | 2 1 + 1 - 0 !
sage/src/setup.py | 4 3 + 1 - 0 !
2 files changed, 4 insertions(+), 2 deletions(-)

 add gap library directory
 Search libraries in gap's subdirectory where libgap is located.
d0 maxima.patch | (download)

sage/src/bin/sage | 2 1 + 1 - 0 !
sage/src/doc/en/constructions/plotting.rst | 2 1 + 1 - 0 !
sage/src/sage/interfaces/expect.py | 2 1 + 1 - 0 !
sage/src/sage/interfaces/maxima.py | 4 2 + 2 - 0 !
sage/src/sage/interfaces/maxima_abstract.py | 11 4 + 7 - 0 !
5 files changed, 9 insertions(+), 12 deletions(-)

 change to work with debian's maxima-sage packages
d0 mathjax.patch | (download)

sage/src/doc/common/conf.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 change mathjax_path
 _static/mathjax are symlinks to /usr/share/javascript/mathjax created in debian/rules.
d0 nauty.patch | (download)

sage/src/sage/graphs/digraph_generators.py | 2 1 + 1 - 0 !
sage/src/sage/graphs/graph_generators.py | 4 2 + 2 - 0 !
sage/src/sage/graphs/hypergraph_generators.py | 2 1 + 1 - 0 !
3 files changed, 4 insertions(+), 4 deletions(-)

---
d0 rubiks.patch | (download)

sage/src/sage/interfaces/rubik.py | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 find rubiks binaries
d0 singular.patch | (download)

sage/src/sage/env.py | 2 1 + 1 - 0 !
sage/src/sage/interfaces/singular.py | 2 1 + 1 - 0 !
sage/src/sage/misc/compat.py | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 additional changes to work with the debian package of singular
 We search for a specific SOVERSION of libsingular-Singular, to allow us to
 runtime-Depend on libsingular4 and not libsingular4-dev.
d0 threejs default in notebooks.patch | (download)

sage/src/sage/plot/plot3d/base.pyx | 4 2 + 2 - 0 !
sage/src/sage/repl/rich_output/backend_ipython.py | 2 1 + 1 - 0 !
sage/src/sage/repl/rich_output/backend_sagenb.py | 2 1 + 1 - 0 !
3 files changed, 4 insertions(+), 4 deletions(-)

 use threejs as default 3d viewer in jupyter and sagenb notebooks
 In Debian we have jmol, which can be used from the sage command line,
 but not jsmol, which is necessary to use jmol in the notebooks. This patch
 makes sure that jmol is the default 3D viewer on the command line and threejs
 is the default in the notebooks.
d0 disable jsmol.patch | (download)

sage/src/sage/repl/display/jsmol_iframe.py | 13 13 + 0 - 0 !
sage/src/sage/repl/ipython_kernel/install.py | 1 0 + 1 - 0 !
2 files changed, 13 insertions(+), 1 deletion(-)

 disable installation of jsmol nbextension
d0 paths.patch | (download)

sage/build/bin/sage-python23 | 4 2 + 2 - 0 !
sage/src/sage/libs/lcalc/lcalc_sage.h | 2 1 + 1 - 0 !
sage/src/sage/repl/ipython_kernel/install.py | 2 1 + 1 - 0 !
3 files changed, 4 insertions(+), 4 deletions(-)

 hard-code paths to external system run-time dependencies
d0 threejs offline paths.patch | (download)

sage/src/sage/repl/rich_output/backend_ipython.py | 26 7 + 19 - 0 !
sage/src/sage/repl/rich_output/backend_sagenb.py | 6 4 + 2 - 0 !
2 files changed, 11 insertions(+), 21 deletions(-)

---
d1 install paths.patch # many things in here could be split into an upstreamable patch | (download)

sage/configure.ac | 3 1 + 2 - 0 !
sage/sage | 1 1 + 0 - 0 !
sage/src/Makefile.in | 2 1 + 1 - 0 !
sage/src/module_list.py | 2 1 + 1 - 0 !
sage/src/sage/env.py | 2 1 + 1 - 0 !
sage/src/sage/interacts/debugger.py | 4 2 + 2 - 0 !
sage/src/sage_setup/clean.py | 2 1 + 1 - 0 !
sage/src/sage_setup/find.py | 7 3 + 4 - 0 !
sage/src/setup.py | 6 3 + 3 - 0 !
9 files changed, 14 insertions(+), 15 deletions(-)

 install to debian paths
 TODO: upstream hard-codes "site-packages" in a bunch of places; these should
 be fixed to use SAGE_LIB instead and forwarded upstream. Then this patch could
 be a lot smaller.
d1 sage cli.patch | (download)

sage/src/bin/sage | 396 3 + 393 - 0 !
sage/src/sage/tests/cmdline.py | 47 0 + 47 - 0 !
2 files changed, 3 insertions(+), 440 deletions(-)

 patch the sage startup script
 This patch removes options that do not work for us
 and removes a check for if we are in a sage source directory.
 It has only minor modifications from the sage-on-gentoo version.
d1 sage env.patch | (download)

sage/build/make/deps | 2 1 + 1 - 0 !
sage/build/make/install | 2 1 + 1 - 0 !
sage/src/bin/sage | 34 21 + 13 - 0 !
sage/src/bin/sage-env | 32 10 + 22 - 0 !
sage/src/doc/en/developer/sage_manuals.rst | 2 1 + 1 - 0 !
sage/src/doc/en/faq/faq-general.rst | 2 1 + 1 - 0 !
sage/src/doc/en/installation/source.rst | 2 1 + 1 - 0 !
sage/src/sage/env.py | 35 13 + 22 - 0 !
sage/src/sage_setup/docbuild/__init__.py | 2 1 + 1 - 0 !
9 files changed, 50 insertions(+), 63 deletions(-)

 patch sage-env and env.py
 Note that the patched sage-env is only used during the package build and not installed.
 Instead the file debian/adhoc/sage-env is installed.
 .
 The LD_LIBRARY_PATH can probably be forwarded upstream, either way is fine.
d1 fakeroot.patch | (download)

sage/configure.ac | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 we are building with fakeroot which makes this check fail.
 dpkg-buildpackage uses `fakeroot debian/rules clean` so this is needed
d1 multiarch python paths.patch | (download)

sage/src/sage/misc/sageinspect.py | 8 7 + 1 - 0 !
1 file changed, 7 insertions(+), 1 deletion(-)

 correctly handle debian's python multiarch extension module names
 We need to strip that part in order to return the correct ".pyx" filename.
 Otherwise a few post-install tests break.
d1 doc docs.patch | (download)

sage/src/sage/misc/copying.py | 2 1 + 1 - 0 !
sage/src/sage/misc/sagedoc.py | 4 2 + 2 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

---
df revert minor feature dependent on python patch.patch | (download)

sage/src/sage/rings/integer.pyx | 10 0 + 10 - 0 !
1 file changed, 10 deletions(-)

 revert sage commit 5dbc699911095dd03f0141a7c1b7ba1c7056ceef
 This is dependent on a python patch that hasn't landed upstream or in Debian
 yet. It adds a minor feature used nowhere except the doctests, so just revert
 it because we know it will break.
df sage gap reset doctest.patch | (download)

sage/src/sage/interfaces/gap.py | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 reset the sage-local gap workspace before the first test
 Otherwise it causes test errors, if the workspace contains files from older
 versions of gap.
df silence_ecl_opt_signals.patch | (download)

sage/src/sage/libs/ecl.pyx | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
df subprocess sphinx.patch | (download)

sage/src/sage_setup/docbuild/__init__.py | 25 2 + 23 - 0 !
sage/src/sage_setup/docbuild/sphinxbuild.py | 5 5 + 0 - 0 !
2 files changed, 7 insertions(+), 23 deletions(-)

 use subprocess to run parallel sphinx build
 The upstream sphinx parallel build segfaults because we don't patch Python,
 see our revert-lazy-import patches for details. (Those reverts are needed to
 make the serial build not segfault, but the parallel build still segfaults.)
 .
 We used to disable parallel build completely, but it was too slow. This
 alternative method of running the parallel build seems to work OK.
 .
 As of SageMath 8.0 the RAM usage seems to be more reasonable (~3-4GB for 4
 threads), but please complain on the mailing list if this eats your machine.
dt version glpk 4.60 extra hacky fixes.patch | (download)

sage/src/sage/libs/glpk/error.pyx | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 work around sage/glpk differences to fix remaining glpk doctests
 Sage upstream patch GLPK. Most of this was accepted by upstream, however they
 rejected one minor part of it:
 https://git.sagemath.org/sage.git/tree/build/pkgs/glpk/patches/error_recovery.patch?id=3e8450b13d5c5353cd45d5881acf59994cf28b6b
 This is described in some more detail here:
 https://trac.sagemath.org/ticket/20710#comment:18
 It turns out this is quite important for Sage:
 .
 Since we don't patch GLPK the same way in Debian, this means that if GLPK in
 Sage causes one error, and this is caught by Sage and recovered from, then
 later (because upstream GLPK is not clear the "error" flag) Sage will append
 all subsequent terminal output of GLPK into the error_message string but not
 actually forward it to the user's terminal. This breaks some doctests.
 .
 The patch below disables the terminal supression, so that doctests work again.
 In this sense, it is not *this patch* that is hacky; this patch can remain -
 all it does is print some extra messages to the terminal. However, this
 inherent incompatibility between what upstream GLPK does and what Sage
 expects, may cause other problems for us later, so I am just documenting this
 in detail for future maintainers.
dt version glpk 4.65 ignore warnings.patch | (download)

sage/src/sage/doctest/parsing.py | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 ignore warnings of glpk 4.65 when parsing doctests
 GLPK 4.65 prints warnings which lead to failing doctests.
 Upstream does not use GLPK 4.65 yet. Ignore the warnings until a
 solution is found.
dt more fix test cases.patch | (download)

sage/src/doc/en/constructions/algebraic_geometry.rst | 6 3 + 3 - 0 !
sage/src/doc/en/developer/coding_in_other.rst | 7 0 + 7 - 0 !
sage/src/sage/interfaces/tests.py | 2 1 + 1 - 0 !
3 files changed, 4 insertions(+), 11 deletions(-)

 temporary fixes to some more test cases
 Every override in this file should be accompanied by an explanation on why
 it's only going to be temporary and when it can be expected to be removed.
dt work around doc common conf.patch | (download)

sage/src/doc/common/conf.py | 7 6 + 1 - 0 !
sage/src/doc/en/introspect/conf.py | 7 5 + 2 - 0 !
sage/src/sage/misc/sphinxify.py | 4 3 + 1 - 0 !
3 files changed, 14 insertions(+), 4 deletions(-)

 move runtime documentation python modules into src/sage
 This is a temporary workaround; upstream is working on a proper fix.
 When you remove this patch, also be sure to remove the hacky entries in
 sagemath-common.install
dt work around singular mips64el segfault.patch | (download)

sage/src/bin/sage | 6 6 + 0 - 0 !
1 file changed, 6 insertions(+)

---
dt version ipywidgets 6 revert 23177.patch | (download)

sage/src/sage/cpython/debug.pyx | 2 1 + 1 - 0 !
sage/src/sage/interacts/test_jupyter.rst | 165 82 + 83 - 0 !
sage/src/sage/repl/ipython_kernel/interact.py | 36 18 + 18 - 0 !
sage/src/sage/repl/ipython_kernel/widgets.py | 20 10 + 10 - 0 !
sage/src/sage/repl/ipython_kernel/widgets_sagenb.py | 72 36 + 36 - 0 !
5 files changed, 147 insertions(+), 148 deletions(-)

 upgrade to ipywidgets 7