## Package: sagemath / 8.6-6

### Metadata

Package | Version | Patches format |
---|---|---|

sagemath | 8.6-6 | 3.0 (quilt) |

### Patch series

view the series filePatch | File delta | Description |
---|---|---|

u0 version numpy 1.16 inline fortran.patch #27061 | (download) |
sage/src/sage/misc/inline_fortran.py |
53 30 + 23 - 0 ! |
fix sage.misc.inline_fortran to work with numpy 1.16 Numpy 1.16 introduced a slight backwards incompatibility such that the way we were calling f2py.compile() would no longer work for capturing a log of the f2py output. It turns out f2py.compile() doesn't do anything very interesting anyways and has many redundancies with what we do here: It's easy to call f2py in a subprocess ourselves with the correct arguments and handle the output. |

u0 version ecl 16.1.3.patch #22191 | (download) |
sage/src/sage/libs/ecl.pyx |
18 16 + 2 - 0 ! |
set ecl to not trap floating point exceptions, so that sigfpe will not occur |

u0 version sphinx 1.8 dependency.patch #26949 | (download) |
sage/src/sage_setup/docbuild/ext/sage_autodoc.py |
829 284 + 545 - 0 ! |
make sage autodoc work for both py2 and py3 |

u0 version sphinx 1.8.patch #26451 | (download) |
sage/src/doc/common/conf.py |
2 1 + 1 - 0 ! |
call sphinx() 1.8 constructor i.e., do not make srcdir and outdir the same as Sphinx does not allow that anymore. |

u1 sphinx 1.8 doctest transform.patch | (download) |
sage/src/doc/common/conf.py |
2 1 + 1 - 0 ! |
add sphinx extension to modify lines in codeblocks starting with 'sage:' In particular this removes <BLANKLINE> from doctest codeblocks in the documentation. |

u1 pkgconfig extra link flags.patch #27205 | (download) |
sage/src/sage/env.py |
6 6 + 0 - 0 ! |
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 ! |
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 ! |
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 ! |
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 |
31 30 + 1 - 0 ! |
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 ! |
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 ! |
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 ! |
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 ! |
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. |

u2 libgap symbol loading.patch | (download) |
sage/src/sage/libs/gap/util.pyx |
14 14 + 0 - 0 ! |
force all symbols in libgap.so to be loaded This fixes a bug that occurs when trying to load compiled GAP packages using libgap as opposed to the gap executable. The problem is caused by the fact that compiled GAP packages are not currently linked with -lgap; rather they assume they will be loaded by running the gap executable, which has all of the GAP library compiled into it and thus is able to resolve all the symbols it uses at runtime. However, when using libgap, symbols are resolved lazily by default (this is in turn due to the dlopen flags that Python uses when importing a module), and when libgap in turn tries to dlopen() a compiled GAP module such as io.so, since io.so does not have a DT_NEEDED entry for libgap it fails to find some of the symbols it needs that haven't been resolved yet. This fixes the issue in Sage's libgap interface by immediately, before initializing GAP, re-dlopen()-ing libgap.so with the RTLD_GLOBAL | RTLD_NOW flagset, forcing all symbols in the library to be resolved. |

d0 arb.patch | (download) |
sage/src/module_list.py |
4 2 + 2 - 0 ! |
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 ! |
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/setup.py |
4 3 + 1 - 0 ! |
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 ! |
change to work with debian's maxima-sage packages |

d0 mathjax.patch | (download) |
sage/src/doc/common/conf.py |
2 1 + 1 - 0 ! |
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 ! |
--- |

d0 rubiks.patch | (download) |
sage/src/sage/interfaces/rubik.py |
6 3 + 3 - 0 ! |
find rubiks binaries |

d0 singular.patch | (download) |
sage/src/sage/env.py |
2 1 + 1 - 0 ! |
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 ! |
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 ! |
disable installation of jsmol nbextension |

d0 paths.patch | (download) |
sage/build/bin/sage-python23 |
4 2 + 2 - 0 ! |
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 ! |
--- |

d1 install paths.patch # many things in here could be split into an upstreamable patch | (download) |
sage/configure.ac |
3 1 + 2 - 0 ! |
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 |
389 3 + 386 - 0 ! |
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 ! |
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 ! |
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 ! |
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 ! |
--- |

d1 disable post install tests.patch | (download) |
sage/src/sage/all.py |
8 0 + 8 - 0 ! |
disable some post-install tests We don't need to test these pre-install either because they're already implicitly tested by other parts of the build process. |

df revert minor feature dependent on python patch.patch | (download) |
sage/src/sage/rings/integer.pyx |
10 0 + 10 - 0 ! |
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 python_security.patch | (download) |
sage/src/sage/doctest/control.py |
25 13 + 12 - 0 ! |
--- |

df sage gap reset doctest.patch | (download) |
sage/src/sage/interfaces/gap.py |
1 1 + 0 - 0 ! |
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 ! |
--- |

df subprocess sphinx.patch | (download) |
sage/src/sage_setup/docbuild/__init__.py |
27 2 + 25 - 0 ! |
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 ! |
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. |