[Debian-science-sagemath] Sage with gap 4.10 status

[Tobias Hansen]

On 1/2/19 3:20 PM, E. Madison Bray wrote:
> On Wed, Jan 2, 2019 at 1:48 PM Tobias Hansen <thansen at debian.org> wrote:
>> On 1/2/19 1:07 PM, E. Madison Bray wrote:
>>> On Wed, Jan 2, 2019 at 12:57 PM Tobias Hansen <thansen at debian.org> wrote:
>>>> From the gap 4.10 ticket I take that you install
>>>>
>>>> + pkg/autpgrp-* \
>>>> + pkg/alnuth-* \
>>>> + pkg/crisp-* \
>>>> + pkg/ctbllib \
>>>> + pkg/FactInt-* \
>>>> + pkg/fga \
>>>> + pkg/irredsol-* \
>>>> + pkg/laguna-* \
>>>> + pkg/polenta-* \
>>>> + pkg/polycyclic-* \
>>>> + pkg/resclasses-* \
>>>> + pkg/sophus-* \
>>>> + pkg/tomlib-* \
>>>> and atlasrep.
>>>>
>>>> When I installed more gap libraries (gap-atlasrep, gap-autpgrp, gap-factint, gap-laguna, gap-polycyclic) I got an error during the docbuild (see attached sagemath_docbuild_error.build).
>>> Did you also include the patches from
>>> https://trac.sagemath.org/ticket/26856 and its dependency
>>> https://trac.sagemath.org/ticket/26889 ?
>>> This updated support for various additional GAP packages with 4.10,
>>> including all the packages you listed above, among others.
>> No, I didn't. I am running a test build with these two patches now. Are there any gap libs that change particularly many test results when they are installed? Ideally the sagemath package shouldn't depend on additional gap libs (apart from the package gap-libs).
> It's not so much a question of changing test results (although
> obviously that is a side-effect) as there are GAP packages that change
> the behavior of GAP, sometimes in significant ways.  Therefore code
> that uses GAP sometimes may need additional logic to account for
> differences in results that occur depending on what packages are
> loaded.  It's quite frustrating and confusing.

Ok, adding the two patches and depending on the Debian packages gap-primgrp, gap-smallgrp and gap-transgrp I get much less test failures. I uploaded an updated sage 8.4-4.

I also updated the package to 8.6.beta1 (in the branch 8.6), skipping 8.5 because it's better to avoid the large gap related patches. I uploaded cython 0.29.2 and cypari2 1.3.1 to experimental. The only other change that sage 8.6.beta1 needs to get through compilation is the patch using_namespace_std.patch for lcalc, which breaks sage 8.4. If anyone wants to test, this needs to be applied locally for now.

The main reason 8.6.beta1 has significantly more test failures than 8.4 seem to be many variations of this error:

File "src/sage/misc/bindable_class.py", line 180, in sage.misc.bindable_class.BoundClass
Failed example:
    sage_getdoc(c)
Exception raised:
    Traceback (most recent call last):
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/doctest/forker.py", line 671, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/doctest/forker.py", line 1086, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.misc.bindable_class.BoundClass[7]>", line 1, in <module>
        sage_getdoc(c)
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/misc/sageinspect.py", line 1923, in sage_getdoc
        s = sage.misc.sagedoc.format(r, embedded=(embedded_override or EMBEDDED_MODE))
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/misc/sagedoc.py", line 711, in format
        s = detex(s, embedded=embedded)
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/misc/sagedoc.py", line 228, in detex
        s = sphinxify(s, format='text')
      File "/<<PKGBUILDDIR>>/debian/build/usr/lib/python2.7/dist-packages/sage/misc/sphinxify.py", line 99, in sphinxify
        confoverrides, None, None, True)
      File "/usr/lib/python2.7/dist-packages/sphinx/application.py", line 160, in __init__
        raise ApplicationError(__('Source directory and destination '
    ApplicationError: Source directory and destination directory cannot be identical


If we could fix this we could upload sage 8.6 to experimental.

I will be on vacation next week (January 6-13) with no possibility to work on this.

Best,

Tobias