Upgrade GAP, libsemigroups by trevorkarn · Pull Request #41700 · sagemath/sage

trevorkarn · 2026-02-26T02:39:37Z

Upgrade GAP to 4.15.1 and libsemigroups to 3.5.1.

Fixes #41653 and implicitly #40186

📝 Checklist

The title is concise and informative.
The description explains in detail what this PR is about.
I have linked a relevant issue or discussion.
I have created tests covering the changes.
I have updated the documentation and checked the documentation preview.

⌛ Dependencies

Bump libsemigroups

github-actions · 2026-02-26T03:42:04Z

Documentation preview for this PR (built with commit c92ca31; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

antonio-rojas · 2026-02-26T07:34:56Z

libsemigroups can't be updated to v3 because the GAP semigroups package only supports v2. There is also a new version 5.5.4 of semigroups, it makes sense to update it too.

dimpase · 2026-02-26T20:21:11Z

[gap_packages-4.15.1] [......................................................................]
[gap_packages-4.15.1] Setting up build directory /Users/dima/software/sage/local/var/tmp/sage/build/gap_packages-4.15.1
[gap_packages-4.15.1] Applying patches from ../patches...
[gap_packages-4.15.1] Applying ../patches/digraphs-planarity-4.x.patch
[gap_packages-4.15.1] patching file 'pkg/digraphs/src/planar.c'
[gap_packages-4.15.1] 1 out of 1 hunks failed--saving rejects to 'pkg/digraphs/src/planar.c.rej'
[gap_packages-4.15.1] Error applying '../patches/digraphs-planarity-4.x.patch'
[gap_packages-4.15.1] ************************************************************************
[gap_packages-4.15.1] Error applying patches
[gap_packages-4.15.1] ************************************************************************
[gap_packages-4.15.1] Please email sage-devel (http://groups.google.com/group/sage-devel)
[gap_packages-4.15.1] explaining the problem and including the log files
[gap_packages-4.15.1]   /Users/dima/software/sage/logs/pkgs/gap_packages-4.15.1.log

more patches to take care of

trevorkarn · 2026-02-26T21:42:11Z

[gap_packages-4.15.1] [......................................................................]
[gap_packages-4.15.1] Setting up build directory /Users/dima/software/sage/local/var/tmp/sage/build/gap_packages-4.15.1
[gap_packages-4.15.1] Applying patches from ../patches...
[gap_packages-4.15.1] Applying ../patches/digraphs-planarity-4.x.patch
[gap_packages-4.15.1] patching file 'pkg/digraphs/src/planar.c'
[gap_packages-4.15.1] 1 out of 1 hunks failed--saving rejects to 'pkg/digraphs/src/planar.c.rej'
[gap_packages-4.15.1] Error applying '../patches/digraphs-planarity-4.x.patch'
[gap_packages-4.15.1] ************************************************************************
[gap_packages-4.15.1] Error applying patches
[gap_packages-4.15.1] ************************************************************************
[gap_packages-4.15.1] Please email sage-devel (http://groups.google.com/group/sage-devel)
[gap_packages-4.15.1] explaining the problem and including the log files
[gap_packages-4.15.1]   /Users/dima/software/sage/logs/pkgs/gap_packages-4.15.1.log

more patches to take care of

Thanks - is this your output of make? I didn't see this error when building gap_packages on my system, should I expect something different with a different OS?

dimpase · 2026-02-26T22:31:14Z

Thanks - is this your output of make?
yes
I didn't see this error when building gap_packages on my system, should I expect something different with a different OS?

This patch comes from #40153

I have hard time imagining it would fail on macOS, but somehow magically work on Linux.

You either have to enable building gap_packages via ./configure, or
explicitly run make gap_packages

dimpase

make sure make gap_packages works, and then run tests

trevorkarn · 2026-02-27T16:00:22Z

Thanks - is this your output of make?
yes
I didn't see this error when building gap_packages on my system, should I expect something different with a different OS?

This patch comes from #40153

I have hard time imagining it would fail on macOS, but somehow magically work on Linux.

You either have to enable building gap_packages via ./configure, or explicitly run make gap_packages

Indeed. I can reproduce your patch issue when I explicitly run make gap_packages.

trevorkarn · 2026-02-28T21:15:45Z

All tests pass locally when I run sage -tp 10 -a --long. Does this include the gap_packages as well, or do I have to manually test them somehow?

antonio-rojas · 2026-02-28T21:24:29Z

As mentioned above, you need to revert the libsemigroups upgrade, the semigroups package shipped by sage does not support v3.

trevorkarn · 2026-02-28T21:33:08Z

As mentioned above, you need to revert the libsemigroups upgrade, the semigroups package shipped by sage does not support v3.

Thanks for the reminder. Do you have a case in mind of where this causes a failure? I ask because it feels slightly misleading to have all of the tests pass when the semigroups package doesn't support v3. So I'd like to add a test that fails on v3 and passes with any compatible version.

antonio-rojas · 2026-02-28T21:38:20Z

As mentioned above, you need to revert the libsemigroups upgrade, the semigroups package shipped by sage does not support v3.

Thanks for the reminder. Do you have a case in mind of where this causes a failure? I ask because it feels slightly misleading to have all of the tests pass when the semigroups package doesn't support v3. So I'd like to add a test that fails on v3 and passes with any compatible version.

Just try to install the semigroups package, it will not even compile.

dimpase · 2026-02-28T21:39:18Z

look for gap_packages in the output of ./configure -h and act accordingly

trevorkarn · 2026-02-28T22:03:58Z

As mentioned above, you need to revert the libsemigroups upgrade, the semigroups package shipped by sage does not support v3.

Thanks for the reminder. Do you have a case in mind of where this causes a failure? I ask because it feels slightly misleading to have all of the tests pass when the semigroups package doesn't support v3. So I'd like to add a test that fails on v3 and passes with any compatible version.

Just try to install the semigroups package, it will not even compile.

Indeed it does not even compile. Is this something that we should update on a separate PR, or is it fine to leave it as v2 indefinitely?

trevorkarn · 2026-02-28T22:45:36Z

look for gap_packages in the output of ./configure -h and act accordingly

I see that this output tells me how to install gap_packages (by running ./configure --enable-gap_packages). I'm not seeing anything about how to run tests in the output of ./configure -h. Am I missing something?

dimpase · 2026-02-28T23:34:54Z

if gap_packages is installed then it will be tested

dimpase · 2026-02-28T23:36:36Z

As mentioned above, you need to revert the libsemigroups upgrade, the semigroups package shipped by sage does not support v3.

Thanks for the reminder. Do you have a case in mind of where this causes a failure? I ask because it feels slightly misleading to have all of the tests pass when the semigroups package doesn't support v3. So I'd like to add a test that fails on v3 and passes with any compatible version.

Just try to install the semigroups package, it will not even compile.

Indeed it does not even compile. Is this something that we should update on a separate PR, or is it fine to leave it as v2 indefinitely?

leave it as the highest version supported by Semigroups package as packaged by GAP

trevorkarn · 2026-03-01T00:47:35Z

Ok I think most recent push addresses all comments

antonio-rojas · 2026-03-06T07:38:48Z

semigroups 5.6.0 with support for libsemigroups v3 was just released, so those can now be upgraded too.

dimpase · 2026-03-06T13:23:52Z

semigroups 5.6.0 with support for libsemigroups v3 was just released, so those can now be upgraded too.

This would need splitting Semigroups into its own spkg?

antonio-rojas · 2026-03-06T13:37:32Z

semigroups 5.6.0 with support for libsemigroups v3 was just released, so those can now be upgraded too.

This would need splitting Semigroups into its own spkg?

It is its own spkg already

antonio-rojas · 2026-03-08T16:42:37Z

Note that there is a bug in the semigroups tarball that breaks building with external libsemigroups. A workaround is echo "3.5.1" > .LIBSEMIGROUPS_VERSION

See semigroups/Semigroups#1143 (comment)

trevorkarn · 2026-03-09T18:25:47Z

Note that there is a bug in the semigroups tarball that breaks building with external libsemigroups. A workaround is echo "3.5.1" > .LIBSEMIGROUPS_VERSION

See semigroups/Semigroups#1143 (comment)

In which directory should I do this? I tried in the build directory SAGE_ROOT/local/var/tmp/sage/build/semigroups-5.6.0 and in SAGE_ROOT/local/var/tmp/sage/build/semigroups-5.6.0/src, and reran with KEEP_BUILT_SPKGS=yes and neither of those work. Also how should we get this into Sage? Should this go in the patches directory? Or should we wait until it is fixed upstream?

antonio-rojas · 2026-03-09T21:17:30Z

In which directory should I do this? I tried in the build directory SAGE_ROOT/local/var/tmp/sage/build/semigroups-5.6.0 and in SAGE_ROOT/local/var/tmp/sage/build/semigroups-5.6.0/src, and reran with KEEP_BUILT_SPKGS=yes and neither of those work. Also how should we get this into Sage? Should this go in the patches directory? Or should we wait until it is fixed upstream?

In spkg-install.in, right before the sdh_configure call. You'll need to run autogen.sh too.

dimpase · 2026-03-09T21:56:15Z

hmm, no, I think this should be a patch?
in SAGEROOT/build/pkgs/semigroup/patches/

un-tar the tarball somewhere,
run "git init", "git commit -m1", create the file, "git add" it, hen put the output of "git diff" in the sudirectory patches/, with suffix ".patch"

dimpase · 2026-03-09T21:56:54Z

or is it an unconfigured tarball?

trevorkarn · 2026-03-10T00:21:24Z

or is it an unconfigured tarball?

I'm not sure, but it seems to work with the patch approach. Does that answer the question?

dimpase · 2026-03-10T01:10:09Z

or is it an unconfigured tarball?

I'm not sure, but it seems to work with the patch approach. Does that answer the question?

Yep, all good then.

trevorkarn · 2026-03-10T13:26:51Z

or is it an unconfigured tarball?

I'm not sure, but it seems to work with the patch approach. Does that answer the question?

Yep, all good then.

Ok great - is there anything else I should do for this pr?

dimpase · 2026-03-10T14:15:01Z

do the tests pass with gap_packages spkg correctly installed?

trevorkarn · 2026-03-11T16:03:09Z

do the tests pass with gap_packages spkg correctly installed?

I believe so. Here is the test log to make sure I am interpreting it correctly.
sagetest.log

dimpase

lgtm

sagemathgh-41700: Upgrade GAP, libsemigroups Upgrade GAP to 4.15.1 and libsemigroups to 3.5.1.       Fixes sagemath#41653 and implicitly sagemath#40186 ### 📝 Checklist  - [x] The title is concise and informative. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [x] I have created tests covering the changes. - [ ] I have updated the documentation and checked the documentation preview. ### ⌛ Dependencies    URL: sagemath#41700 Reported by: trevorkarn Reviewer(s): Chenxin Zhong, Dima Pasechnik

Bump gap package/--long tests pass in src/sage/groups

db0ca36

Bump libsemigroups

trevorkarn requested a review from dimpase February 26, 2026 02:39

github-actions bot added the s: needs review label Feb 26, 2026

Merge branch 'develop' into bumpgap-4.15.1

2a8a0cc

antonio-rojas added s: needs work and removed s: needs review labels Feb 26, 2026

dimpase suggested changes Feb 26, 2026

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Remove digraphs-planarity patch and fix test in permgroup.py

56575d2

github-actions bot added s: needs review and removed s: needs work labels Feb 28, 2026

trevorkarn added s: needs work and removed s: needs review labels Feb 28, 2026

Revert libsemigroups

933d2dc

github-actions bot added s: needs review and removed s: needs work labels Mar 1, 2026

cxzhong approved these changes Mar 2, 2026

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cxzhong requested a review from dimpase March 2, 2026 07:27

trevorkarn added 2 commits March 8, 2026 10:26

Revert 'revert libsamegroups'

a8e04bf

Update Semigroups version/checksums

627ca6d

Add libsemigroup version patch

c92ca31

trevorkarn self-assigned this Mar 10, 2026

dimpase approved these changes Mar 17, 2026

View reviewed changes

dimpase added s: positive review and removed s: needs review labels Mar 17, 2026

vbraun merged commit c23795d into sagemath:develop Mar 22, 2026
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github-actions bot removed the s: positive review label Mar 22, 2026

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