Upgrade GAP, libsemigroups

[trevorkarn]

Upgrade GAP to 4.15.1 and libsemigroups to 3.5.1.

Fixes #41653 and implicitly #40186

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[antonio-rojas]

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]

[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]

[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]

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]

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]

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]

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

[trevorkarn]

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]

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]

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

[trevorkarn]

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]

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]

if gap_packages is installed then it will be tested

[dimpase]

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]

Ok I think most recent push addresses all comments

[antonio-rojas]

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

[dimpase]

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]

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]

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]

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]

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]

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]

or is it an unconfigured tarball?

[trevorkarn]

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]

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]

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]

do the tests pass with gap_packages spkg correctly installed?

[trevorkarn]

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