To determine GAP_SO sage.env looks for libgap.so but it should look for libgap.so* by dimpase · Pull Request #35094 · sagemath/sage

dimpase · 2023-02-12T16:45:16Z

📚 Description

In short, sometimes there is no lib**.so available, but only lib**.so.*. This breaks GAP and Singular related things.
See #33446 for details.

Closes #33446

⌛ Dependencies

Depends on #35093 #34391 (GAP update to 4.12.2)

adjust doctests

also add a workaround for Semigroups (see comment in the code)

`make install` installs files in both paths

The 'packagemanager' package does not load without it

This needs the soname (as in sage.env.GAP_SO) which has issues for system gap as explained in sagemath#33446. Instead we dlopen() the extension module sage.libs.gap.util which, having a link time dependency to libgap, will indirectly dlopen() it. For the record: by the time we run dlopen() the libgap should be already loaded. The purpose of doing it is to change mode to RTLD_GLOBAL so that symbols in libgap are placed in the global symbol table. This is required to compiled load gap packages. An easy test that this is working ok is: sage: libgap.LoadPackage("io") true This requires optional spkg `gap_packages` to be installed.

Same as for gap in the previous commit. Instead of requiring the soname (as in sage.env.LIBSINGULAR_PATH) we dlopen() the extension module sage.libs.singular.singular which will indirectly dlopen() libSingular.

…isambiguate the workspace file, not SAGE_LOCAL" This reverts commit a801e6d. See sagemath#33446.

codecov-commenter · 2023-02-12T19:25:45Z

Codecov Report

Base: 88.57% // Head: 88.58% // Increases project coverage by +0.01% 🎉

Coverage data is based on head (ac4b671) compared to base (52a81cb).
Patch coverage: 100.00% of modified lines in pull request are covered.

❗ Current head ac4b671 differs from pull request most recent head 406e21b. Consider uploading reports for the commit 406e21b to get more accurate results

Additional details and impacted files

@@             Coverage Diff             @@
##           develop   #35094      +/-   ##
===========================================
+ Coverage    88.57%   88.58%   +0.01%     
===========================================
  Files         2140     2136       -4     
  Lines       397273   396119    -1154     
===========================================
- Hits        351891   350915     -976     
+ Misses       45382    45204     -178

Impacted Files	Coverage Δ
src/sage/coding/linear_code.py	`81.12% <ø> (ø)`
src/sage/combinat/posets/posets.py	`93.87% <ø> (ø)`
...mbinat/root_system/hecke_algebra_representation.py	`93.11% <ø> (ø)`
src/sage/combinat/symmetric_group_algebra.py	`94.35% <ø> (ø)`
src/sage/groups/finitely_presented.py	`95.88% <ø> (ø)`
src/sage/groups/fqf_orthogonal.py	`88.48% <ø> (ø)`
src/sage/groups/matrix_gps/finitely_generated.py	`90.50% <ø> (ø)`
src/sage/groups/perm_gps/permgroup.py	`90.56% <ø> (-0.49%)`	⬇️
src/sage/tests/gap_packages.py	`94.59% <ø> (ø)`
src/sage/env.py	`88.77% <100.00%> (+0.77%)`	⬆️
... and 107 more

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dimpase · 2023-02-12T19:32:52Z

the test failure (yes, just 1) is unrelated, and addressed by #35058

sage -t --random-seed=136480729433508966711661003720220671146 sage/schemes/toric/sheaf/klyachko.py
**********************************************************************
File "sage/schemes/toric/sheaf/klyachko.py", line 951, in sage.schemes.toric.sheaf.klyachko.KlyachkoBundle_class.random_deformation
Failed example:
    Vtilde.cohomology(dim=True, weight=(0,))
Expected:
    (1, 0)
Got:
    (0, 0)

tornaria · 2023-02-26T14:09:54Z

@dimpase dont forget to rebase this one as well on top of dimpase:u/dimpase/packages/gap/4_12_2

tornaria · 2023-03-06T19:08:42Z

@vbraun @mkoeppe can we please get #35093 and #35094 in? The sooner the better... it almost made it into 9.8. It is the largest and more intrusive patch I'm carrying, and I can't use develop branch at all without merging this so testing other PR is a pain.

mkoeppe · 2023-03-06T20:22:42Z

I've now set it to "blocker", which used to be the way to give a ticket priority in merging.
But it seems that @vbraun's new merging script does not take priority into account.
@vbraun is this by intentional design or is it something that should be fixed in https://github.com/sagemath/sage-release-management?

github-actions · 2023-03-07T13:58:32Z

Documentation preview for this PR is ready! 🎉
Built with commit: 6c3afe6

gh-35285: System package information tox ini gh actions for alpine linux ### 📚 system pkgs info and GH actions for alpine linux Will fix #33083. This is the rebase of the branch of the latter on top of 10.0.beta4, reduced to the scripts and package lists. Workarounds for musl libc from #33083 will be revisited in a follow up. ### 📝 Checklist - [X] I have made sure that the title is self-explanatory and the description concisely explains the PR. - [X] I have linked an issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### Dependencies - #35290 - pplpy 0.8.7 - #35094 - saner libsingular linking URL: #35285 Reported by: Dima Pasechnik Reviewer(s): Dima Pasechnik, Matthias Köppe

antonio-rojas and others added 30 commits February 12, 2023 16:30

Adapt to API changes in OpenOutputStream and CloseOutput

8b272d3

Disable colored prompt as it breaks the pexpect interface

1c8832f

Port NaturalHomomorphism uses

4b5ed43

Fix tests with GAP 4.12

b1a8121

Adapt test to new is_transitive and is_primitive behavior

b24d42e

Mark test as random. With gap 4.12 on x86_64 it is no longer 2

271a5ba

Remove test that is now redundant, all seeds give the same answer

8c8d756

install gap 4.12.0

21537e7

upgrade libsemigroup and gap_packages

da558e1

adjust doctests

add GAP upstream PR 5077

821f9da

also, fix the package names etc

c5410a2

update GAP to 4.12.1

f30806e

install GAP package singular - new dependency of liepring

ca2d08d

moved install of radiroot to gap from gap_packages

41cf212

moved install of autodoc and utils to gap from gap_packages

2f552b0

don't use SAGE_LOCAL/share/gap, switch to GAP's "make install"

32c4a63

also add a workaround for Semigroups (see comment in the code)

Search for files in both lib/gap and share/gap

85849a2

`make install` installs files in both paths

Create lib/gap/bin on install

575c6b2

The 'packagemanager' package does not load without it

ensure make gap-clean still works

3a73005

with SAGE_CHECK=yes, one needs io installed to prevent hangs

3c1d422

backport GAP PR 5235

b335ec9

update GAP to 4.12.2

5ed4447

bump libsemigroups to v2.3.2

c70ae12

singular: do not directly dlopen() the singular library

177eb5d

Same as for gap in the previous commit. Instead of requiring the soname (as in sage.env.LIBSINGULAR_PATH) we dlopen() the extension module sage.libs.singular.singular which will indirectly dlopen() libSingular.

singular: remove LIBSINGULAR_PATH, no longer needed

3a46e87

Revert "src/sage/interfaces/gap_workspace.py: Use hash of GAP_SO to d…

b8058e9

…isambiguate the workspace file, not SAGE_LOCAL" This reverts commit a801e6d. See sagemath#33446.

gap: remove GAP_SO, no longer needed

5919d54

gap_workspace_file: include hostname and gap version

e115716

gap_workspace_file: use GAP_LIB_DIR and GAP_SHARE_DIR

ac4b671

This was referenced Feb 13, 2023

update GAP to 4.12.2 #35093

Merged

Rebase gap PR #35094 on top of #35093 dimpase/sage#2

Closed

Merge branch 'develop' into u/dimpase/33446/gap-and-singular-dlopen

406e21b

dimpase requested a review from mkoeppe February 27, 2023 13:39

mkoeppe approved these changes Feb 27, 2023

View reviewed changes

tornaria added this to the sage-10.0 milestone Mar 6, 2023

Merge branch 'develop' into u/dimpase/33446/gap-and-singular-dlopen

6c3afe6

dimpase mentioned this pull request Mar 15, 2023

System package information tox ini gh actions for alpine linux #35285

Merged

4 tasks

vbraun merged commit dc933bd into sagemath:develop Mar 19, 2023

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To determine GAP_SO sage.env looks for libgap.so but it should look for libgap.so*#35094

To determine GAP_SO sage.env looks for libgap.so but it should look for libgap.so*#35094
vbraun merged 32 commits intosagemath:developfrom
dimpase:u/dimpase/33446/gap-and-singular-dlopen

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dimpase commented Feb 12, 2023

📚 Description

⌛ Dependencies

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