`igraph`: Update to 0.10.12, fix spkg-check; `python_igraph`: Update to 0.11.5, remove spkg-install workarounds #37819

mkoeppe · 2024-04-17T02:34:07Z

📝 Checklist

https://github.com/igraph/python-igraph/blob/main/CHANGELOG.md

Increasing the lower bound for system cmake to 3.18. This will cause system cmake on ubuntu-focal to be rejected, so cmake will be built from source on this platform. https://repology.org/project/cmake/versions

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

CI: Fix handling of deletions/renames; Build&Test: Uninstall/build changed packages; Linux Incremental: Update platforms #38144 (merged here for testing)

github-actions · 2024-04-17T03:05:39Z

Documentation preview for this PR (built with commit 4f748fe; changes) is ready! 🎉
This preview will update shortly after each push to this PR.

dcoudert

I have igraph 0.10.11 installed via homebrew

MAC-04017247:sage dcoudert$ ls -l /opt/homebrew/Cellar/igraph/
total 0
drwxr-xr-x  12 dcoudert  admin  384 17 avr 09:15 0.10.11

in a fresh shell session, I did:

make distclean
./bootstrap
source .homebrew-build-env
./configure
make build
./sage -i python_igraph

For some reason, it installs igraph from source and don't use my homebrew version.
How to fix that ?

mkoeppe · 2024-04-17T19:30:32Z

Thanks for testing! I had forgotten to check/update the spkg-configure file. Fixed now

dcoudert

Installation and tests ok on macOS 12.7.4.

LGTM.

dcoudert · 2024-04-18T10:02:22Z

I have some doubts about all the failing CI. That's why I'm not seeing this PR to positive review yet.

szhorvat · 2024-05-07T18:27:41Z

igraph 0.10.12 and python-igraph 0.11.5 are released now. I suggest going directly for these new versions.

…el condition

…-linux-incremental.yml)

…container if nothing to be tested

…of the default platform (ubuntu-jammy)

…dora-38 by latest

…t from build.yml, use ptest-nodoc to avoid duplicate doc-html build

… /new at the end

…e new .git file at the end

…g-settings now, as we have setuptools>=64 with pypa/setuptools#3380

…ep-517 explicitly

dcoudert

Works fine on macOS with homebrew igraph.

LGTM.

dcoudert · 2024-06-05T14:16:47Z

Some errors are reported by the CI on the uninstall part.

mkoeppe · 2024-06-05T17:24:06Z

Not sure what you mean by the "uninstall part" but there is a problem with cmake.
test / linux (fedora-30, standard)

#29 40.36   [igraph-0.10.12]   No spkg-legacy-uninstall script; nothing to do
#29 40.36   [igraph-0.10.12]   [spkg-install] Configuring igraph-0.10.12 with cmake
#29 40.36   [igraph-0.10.12]   [spkg-install] CMake Error at CMakeLists.txt:8 (cmake_minimum_required):
#29 40.36   [igraph-0.10.12]   [spkg-install]   CMake 3.18 or higher is required.  You are running version 3.17.2
#29 40.36   [igraph-0.10.12]   [spkg-install] 
#29 40.36   [igraph-0.10.12]   [spkg-install] 
#29 40.36   [igraph-0.10.12]   [spkg-install] -- Configuring incomplete, errors occurred!
#29 40.36   [igraph-0.10.12]   [spkg-install] ********************************************************************************
#29 40.36   [igraph-0.10.12]   [spkg-install] Error configuring igraph-0.10.12 with cmake
#29 40.36   [igraph-0.10.12]   [spkg-install] ********************************************************************************

…hich begin with a hyphen correctly

dcoudert · 2024-06-05T20:06:27Z

The issue is not yet fixed https://github.com/sagemath/sage/actions/runs/9388680174/job/25854493223?pr=37819#step:11:12925

mkoeppe · 2024-06-05T20:09:38Z

What I see there is this test failure:

sage -t --random-seed=302171850113617614625936987131470123946 src/sage/graphs/generators/random.py
#30 2631.5 **********************************************************************
#30 2631.5 File "src/sage/graphs/generators/random.py", line 1605, in sage.graphs.generators.random.RandomPartialKTree
#30 2631.5 Failed example:
#30 2631.5     G.treewidth()
#30 2631.5 Expected:
#30 2631.5     5
#30 2631.5 Got:
#30 2631.5     6
#30 2633.3

Do you know something about this test?

dcoudert · 2024-06-06T08:52:35Z

it seems to be

What I see there is this test failure:

sage -t --random-seed=302171850113617614625936987131470123946 src/sage/graphs/generators/random.py
#30 2631.5 **********************************************************************
#30 2631.5 File "src/sage/graphs/generators/random.py", line 1605, in sage.graphs.generators.random.RandomPartialKTree
#30 2631.5 Failed example:
#30 2631.5     G.treewidth()
#30 2631.5 Expected:
#30 2631.5     5
#30 2631.5 Got:
#30 2631.5     6
#30 2633.3

Do you know something about this test?

This seems to be an error from tdlib.

sage: from sage.graphs.graph_decompositions.tree_decomposition import width_of_tree_decomposition
sage: G = Graph('q~~|~q{mLhUo}?v?EO`{?h`?wo@w?fo?As_?lG?Cp_?Uc??{?_?|???Y_G?@gH??{?_?A{???Dp???Dk???Ax????l????Dh????Qo???GkG???_lG????Q_???I@p?G???uO????As????@@gH????FG??A??AW_??A??d????CG@w?C????PE?@????D@G?C???t?O??????')
sage: G.treewidth(algorithm='sage')
5
sage: G.treewidth(algorithm='tdlib')
6
sage: T = G.treewidth(algorithm='tdlib', certificate=True)
sage: width_of_tree_decomposition(G, T)
6

May be we should first try to update tdlib to see if it fixes this issue, and otherwise report upstream.

dcoudert · 2024-06-06T13:00:59Z

I have opened #38159

dcoudert · 2024-06-06T13:02:54Z

This PR looks good to me. Let me know if ready for review (currently in needs work).

mkoeppe · 2024-06-06T17:52:11Z

Thanks. It's ready for review

dcoudert

LGTM.

mkoeppe · 2024-06-06T19:39:09Z

Thank you!

dcoudert reviewed Apr 17, 2024

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dcoudert approved these changes Apr 18, 2024

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Matthias Koeppe added 7 commits June 2, 2024 22:50

.github/workflows/ci-linux-incremental.yml (sitepackages): Remove lab…

421b552

…el condition

.github/workflows/build.yml: Determine build_targets (adapted from ci…

e90d737

…-linux-incremental.yml)

.github/workflows/build.yml: Combine calls of tj-actions/changed-files

dae0ff1

.github/workflows/build.yml (test-new): Do not push and do not start …

62ade48

…container if nothing to be tested

.github/workflows/ci-linux-incremental.yml: Remove duplicate testing …

9d3a3f2

…of the default platform (ubuntu-jammy)

.github/workflows/ci-linux-incremental.yml: Replace ubuntu-mantic, fe…

4db3313

…dora-38 by latest

.github/workflows/ci-linux-incremental.yml: Update build_target scrip…

3586090

…t from build.yml, use ptest-nodoc to avoid duplicate doc-html build

vbraun force-pushed the develop branch from eba5e19 to e5f42fa Compare June 3, 2024 22:15

Matthias Koeppe added 13 commits June 3, 2024 18:27

.ci/retrofit-worktree.sh: Commit /new

1df4f5a

.ci/write-dockerfile.sh: Remove old /new at the beginning, remove new…

8d0c849

… /new at the end

.ci/write-dockerfile.sh: Remove duplicated ADD

d068c8d

.ci/write-dockerfile.sh: Remove old .git file at the beginning, remov…

7fb0323

…e new .git file at the end

build/pkgs/igraph: Update to 0.10.11

41b88e1

build/pkgs/python_igraph/spkg-install.in: We can pass another --confi…

2299e06

…g-settings now, as we have setuptools>=64 with pypa/setuptools#3380

build/pkgs/python_igraph/spkg-install.in: No more need to use --use-p…

0a9bf9f

…ep-517 explicitly

build/pkgs/igraph/spkg-check.in: Fix

176cbaf

build/pkgs/igraph/spkg-configure.m4: Accept system igraph 0.10.11

8010f7f

build/pkgs/python_igraph: Update to 0.11.4

645757c

build/pkgs/igraph: Update to 0.10.12

bd02730

build/pkgs/python_igraph: Update to 0.11.5

735a90e

build/pkgs/igraph/spkg-configure.m4: Only accept igraph 0.10.12

254adac

github-actions bot added the v: moderate label Jun 5, 2024

.github/workflows/*build*.yml: Survive GHA cache upload timeouts

5726013

dcoudert approved these changes Jun 5, 2024

View reviewed changes

Matthias Koeppe added 3 commits June 5, 2024 10:24

build/bin/sage-dist-helpers (sdh_pip_install): Pass config-settings w…

2693e1c

…hich begin with a hyphen correctly

build/pkgs/cmake/spkg-configure.m4: Require at least 3.18 (for igraph)

0996d95

Merge branch 'merge_ci_linux' into igraph-0.10.11

4f748fe

dcoudert approved these changes Jun 6, 2024

View reviewed changes

dcoudert added s: positive review and removed s: needs review labels Jun 6, 2024

vbraun merged commit a09048c into sagemath:develop Jun 9, 2024

github-actions bot removed the s: positive review label Jun 9, 2024

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igraph: Update to 0.10.12, fix spkg-check; python_igraph: Update to 0.11.5, remove spkg-install workarounds #37819

igraph: Update to 0.10.12, fix spkg-check; python_igraph: Update to 0.11.5, remove spkg-install workarounds #37819

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📝 Checklist

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`igraph`: Update to 0.10.12, fix spkg-check; `python_igraph`: Update to 0.11.5, remove spkg-install workarounds #37819

`igraph`: Update to 0.10.12, fix spkg-check; `python_igraph`: Update to 0.11.5, remove spkg-install workarounds #37819

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