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Support networkx 3.1#35584

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tornaria:networkx-3.1
May 28, 2023
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Support networkx 3.1#35584
vbraun merged 2 commits intosagemath:developfrom
tornaria:networkx-3.1

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@tornaria tornaria commented Apr 29, 2023

📚 Description

The functions number_of_cliques() and cliques_containing_node() are deprecated in networkx 3.1.

This commit reimplements both functions based on method cliques_maximal().

This PR is critical to upgrade networkx to 3.1 in void linux.

📝 Checklist

  • The title is concise, informative, and self-explanatory.
  • The description explains in detail what this PR is about.
  • I have created tests covering the changes.

@tornaria tornaria added this to the sage-10.0 milestone Apr 29, 2023
@tornaria tornaria requested review from dcoudert and tscrim April 29, 2023 01:06
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tornaria commented Apr 29, 2023

Lint failure is unrelated:

Run tox -e pycodestyle-minimal
pycodestyle-minimal: freeze> python -m pip freeze --all
pycodestyle-minimal: pip==23.1.2,setuptools==67.7.2,wheel==0.40.0
pycodestyle-minimal: commands[0]> tox -c /home/runner/work/sage/sage/src/tox.ini -e pycodestyle-minimal --
pycodestyle-minimal: install_deps /home/runner/work/sage/sage/src> python -I -m pip install pycodestyle
pycodestyle-minimal: commands[0] /home/runner/work/sage/sage/src> pycodestyle --select E111,E211,E271,E306,E401,E502,E701,E702,E703,W291,W391,W605,E711,E712,E713,E721,E722
pycodestyle-minimal: commands[1] /home/runner/work/sage/sage/src> pycodestyle --select E111,E306,E401,E703,W293,W391,W605,E712,E713,E714,E721,E722 --filename '*.pyx'
./sage/rings/real_double.pyx:1525:1: W293 blank line contains whitespace
./sage/rings/real_mpfr.pyx:2995:1: W293 blank line contains whitespace
2       W293 blank line contains whitespace
pycodestyle-minimal: exit 1 (20.78 seconds) /home/runner/work/sage/sage/src> pycodestyle --select E111,E306,E401,E703,W293,W391,W605,E712,E713,E714,E721,E722 --filename '*.pyx' pid=1864
  pycodestyle-minimal: FAIL code 1 (92.31=setup[1.42]+cmd[70.11,20.78] seconds)
  evaluation failed :( (92.38 seconds)
pycodestyle-minimal: exit 1 (92.55 seconds) /home/runner/work/sage/sage> tox -c /home/runner/work/sage/sage/src/tox.ini -e pycodestyle-minimal -- pid=1739
  pycodestyle-minimal: FAIL code 1 (93.75=setup[1.20]+cmd[92.55] seconds)
  evaluation failed :( (93.91 seconds)
Error: Process completed with exit code 1.

Is this a bug in 10.0.rc0 ? Or is this a case of workflow changing without making sure develop passes?

This was referenced Apr 29, 2023
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tornaria commented Apr 30, 2023

@vbraun @mkoeppe I rebased to rc1 but it's still failng lint. Can we get CI fixed please?

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LGTM. I support merging it in 10.0 to make downstream packaging easier.

dcoudert
dcoudert requested changes May 4, 2023
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it's to comply with the coding style

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LGTM.

tornaria added 2 commits May 10, 2023 09:41
@tornaria
Support networkx 3.1
0cf50a2 
The functions `number_of_cliques()` and `cliques_containing_node()` are
deprecated in networkx 3.1.

This commit reimplements both functions based on method `cliques_maximal()`.
@tornaria
Improve cliques_number_of() and cliques_containing_vertices()
e599562 
The previous implementation was taken from the ones that are deprecated
in networkx 3.1.

We replace it by a better implementation suggested by David Coudert.
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tornaria commented May 10, 2023

Rebased to 10.0.rc2 without any change (removes spurious "fix the linter commits")

@tornaria tornaria mentioned this pull request May 10, 2023
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github-actions bot commented May 10, 2023

Documentation preview for this PR is ready! 🎉
Built with commit: e599562

@vbraun vbraun merged commit be0aab7 into sagemath:develop May 28, 2023
@tornaria tornaria deleted the networkx-3.1 branch May 29, 2023 18:08
vbraun pushed a commit that referenced this pull request Jun 11, 2023
6ca634a 
gh-35671: Upgrade networkx to 3.1, igraph/python_igraph to 0.10.4 
    
<!-- Please provide a concise, informative and self-explanatory title.
-->
<!-- Don't put issue numbers in the title. Put it in the Description
below. -->
<!-- For example, instead of "Fixes #12345", use "Add a new method to
multiply two integers" -->

### 📚 Description

<!-- Describe your changes here in detail. -->
https://networkx.org/documentation/stable/release/index.html; still
supports Python >= 3.8 (see #35404)
- https://networkx.org/documentation/stable/release/release_3.1.html
- https://networkx.org/documentation/stable/release/release_3.0.html

python_igraph still supports Python >= 3.7.
- https://igraph.org/2023/01/27/igraph-0.10.4-c.html
- https://igraph.org/2022/12/30/igraph-0.10.3-c.html

<!-- Why is this change required? What problem does it solve? -->
<!-- If this PR resolves an open issue, please link to it here. For
example "Fixes #12345". -->
<!-- If your change requires a documentation PR, please link it
appropriately. -->

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. It should be `[x]` not `[x
]`. -->

- [x] The title is concise, informative, and self-explanatory.
- [x] 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 accordingly.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on
- #12345: short description why this is a dependency
- #34567: ...
-->
- Depends on #35584

<!-- If you're unsure about any of these, don't hesitate to ask. We're
here to help! -->
    
URL: #35671
Reported by: Matthias Köppe
Reviewer(s): David Coudert
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@dcoudert dcoudert dcoudert approved these changes

@tscrim tscrim Awaiting requested review from tscrim

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@mkoeppe mkoeppe mkoeppe approved these changes

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