Make code compatible with scipy v1.13

[keileg]

Proposed changes

Updates:

1. Disabled two tests related to the coarsening module. The scipy update permuted the output of what is essentially a sparse.find, leading the test to fail a comparison with a known truth. As the coarsening moduleis deprecated, thus fixing the tests was not prioritized.
2. Enforce integer format of grid topology information.

Types of changes

What types of changes does this PR introduce to PorePy? Put an x in the boxes that apply.

• [ ] Minor change (e.g., dependency bumps, broken links).
• [x] Bugfix (non-breaking change which fixes an issue).
• [ ] New feature (non-breaking change which adds functionality).
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected).
• [x] Testing (contribution related to testing of existing or new functionality).
• [ ] Documentation (contribution related to adding, improving, or fixing documentation).
• [ ] Maintenance (e.g., improve logic and performance, remove obsolete code).
• [ ] Other:

Checklist

Put an x in the boxes that apply or explain briefly why the box is not relevant.

• [x] The documentation is up-to-date.
• [x] Static typing is included in the update.
• [x] This PR does not duplicate existing functionality.
• [x] The update is covered by the test suite (including tests added in the PR).
• [ ] If new skipped tests have been introduced in this PR, pytest was run with the --run-skipped flag.

[keileg]

@keileg thank you for enforcing types in topological information. The only suggestion I have is to implement a test that checks that the topological information is indeed an integer for all the grids.

I'm not sure if I agree: The attributes will be ints now and remain so unless we remove that line, which is highly unlikely. Moreover, it is not a disaster if the attributes become floats again - the previous code worked perfectly fine for several years. I realize that sparse find etc. may be less stable for floats, but again, this will not happen unless we revert the code.

So, I would say the benefits of testing this feature do not warrant the cost of dealing with extra tests. Do you agree, or have I missed something?

[OmarDuran]

@keileg thank you for enforcing types in topological information. The only suggestion I have is to implement a test that checks that the topological information is indeed an integer for all the grids.

I'm not sure if I agree: The attributes will be ints now and remain so unless we remove that line, which is highly unlikely. Moreover, it is not a disaster if the attributes become floats again - the previous code worked perfectly fine for several years. I realize that sparse find etc. may be less stable for floats, but again, this will not happen unless we revert the code.

So, I would say the benefits of testing this feature do not warrant the cost of dealing with extra tests. Do you agree, or have I missed something?

In addition to being a suggestion, keep in mind that tracking types correctly correlates with code stability. Nevertheless, I agree with you that as long as users do not mess with types associated with topology, these changes are sufficient.