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Update scipy requirement from <=1.10 to <=1.11.1 #932

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merged 22 commits into from
Dec 7, 2023

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@dependabot dependabot bot commented on behalf of github Jun 29, 2023

Updates the requirements on scipy to permit the latest version.

Release notes

Sourced from scipy's releases.

SciPy 1.11.1 Release Notes

SciPy 1.11.1 is a bug-fix release with no new features compared to 1.11.0. In particular, a licensing issue discovered after the release of 1.11.0 has been addressed.

Authors

  • Name (commits)
  • h-vetinari (1)
  • Robert Kern (1)
  • Ilhan Polat (4)
  • Tyler Reddy (8)

A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

Commits
  • cfe8011 REL: 1.11.1 rel commit [wheel build]
  • 450d8aa Merge pull request #18779 from tylerjereddy/treddy_1_11_1_prep
  • 6f942e8 DOC: update 1.11.1 relnotes
  • 145cec5 MAINT: fix unuran licensing
  • 0760bab MAINT:linalg.det:Return scalars for singleton inputs (#18763)
  • a1c6f99 MAINT:linalg:Use only NumPy types in lu
  • 5cdc2fe MAINT:linalg:Remove memcpy from lu
  • d9ac3f3 FIX:linalg:Guard against possible permute_l out of bound behavior
  • 7ec5010 BUG: fix handling for factorial(..., exact=False) for 0-dim array inputs (#...
  • 90415c6 BUG: Fix work array construction for various weight shapes. (#18741)
  • Additional commits viewable in compare view

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Updates the requirements on [scipy](https://github.com/scipy/scipy) to permit the latest version.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v0.1.0...v1.11.1)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Jun 29, 2023
@keileg
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keileg commented Jul 14, 2023

This is connected with some possibly deep changes in scipy's sparse data formats. We should not upgrade before having explored the consequences.

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keileg commented Aug 16, 2023

Having looked at this in some more detail, it seems to me that Scipy's new array format is not yet a drop-in replacement for the old matrix classes. For instance, slicing operations are for the moment not fully implemented, see https://docs.scipy.org/doc/scipy/reference/sparse.html#module-scipy.sparse.

My suggestion is:

  1. We do not actively replace sparse matrices with arrays, but we may do this while doing general maintenance. Similarly, we should aim for gradually replacing * with @ as the operator for matrix multiplication.
  2. Since the arrays seem to be the future, we should try to use these when developing new code, provided we are not hampered by limitations in the implementation (e.g., slicing).

@IvarStefansson, @OmarDuran: Does this make sense to you?

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Yes, I think so. But I'm not overly confident in my opinion, not having looked into this.

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I completely agree with both suggestions. In the case of updating the requirement, this will simplify the process.

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dependabot bot commented on behalf of github Aug 18, 2023

A newer version of scipy exists, but since this PR has been edited by someone other than Dependabot I haven't updated it. You'll get a PR for the updated version as normal once this PR is merged.

@keileg keileg added this to the Release 1.8 milestone Oct 18, 2023
@keileg keileg removed this from the Release 1.8 milestone Oct 30, 2023
@OmarDuran OmarDuran added the enhancement New feature or request. label Dec 1, 2023
@OmarDuran OmarDuran added the PR - waiting on reviewer(s) A PR that is waiting for the reviewer(s). label Dec 1, 2023
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My only major question regards a parametrized test of mortar projection where one case was commented out.

examples/mandel_biot.py Outdated Show resolved Hide resolved
src/porepy/grids/grid.py Outdated Show resolved Hide resolved
src/porepy/grids/grid_extrusion.py Outdated Show resolved Hide resolved
src/porepy/numerics/linalg/matrix_operations.py Outdated Show resolved Hide resolved
src/porepy/numerics/linalg/matrix_operations.py Outdated Show resolved Hide resolved
src/porepy/numerics/linalg/matrix_operations.py Outdated Show resolved Hide resolved
tests/numerics/ad/test_operators.py Outdated Show resolved Hide resolved
tests/numerics/vem/test_dual_vem.py Outdated Show resolved Hide resolved
tests/numerics/vem/test_rt0.py Show resolved Hide resolved
STY: formatter

Update src/porepy/grids/grid_extrusion.py

Update src/porepy/grids/grid.py

DOC:  Removing comment and turn lower case local variable

DOC: Formatting documentation

STY: black on mandel_biot.py
Co-Authored-By: Eirik Keilegavlen <Eirik.Keilegavlen@uib.no>
@OmarDuran OmarDuran force-pushed the dependabot/pip/scipy-lte-1.11.1 branch from ed97bf1 to d7606ee Compare December 6, 2023 17:57
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One final reformatting. Feel free to resolve and merge when you have considered that one.

src/porepy/numerics/linalg/matrix_operations.py Outdated Show resolved Hide resolved
Co-authored-by: Eirik Keilegavlen <Eirik.Keilegavlen@uib.no>
@OmarDuran OmarDuran merged commit 17b280e into develop Dec 7, 2023
@OmarDuran OmarDuran deleted the dependabot/pip/scipy-lte-1.11.1 branch December 7, 2023 18:48
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3 participants