fix: Add temporary upper bounds on NumPy and SciPy to pass tests

[matthewfeickert]

Description

To get development up and running again without having to deal with additional changes yet to the codebase, just get the existing code passing without changing library code and then go from there. We should then pull in the parts of @kratsg's PR #2566 that are needed. Docs will get fixed in another PR.

Resolves #2553

• Add upper bound of SciPy v1.16.0 as there are numerical differences compared to v1.15.x and convergence issues that can lead to 'Singular matrix E in LSQ subproblem'.
  • c.f. SciPy v1.16.0 gives different numerical results and Singular matrix E in LSQ subproblem #2593
• Add upper bound of NumPy v2.0 to the PyTorch extra as PyTorch is currently incompatible with NumPy v2.0.
  • c.f. dynamo+numpy 2.0 issue: TypeError: 'numpy.bool' object cannot be interpreted as an integer pytorch/pytorch#157973
• Add try-except for from click.testing.CliRunner to work with versions of Click older than v8.2.0.
• Use typing.cast to have all NumPy backend operations be cast to type numpy.typing.ArrayLike to satisfy mypy.
• Add pytest fixture to disable CUDA acceleration by default for GPU enabled machines so that the tests will run in CPU mode by default.
  • Add --enable-cuda flag that can be passed to let CUDA backends be turned on.
• Remove pyhf CLI command with no arguments from Docker image test as it results in an exit code of 2.
• Add ignores to filterwarning for Click, papermill, and PyTorch.

   - DeprecationWarning: 'MultiCommand' is deprecated and will be removed in Click 9.0. Use 'Group' instead.
   - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs given by the platformdirs library.  To remove this warning and see the appropriate new directories, set the environment variable `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`. The use of platformdirs will be the default in `jupyter_core` v6.
   - DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).
   - DeprecationWarning: In future, it will be an error for 'np.bool' scalars to be interpreted as an index.
   - DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword arguments.

• c.f. https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword

Checklist Before Requesting Reviewer

• Tests are passing
• "WIP" removed from the title of the pull request
• Selected an Assignee for the PR to be responsible for the log summary

Before Merging

For the PR Assignees:

• Summarize commit messages into a comprehensive review of the PR

* Add upper bound of SciPy v1.16.0 as there are numerical differences compared to
  v1.15.x and convergence issues that can lead to 'Singular matrix E in LSQ subproblem'.
   - c.f. https://github.com/scikit-hep/pyhf/issues/2593
* Add upper bound of NumPy v2.0 to the PyTorch extra as PyTorch is currently
  incompatible with NumPy v2.0.
   - c.f. https://github.com/pytorch/pytorch/issues/157973
* Add try-except for from `click.testing.CliRunner` to work with versions of Click
  older than v8.2.0.
* Use typing.cast to have all NumPy backend operations be cast to type
  numpy.typing.ArrayLike to satisfy mypy.
* Add pytest fixture to disable CUDA acceleration by default for GPU enabled machines
  so that the tests will run in CPU mode by default.
   - Add `--enable-cuda` flag that can be passed to let CUDA backends be turned on.
* Remove `pyhf` CLI command with no arguments from Docker image test as it results
  in an exit code of 2.
* Add ignores to filterwarning for Click, papermill, and PyTorch.
   - DeprecationWarning: 'MultiCommand' is deprecated and will be removed in Click 9.0.
     Use 'Group' instead.
   - DeprecationWarning: Jupyter is migrating its paths to use standard platformdirs
     given by the platformdirs library. To remove this warning and see the appropriate
     new directories, set the environment variable `JUPYTER_PLATFORM_DIRS=1` and then
     run `jupyter --paths`. The use of platformdirs will be the default in `jupyter_core`
     v6.
   - DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for
     removal in a future version. Use timezone-aware objects to represent datetimes
     in UTC: datetime.datetime.now(datetime.UTC).
   - DeprecationWarning: In future, it will be an error for 'np.bool' scalars to be
     interpreted as an index.
   - DeprecationWarning: __array__ implementation doesn't accept a copy keyword, so
     passing copy=False failed. __array__ must implement 'dtype' and 'copy' keyword
     arguments.
   - c.f. https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword

Co-authored-by: Giordon Stark <kratsg@gmail.com>

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.23%. Comparing base (3d26434) to head (ebfd2b3).
⚠️ Report is 24 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2592      +/-   ##
==========================================
+ Coverage   98.21%   98.23%   +0.02%     
==========================================
  Files          69       69              
  Lines        4543     4545       +2     
  Branches      804      612     -192     
==========================================
+ Hits         4462     4465       +3     
  Misses         48       48              
+ Partials       33       32       -1     

Flag	Coverage Δ
contrib	?
doctest	98.10% <100.00%> (+0.02%)	⬆️
unittests-3.10	?
unittests-3.11	96.25% <100.00%> (+0.02%)	⬆️
unittests-3.12	96.25% <100.00%> (+0.02%)	⬆️
unittests-3.8	96.25% <100.00%> (+<0.01%)	⬆️
unittests-3.9	96.30% <100.00%> (+0.02%)	⬆️

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[kratsg]

bypassing rules as docs are expected to fail and will be fixed in a different PR.