Bump scipy, pytest and sphinx-autodoc-typehints

[github-actions]

Bumps scipy, pytest and sphinx-autodoc-typehints. These dependencies needed to be updated together.
Updates scipy from 1.10.1 to 1.11.0

Release notes

Sourced from scipy's releases.

SciPy 1.11.0 Release Notes

SciPy 1.11.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.11.x branch, and on adding new features on the main branch.

This release requires Python 3.9+ and NumPy 1.21.6 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

• Several scipy.sparse array API improvements, including sparse.sparray, a new public base class distinct from the older sparse.spmatrix class, proper 64-bit index support, and numerous deprecations paving the way to a modern sparse array experience.
• scipy.stats added tools for survival analysis, multiple hypothesis testing, sensitivity analysis, and working with censored data.
• A new function was added for quasi-Monte Carlo integration, and linear algebra functions det and lu now accept nD-arrays.
• An axes argument was added broadly to ndimage functions, facilitating analysis of stacked image data.

New features

scipy.integrate improvements

• Added scipy.integrate.qmc_quad for quasi-Monte Carlo integration.
• For an even number of points, scipy.integrate.simpson now calculates a parabolic segment over the last three points which gives improved accuracy over the previous implementation.

scipy.cluster improvements

• disjoint_set has a new method subset_size for providing the size of a particular subset.

... (truncated)

Commits

• 2e16ec5 REL: 1.11.0 round 2 [wheel build]
• 58c5d60 Merge pull request #18743 from tylerjereddy/treddy_1_11_0_arm_shims
• 084357e DOC: update 1.11.0 relnotes
• 78973aa TST: flaky test_complex_iir_dlti
• db11851 TST: flaky TestSOSFreqz::test_fs_param
• 7c317cb REL: 1.11.0 "final" [wheel build]
• 8db01f2 Merge pull request #18724 from tylerjereddy/treddy_1_11_0_final_prep
• c717774 DOC: update 1.11.0 relnotes
• 9eba5e4 DEP: interpolate: delay interp2d deprecation and update link (#18698)
• 7dbf2b9 TST: PR 18697 revisions
• Additional commits viewable in compare view

Updates pytest from 7.3.2 to 7.4.0

Release notes

Sourced from pytest's releases.

7.4.0

pytest 7.4.0 (2023-06-23)

Features

• #10901: Added ExceptionInfo.from_exception() <pytest.ExceptionInfo.from_exception>{.interpreted-text role="func"}, a simpler way to create an ~pytest.ExceptionInfo{.interpreted-text role="class"} from an exception. This can replace ExceptionInfo.from_exc_info() <pytest.ExceptionInfo.from_exc_info()>{.interpreted-text role="func"} for most uses.

Improvements

• #10872: Update test log report annotation to named tuple and fixed inconsistency in docs for pytest_report_teststatus{.interpreted-text role="hook"} hook.

• #10907: When an exception traceback to be displayed is completely filtered out (by mechanisms such as __tracebackhide__, internal frames, and similar), now only the exception string and the following message are shown:

  "All traceback entries are hidden. Pass [--full-trace]{.title-ref} to see hidden and internal frames.".

  Previously, the last frame of the traceback was shown, even though it was hidden.

• #10940: Improved verbose output (-vv) of skip and xfail reasons by performing text wrapping while leaving a clear margin for progress output.

  Added TerminalReporter.wrap_write() as a helper for that.

• #10991: Added handling of %f directive to print microseconds in log format options, such as log-date-format.

• #11005: Added the underlying exception to the cache provider's path creation and write warning messages.

• #11013: Added warning when testpaths{.interpreted-text role="confval"} is set, but paths are not found by glob. In this case, pytest will fall back to searching from the current directory.

• #11043: When [--confcutdir]{.title-ref} is not specified, and there is no config file present, the conftest cutoff directory ([--confcutdir]{.title-ref}) is now set to the rootdir <rootdir>{.interpreted-text role="ref"}. Previously in such cases, [conftest.py]{.title-ref} files would be probed all the way to the root directory of the filesystem. If you are badly affected by this change, consider adding an empty config file to your desired cutoff directory, or explicitly set [--confcutdir]{.title-ref}.

• #11081: The norecursedirs{.interpreted-text role="confval"} check is now performed in a pytest_ignore_collect{.interpreted-text role="hook"} implementation, so plugins can affect it.

  If after updating to this version you see that your [norecursedirs]{.title-ref} setting is not being respected, it means that a conftest or a plugin you use has a bad [pytest_ignore_collect]{.title-ref} implementation. Most likely, your hook returns [False]{.title-ref} for paths it does not want to ignore, which ends the processing and doesn't allow other plugins, including pytest itself, to ignore the path. The fix is to return [None]{.title-ref} instead of [False]{.title-ref} for paths your hook doesn't want to ignore.

• #8711: caplog.set_level() <pytest.LogCaptureFixture.set_level>{.interpreted-text role="func"} and caplog.at_level() <pytest.LogCaptureFixture.at_level>{.interpreted-text role="func"} will temporarily enable the requested level if level was disabled globally via logging.disable(LEVEL).

Bug Fixes

... (truncated)

Commits

• d9bf9db Prepare release version 7.4.0
• 64319db Merge pull request #11128 from bluetech/pythonpath-note
• 1e8135d reference: add note that pythonpath does not affect -p
• 1e32a4b Merge pull request #10935 from nondescryptid/10328
• faa1f9d Merge pull request #11125 from bluetech/initial-conftests-testpaths
• 1489032 config: fix the paths considered for initial conftest discovery
• d97d44a config: extract initial paths/nodeids args logic to a function
• f6b995e Use utf-8 debug file
• 661b938 Add encoding in more tests
• 7e51076 Encoding for subprocess.run
• Additional commits viewable in compare view

[codecov]

Codecov Report

Merging #2146 (f9d765e) into main (997e288) will increase coverage by 5.74%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #2146      +/-   ##
==========================================
+ Coverage   80.82%   86.57%   +5.74%     
==========================================
  Files          44       44              
  Lines        7489     7455      -34     
==========================================
+ Hits         6053     6454     +401     
+ Misses       1436     1001     -435     

[germa89]

the new sphinx-autodoc-typehints requires sphinx > 7.0 which is not allowed by ansys-sphinx-theme. Hence, adding that the multibot exceptions.