Cleanup of warnings from the test suite

[oscarbenjamin]

References to other Issues or PRs

• Partial fix for Test failures and warnings in master #23061
• Extracts the more straight-forward parts of maint(test): suppress warnings from the test suite #23745

Brief description of what is fixed or changed

Various fixes related to things that give warnings in the test suite (including some warnings that are hidden by default):

• Not closing files properly (i.e. use with open())
• Not closing subprocesses properly (use communicate etc)
• Using the deprecated imp module
• Using the deprecated np.matrix type
• Plotting code that passes out of range values to numpy functions

Also:

• Aesara has deprecated the broadcastable argument in favour of shape.
• Some warnings from Aesara are now suppressed (in the test suite).
• Autowrap now sets language_level=3 in the generated cython code.

Other comments

I would like to merge this as a bunch of minor fixes and then rebase #23745 and think more generally about how to handle warnings in CI.

Release Notes

• utilities
  • The autowrap module now sets language_level = 3 in the generated Cython code.

[sympy-bot]

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• utilities
  • The autowrap module now sets language_level = 3 in the generated Cython code. (#23754 by @oscarbenjamin)

This will be added to https://github.com/sympy/sympy/wiki/Release-Notes-for-1.11.

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#### References to other Issues or PRs
<!-- If this pull request fixes an issue, write "Fixes #NNNN" in that exact
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- Partial fix for #23061
- Extracts the more straight-forward parts of #23745

#### Brief description of what is fixed or changed

Various fixes related to things that give warnings in the test suite (including some warnings that are hidden by default):

- Not closing files properly (i.e. use `with open()`)
- Not closing subprocesses properly (use `communicate` etc)
- Using the deprecated `imp` module
- Using the deprecated `np.matrix` type
- Plotting code that passes out of range values to numpy functions

Also:

- Aesara has deprecated the `broadcastable` argument in favour of `shape`.
- Some warnings from Aesara are now suppressed (in the test suite).
- Autowrap now sets `language_level=3` in the generated cython code.

#### Other comments

I would like to merge this as a bunch of minor fixes and then rebase #23745 and think more generally about how to handle warnings in CI.

#### Release Notes

<!-- Write the release notes for this release below between the BEGIN and END
statements. The basic format is a bulleted list with the name of the subpackage
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* solvers
  * Added a new solver for logarithmic equations.

* functions
  * Fixed a bug with log of integers.

or if no release note(s) should be included use:

NO ENTRY

See https://github.com/sympy/sympy/wiki/Writing-Release-Notes for more
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<!-- BEGIN RELEASE NOTES -->
* utilities
  * The autowrap module now sets `language_level = 3` in the generated Cython code.
<!-- END RELEASE NOTES -->

Update

The release notes on the wiki have been updated.

[github-actions]

Benchmark results from GitHub Actions

Lower numbers are good, higher numbers are bad. A ratio less than 1
means a speed up and greater than 1 means a slowdown. Green lines
beginning with + are slowdowns (the PR is slower then master or
master is slower than the previous release). Red lines beginning
with - are speedups.

Significantly changed benchmark results (PR vs master)

Significantly changed benchmark results (master vs previous release)

       before           after         ratio
     [77f1d79c]       [cace0875]
     <sympy-1.10.1^0>                 
+      97.9±0.4ms          179±1ms     1.83  sum.TimeSum.time_doit

Full benchmark results can be found as artifacts in GitHub Actions
(click on checks at the top of the PR).

[oscarbenjamin]

This change is incompatible with Theano: #23745 (comment)

[oscarbenjamin]

I've reverted this change. We will need to consider separately how easy it will be to support both Theano and Aesara going forwards. At some point it definitely makes sense to just drop support for Theano.

[oscarbenjamin]

This is ready for review.

[oscarbenjamin]

Thanks!