Switch to src layout with separate tests directory

[namurphy]

Description

This PR changes the layout to be aligned with what is now recommended in the PyPA Python Packaging Guide. The following changes are made:

• The plasmapy/ directory has been changed to src/plasmapy/
• Tests have been moved to a separate top-level tests/ directory.
• The contributor guide has been updated to reflect changes in the locations of things

Below I included my suggestions for other projects on switching to an src layout.

Motivation and context

See #2581 for the motivation. Essentially, the src layout can prevent a variety of easy-to-overlook problems. My hope is to get this merged well ahead of the summer school, since we're hoping to welcome new & potential contributors.

Code review checklist

While this PR says it modifies ∼239 files 😱, nearly all of the files were moved without being changed and don't require review. 😮‍💨 The files that warrant the most attention are:

• docs/contributing/testing_guide.rst
• changelog/2598.internal.rst
• pyproject.toml
• tests/__init__.py

Thank you! 🙏🏻

Task checklist

• git mv plasmapy src/plasmapy
• Move tests to tests/
• Update .gitignore paths
• Update & consolidate paths in MANIFEST.in
• Update paths in .pre-commit-config.yaml
• Update paths in contributor guide
• Describe location of source code & tests in contributor guide
• Update/regenerate per-file ignores in mypy.ini
• pyproject.toml: update setuptools & setuptools_scm paths
• pyproject.toml: update testpaths in pytest
• pyproject.toml: update coverage settings (define source and update paths in omit)
• Verify that code coverage is unchanged
• pyproject.toml: in isort settings, add plasmapy as known-first-party
• pyproject.toml: update ruff per-file ignores
• Update paths included in comments throughout the package
• tox.ini: update pytest command
• tox.ini: Update mypy command

Related issues

Closes #2581.

[namurphy]

📝 This line is probably not necessary because everything within src is now included.

[namurphy]

❔ I'm not sure if we want to include tests/ in MANIFEST.in. I'd like the tests to be included in source distributions for completeness, but not included in wheels.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.18%. Comparing base (923ab22) to head (2c311a0).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2598   +/-   ##
=======================================
  Coverage   95.17%   95.18%           
=======================================
  Files         104      103    -1     
  Lines        9417     9412    -5     
  Branches     2154     2153    -1     
=======================================
- Hits         8963     8959    -4     
  Misses        276      276           
+ Partials      178      177    -1     

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[namurphy]

Preview of admonition from GitHub Action to post on PRs:

Note

PlasmaPy recently switched to an src layout. The source code previously in plasmapy/ is now in src/plasmapy/. Tests are now in tests/.

[pheuer]

@namurphy FYI I had to re-do the editable installation in order to get internal imports working again after this merge, e.g. import plasmapy worked but from plasmapy.diagnostics import thomson did not until I re-ran pip install -e . Assuming there's no way around this, we may want to prominently note that this needs to be done?

Also, the plasmapy folder is still there (I guess Git doesn't delete the folder) so people may be confused looking for where the source code went if they aren't following the PRs

[namurphy]

@pheuer — thank you for the follow-up! I'll add something to README.md noting what you said.

(Also I'm at UCLA working next to @rocco8773 today, and just saw two of your posters in the hallway here!)