Type annotations, mypy config, pydoclint setup, and other changes

[VeckoTheGecko]

Overview

This PR introduces typing to the Parcels codebase, providing:

• useful information to users regarding the types of parameters
• useful information to developers regarding the types of variables
• a mechanism to bring types into active consideration, where complicated typing can be a "code smell" indicating a deeper problem with the code

The coverage for this isn't 100% yet (as doing so is quite difficult with the current codebase), but as we refactor code it will get easier to increase our coverage.

Changes

Typing:

• Add mypy to check types (also with a CI workflow)
• Add mypy config, with list of files to check for types (this list will be included). Note that this list is only the source files (i.e., entrypoint for mypy). Types with imported parcels functions/methods are also checked
• Add typing to various files
• Introduce a _typing.py file to define types used throughout Parcels

Other:

• add pydoclint tooling to pre-commit to help capture docstring errors not picked up by Ruff
• add _compat.py file to help with compatibility between installations when using mpi
• Implement some suggestions from repo-review tool
  • Notably:
    • concurrency with GHA (i.e., repeated pushes to a branch will cancel already running workflows on prior commits)
    • dependabot to automatically open PRs to update GHA workflow versions monthly
• Fix unit-test badge in README and add Ruff badge
• Clean up some code involving casting to arrays

[codecov]

Codecov Report

Attention: Patch coverage is 98.10427% with 4 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
parcels/tools/interpolation_utils.py	90.90%	2 Missing ⚠️
parcels/field.py	97.77%	1 Missing ⚠️
parcels/fieldset.py	97.82%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (997e3f8) and HEAD (6fa0515). Click for more details.

HEAD has 8 uploads less than BASE

Flag	BASE (997e3f8)	HEAD (6fa0515)
unit-tests	10	5
integration-tests	6	3

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1660      +/-   ##
==========================================
- Coverage   86.40%   81.03%   -5.38%     
==========================================
  Files          67       69       +2     
  Lines       11746    13118    +1372     
  Branches        0      125     +125     
==========================================
+ Hits        10149    10630     +481     
- Misses       1597     2451     +854     
- Partials        0       37      +37     

Flag	Coverage Δ
integration-tests	64.86% <89.47%> (+0.02%)	⬆️
mypy	14.90% <75.96%> (?)
unit-tests	80.87% <92.48%> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
parcels/_compat.py	100.00% <100.00%> (ø)
parcels/_typing.py	100.00% <100.00%> (ø)
parcels/compilation/codecompiler.py	91.42% <100.00%> (-4.32%)	⬇️
parcels/compilation/codegenerator.py	78.61% <100.00%> (-6.30%)	⬇️
parcels/fieldfilebuffer.py	70.01% <100.00%> (-3.32%)	⬇️
parcels/grid.py	73.02% <100.00%> (-18.86%)	⬇️
parcels/interaction/interactionkernel.py	78.44% <100.00%> (+2.41%)	⬆️
parcels/kernel.py	76.70% <100.00%> (-9.69%)	⬇️
parcels/particledata.py	71.05% <100.00%> (-10.63%)	⬇️
parcels/particlefile.py	77.41% <100.00%> (-17.95%)	⬇️
... and 8 more

... and 10 files with indirect coverage changes

[VeckoTheGecko]

Fixes #1653 . Refactoring to reduce code duplication in fieldset.py will be done in a future PR