🔧 Make mypy and doc string linters opt out instead of opt in

[s-weigand]

Changed the mypy and flake8-docs pre-commit hooks to be opt out instead of opt in and fixed some docstring and typing issues along the way.

Change summary

• 🔧⌨️ Made mypy optout instead of opt in and fixed some typing issues
• 🔧👌 Moved mypy config from setup.cfg to pyproject.toml
• 🔧👌 Made docstring linter opt out instead of opt in
• 🩹 Fix yesqa by moving count from the config to the hook args

Checklist

• ✔️ Passing the tests (mandatory for all PR's)
• 🚧 Added changes to changelog (mandatory for all PR's)
• 👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)

Closes issues

closes #1001

[sourcery-ai]

Sourcery Code Quality Report

Merging this PR leaves code quality unchanged.

Quality metrics	Before	After	Change
Complexity	4.30 ⭐	4.29 ⭐	-0.01 👍
Method Length	74.88 🙂	71.14 🙂	-3.74 👍
Working memory	7.75 🙂	7.75 🙂	0.00
Quality	67.16% 🙂	67.16% 🙂	0.00%

Other metrics	Before	After	Change
Lines	1637	1741	104

Changed files	Quality Before	Quality After	Quality Change
benchmark/benchmarks/unit/analysis/bench_optimize.py	58.05% 🙂	58.05% 🙂	0.00%
glotaran/init.py	92.05% ⭐	92.05% ⭐	0.00%
glotaran/builtin/io/init.py	%	%	%
glotaran/builtin/io/netCDF/init.py	%	%	%
glotaran/builtin/io/netCDF/netCDF.py	89.94% ⭐	89.77% ⭐	-0.17% 👎
glotaran/builtin/io/sdt/init.py	%	%	%
glotaran/builtin/io/sdt/sdt_file_reader.py	36.78% 😞	36.78% 😞	0.00%
glotaran/builtin/io/yml/init.py	%	%	%
glotaran/builtin/io/yml/utils.py	83.36% ⭐	82.68% ⭐	-0.68% 👎
glotaran/builtin/io/yml/yml.py	72.30% 🙂	72.28% 🙂	-0.02% 👎
glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py	46.35% 😞	46.35% 😞	0.00%
glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py	55.92% 🙂	55.92% 🙂	0.00%
glotaran/io/init.py	%	%	%
glotaran/io/interface.py	88.22% ⭐	88.22% ⭐	0.00%
glotaran/io/prepare_dataset.py	65.64% 🙂	65.63% 🙂	-0.01% 👎
glotaran/model/model.py	77.55% ⭐	77.54% ⭐	-0.01% 👎
glotaran/testing/simulated_data/sequential_spectral_decay.py	62.34% 🙂	62.34% 🙂	0.00%
glotaran/typing/protocols.py	81.59% ⭐	81.44% ⭐	-0.15% 👎

Here are some functions in these files that still need a tune-up:

File	Function	Complexity	Length	Working Memory	Quality	Recommendation
glotaran/builtin/io/sdt/sdt_file_reader.py	SdtDataIo.load_dataset	15 🙂	267 ⛔	12 😞	36.78% 😞	Try splitting into smaller methods. Extract out complex expressions
glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py	test_coherent_artifact	6 ⭐	500 ⛔	9 🙂	46.35% 😞	Try splitting into smaller methods
glotaran/builtin/io/yml/yml.py	YmlProjectIo.save_model	15 🙂	117 🙂	13 😞	47.50% 😞	Extract out complex expressions
glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py	test_kinetic_model	4 ⭐	325 ⛔	9 🙂	50.55% 🙂	Try splitting into smaller methods
benchmark/benchmarks/unit/analysis/bench_optimize.py	BenchmarkOptimize.setup	4 ⭐	180 😞	12 😞	52.42% 🙂	Try splitting into smaller methods. Extract out complex expressions

Legend and Explanation

The emojis denote the absolute quality of the code:

• ⭐ excellent
• 🙂 good
• 😞 poor
• ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

---

Please see our documentation here for details on how these metrics are calculated.

We are actively working on this report - lots more documentation and extra metrics to come!

Help us improve this quality report!

[github-actions]

👈 Launch a binder notebook on branch s-weigand/pyglotaran/mypy-opt-out

[codecov]

Codecov Report

Base: 87.6% // Head: 87.6% // Increases project coverage by +0.0% 🎉

Coverage data is based on head (a880ed9) compared to base (ece973f).
Patch coverage: 60.0% of modified lines in pull request are covered.

Additional details and impacted files

@@          Coverage Diff          @@
##            main   #1173   +/-   ##
=====================================
  Coverage   87.6%   87.6%           
=====================================
  Files        103     103           
  Lines       4896    4898    +2     
  Branches     806     806           
=====================================
+ Hits        4289    4291    +2     
  Misses       489     489           
  Partials     118     118           

Impacted Files	Coverage Δ
glotaran/__init__.py	100.0% <ø> (ø)
glotaran/builtin/io/netCDF/netCDF.py	100.0% <ø> (ø)
glotaran/builtin/io/sdt/sdt_file_reader.py	62.1% <0.0%> (ø)
glotaran/builtin/io/yml/yml.py	88.4% <ø> (ø)
glotaran/io/__init__.py	100.0% <ø> (ø)
glotaran/io/interface.py	100.0% <ø> (ø)
glotaran/io/prepare_dataset.py	65.3% <0.0%> (ø)
...esting/simulated_data/sequential_spectral_decay.py	100.0% <ø> (ø)
glotaran/typing/protocols.py	0.0% <ø> (ø)
glotaran/builtin/io/yml/utils.py	100.0% <100.0%> (ø)
... and 1 more

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[lgtm-com]

This pull request fixes 1 alert when merging b9cb524 into ece973f - view on LGTM.com

fixed alerts:

• 1 for Comparison using is when operands support `__eq__`

[lgtm-com]

This pull request fixes 1 alert when merging 4fffe9c into ece973f - view on LGTM.com

fixed alerts:

• 1 for Comparison using is when operands support `__eq__`

[jsnel]

Small stylistic improvements.

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[lgtm-com]

This pull request fixes 1 alert when merging a880ed9 into ece973f - view on LGTM.com

fixed alerts:

• 1 for Comparison using is when operands support `__eq__`

[jsnel]

Thanks for incorporating the suggested changes! LGTM.