Use ruff to improve code quality

[seisman]

It seems ruff has been very hot recently. The README says it can replace flake8 and pylint, and more importantly, it's 10-100x faster.

Someone interested may try it and tell us how it works for the PyGMT project.

[weiji14]

Opened a PR to replace flakeheaven and isort with ruff at #2747, so that we can move ahead with the Python 3.12 support.

It should also be possible to replace pylint with ruff (see https://docs.astral.sh/ruff/faq/#how-does-ruff-compare-to-pylint), which would:

• Pro:
  • Allow us to remove make lint (which is slow) from the Makefile (i.e. only have make check and make format)
  • Bonus is that ruff can actually automatically fix some pylint rules (see those marked with 🛠️ at https://docs.astral.sh/ruff/rules/#pylint-pl)
• Con: Not all pylint rules are applied (see Implement Pylint astral-sh/ruff#970), but I'm not sure if we even need to check all of them...

So should we replace pylint with ruff? Vote 👍 for yes, 👎 for no. If everyone is generally in favour, we can open a PR after #2747 is merged.

[seisman]

So should we replace pylint with ruff?

Instead of replacing pylint with ruff, I think we can use both to see if there are any linting issues reported by pylint but not detected by ruff. We can then decide if we want to remove pylint before releasing v0.11.0. So I propose to have two separate PRs:

• Configure ruff as a linting tool
• Remove pylint before v0.11.0

[seisman]

ruff supports many groups of rules (https://docs.astral.sh/ruff/rules/). I think we should go through the available rules and apply the rules that make sense to our project.

ruff v0.1.8 provides the following linters/rules:

ruff linter | awk '{printf("- [ ] [`%s`](https://docs.astral.sh/ruff/rules/#%s-%s): %s\n"), $1, tolower($2), tolower($1), $2}' 

• F: Pyflakes Replace flakeheaven and isort with ruff #2747
• E/W: pycodestyle Replace flakeheaven and isort with ruff #2747
• C90: mccabe [Some functions have high complexity but it's a lot of work to refactor them]
• I: isort Replace flakeheaven and isort with ruff #2747
• N: pep8-naming Enable ruff's pep8-naming (N) rules #2877
• D: pydocstyle [Enable this ruleset will cause too many changes]
• UP: pyupgrade Enable ruff's pyupgrade (UP) rules #2749
• YTT: flake8-2020 Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• ANN: flake8-annotations [This ruleset checks annotations of all parameters. So, we can't enable this ruleset until we're 100% type-complete]
• ASYNC: flake8-async [async is not used in pygmt]
• TRIO: flake8-trio [trio is not used in pygmt]
• S: flake8-bandit Enable ruff's flake8-bandit (S) rules #2892
• BLE: flake8-blind-except Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• FBT: flake8-boolean-trap [This ruleset causes too many errors. Better to refactor the function definition in Improve function signatures to use positional-only, positional-or-keyword, or keyword-only parameter #2893 first]
• B: flake8-bugbear Enable ruff's flake8-bugbear (B) rules #2825
• A: flake8-builtins Enable ruff's flake8-builtins (A) rules #2882
• COM: flake8-commas [COM812 causes too many changes]
• CPY: flake8-copyright [we don't have copyright in any files]
• C4: flake8-comprehensions Enable ruff's flake8-comprehensions (C4) rules #2887
• DTZ: flake8-datetimez [I think we usually don't care about timezones)
• T10: flake8-debugger [no debugger information in pygmt]
• DJ: flake8-django [not a django project]
• EM: flake8-errmsg [The rules make sense, but we have too many violations, and fixing all of them make minor improvements. So better not enable this ruleset]
• EXE: flake8-executable Enable ruff's flake8-executable (EXE) rules #2898
• FA: flake8-future-annotations Enable ruff's flake8-future-annotations (FA) rules #2855
• ISC: flake8-implicit-str-concat Enable ruff's flake8-implicit-str-concat (ISC) rules #2837
• ICN: flake8-import-conventions Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• G: flake8-logging-format [logging is not used in pygmt]
• INP: flake8-no-pep420 [report too many errors about examples]
• PIE: flake8-pie Enable ruff's flake8-pie (PIE) rules #2866
• T20: flake8-print Enable ruff's flake8-print (T20) rules #2894
• PYI: flake8-pyi [PyGMT doesn't provide .pyi files]
• PT: flake8-pytest-style Enable ruff's flake8-pytest-style (PT) rules #2899
• Q: flake8-quotes [ruff format already enforces consistent quote style. The rules are redundant]
• RSE: flake8-raise Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• RET: flake8-return Enable ruff's flake8-return (RET) rules and ignore RET504 #2897
• SLF: flake8-self [I believe we only access class private members when necessary]
• SLOT: flake8-slots [pygmt has no subclasses of immutable types]
• SIM: flake8-simplify Enable ruff's flake8-simplify (SIM) rules #2829
• TID: flake8-tidy-imports Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• TCH: flake8-type-checking Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• INT: flake8-gettext [gettext is not used in pygmt]
• ARG: flake8-unused-arguments Enable ruff's flake8-unused-arguments (ARG) rules #2900
• PTH: flake8-use-pathlib [too many violations. Address Replace os.path with pathlib #1834 first]
• TD: flake8-todos [TODO is not used in pygmt]
• FIX: flake8-fixme [FIXME is not used in pygmt]
• ERA: eradicate [This linter has one rule to check commented-out Python code. It raises many errors because sometimes we have code-like comments.]
• PD: pandas-vet Enable ruff's pandas-vet (PD) rules #2830
• PGH: pygrep-hooks Enable ruff's BLE/ICN/PGH/RSE/TCH/TID/YTT rules #2878
• PL: Pylint Enable ruff's pylint rules (PL) and remove pylint #2815
• TRY: tryceratops [too many violations. Need to refactor our exceptions first]
• FLY: flynt Enable ruff's flynt (FLY) rules #2835
• NPY: NumPy-specific Enable ruff's NumPy-specific rules #2782
• AIR: Airflow [unrelated to airflow]
• PERF: Perflint Enable ruff's perflint (PERF) rules #2886
• FURB: refurb [preview only]
• LOG: flake8-logging [no logging in pygmt]
• RUF: Ruff-specific Enable ruff's ruff-specific (RUF) rules #2901

[seisman]

I've enabled ~32 rulesets that make sense to our project. Closing the issue now and we may revisit it in the feature if new ruff versions provide more rulesets.