Merge branch 'lint_check' into 'dev'

Use ruff format and auto-fix for release lint

See merge request mass-spectrometry/corems!257

Author: kheal

CONTRIBUTING.md

@@ -88,7 +88,7 @@ Reviewers check these before merging into **`dev`**:
 
 - Docstrings follow the [NumPy style](https://numpydoc.readthedocs.io/en/latest/format.html).
 - API docs are built with [pdoc](https://github.com/mitmproxy/pdoc) (`make docu`). The package landing page (`corems.__doc__`) includes `README.md` and `docs/user/installation.md` so install content uses the same pdoc styling as the API.
-- Maintainers: before cutting a release, run package lint (`make lint`) as described in [RELEASE.md](./RELEASE.md). Dev tooling is installed via `pip install -e ".[dev]"`.
+- Maintainers: before cutting a release, run `make lint` as described in [RELEASE.md](./RELEASE.md). That command **rewrites** package Python (`ruff format` + `ruff check --fix`). Do not run it on a feature branch unless you intend to commit the diff. Dev tooling is installed via `pip install -e ".[dev]"`.
 
 ## Issue reporting
 

Makefile

@@ -149,14 +149,17 @@ uml:
 docu: uml
 	pdoc --output-dir docs --docformat numpy corems
 
-# Package lint (release prep). Requires corems[dev] (pylint). Config: pyproject.toml.
-# Advisory for maintainers — see RELEASE.md. Exit code may be non-zero when issues remain.
+# Format + auto-fix (release prep). Rewrites files — see RELEASE.md.
+# Requires corems[dev] (ruff). Config: pyproject.toml.
+# Do not use --unsafe-fixes.
 lint:
-	$(PYTHON) -m pylint corems
+	$(PYTHON) -m ruff format corems
+	$(PYTHON) -m ruff check --fix corems
 
-# Broader first-party Python (package + tests + support scripts). Still advisory.
+# Broader first-party Python (package + tests + support scripts). Also rewrites.
 lint-all:
-	$(PYTHON) -m pylint corems tests support_code
+	$(PYTHON) -m ruff format corems tests support_code
+	$(PYTHON) -m ruff check --fix corems tests support_code
 
 SKIP_LIPIDOMICS_DB ?= 0
 SKIP_MOLECULAR_DB ?= 0

RELEASE.md

@@ -23,7 +23,7 @@ Release when `dev` has a coherent set of changes ready for users (features, fixe
 | `make minor` | Backwards-compatible new features |
 | `make major` | Incompatible API changes |
 
-Each of those updates version metadata (see `.bumpversion.cfg`) and regenerates docs via `make docu` (UML class diagrams via `make uml` / pyreverse + Graphviz, then pdoc). The install how-to source is `docs/user/installation.md`, included on the package landing page through `corems.__doc__`. Maintainers need the `dev` extra (`pylint`) and system Graphviz (`dot`) installed so `make uml` succeeds during a version bump.
+Each of those updates version metadata (see `.bumpversion.cfg`) and regenerates docs via `make docu` (UML class diagrams via `make uml` / pyreverse + Graphviz, then pdoc). The install how-to source is `docs/user/installation.md`, included on the package landing page through `corems.__doc__`. Maintainers need the `dev` extra (`ruff` for `make lint`, `pylint` for `pyreverse` / `make uml`, `pdoc`, …) and system Graphviz (`dot`) so format and docs steps succeed during a version bump.
 
 ## Release steps (GitLab)
 
@@ -33,21 +33,21 @@ All release steps should be done on the `dev` branch and then merged into `maste
    - Gitlab CI green on `dev`.
    - Changelog or release notes drafted (these will be copied into the MR description and later into the release on GitHub).
    - No open blockers for the intended version.
-   - **Lint the package** (advisory maintainer review; not a hard CI gate):
-     1. Activate the same environment you use for CoreMS development and install/update dev extras so `pylint` is available, e.g.:
+   - **Format and auto-fix the package** (release prep; not a hard CI gate). This **rewrites files**.
+     1. Activate the same environment you use for CoreMS development and install/update dev extras so `ruff` is available, e.g.:
         ```bash
         pip install -e ".[dev]"
         ```
      2. From the repo root run:
         ```bash
         make lint
         ```
-        This runs `pylint` on `corems` with project config from `pyproject.toml` (high-volume legacy style noise disabled so the report is usable). Use the venv’s Python (activate the venv first, or `make lint PYTHON=.venv/bin/python`) so import resolution matches a real install.
-     3. Optional broader pass (tests and support scripts):
+        This runs `ruff format` then `ruff check --fix` on `corems` (config in `pyproject.toml`). Use the venv’s Python (activate the venv first, or `make lint PYTHON=.venv/bin/python`). The first run after ruff is introduced will produce a large diff; later releases should be small.
+     3. Optional broader pass (tests and support scripts; also rewrites):
         ```bash
         make lint-all
         ```
-     4. Review the report: fix release-blocking issues you care about; residual warnings are OK for this step. Proceed when you are satisfied—the step does not require a perfect score or exit code 0.
+     4. Review `git diff` and commit the formatted/fixed files (a dedicated commit is fine, especially the first time). Findings that `--fix` cannot apply may remain and may make the command exit non-zero; that does not block the release. Do not use `--unsafe-fixes`.
 
 2. **Bump version on `dev` (or a short-lived release branch from `dev`)**
    ```bash

docs/user/installation.md

@@ -41,10 +41,10 @@ By default the molecular formula database uses **SQLite** (local file; no extra
 Install extras from `pyproject.toml` as needed:
 
 ```bash
-pip install "corems[dev]"          # tests, pylint, docs tooling (incl. pdoc)
+pip install "corems[dev]"          # tests, ruff, docs tooling (incl. pdoc)
 ```
 
-With `corems[dev]`, maintainers can run package lint via `make lint` (see [RELEASE.md](../../RELEASE.md)).
+With `corems[dev]`, maintainers can format and auto-fix the package via `make lint` at release time (see [RELEASE.md](../../RELEASE.md)). That command rewrites files.
 
 Check the installed package metadata or `pyproject.toml` for the current list of extras.
 

pyproject.toml

@@ -59,7 +59,8 @@ Documentation = "https://emsl-computing.github.io/CoreMS/corems.html"
 
 [project.optional-dependencies]
 dev = [
-    "pylint>=3.0",
+    "ruff>=0.8",
+    "pylint>=3.0",  # pyreverse for make uml / make docu
     "pytest>=8.3.2",
     "pytest-cov>=5.0.0",
     "pytest-xdist>=3.6.1",
@@ -107,48 +108,25 @@ exclude_lines = [
 ]
 
 # ---------------------------------------------------------------------------
-# Pylint (release / maintainer lint via `make lint`; see RELEASE.md)
-# Disable high-volume project-wide style debt so the report is reviewable.
-# Tighten this list over time as the codebase is cleaned up.
+# Ruff (release / maintainer format+fix via `make lint`; see RELEASE.md)
+# `make lint` rewrites files. Do not run it except during release prep
+# unless you intend to commit the diff. Default rule set only.
 # ---------------------------------------------------------------------------
-[tool.pylint.main]
-jobs = 0
-py-version = "3.10"
-ignore-paths = [
-    "^.venv/.*",
-    "^corems/mass_spectra/input/win_only/.*",
+[tool.ruff]
+target-version = "py310"
+line-length = 88
+src = ["corems"]
+extend-exclude = [
+    "corems/mass_spectra/input/win_only",
 ]
 
-[tool.pylint.messages_control]
-disable = [
-    # Legacy / project-wide naming and structure
-    "invalid-name",
-    "too-few-public-methods",
-    "too-many-arguments",
-    "too-many-positional-arguments",
-    "too-many-locals",
-    "too-many-statements",
-    "too-many-branches",
-    "too-many-instance-attributes",
-    "too-many-public-methods",
-    "too-many-return-statements",
-    "too-many-nested-blocks",
-    "too-many-lines",
-    "duplicate-code",
-    # Formatting and docstring debt
-    "line-too-long",
-    "trailing-whitespace",
-    "missing-module-docstring",
-    "missing-class-docstring",
-    "missing-function-docstring",
-    # Common style nits in this codebase
-    "no-else-return",
-    "consider-using-f-string",
-    "import-outside-toplevel",
-    "wrong-import-order",
-    "ungrouped-imports",
-    "protected-access",
-    "attribute-defined-outside-init",
-    # Dynamic attributes (numpy / instrument APIs) — high false-positive rate
-    "no-member",
-]
+[tool.ruff.lint]
+# Pin ruff defaults so a newer ruff does not enable extra families at release.
+select = ["E4", "E7", "E9", "F"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+