Pre-commit: add Ruff (#261)

* Replaces flake8 and all its enabled plugins with Ruff * Use Ruff formatter as a drop-in replacement of Black * Simplifies the configuration using a single `pyproject.toml` instead of multiple files (`pytest.ini`, `flake8`).
empa-scientific-it · Nov 20, 2024 · 04ab64c · 04ab64c
1 parent 5a3fa10
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diff --git a/.flake8 b/.flake8
diff --git a/.github/workflows/build-docker-image.yml b/.github/workflows/build-docker-image.yml
@@ -1,30 +1,28 @@
 ---
 name: Build Tutorial Container
 on:
-    push:
-        branches:
-            - main
-        paths-ignore:
-            - '*.md'
-            - slides/**
-            - images/**
-            - .gitignore
-    workflow_dispatch:
-
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - '*.md'
+      - slides/**
+      - images/**
+      - .gitignore
+  workflow_dispatch:
 jobs:
-    repo2docker:
-        runs-on: ubuntu-latest
-        permissions:
-            packages: write
-        steps:
-            - name: checkout files in repo
-              uses: actions/checkout@main
-
-            - name: update jupyter dependencies with repo2docker
-              uses: jupyterhub/repo2docker-action@master
-              with:
-                  DOCKER_USERNAME: ${{ github.actor }}
-                  DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
-                  DOCKER_REGISTRY: ghcr.io
-                  IMAGE_NAME: ${{ github.repository }}
-                  FORCE_REPO2DOCKER_VERSION: jupyter-repo2docker==2023.06.0
+  repo2docker:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+    steps:
+      - name: checkout files in repo
+        uses: actions/checkout@main
+      - name: update jupyter dependencies with repo2docker
+        uses: jupyterhub/repo2docker-action@master
+        with:
+          DOCKER_USERNAME: ${{ github.actor }}
+          DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
+          DOCKER_REGISTRY: ghcr.io
+          IMAGE_NAME: ${{ github.repository }}
+          FORCE_REPO2DOCKER_VERSION: jupyter-repo2docker==2023.06.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,68 +1,34 @@
 ---
 ci:
-    autoupdate_schedule: quarterly
-
+  autoupdate_schedule: quarterly
 repos:
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
-      hooks:
-          - id: end-of-file-fixer
-          - id: trailing-whitespace
-            exclude: miscellaneous/structures/SiO2.xyz
-          - id: check-yaml
-          - id: check-added-large-files
-            args: [--maxkb=6000]
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-          - id: isort
-            args: [--profile, black, --filter-files]
-    - repo: https://github.com/PyCQA/autoflake
-      rev: v2.3.1
-      hooks:
-          - id: autoflake
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.16.0
-      hooks:
-          - id: pyupgrade
-            args: [--py38-plus]
-    - repo: https://github.com/psf/black
-      rev: 24.4.2
-      hooks:
-          - id: black
-            language_version: python3 # Should be a command that runs python3.6+
-    - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.0
-      hooks:
-          - id: flake8
-            args: [--count, --show-source, --statistics]
-            additional_dependencies:
-                - flake8-bugbear
-                - flake8-builtins
-                - flake8-comprehensions
-                - flake8-debugger
-                - flake8-logging-format
-                - pep8-naming
-                - pyflakes
-                - tryceratops
-    # - repo: https://github.com/pre-commit/mirrors-mypy
-    #   rev: v1.5.1
-    #   hooks:
-    #       - id: mypy
-    #         additional_dependencies:
-    #             - types-click-spinner
-    #             - types-requests
-    #             - types-tabulate
-    #             - types-toml
-    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
-      rev: 0.2.3
-      hooks:
-          - id: yamlfmt
-    - repo: https://github.com/asottile/setup-cfg-fmt
-      rev: v2.5.0
-      hooks:
-          - id: setup-cfg-fmt
-    - repo: https://github.com/kynan/nbstripout
-      rev: 0.7.1
-      hooks:
-          - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+      - id: check-added-large-files
+        args: [--maxkb=6000]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.4
+    hooks:
+      # Ruff fix
+      - id: ruff
+        types_or: [python, pyi]
+        args: [--fix]
+        name: ruff (fix)
+      # Ruff formatter
+      - id: ruff-format
+        types_or: [python, pyi]
+        name: ruff (format)
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.14.0
+    hooks:
+      - id: yamlfmt
+        name: YAML (format)
+        types: [yaml]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
diff --git a/.yamlfmt b/.yamlfmt
@@ -0,0 +1,5 @@
+formatter:
+  type: basic
+  include_document_start: true
+  retain_line_breaks: true
+output_format: line
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -1,23 +1,23 @@
 ---
 name: python-tutorial
 channels:
-    - conda-forge
+  - conda-forge
 dependencies:
-    - python=3.10
-    - pip
-    - pip:
-          - numpy
-          - matplotlib
-          - pandas
-          - ipywidgets
-          - ipynbname
-          - jupyterlab
-          - pytest
-          - pytest-timeout
-          - markdown
-          - pre-commit
-          - geostatspy
-          - gstools
-          - scikit-learn
-          - attrs
-          - multiprocess
+  - python=3.10
+  - pip
+  - pip:
+      - numpy
+      - matplotlib
+      - pandas
+      - ipywidgets
+      - ipynbname
+      - jupyterlab
+      - pytest
+      - pytest-timeout
+      - markdown
+      - pre-commit
+      - geostatspy
+      - gstools
+      - scikit-learn
+      - attrs
+      - multiprocess
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,58 @@
+[tool.ruff]
+# Line length (Black default)
+line-length = 88
+
+# Python target version
+target-version = "py38"
+
+# Ignored rules for the entire project
+[tool.ruff.lint]
+ignore = [
+    "E501", # Line too long
+    "E203", # Whitespace before ':'
+    # "TRY301", # Raise within try block (this is actually a good practice)
+    # "W503"  # Line break before binary operator (not PEP8 enforced, so not implemented in Ruff)
+]
+
+# flake8 plugins to enable:
+#   - flake8-bugbear          B
+#   - flake8-builtins         A
+#   - flake8-comprehensions   C4
+#   - flake8-debugger         T10
+#   - flake8-logging-format   G
+#   - pep8-naming             N
+#   - pyflakes                F
+#   - tryceratops             TRY
+select = [
+    "A",   # flake8-builtins
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "T10", # flake8-debugger
+    "G",   # flake8-logging-format
+    "N",   # pep8-naming
+    "F",   # pyflakes
+    "TRY", # tryceratops
+    "I",   # isort
+    "E",   # pycodestyle errors
+    "UP",  # pyupgrade
+]
+
+# Per-file rule ignores
+[tool.ruff.lint.per-file-ignores]
+# Trailing whitespace in comment
+"binder/ipython_config.py" = ["E266"]
+# suppress `raise ... from err`
+# Why we ignore B904 from the object-oriented tests?
+# We do want to raise an assertion error if the check on the solution function attributes fails,
+# but Python by default will raise a TypeError via vars(solution_result)
+# if the result is not a class and therefore doesn't have a __dict__ attribute.
+"tutorial/tests/test_object_oriented_programming.py" = ["B904"]
+
+# Ruff formatting
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+
+# pytest
+[tool.pytest.ini_options]
+addopts = "-v --tb=short"
diff --git a/pytest.ini b/pytest.ini
diff --git a/tutorial/tests/test_functional_programming.py b/tutorial/tests/test_functional_programming.py
@@ -143,7 +143,7 @@ def reference_exercise6(my_list: List[Tuple[str, int]]) -> List[Tuple[str, float
 
 
 def test_exercise6(
-    function_to_test: Callable[[List[Tuple[str, int]]], List[Tuple[str, float]]]
+    function_to_test: Callable[[List[Tuple[str, int]]], List[Tuple[str, float]]],
 ):
     input_data = reference_exercise5(get_data_exercise5())
     assert function_to_test(input_data) == reference_exercise6(input_data)

diff --git a/tutorial/tests/test_input_output.py b/tutorial/tests/test_input_output.py
@@ -98,9 +98,7 @@ def test_write_file(function_to_test, tmp_path: pl.Path):
     function_to_test(tmp_user)
     reference_write_file(tmp_test)
 
-    assert (
-        tmp_user.exists()
-    ), """The file was not created. Make sure to create the file in the function. Hint: use `open(output_file, "w")`"""
+    assert tmp_user.exists(), """The file was not created. Make sure to create the file in the function. Hint: use `open(output_file, "w")`"""
 
     assert (
         tmp_user.read_text() == tmp_test.read_text()

diff --git a/tutorial/tests/test_object_oriented_programming.py b/tutorial/tests/test_object_oriented_programming.py
@@ -177,8 +177,8 @@ def test_oop_str_and_repr(first_name, last_name, function_to_test):
     validate_oop_str_method(solution_result)
     validate_oop_repr_method(solution_result)
 
-    assert str(solution_result) == str(
-        reference_result
+    assert (
+        str(solution_result) == str(reference_result)
     ), "The __str__() result does not match the template 'My name is {first_name} {last_name}'."
     assert (
         solution_result.__repr__() == reference_result.__repr__()

diff --git a/tutorial/toc.py b/tutorial/toc.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """CLI script to build a table of contents for an IPython notebook"""
+
 import argparse as ap
 import pathlib
 import re