Feature/pre commit (#64)

* add pre-commit for ruff

* add pre commit

* add precommit github workflow

* update pre-commit version

* add pre-commit task

* run pre-commit

* enable more pre-commit checks

* remove black

* update pixi.lock

* add typo

* add precommit to docker

* remove black settings

* extract ruff settings into ruff.toml

* extract ruff settings into ruff.toml

* update pre-commit hooks

.devcontainer/Dockerfile

@@ -10,4 +10,4 @@ RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix
 USER vscode
 WORKDIR /home/vscode
 
-RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.gitattributes

@@ -43,4 +43,4 @@
 # numpy file format
 *.npy filter=lfs diff=lfs merge=lfs -text
 # GitHub syntax highlighting
-pixi.lock linguist-language=YAML merge=ourslock
+pixi.lock linguist-language=YAML merge=ourslock

.github/workflows/ci.yml

@@ -29,4 +29,4 @@ jobs:
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v4
         env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pre-commit.yaml

@@ -0,0 +1,10 @@
+name: pre-commit
+
+on: [pull_request]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: pre-commit/action@v3.0.0

.github/workflows/publish.yml

@@ -15,4 +15,4 @@ jobs:
       with:
         pypi-token: ${{ secrets.PYPI_API_TOKEN }}
         gh-token: ${{ secrets.GITHUB_TOKEN }}
-        parse-changelog: true
+        parse-changelog: true

.pre-commit-config.yaml

@@ -0,0 +1,44 @@
+# To use:
+#
+#     pre-commit run -a
+#
+# Or:
+#
+#     pre-commit install  # (runs every time you commit in git)
+#
+# To update this file:
+#
+#     pre-commit autoupdate
+#
+# See https://github.com/pre-commit/pre-commit
+
+repos:
+  # Standard hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+        args: ['--unsafe']  # Fixes errors parsing custom jinja templates
+      # - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      # - id: trailing-whitespace
+      - id: fix-byte-order-marker
+
+  # Formatter for python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [ python, pyi ]

.vscode/extensions.json

@@ -14,4 +14,4 @@
         "ryanluker.vscode-coverage-gutters",
         "jjjermiah.pixi-vscode"       
     ]
-}
+}

.vscode/settings.json

@@ -11,4 +11,4 @@
 		"/home/vscode/.local/lib/python3.10/site-packages/python_template/**": true
 	},
 	"python.analysis.autoImportCompletions": false //vscode gets it wrong more than right and mostly gets in the way
-}
+}

CHANGELOG.md

@@ -3,5 +3,3 @@
 ## python_template
 
 ## [0.0.0]
-
-

README.md

@@ -94,6 +94,3 @@ There are two core tasks.
 2. run \<cfg\>
 
     This runs python with the file set in \<cfg\>
-
-
-

docs/requirements.txt

@@ -1,3 +1,3 @@
 sphinxcontrib-napoleon
 sphinx-rtd-theme
-sphinx-autoapi
+sphinx-autoapi

pyproject.toml

@@ -34,13 +34,13 @@ python_template = { path = ".", editable = true }
 
 [project.optional-dependencies]
 test = [
-  "black>=23,<=24.10.0",
   "pylint>=3.2.5,<=3.3.1",
   "pytest-cov>=4.1,<=6.0.0",
   "pytest>=7.4,<=8.3.3",
   "hypothesis>=6.104.2,<=6.116.0",
   "ruff>=0.5.0,<=0.7.2",
   "coverage>=7.5.4,<=7.6.4",
+  "pre-commit<=4.0.1"
 ]
 
 [build-system]
@@ -60,7 +60,9 @@ py313 = ["py313","test"]
 
 
 [tool.pixi.tasks]
-format = "black ."
+pre-commit = "pre-commit run -a"
+pre-commit-update = "pre-commit autoupdate"
+format = "ruff format ."
 check-clean-workspace = "git diff --exit-code"
 ruff-lint = "ruff check . --fix"
 pylint = "pylint --version && echo 'running pylint...' && pylint $(git ls-files '*.py')"
@@ -90,26 +92,6 @@ jobs = 16                           #detect number of cores
 disable = "C,logging-fstring-interpolation,line-too-long,fixme,broad-exception-caught,missing-module-docstring,too-many-instance-attributes,too-few-public-methods,too-many-arguments,too-many-locals,too-many-branches,too-many-statements,use-dict-literal,cyclic-import,duplicate-code,too-many-public-methods"
 enable = "no-else-return,consider-using-in"
 
-[tool.black]
-line-length = 100
-
-[tool.ruff]
-line-length = 100 # Same as Black.
-
-target-version = "py310"
-
-[tool.ruff.lint]
-# Never enforce `E501` (line length violations).
-#"F841" will auto remove unused variables which is annoying during development, pylint catches this anyway
-ignore = ["E501", "E902", "F841"]
-# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
-
-# Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
-
-
 [tool.coverage.run]
 omit = ["*/test/*", "__init__.py"]
 

python_template.deps.yaml

@@ -7,3 +7,4 @@ apt_tools:
 pip_language-toolchain:
   - uv #use uv instead of pip
   - pip #update to the latest pip
+  - pre-commit

ruff.toml

@@ -0,0 +1,16 @@
+line-length = 100
+
+[lint]
+# E501: Lines too long (maximum of 79 characters).
+ignore = [
+    "E501", # Long line that exceeds maximum allowed length.
+    "F841", # Local variable referenced before assignment, this is annoying during development.
+]
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+# Ignore `E402` (import violations) in all `__init__.py` files, and in `path/to/file.py`.
+[lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
+"**/{tests,docs,tools}/*" = ["E402"]

scripts/setup_host.sh

@@ -56,4 +56,4 @@ echo 'eval "$(pixi completion --shell bash)"' >> ~/.bashrc
 
 sudo groupadd docker
 sudo usermod -aG docker $USER
-newgrp docker || true
+newgrp docker || true