Feature/pre commit

.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/[email protected]

.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 +1,60 @@
+# 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-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: name-tests-test
+      - id: detect-private-key
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-xml
+      - id: check-yaml
+        args: ['--unsafe']  # Fixes errors parsing custom jinja templates
+      # - id: check-json
+      # - id: pretty-format-json
+      #   args: ['--autofix']  
+      - 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 ]
+  # Checks for spelling mistakes
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0 #TODO latest version  2.3.0 finds a lot of spelling mistakes but fails on "assertIn"
+    hooks:
+      - id: codespell
+        args: ['--write-changes']
+        exclude: \.(svg|pyc|lock|json)$

.vscode/extensions.json

@@ -1,17 +1,17 @@
 {
-    "recommendations": [
-        "ms-python.python",
-        "ms-python.vscode-pylance",
-        "ms-python.pylint",
-        "ms-python.black-formatter",
-        "njpwerner.autodocstring",
-        "charliermarsh.ruff",
-        "mhutchie.git-graph",
-        "eamodio.gitlens",
-        "tamasfe.even-better-toml",
-        "Codium.codium",
-        "ms-azuretools.vscode-docker",
-        "ryanluker.vscode-coverage-gutters",
-        "jjjermiah.pixi-vscode"       
-    ]
-}
+  "recommendations": [
+    "ms-python.python",
+    "ms-python.vscode-pylance",
+    "ms-python.pylint",
+    "ms-python.black-formatter",
+    "njpwerner.autodocstring",
+    "charliermarsh.ruff",
+    "mhutchie.git-graph",
+    "eamodio.gitlens",
+    "tamasfe.even-better-toml",
+    "Codium.codium",
+    "ms-azuretools.vscode-docker",
+    "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

@@ -81,7 +81,7 @@ If you don't want to install rocker on your system but want to use vscode, you c
 
 ## Troubleshooting
 
-The main pixi tasks are related to CI.  Github actions runs the pixi task "ci".  The CI is mostly likey to fail from a lockfile mismatch.  Use `pixi run fix` to fix any lockfile related problems. 
+The main pixi tasks are related to CI.  Github actions runs the pixi task "ci".  The CI is mostly likely to fail from a lockfile mismatch.  Use `pixi run fix` to fix any lockfile related problems. 
 
 ## vscode tasks
 
@@ -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