Add pre commit config (#68)

ocefpaf · web-flow · commit 9c6cf48549e7 · 2025-06-11T08:17:54.000-07:00
* basic pre-commit fixes

* codespell

* pyproject-fmt

* ruff fixes

* add pre-commit config

* add ruff format

* add zizmor

* zizmor fixes and let linting happen in pre-commit-ci

* docstring check

* run pre-commits

* refresh lockfile

* enable blackdoc
diff --git a/.gitattributes b/.gitattributes
@@ -1,3 +1,2 @@
 # GitHub syntax highlighting
 pixi.lock linguist-language=YAML
-
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -10,9 +10,13 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest", "macos-latest"]
         environment: [test310, test311, test312, test313]
-    
+    permissions:
+      actions: none
+
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683  # v4.2.2
+        with:
+          persist-credentials: false
       - name: Setup pixi
         uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da  # v0.8.8
         with:
@@ -21,11 +25,3 @@ jobs:
       - name: Tests
         run: >
           pixi run --environment ${{ matrix.environment }} test
-        
-      - name: Lint
-        if: contains(${{ matrix.os }}, "ubuntu") && ${{ matrix.environment }} == "test310"
-        run: >
-          pixi run --environment test310 lint
-
-
-
diff --git a/.gitignore b/.gitignore
@@ -165,4 +165,4 @@ xarray_subset_grid/_version.py
 .pixi
 *.egg-info
 
-.ruff_cache/
+.ruff_cache/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,55 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: check-ast
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: check-docstring-first
+    - id: check-added-large-files
+      exclude_types: [yaml]
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.10
+  hooks:
+    - id: blackdoc
+
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+    - id: codespell
+      exclude: >
+          (?x)^(
+              .*\.ipynb
+          )$
+      args:
+        - --ignore-words-list=astroid,fo
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.11.13
+  hooks:
+    - id: ruff
+      args: ["--fix", "--show-fixes"]
+    - id: ruff-format
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: v2.6.0
+  hooks:
+    - id: pyproject-fmt
+
+- repo: https://github.com/woodruffw/zizmor-pre-commit
+  rev: v1.9.0
+  hooks:
+    - id: zizmor
+
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+        for more information, see https://pre-commit.ci
+    autofix_prs: false
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: []
+    submodules: false
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -10,4 +10,4 @@ sphinx:
 
 python:
   install:
-    - requirements: docs/requirements.txt
+    - requirements: docs/requirements.txt
diff --git a/DevelopmentNotes.txt b/DevelopmentNotes.txt
@@ -13,5 +13,3 @@ First point is not repeated.
 Bounding Box:
 
 A tuple of floats: (min_lon, min_lat, max_lon, max_lat).
-
-
diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ Or clone the project from git and build / install it from there.
 
 ## Usage
 
-This package is designed to be used in conjuction with [`xarray`](https://xarray.dev/). Given a [CF Compliant](https://cfconventions.org/) `xarray` dataset named `ds`, this package can be accessed using the `xsg` accessor:
+This package is designed to be used in conjunction with [`xarray`](https://xarray.dev/). Given a [CF Compliant](https://cfconventions.org/) `xarray` dataset named `ds`, this package can be accessed using the `xsg` accessor:
 
 ```python
 # Get the interprested grid class
@@ -31,9 +31,9 @@ ds_subset_bbox = ds.xsg.subset_bbox([-72, 32, -70, 35])
 # or by polygon
 poly = np.array([
     [-72, 32],
-    [-72, 33], 
-    [-73, 33], 
-    [-73, 31], 
+    [-72, 33],
+    [-73, 33],
+    [-73, 31],
     [-72, 32],
 ])
 ds_subset_poly = ds.xsg.subset_polygon(poly)
@@ -58,7 +58,7 @@ Then install the project in local edit mode:
 pip install -e .
 ```
 
-Once installed, the tests can be run: 
+Once installed, the tests can be run:
 
 ```bash
 python -m pytest
diff --git a/conda_requirements_dev.txt b/conda_requirements_dev.txt
@@ -11,4 +11,3 @@ pytest
 pytest-cov
 sphinx
 sphinx-rtd-theme
-
diff --git a/docs/design.rst b/docs/design.rst
@@ -33,4 +33,3 @@ utils
    :members:
    :undoc-members:
    :show-inheritance:
-
diff --git a/docs/examples/README.md b/docs/examples/README.md
@@ -4,4 +4,4 @@
 
 [roms.ipynb](./roms.ipynb): Read and subset [WCOFS](https://tidesandcurrents.noaa.gov/ofs/wcofs/wcofs.html) model data in space and view a plot of the resulting data
 
-[sscofs.ipynb](./sscofs.ipynb): Read [SSCOFS](https://tidesandcurrents.noaa.gov/ofs/dev/sscofs/sscofs_info.html) model data and assign cf compliant topology to allow for subsetting
+[sscofs.ipynb](./sscofs.ipynb): Read [SSCOFS](https://tidesandcurrents.noaa.gov/ofs/dev/sscofs/sscofs_info.html) model data and assign cf compliant topology to allow for subsetting
diff --git a/docs/examples/RegularGridTHREDDS.ipynb b/docs/examples/RegularGridTHREDDS.ipynb
@@ -21,7 +21,7 @@
    "outputs": [],
    "source": [
     "import xarray as xr\n",
-    "import xarray_subset_grid\n",
+    "\n",
     "from xarray_subset_grid.utils import format_bytes\n"
    ]
   },
diff --git a/docs/grids.rst b/docs/grids.rst
@@ -31,4 +31,4 @@ UGrid
 .. automodule:: xarray_subset_grid.grids.ugrid
    :members:
    :undoc-members:
-   :show-inheritance:
+   :show-inheritance:
diff --git a/docs/index.rst b/docs/index.rst
@@ -16,4 +16,4 @@ Contents:
    design
    grids
    notebooks
-   contributing
+   contributing
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -80,7 +80,7 @@ Source (Github)
 Install `Git <https://git-scm.com/book/en/v2/Getting-Started-Installing-Git>`__
 on your system if not already available (check with ``git --version`` at the command line.)
 
-If you are interested in installing xarray-subset-grid from source, 
+If you are interested in installing xarray-subset-grid from source,
 you will first need to get the latest version of the code
 ::
 
@@ -91,4 +91,3 @@ Run the following command from the root-directory
 ::
 
     pip install .
-
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,8 +1,8 @@
-sphinx 
+sphinx
 sphinx-autodoc-typehints
 myst_nb
 xarray_subset_grid@git+https://github.com/asascience-open/xarray-subset-grid.git
 sphinxcontrib-bibtex
 matplotlib
 cf_xarray
-xarray
+xarray
diff --git a/pixi.lock b/pixi.lock
diff --git a/profiling/README.md b/profiling/README.md
@@ -1,2 +1 @@
 Use this dir for performance testing and profiling -- code and notes.
-
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/tests/test_grids/test_regular_grid.py b/tests/test_grids/test_regular_grid.py
diff --git a/tests/test_grids/test_ugrid.py b/tests/test_grids/test_ugrid.py
diff --git a/xarray_subset_grid/grid.py b/xarray_subset_grid/grid.py
diff --git a/xarray_subset_grid/selector.py b/xarray_subset_grid/selector.py
diff --git a/xarray_subset_grid/visualization/mpl_plotting.py b/xarray_subset_grid/visualization/mpl_plotting.py

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,2 @@`
`1`	`1`	`# GitHub syntax highlighting`
`2`	`2`	`pixi.lock linguist-language=YAML`
`3`		`-`
Original file line number	Diff line number	Diff line change
`@@ -4,4 +4,4 @@`
`4`	`4`
`5`	`5`	`[roms.ipynb](./roms.ipynb): Read and subset [WCOFS](https://tidesandcurrents.noaa.gov/ofs/wcofs/wcofs.html) model data in space and view a plot of the resulting data`
`6`	`6`
`7`		`-[sscofs.ipynb](./sscofs.ipynb): Read [SSCOFS](https://tidesandcurrents.noaa.gov/ofs/dev/sscofs/sscofs_info.html) model data and assign cf compliant topology to allow for subsetting`
	`7`	`+[sscofs.ipynb](./sscofs.ipynb): Read [SSCOFS](https://tidesandcurrents.noaa.gov/ofs/dev/sscofs/sscofs_info.html) model data and assign cf compliant topology to allow for subsetting`