run pre-commit

Author: VeckoTheGecko

.github/CONTRIBUTING.md

@@ -1 +1 @@
-Follow the instructions in our [contributing page](./contributing.md).
+Follow the instructions in our [contributing page](./contributing.md).

.github/workflows/publish-to-pypi.yml

@@ -8,106 +8,106 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.x"
-    - name: Install pypa/build
-      run: python3 -m pip install build --user
-    - name: Build a binary wheel and a source tarball
-      run: python3 -m build
-    - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: python3 -m pip install build --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
 
   publish-to-pypi:
     name: >-
       Publish Python 🐍 distribution 📦 to PyPI
-    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
     needs:
-    - build
+      - build
     runs-on: ubuntu-latest
     environment:
       name: pypi
       url: https://pypi.org/p/pyglider
     permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+      id-token: write # IMPORTANT: mandatory for trusted publishing
 
     steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
   github-release:
     name: >-
       Sign the Python 🐍 distribution 📦 with Sigstore
       and upload them to GitHub Release
     needs:
-    - publish-to-pypi
+      - publish-to-pypi
     runs-on: ubuntu-latest
 
     permissions:
-      contents: write  # IMPORTANT: mandatory for making GitHub Releases
-      id-token: write  # IMPORTANT: mandatory for sigstore
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write # IMPORTANT: mandatory for sigstore
 
     steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v2.1.1
-      with:
-        inputs: >-
-          ./dist/*.tar.gz
-          ./dist/*.whl
-    - name: Create GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      run: >-
-        gh release create
-        '${{ github.ref_name }}'
-        --repo '${{ github.repository }}'
-        --notes ""
-    - name: Upload artifact signatures to GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload
-        '${{ github.ref_name }}' dist/**
-        --repo '${{ github.repository }}'
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v2.1.1
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'
 
   publish-to-testpypi:
     name: Publish Python 🐍 distribution 📦 to TestPyPI
     needs:
-    - build
+      - build
     runs-on: ubuntu-latest
 
     environment:
       name: testpypi
       url: https://test.pypi.org/p/pyglider
 
     permissions:
-      id-token: write  # IMPORTANT: mandatory for trusted publishing
+      id-token: write # IMPORTANT: mandatory for trusted publishing
 
     steps:
-    - name: Download all the dists
-      uses: actions/download-artifact@v4
-      with:
-        name: python-package-distributions
-        path: dist/
-    - name: Publish distribution 📦 to TestPyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        repository-url: https://test.pypi.org/legacy/
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -5,4 +5,4 @@ docs/pyglider
 dist
 
 *.png
-.DS_Store
+.DS_Store

.readthedocs.yaml

@@ -8,4 +8,4 @@ sphinx:
   configuration: docs/conf.py
 
 conda:
-  environment: environment.yml
+  environment: environment.yml

LICENSE

@@ -188,4 +188,4 @@ third-party archives.
    distributed under the License is distributed on an "AS IS" BASIS,
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
-   limitations under the License.
+   limitations under the License.

README.md

@@ -1,11 +1,11 @@
 ![](docs/_static/PyGliderHorizontal.svg)
 
-Python tools for interacting with ocean glider data.   PyGlider takes data from
+Python tools for interacting with ocean glider data. PyGlider takes data from
 Teledyne/Webb Slocum gliders and Alseamar SeaExplorers and creates CF-compliant
 NetCDF files.
 
 For documentation, please see <http://pyglider.readthedocs.io>
 
 ### Contact
 
-Get in touch with us using Discussion above or by opening an issue.
+Get in touch with us using Discussion above or by opening an issue.

codecov.yml

@@ -20,10 +20,10 @@ coverage:
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
-        paths: '!tests/.*'
+        paths: "!tests/.*"
       tests:
         target: auto
         if_no_uploads: error
         if_not_found: success
         if_ci_failed: failure
-        paths: 'tests/.*'
+        paths: "tests/.*"

docs/Install.md

@@ -2,8 +2,8 @@
 
 ## conda/pip
 
-PyGlider depends on `dask` and `netcdf4`, both of which can be tricky to install using ``pip``,
-hence we recommend these be installed with [``conda``](https://www.anaconda.com/).  To install
+PyGlider depends on `dask` and `netcdf4`, both of which can be tricky to install using `pip`,
+hence we recommend these be installed with [`conda`](https://www.anaconda.com/). To install
 PyGlider, create an environment, and do
 
 ```

docs/conf.py

@@ -25,16 +25,16 @@
 # The full version, including alpha/beta/rc tags
 release = __version__
 
-master_doc = "index"
+master_doc = 'index'
 source_suffix = ['.rst', '.md']
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    "numpydoc",
-    "myst_parser",
+    'numpydoc',
+    'myst_parser',
     'sphinx.ext.autodoc',
     'sphinx.ext.inheritance_diagram',
     'autoapi.extension',
@@ -43,9 +43,9 @@
 extensions.append('sphinx.ext.intersphinx')
 
 intersphinx_mapping = {
-  'xarray': ('http://xarray.pydata.org/en/stable/', None),
-  'python': ('https://docs.python.org/3/', None),
-  }
+    'xarray': ('http://xarray.pydata.org/en/stable/', None),
+    'python': ('https://docs.python.org/3/', None),
+}
 
 autoapi_dirs = ['../pyglider']
 
@@ -63,40 +63,41 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "pydata_sphinx_theme"
+html_theme = 'pydata_sphinx_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-html_logo = "_static/PyGliderHorizontal.svg"
+html_logo = '_static/PyGliderHorizontal.svg'
 
 html_context = {
     # "github_url": "https://github.com", # or your GitHub Enterprise interprise
-    "github_user": "c-proof",
-    "github_repo": "pyglider",
-    "doc_path": "docs/",
+    'github_user': 'c-proof',
+    'github_repo': 'pyglider',
+    'doc_path': 'docs/',
 }
 html_theme_options = {
-    "icon_links": [
+    'icon_links': [
         {
             # Label for this link
-            "name": "GitHub",
+            'name': 'GitHub',
             # URL where the link will redirect
-            "url": "https://github.com/c-proof/pyglider",  # required
+            'url': 'https://github.com/c-proof/pyglider',  # required
             # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
-            "icon": "fab fa-github-square",
+            'icon': 'fab fa-github-square',
             # The type of image to be used (see below for details)
-            "type": "fontawesome",
+            'type': 'fontawesome',
         },
         {
-            "name": "PyPI",
-            "url": "https://pypi.org/project/pyglider",
-            "icon": "fas fa-box",
+            'name': 'PyPI',
+            'url': 'https://pypi.org/project/pyglider',
+            'icon': 'fas fa-box',
         },
         # {   "name": "conda-forge",
         #     "url": "https://anaconda.org/conda-forge/pyglider",
         #     "icon": "fas fa-box"
         # }
-   ]}
+    ]
+}

docs/contributing.md

@@ -1,6 +1,7 @@
 # Contributing
 
 ## Create a fork
+
 ```{note}
 TODO: Create contributing page noting:
 - the forking process (trimmed down)
@@ -20,6 +21,7 @@ Then install the dependencies:
 ```bash
 conda env update -f environment.yml -n pyglider-dev
 ```
+
 And install the package in editable mode:
 
 ```bash
@@ -30,7 +32,7 @@ Done!
 
 ---
 
-From here, you can make the changes you want, and add tests.  When you are ready, you can create a pull request into the codebase.
+From here, you can make the changes you want, and add tests. When you are ready, you can create a pull request into the codebase.
 
 ## Running tests