modernize the pre-commit hooks

.devcontainer/scipy2023/jupyter_lab_config.py

@@ -1,3 +1,3 @@
 c = get_config()  # noqa
-c.LabApp.default_url = '/lab/tree/workshops/scipy2023/index.ipynb'
-c.ServerApp.allow_origin = '*'
+c.LabApp.default_url = "/lab/tree/workshops/scipy2023/index.ipynb"
+c.ServerApp.allow_origin = "*"

.devcontainer/scipy2024/jupyter_lab_config.py

@@ -1,3 +1,3 @@
 c = get_config()  # noqa
-c.LabApp.default_url = '/lab/tree/workshops/scipy2024/index.ipynb'
-c.ServerApp.allow_origin = '*'
+c.LabApp.default_url = "/lab/tree/workshops/scipy2024/index.ipynb"
+c.ServerApp.allow_origin = "*"

.github/actions/setup-pixi/action.yml

@@ -1,8 +1,8 @@
-name: "Setup Pixi"
-description: "Create Python environment for GitHub Action Job"
+name: 'Setup Pixi'
+description: 'Create Python environment for GitHub Action Job'
 
 runs:
-  using: "composite"
+  using: 'composite'
   steps:
     - uses: prefix-dev/setup-pixi@v0.8.10
       with:

.github/dependabot.yml

@@ -1,7 +1,7 @@
 # Regularly update Docker tags and Actions steps
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/.github"
+  - package-ecosystem: 'github-actions'
+    directory: '/.github'
     schedule:
-      interval: "monthly"
+      interval: 'monthly'

.github/workflows/main.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches: main
     paths-ignore:
-      - ".devcontainer/**"
+      - '.devcontainer/**'
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:

.github/workflows/pull_request.yaml

@@ -4,7 +4,7 @@ on:
   pull_request:
     types: [opened, synchronize, reopened, closed]
     paths-ignore:
-      - ".devcontainer/**"
+      - '.devcontainer/**'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/qaqc.yaml

@@ -6,7 +6,7 @@ on:
     branches:
       - main
     paths-ignore:
-      - ".devcontainer/**"
+      - '.devcontainer/**'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -28,7 +28,7 @@ jobs:
         with:
           check_filenames: true
           check_hidden: true
-          skip: ".git,*.js,qaqc.yml"
+          skip: '.git,*.js,qaqc.yml'
           ignore_words_list: hist,nd
 
       # borrowed from https://github.com/ProjectPythia/pythia-foundations/blob/main/.github/workflows/link-checker.yaml

.github/workflows/surge_preview.yml

@@ -2,7 +2,7 @@ name: Pull Request Preview
 
 on:
   workflow_run:
-    workflows: ["Pull Request Build"]
+    workflows: ['Pull Request Build']
     types:
       - completed
 

.pre-commit-config.yaml

@@ -11,10 +11,9 @@ repos:
       - id: check-json
         exclude: ^.devcontainer/
       - id: check-yaml
-      - id: double-quote-string-fixer
 
   - repo: https://github.com/codespell-project/codespell
-    rev: "v2.4.1"
+    rev: 'v2.4.1'
     hooks:
       - id: codespell
 
@@ -28,21 +27,28 @@ repos:
     rev: v0.4.6
     hooks:
       - id: blackdoc
+        additional_dependencies: ['black==26.1.0']
+      - id: blackdoc-autoupdate-black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.15
     hooks:
-      - id: flake8
+      - id: ruff-check
+        args: ['--fix', '--show-fixes']
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 8.0.1
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.8.3
     hooks:
-      - id: isort
+      - id: prettier
+        args: ['--cache-location=.prettier_cache/cache']
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: prettier
+      - id: taplo-format
+        args: ['--option', 'array_auto_collapse=false']
+      - id: taplo-lint
+        args: ['--no-schema']
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.9.1

_config.yml

@@ -1,7 +1,7 @@
 # Learn more at https://jupyterbook.org/customize/config.html
-title: ""
+title: ''
 author: The Xarray Community
-copyright: "2025"
+copyright: '2025'
 logo: images/logo.png
 only_build_toc_files: true
 exclude_patterns: [.github, .pixi]
@@ -18,7 +18,7 @@ html:
   extra_footer: '<p>Xarray is a fiscally sponsored project of <a href="https://numfocus.org">NumFOCUS</a>, a nonprofit dedicated to supporting the open-source scientific computing community.<br> Theme by the <a href="https://ebp.jupyterbook.org">Executable Book Project</a>.</p> Content licensed under the terms of the <a href="https://www.apache.org/licenses/LICENSE-2.0.html">Apache 2.0 License</a>.'
   analytics:
     google_analytics_id: G-JRQHYVFQR7
-  favicon: "images/favicon.ico"
+  favicon: 'images/favicon.ico'
 
 parse:
   # https://jupyterbook.org/content/content-blocks.html?highlight=myst%20substitution#define-substitutions-for-your-whole-book
@@ -40,7 +40,7 @@ parse:
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: "cache"
+  execute_notebooks: 'cache'
   allow_errors: false
   # Per-cell notebook execution limit (seconds)
   timeout: 300
@@ -53,11 +53,11 @@ latex:
 # Configure your Binder links, such as the URL of the BinderHub.
 launch_buttons:
   notebook_interface: jupyterlab
-  binderhub_url: "https://mybinder.org"
+  binderhub_url: 'https://mybinder.org'
 
 # Information about where the book exists on the web
 repository:
-  url: "https://github.com/xarray-contrib/xarray-tutorial"
+  url: 'https://github.com/xarray-contrib/xarray-tutorial'
   branch: main
 
 # Bibliography
@@ -78,7 +78,7 @@ sphinx:
   config:
     language: en # accessibility
     # application/vnd.holoviews_load.v0+json, application/vnd.holoviews_exec.v0+json
-    suppress_warnings: ["mystnb.unknown_mime_type", "misc.highlighting_failure"]
+    suppress_warnings: ['mystnb.unknown_mime_type', 'misc.highlighting_failure']
     codeautolink_concat_default: True
     notfound_context:
       body: "<h1>Whoops! 404 Page Not Found</h1>\n\n<p>Sorry, this page doesn't exist. Many sections of this book have been updated recently.</p><p> Try the search box 🔎 to find what you're looking for!</p>"

_static/style.css

@@ -5,7 +5,7 @@
 /* workaround Pydata Sphinx theme using light colors for widget cell outputs in dark-mode */
 /* works for many widgets but not for Xarray html reprs */
 /* https://github.com/pydata/pydata-sphinx-theme/issues/2189 */
-html[data-theme="dark"] div.cell_output .text_html:has(div.xr-wrap) {
+html[data-theme='dark'] div.cell_output .text_html:has(div.xr-wrap) {
   background-color: var(--pst-color-on-background) !important;
   color: var(--pst-color-text-base) !important;
 }

advanced/accessors/01_accessor_examples.ipynb

@@ -98,7 +98,7 @@
    "outputs": [],
    "source": [
     "ds = xr.tutorial.load_dataset(\"air_temperature\")\n",
-    "ds[\"skewair\"] = ds['air'].stats.skewness(dim=\"time\")\n",
+    "ds[\"skewair\"] = ds[\"air\"].stats.skewness(dim=\"time\")\n",
     "ds"
    ]
   },
@@ -126,8 +126,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import os\n",
+    "\n",
+    "import numpy as np\n",
     "import pandas as pd\n",
     "import xarray as xr\n",
     "\n",
@@ -151,7 +152,7 @@
     "\n",
     "    @staticmethod\n",
     "    def _validate(self, req_dim=None, req_vars=None):\n",
-    "        '''\n",
+    "        \"\"\"\n",
     "        Make sure the xarray dataset has the correct dimensions and variables.\n",
     "\n",
     "        Running this function will check that my dataset has all the needed dimensions and variables\n",
@@ -164,7 +165,7 @@
     "            List of all required dimension names\n",
     "        req_vars : list of str\n",
     "            List of all required variable  names\n",
-    "        '''\n",
+    "        \"\"\"\n",
     "\n",
     "        if req_dim is not None:\n",
     "            if all([dim not in list(self._xrds.dims) for dim in req_dim]):\n",
@@ -179,8 +180,8 @@
     "\n",
     "    def change_vars_to_coords(\n",
     "        self,\n",
-    "        req_dim=['ny', 'nx'],\n",
-    "        req_vars={'xaxis': ['nx'], 'yaxis': ['ny']},\n",
+    "        req_dim=[\"ny\", \"nx\"],\n",
+    "        req_vars={\"xaxis\": [\"nx\"], \"yaxis\": [\"ny\"]},\n",
     "    ):\n",
     "        \"\"\"\n",
     "        Turn the xaxis and y axis variables into coordinates.\n",
@@ -195,8 +196,8 @@
     "\n",
     "        self._validate(self, req_dim, req_vars)\n",
     "\n",
-    "        self._xrds = self._xrds.swap_dims({'ny': 'yaxis', 'nx': 'xaxis'})\n",
-    "        self._xrds = self._xrds.rename({'xaxis': 'x', 'yaxis': 'y'})\n",
+    "        self._xrds = self._xrds.swap_dims({\"ny\": \"yaxis\", \"nx\": \"xaxis\"})\n",
+    "        self._xrds = self._xrds.rename({\"xaxis\": \"x\", \"yaxis\": \"y\"})\n",
     "\n",
     "        return self._xrds\n",
     "\n",
@@ -207,7 +208,7 @@
     "        \"\"\"\n",
     "\n",
     "        reorged = []\n",
-    "        for reorg_var in ['vx', 'vy', 'err']:\n",
+    "        for reorg_var in [\"vx\", \"vy\", \"err\"]:\n",
     "            ds = self.reorg_var_time(reorg_var)\n",
     "            reorged.append(ds)\n",
     "\n",
@@ -232,12 +233,12 @@
     "        das_to_reorg = [self._xrds[var] for var in to_reorg]\n",
     "\n",
     "        # add the time dimension\n",
-    "        das_to_reorg = [das_to_reorg[var].expand_dims('time') for var in range(len(das_to_reorg))]\n",
+    "        das_to_reorg = [das_to_reorg[var].expand_dims(\"time\") for var in range(len(das_to_reorg))]\n",
     "\n",
     "        # update variable name to remove time\n",
     "        das_to_reorg = [das_to_reorg[var].rename(reorg_var) for var in range(len(das_to_reorg))]\n",
     "\n",
-    "        ds = xr.concat(das_to_reorg, dim='time')\n",
+    "        ds = xr.concat(das_to_reorg, dim=\"time\")\n",
     "\n",
     "        return ds"
    ]
@@ -248,7 +249,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ds = xr.tutorial.open_dataset('ASE_ice_velocity.nc')"
+    "ds = xr.tutorial.open_dataset(\"ASE_ice_velocity.nc\")"
    ]
   },
   {
@@ -311,15 +312,15 @@
     "        # as specific to my workflow, saving time and headache later if they were missing and the computation fails\n",
     "        # partway through.\n",
     "        self._validate(\n",
-    "            self, req_dim=['x', 'y', 'dtime'], req_vars={'elevation': ['x', 'y', 'dtime']}\n",
+    "            self, req_dim=[\"x\", \"y\", \"dtime\"], req_vars={\"elevation\": [\"x\", \"y\", \"dtime\"]}\n",
     "        )\n",
     "\n",
     "    # ----------------------------------------------------------------------\n",
     "    # Methods\n",
     "\n",
     "    @staticmethod\n",
     "    def _validate(self, req_dim=None, req_vars=None):\n",
-    "        '''\n",
+    "        \"\"\"\n",
     "        Make sure the xarray dataset has the correct dimensions and variables\n",
     "\n",
     "        Parameters\n",
@@ -328,7 +329,7 @@
     "            List of all required dimension names\n",
     "        req_vars : list of str\n",
     "            List of all required variable  names\n",
-    "        '''\n",
+    "        \"\"\"\n",
     "\n",
     "        if req_dim is not None:\n",
     "            if all([dim not in list(self._xrds.dims) for dim in req_dim]):\n",
@@ -340,8 +341,8 @@
     "    # Notice that 'geoid' has been added to the req_vars list\n",
     "    def to_geoid(\n",
     "        self,\n",
-    "        req_dim=['dtime', 'x', 'y'],\n",
-    "        req_vars={'elevation': ['x', 'y', 'dtime', 'geoid']},\n",
+    "        req_dim=[\"dtime\", \"x\", \"y\"],\n",
+    "        req_vars={\"elevation\": [\"x\", \"y\", \"dtime\", \"geoid\"]},\n",
     "        source=None,\n",
     "    ):\n",
     "        \"\"\"\n",
@@ -361,11 +362,11 @@
     "\n",
     "        # check to make sure you haven't already run this function (and are thus applying the offset twice)\n",
     "        try:\n",
-    "            values = self._xrds.attrs['offset_names']\n",
-    "            assert 'geoid_offset' not in values, \"You've already applied the geoid offset!\"\n",
-    "            values = list([values]) + ['geoid_offset']\n",
+    "            values = self._xrds.attrs[\"offset_names\"]\n",
+    "            assert \"geoid_offset\" not in values, \"You've already applied the geoid offset!\"\n",
+    "            values = list([values]) + [\"geoid_offset\"]\n",
     "        except KeyError:\n",
-    "            values = ['geoid_offset']\n",
+    "            values = [\"geoid_offset\"]\n",
     "\n",
     "        self._validate(self, req_dim, req_vars)\n",
     "\n",
@@ -374,12 +375,12 @@
     "        # them to. If not, you will need to reproject and/or resample them to match the data to which you are applying them.\n",
     "        # That step is not included here to emphasize the accessor aspect of the workflow.\n",
     "        with rasterio.open(source) as src:\n",
-    "            geoid = src['geoid_varname']\n",
+    "            geoid = src[\"geoid_varname\"]\n",
     "\n",
     "        # As noted above, this step will fail or produce unreliable results if your data is not properly gridded\n",
-    "        self._xrds['elevation'] = self._xrds.elevation - geoid\n",
+    "        self._xrds[\"elevation\"] = self._xrds.elevation - geoid\n",
     "\n",
-    "        self._xrds.attrs['offset_names'] = values\n",
+    "        self._xrds.attrs[\"offset_names\"] = values\n",
     "\n",
     "        return self._xrds"
    ]
@@ -401,7 +402,7 @@
    },
    "outputs": [],
    "source": [
-    "ds = ds.geoidxr.to_geoid(source='/Path/to/Custom/source/file.nc')\n",
+    "ds = ds.geoidxr.to_geoid(source=\"/Path/to/Custom/source/file.nc\")\n",
     "ds"
    ]
   }

advanced/apply_ufunc/automatic-vectorizing-numpy.ipynb

@@ -107,8 +107,8 @@
    "source": [
     "%xmode minimal\n",
     "\n",
-    "import xarray as xr\n",
     "import numpy as np\n",
+    "import xarray as xr\n",
     "\n",
     "xr.set_options(display_expand_data=False)\n",
     "\n",

advanced/apply_ufunc/complex-output-numpy.ipynb

@@ -49,8 +49,8 @@
    "source": [
     "%xmode minimal\n",
     "\n",
-    "import xarray as xr\n",
     "import numpy as np\n",
+    "import xarray as xr\n",
     "\n",
     "np.set_printoptions(threshold=10, edgeitems=2)\n",
     "xr.set_options(display_expand_data=False)\n",

advanced/apply_ufunc/example-interp.ipynb

@@ -65,8 +65,8 @@
    "source": [
     "%xmode minimal\n",
     "\n",
-    "import xarray as xr\n",
     "import numpy as np\n",
+    "import xarray as xr\n",
     "\n",
     "# limit the amount of information printed to screen\n",
     "xr.set_options(display_expand_data=False)\n",