Upgrade Environment, Actions Maintenance (#320)

* composite pixi action

* pixi tasks for cache management

* fix dropdown note formatting

* update binder env

* fix intersphinx config, use intersphinx to fix broken links in comp patterns

* fix more links

* reset cache to update intersphinx

* fix more links

Author: scottyhq

.binder/environment.yml

@@ -3,40 +3,40 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - jupyter-book >=1.0.3,<2
-  - pre-commit >=4.1.0,<5
+  - jupyter-book >=1.0.4.post1,<2
+  - pre-commit >=4.2.0,<5
   - dask-labextension >=7.0.0,<8
-  - jupyterlab >=4.3.5,<5
+  - jupyterlab >=4.4.4,<5
   - jupyter_bokeh >=4.0.5,<5
   - jupyterlab-myst >=2.4.2,<3
   - jupyter-resource-usage >=1.1.1,<2
   - cartopy >=0.24.0,<0.25
-  - cf_xarray >=0.10.0,<0.11
-  - dask >=2025.2.0,<2026
-  - datashader >=0.17.0,<0.18
-  - distributed >=2025.2.0,<2026
-  - gcsfs >=2025.2.0,<2026
+  - cf_xarray >=0.10.6,<0.11
+  - dask >=2025.5.1,<2026
+  - datashader >=0.18.1,<0.19
+  - distributed >=2025.5.1,<2026
+  - gcsfs >=2025.5.1,<2026
   - geoviews-core >=1.14.0,<2
   - gsw >=3.6.19,<4
-  - hvplot >=0.11.2,<0.12
-  - h5netcdf >=1.5.0,<2
+  - hvplot >=0.11.3,<0.12
+  - h5netcdf >=1.6.2,<2
   - ipykernel >=6.29.5,<7
-  - matplotlib-base >=3.10.0,<4
+  - matplotlib-base >=3.10.3,<4
   - netcdf4 >=1.7.2,<2
-  - numpy >=2.1.3,<3
-  - pint-xarray >=0.4,<0.5
-  - pydap >=3.5.3,<4
-  - python-graphviz >=0.20.3,<0.21
+  - numpy >=2.2.6,<3
+  - pint-xarray >=0.5.0,<0.6
+  - pydap >=3.5.5,<4
+  - python-graphviz >=0.21,<0.22
   - pooch >=1.8.2,<2
-  - rioxarray >=0.18.2,<0.19
-  - scipy >=1.15.2,<2
-  - sphinx-codeautolink >=0.17.0,<0.18
+  - rioxarray >=0.19.0,<0.20
+  - scipy >=1.16.0,<2
+  - sphinx-codeautolink >=0.17.4,<0.18
   - sphinxcontrib-mermaid >=1.0.0,<2
-  - sphinx-notfound-page >=1.0.4,<2
+  - sphinx-notfound-page >=1.1.0,<2
   - sphinxext-rediraffe >=0.2.7,<0.3
-  - s3fs >=2025.2.0,<2026
-  - xarray >=2025.1.2,<2026
-  - zarr >=3.0.3,<4
-  - flox >=0.10.0,<0.11
+  - s3fs >=2025.5.1,<2026
+  - xarray >=2025.6.1,<2026
+  - zarr >=3.0.8,<4
+  - flox >=0.10.4,<0.11
   - numbagg >=0.9.0,<0.10
   - python >=3.10

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

@@ -0,0 +1,11 @@
+name: "Setup Pixi"
+description: "Create Python environment for GitHub Action Job"
+
+runs:
+  using: "composite"
+  steps:
+    - uses: prefix-dev/setup-pixi@v0.8.10
+      with:
+        manifest-path: pyproject.toml
+        cache: true
+        activate-environment: true

.github/workflows/main.yaml

@@ -30,13 +30,9 @@ jobs:
         with:
           path: _build
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
-          key: jupyterbook-20250221
+          key: jupyterbook-20250701
 
-      - uses: prefix-dev/setup-pixi@v0.8.2
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       - name: Build JupyterBook
         run: |

.github/workflows/nocache.yaml

@@ -21,11 +21,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - uses: prefix-dev/setup-pixi@v0.8.2
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       # https://github.com/xarray-contrib/xarray-tutorial/issues/311
       - name: Configure graphviz

.github/workflows/pull_request.yaml

@@ -24,13 +24,9 @@ jobs:
         with:
           path: _build
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
-          key: jupyterbook-20250221
+          key: jupyterbook-20250701
 
-      - uses: prefix-dev/setup-pixi@v0.8.2
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       - name: Build JupyterBook
         if: github.event.action != 'closed'

.github/workflows/qaqc.yaml

@@ -19,11 +19,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: prefix-dev/setup-pixi@v0.8.2
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       # NOTE: this isn't a comprehensive spellcheck, just common typos
       - name: Spellcheck

.gitignore

@@ -9,6 +9,7 @@ _build/
 *.tiff
 *.tif
 dask-worker-space/
+.jupyter_cache
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

_config.yml

@@ -91,23 +91,23 @@ sphinx:
 
     intersphinx_mapping:
       xarray:
-        - https://docs.xarray.dev/en/latest/
+        - https://docs.xarray.dev/en/stable
         - null
       numpy:
         - https://numpy.org/doc/stable
         - null
+      pandas:
+        - https://pandas.pydata.org/docs
+        - null
       scipy:
         - https://docs.scipy.org/doc/scipy
         - null
-      matplotlib:
-        - https://matplotlib.org/stable/
+      python:
+        - https://docs.python.org/3
         - null
       dask:
-        - https://docs.dask.org/en/latest
+        - https://docs.dask.org/en/stable
         - null
-      python:
-        - https://docs.python.org/3/
-        - null
-      pandas:
-        - https://pandas.pydata.org/pandas-docs/stable
+      matplotlib:
+        - https://matplotlib.org/stable
         - null

fundamentals/03.3_windowed.ipynb

@@ -151,7 +151,7 @@
    "source": [
     "### Custom reductions\n",
     "\n",
-    "While common reductions are implemented by default, sometimes it is useful to apply our own windowed operations. For these uses, Xarray provides the `construct` methods for [DataArray.rolling](https://docs.xarray.dev/en/stable/generated/xarray.core.rolling.DataArrayRolling.construct.html) and [Dataset.rolling](https://docs.xarray.dev/en/stable/generated/xarray.core.rolling.DatasetRolling.construct.html).\n",
+    "While common reductions are implemented by default, sometimes it is useful to apply our own windowed operations. For these uses, Xarray provides the `construct` methods for [DataArray.rolling](https://docs.xarray.dev/en/stable/generated/xarray.computation.rolling.DataArrayRolling.construct.html#xarray.computation.rolling.DataArrayRolling.construct) and [Dataset.rolling](https://docs.xarray.dev/en/stable/generated/xarray.computation.rolling.DatasetRolling.construct.html#xarray.computation.rolling.DatasetRolling.construct).\n",
     "\n",
     "For rolling over a dimension `time` with a window size `N`, `construct` adds a new dimension (with user-provided name) of size `N`. \n",
     "\n",