Merge branch 'xarray-contrib:main' into main

Author: eni-awowale

.binder/environment.yml

@@ -3,40 +3,41 @@ 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 >=1.6.3,<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 >=2025.7.0,<2026
+  - zarr >=3.0.10,<4
+  - flox >=0.10.4,<0.11
   - numbagg >=0.9.0,<0.10
+  - rich >=14.0.0,<15
   - python >=3.10

.devcontainer/Dockerfile

@@ -0,0 +1,13 @@
+FROM mcr.microsoft.com/devcontainers/base:noble
+
+ARG PIXI_VERSION=v0.49.0
+
+RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix-dev/pixi/releases/download/${PIXI_VERSION}/pixi-$(uname -m)-unknown-linux-musl" \
+    && chmod +x /usr/local/bin/pixi \
+    && pixi info
+
+# set some user and workdir settings to work nicely with vscode
+USER vscode
+WORKDIR /home/vscode
+
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.devcontainer/devcontainer.json

@@ -1,17 +1,42 @@
+// https://pixi.sh/latest/integration/editor/vscode/#devcontainer-extension
 {
-  "image": "quay.io/pangeo/pangeo-notebook:latest",
-  "postCreateCommand": {
-    "vscode": "mkdir ${containerWorkspaceFolder}/.vscode && cp ${containerWorkspaceFolder}/.devcontainer/tasks.json ${containerWorkspaceFolder}/.vscode/tasks.json"
-  },
-  "hostRequirements": {
-    "cpus": 2
+  "name": "xarray-tutorial",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
   },
   "customizations": {
-    "codespaces": {
-      "openFiles": ["README.md"]
-    },
     "vscode": {
-      "extensions": ["ms-toolsai.jupyter", "ms-python.python"]
+      "settings": {},
+      "extensions": [
+        "ms-toolsai.jupyter",
+        "ms-python.python",
+        "executablebookproject.myst-highlight"
+      ]
+    }
+  },
+  "features": {
+    // ensure GitHub Codespace 'Open with JupyterLab' works
+    // TODO: figure out why it doesn't work w/ jupyterlab in the pixi environment
+    "ghcr.io/devcontainers/features/python:1": {
+      "version": "3.12",
+      "installTools": false,
+      // NOTE: not working, so install with pip in postCreateCommand
+      // "toolsToInstall":"jupyterlab_myst,pixi-kernel",
+      "installJupyterlab": true
     }
+  },
+  "mounts": [
+    "source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"
+  ],
+  // These should execute in order below
+  "onCreateCommand": {
+    "configure_jupyterlab": "pip install jupyterlab_myst pixi-kernel"
+  },
+  "postCreateCommand": {
+    "set_pixi_permissions": "sudo chown vscode .pixi"
+  },
+  "postStartCommand": {
+    "configure_jupyterlab": "pixi install"
   }
 }

.devcontainer/scipy2025/Dockerfile

@@ -0,0 +1,13 @@
+FROM mcr.microsoft.com/devcontainers/base:noble
+
+ARG PIXI_VERSION=v0.49.0
+
+RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix-dev/pixi/releases/download/${PIXI_VERSION}/pixi-$(uname -m)-unknown-linux-musl" \
+    && chmod +x /usr/local/bin/pixi \
+    && pixi info
+
+# set some user and workdir settings to work nicely with vscode
+USER vscode
+WORKDIR /home/vscode
+
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.devcontainer/scipy2025/devcontainer.json

@@ -0,0 +1,42 @@
+// https://pixi.sh/latest/integration/editor/vscode/#devcontainer-extension
+{
+  "name": "scipy2025-xarray-tutorial",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": "../../"
+  },
+  "customizations": {
+    "vscode": {
+      "settings": {},
+      "extensions": [
+        "ms-toolsai.jupyter",
+        "ms-python.python",
+        "executablebookproject.myst-highlight"
+      ]
+    }
+  },
+  "features": {
+    // ensure GitHub Codespace 'Open with JupyterLab' works
+    // TODO: figure out why it doesn't work w/ jupyterlab in the pixi environment
+    "ghcr.io/devcontainers/features/python:1": {
+      "version": "3.12",
+      "installTools": false,
+      // NOTE: not working, so install with pip in postCreateCommand
+      // "toolsToInstall":"jupyterlab_myst,pixi-kernel",
+      "installJupyterlab": true
+    }
+  },
+  "mounts": [
+    "source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"
+  ],
+  // These should execute in order below
+  "onCreateCommand": {
+    "configure_jupyterlab": "pip install jupyterlab_myst pixi-kernel"
+  },
+  "postCreateCommand": {
+    "set_pixi_permissions": "sudo chown vscode .pixi"
+  },
+  "postStartCommand": {
+    "configure_jupyterlab": "pixi install"
+  }
+}

.devcontainer/tasks.json

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

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

@@ -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/[email protected]
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       - name: Build JupyterBook
         run: |

.github/workflows/main.yaml

@@ -21,11 +21,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - uses: prefix-dev/[email protected]
-        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/nocache.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/[email protected]
-        with:
-          manifest-path: pyproject.toml
-          cache: true
-          activate-environment: true
+      - uses: ./.github/actions/setup-pixi
 
       - name: Build JupyterBook
         if: github.event.action != 'closed'