Merge branch 'main' into engine-flow

.devcontainer/Dockerfile

@@ -1 +1 @@
-FROM pangeo/base-image:2024.06.02
+FROM pangeo/base-image:2024.06.24

.github/dependabot.yml

@@ -1,3 +1,4 @@
+# Regularly update Docker tags and Actions steps
 version: 2
 updates:
   - package-ecosystem: "docker"

.github/workflows/main.yaml

@@ -1,10 +1,10 @@
-name: CI
+name: Deploy Website to GitHub Pages
 
 on:
   push:
     branches: main
-  pull_request:
-    branches: main
+    paths-ignore:
+      - ".devcontainer/**"
 
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
@@ -18,19 +18,19 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build-and-deploy:
+  build:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup JupyterBook Cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: _build
           # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
-          key: jupyterbook-20230707
+          key: jupyterbook-20240517
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1
@@ -50,19 +50,31 @@ jobs:
         run: |
           if (test -a _build/html/reports/*log); then cat _build/html/reports/*log ; fi
 
-      - name: Save Build
+      - name: Save Build Folder
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: build
           path: _build/
 
-      - name: Publish to GitHub Pages
-        if: github.ref == 'refs/heads/main'
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Upload Pages Artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: _build/html
-          publish_branch: gh-pages
-          cname: tutorial.xarray.dev
-          enable_jekyll: false
+          path: _build/html
+
+  # Publish Website to GitHub Pages if built successfully
+  deploy:
+    needs: build
+    if: github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/pull_request.yaml

@@ -0,0 +1,55 @@
+name: Pull Request Build
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
+    paths-ignore:
+      - ".devcontainer/**"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  preview:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Checkout repository
+        if: github.event.action != 'closed'
+        uses: actions/checkout@v4
+
+      - name: Setup JupyterBook Cache
+        if: github.event.action != 'closed'
+        uses: actions/cache@v4
+        with:
+          path: _build
+          # NOTE: change key to "jupyterbook-DATE" to force rebuilding cache
+          key: jupyterbook-20240517
+
+      - name: Install Conda environment with Micromamba
+        if: github.event.action != 'closed'
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: conda/conda-lock.yml
+          environment-name: xarray-tutorial
+          cache-environment: true
+
+      - name: Build JupyterBook
+        if: github.event.action != 'closed'
+        run: |
+          jupyter-book build ./ --warningiserror --keep-going
+
+      - name: Dump Build Logs
+        if: github.event.action != 'closed'
+        run: |
+          if (test -a _build/html/reports/*log); then cat _build/html/reports/*log ; fi
+
+      - name: Upload artifact
+        if: github.event.action != 'closed'
+        uses: actions/upload-artifact@v4
+        with:
+          name: html
+          path: _build/html

.github/workflows/qaqc.yaml

@@ -4,6 +4,8 @@ on:
   pull_request:
     branches:
       - main
+    paths-ignore:
+      - ".devcontainer/**"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -17,7 +19,7 @@ jobs:
         shell: bash -el {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/setup-micromamba@v1

.github/workflows/surge_preview.yml

@@ -0,0 +1,42 @@
+name: Pull Request Preview
+
+on:
+  workflow_run:
+    workflows: ["Pull Request Build"]
+    types:
+      - completed
+
+permissions:
+  pull-requests: write # allow surge-preview to create/update PR comments
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.workflow_run.id }}
+  cancel-in-progress: true
+
+jobs:
+  # NOTE: match job name in pull_request.yaml
+  preview:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success' }}
+
+    steps:
+      # Ensure folder exists for PR 'closed' case
+      - run: mkdir html
+
+      # Download built HTML from PR Build workflow
+      - uses: actions/download-artifact@v4
+        continue-on-error: true
+        with:
+          github-token: ${{ github.token }}
+          run-id: ${{ github.event.workflow_run.id }}
+
+      - name: Manage Surge.sh Deployment
+        id: preview_step
+        uses: afc163/surge-preview@v1
+        with:
+          surge_token: ${{ secrets.SURGE_TOKEN }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          build: echo 'Uploading html/ folder contents to Surge.sh...'
+          dist: html # NOTE: match upload_artifact name in pull_request.yaml
+          failOnError: true
+          teardown: true

.prettierignore

@@ -1 +1 @@
-conda/**
+conda/

advanced/apply_ufunc/automatic-vectorizing-numpy.ipynb

@@ -63,18 +63,17 @@
     "    out[index, :] = np.interp(..., array[index, :], ...)\n",
     "```\n",
     "\n",
-    "\n",
-    "```{exercise}\n",
-    ":label: coreloopdims\n",
-    "\n",
+    "::::{admonition} Exercise\n",
+    ":class: tip\n",
     "Consider the example problem of interpolating a 2D array with dimensions `space` and `time` along the `time` dimension.\n",
     "Which dimension is the core dimension, and which is the \"loop dimension\"?\n",
-    "```\n",
-    "```{solution} coreloopdims\n",
+    "\n",
+    ":::{admonition} Solution\n",
     ":class: dropdown\n",
     "\n",
     "`time` is the core dimension, and `space` is the loop dimension.\n",
-    "```\n",
+    ":::\n",
+    "::::\n",
     "\n",
     "## Vectorization\n",
     "\n",

advanced/apply_ufunc/complex-output-numpy.ipynb

@@ -138,19 +138,20 @@
     "tags": []
    },
    "source": [
-    "```{exercise}\n",
-    ":label: newdim\n",
+    "::::{admonition} Exercise\n",
+    ":class: tip\n",
     "\n",
     "Apply the following function using `apply_ufunc`. It adds a new dimension to the input array, let's call it `newdim`. Specify the new dimension using `output_core_dims`. Do you need any `input_core_dims`?\n",
     "\n",
     "```python\n",
     "def add_new_dim(array):\n",
     "    return np.expand_dims(array, axis=-1)\n",
     "```\n",
-    "````{solution} newdim\n",
+    "\n",
+    ":::{admonition} Solution\n",
     ":class: dropdown\n",
     "\n",
-    "``` python\n",
+    "```python\n",
     "def add_new_dim(array):\n",
     "    return np.expand_dims(array, axis=-1)\n",
     "\n",
@@ -161,7 +162,8 @@
     "    output_core_dims=[[\"newdim\"]],\n",
     ")\n",
     "```\n",
-    "````"
+    ":::\n",
+    "::::"
    ]
   },
   {
@@ -327,8 +329,8 @@
     "tags": []
    },
    "source": [
-    "````{exercise}\n",
-    ":label: generalize\n",
+    "::::{admonition} Exercise\n",
+    ":class: tip\n",
     "\n",
     "We presented the concept of \"core dimensions\" as the \"smallest unit of data the function could handle.\" Do you understand how the above use of `apply_ufunc` generalizes to an array with more than one dimension? \n",
     "\n",
@@ -337,9 +339,8 @@
     "air3d = xr.tutorial.load_dataset(\"air_temperature\").air)\n",
     "``` \n",
     "Your goal is to have a minimum and maximum value of temperature across all latitudes for a given time and longitude.\n",
-    "````\n",
     "\n",
-    "````{solution} generalize\n",
+    ":::{admonition} Solution\n",
     ":class: dropdown\n",
     "\n",
     "We want to use `minmax` to compute the minimum and maximum along the \"lat\" dimension always, regardless of how many dimensions are on the input. So we specify `input_core_dims=[[\"lat\"]]`. The output does not contain the \"lat\" dimension, but we expect two returned variables. So we pass an empty list `[]` for each returned array, so `output_core_dims=[[], []]` just as before.\n",
@@ -352,8 +353,8 @@
     "    input_core_dims=[[\"lat\"]],\n",
     "    output_core_dims=[[],[]],\n",
     ")\n",
-    "```\n",
-    "````"
+    ":::\n",
+    "::::"
    ]
   }
  ],

advanced/apply_ufunc/core-dimensions.ipynb

@@ -335,13 +335,12 @@
     "tags": []
    },
    "source": [
-    "```{exercise}\n",
-    ":label: trapezoid\n",
+    "::::{admonition} Exercise\n",
+    ":class: tip\n",
     "\n",
     "Use `apply_ufunc` to apply `scipy.integrate.trapezoid` along the `time` axis.\n",
-    "```\n",
     "\n",
-    "````{solution} trapezoid\n",
+    ":::{admonition} Solution\n",
     ":class: dropdown\n",
     "\n",
     "```python\n",
@@ -350,7 +349,8 @@
     "\n",
     "xr.apply_ufunc(scipy.integrate.trapezoid, ds, input_core_dims=[[\"time\"]], kwargs={\"axis\": -1})\n",
     "```\n",
-    "````"
+    ":::\n",
+    "::::"
    ]
   }
  ],