Merge pull request #46 from m2lines/fix/preview-5

Fix preview - attempt 5
m2lines · Apr 5, 2024 · f3a7992 · f3a7992
2 parents 0eab033 + f34cae3
commit f3a7992
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Showing 29 changed files with 20 additions and 102 deletions.
diff --git a/.github/workflows/publish-book.yml b/.github/workflows/publish-book.yml
@@ -1,65 +1,22 @@
+
 name: publish-book
 
-# Trigger the workflow on push to main branch
 on:
+  # Trigger the workflow on push to main branch
   push:
     branches:
       - main
-# This job installs dependencies, builds the book, and deploys the html
+  workflow_dispatch:
+
 jobs:
-  build-and-deploy-book:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.9]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Get PR number
-        run: echo "Your PR is ${PR}"
-        env:
-          PR: ${{ github.event.pull_request.number }}
-      - name: 📦 Cache Conda Packages
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if etc/example-environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-linux-64.lock') }}
-      - name: 🐍 Set up Conda environment
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: false
-          activate-environment: DGM2lines
-          environment-file: conda-linux-64.lock
-      - name: 👀 Check Conda environment
-        shell: bash -l {0}
-        run: |
-          pip install -r requirements.txt
-          conda info
-          conda list
-      - name: 📦 Cache Notebooks
-        uses: actions/cache@v2
-        with:
-          path: src/_build/.jupyter_cache
-          key: notebook_cache-${{hashFiles('_toc.yml', '_config.yml', 'environment.yml') }}
-      - name: 📖 Build the book
-        shell: bash -l {0}
-        run: |
-          cd src
-          mkdir -p _notebook_cache
-          jupyter-book build .
-      - name: 📖 Show logs from the book build
-        shell: bash -l {0}
-        run: |
-          find src/_build/html -name "*.log" -print -exec cat {} \;
-      - name: 🚀 Deploy to GitHub Pages
-        # redudant but keeping for testing purposes
-        if: github.ref == 'refs/heads/main'
-        uses: peaceiris/[email protected]
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: src/_build/html
-          keep_files: false
-          force_orphan: true
+  build:
+    uses: ProjectPythia/cookbook-actions/.github/workflows/build-book.yaml@main
+    with:
+      environment_name: DGM2lines
+      path_to_notebooks: 'book'
+
+  deploy:
+    needs: build
+    uses: ProjectPythia/cookbook-actions/.github/workflows/deploy-book.yaml@main
+    with:
+      publish_dir: "book/_build/html"
diff --git a/.github/workflows/trigger-book-build.yml b/.github/workflows/trigger-book-build.yml
@@ -3,47 +3,11 @@ on:
   pull_request:
 
 jobs:
-  install-dependencies:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: [3.9]
-    steps:
-      - uses: actions/checkout@v2
-      - name: Get PR number
-        run: echo "Your PR is ${PR}"
-        env:
-          PR: ${{ github.event.pull_request.number }}
-      - name: 📦 Cache Conda Packages
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if etc/example-environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-linux-64.lock') }}
-      - name: 🐍 Set up Conda environment
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: false
-          activate-environment: DGM2lines
-          environment-file: conda-linux-64.lock
-      - name: 👀 Check Conda environment
-        shell: bash -l {0}
-        run: |
-          pip install -r requirements.txt
-          conda info
-          conda list
-      - name: 📦 Cache Notebooks
-        uses: actions/cache@v2
-        with:
-          path: _build/.jupyter_cache
-          key: notebook_cache-${{hashFiles('_toc.yml', '_config.yml', 'environment.yml') }}
   build:
     uses: ProjectPythia/cookbook-actions/.github/workflows/build-book.yaml@main
     with:
       environment_name: DGM2lines
       artifact_name: book-zip-${{ github.event.number }}
-      path_to_notebooks: "src"
+      path_to_notebooks: "book"
       build_command: "jupyter-book build --keep-going ."
+      # Other input options are possible, see ProjectPythia/cookbook-actions/.github/workflows/build-book.yaml
diff --git a/.github/workflows/trigger-preview.yml b/.github/workflows/trigger-preview.yml
@@ -7,9 +7,6 @@ on:
       - requested
       - completed
 
-permissions:
-  contents: write
-
 jobs:
   find-pull-request:
     uses: ProjectPythia/cookbook-actions/.github/workflows/find-pull-request.yaml@main
@@ -21,8 +18,8 @@ jobs:
       artifact_name: book-zip-${{ needs.find-pull-request.outputs.number }}
       destination_dir: _preview/${{ needs.find-pull-request.outputs.number }} # deploy to subdirectory labeled with PR number
       is_preview: 'true'
-      publish_dir: "src/_build/html"
-      github_token: ${{ secrets.GITHUB_TOKEN }}
+      publish_dir: "book/_build/html"
+      # cname: foundations.projectpythia.org
 
   preview-comment:
     needs: find-pull-request

diff --git a/.gitignore b/.gitignore
@@ -8,7 +8,7 @@ _build/
 *.npz
 *.pth
 _build/*
-src/_build/*
+book/_build/*
 _notebook_cache/*
 notebooks/Source.gv
 notebooks/*.pkl

diff --git a/src/_config.yml → book/_config.yml b/src/_config.yml → book/_config.yml
diff --git a/src/_toc.yml → book/_toc.yml b/src/_toc.yml → book/_toc.yml
diff --git a/src/assets/Aghulas.gif → book/assets/Aghulas.gif b/src/assets/Aghulas.gif → book/assets/Aghulas.gif
diff --git a/src/assets/Atlantic.gif → book/assets/Atlantic.gif b/src/assets/Atlantic.gif → book/assets/Atlantic.gif
diff --git a/src/assets/Global.gif → book/assets/Global.gif b/src/assets/Global.gif → book/assets/Global.gif
diff --git a/src/assets/Pacific.gif → book/assets/Pacific.gif b/src/assets/Pacific.gif → book/assets/Pacific.gif
diff --git a/src/assets/newlogo.png → book/assets/newlogo.png b/src/assets/newlogo.png → book/assets/newlogo.png
diff --git a/src/intro.md → book/intro.md b/src/intro.md → book/intro.md
diff --git a/src/notebooks/MOM6_basic_plotting.ipynb → book/notebooks/MOM6_basic_plotting.ipynb b/src/notebooks/MOM6_basic_plotting.ipynb → book/notebooks/MOM6_basic_plotting.ipynb
diff --git a/src/notebooks/OM4_SE_animation.ipynb → book/notebooks/OM4_SE_animation.ipynb b/src/notebooks/OM4_SE_animation.ipynb → book/notebooks/OM4_SE_animation.ipynb
diff --git a/src/notebooks/OM4_SST_Bias.ipynb → book/notebooks/OM4_SST_Bias.ipynb b/src/notebooks/OM4_SST_Bias.ipynb → book/notebooks/OM4_SST_Bias.ipynb
diff --git a/src/notebooks/OM4_misc.ipynb → book/notebooks/OM4_misc.ipynb b/src/notebooks/OM4_misc.ipynb → book/notebooks/OM4_misc.ipynb
diff --git a/...s/data/N2_ePBL_data_timemean_1978-2002.nc → ...s/data/N2_ePBL_data_timemean_1978-2002.nc b/...s/data/N2_ePBL_data_timemean_1978-2002.nc → ...s/data/N2_ePBL_data_timemean_1978-2002.nc
diff --git a/src/notebooks/data/ocean_static_rm2.nc → book/notebooks/data/ocean_static_rm2.nc b/src/notebooks/data/ocean_static_rm2.nc → book/notebooks/data/ocean_static_rm2.nc
diff --git a/...s/data/so_ePBL_data_timemean_1978-2002.nc → ...s/data/so_ePBL_data_timemean_1978-2002.nc b/...s/data/so_ePBL_data_timemean_1978-2002.nc → ...s/data/so_ePBL_data_timemean_1978-2002.nc
diff --git a/...ta/thetao_ePBL_data_timemean_1978-2002.nc → ...ta/thetao_ePBL_data_timemean_1978-2002.nc b/...ta/thetao_ePBL_data_timemean_1978-2002.nc → ...ta/thetao_ePBL_data_timemean_1978-2002.nc
diff --git a/...ooks/helpers/collection_of_experiments.py → ...ooks/helpers/collection_of_experiments.py b/...ooks/helpers/collection_of_experiments.py → ...ooks/helpers/collection_of_experiments.py
diff --git a/src/notebooks/helpers/computational_tools.py → .../notebooks/helpers/computational_tools.py b/src/notebooks/helpers/computational_tools.py → .../notebooks/helpers/computational_tools.py
diff --git a/src/notebooks/helpers/experiment.py → book/notebooks/helpers/experiment.py b/src/notebooks/helpers/experiment.py → book/notebooks/helpers/experiment.py
diff --git a/src/notebooks/helpers/netcdf_cache.py → book/notebooks/helpers/netcdf_cache.py b/src/notebooks/helpers/netcdf_cache.py → book/notebooks/helpers/netcdf_cache.py
diff --git a/src/notebooks/helpers/plot_helpers.py → book/notebooks/helpers/plot_helpers.py b/src/notebooks/helpers/plot_helpers.py → book/notebooks/helpers/plot_helpers.py
diff --git a/src/notebooks/pycnocline_depth_mom6.ipynb → book/notebooks/pycnocline_depth_mom6.ipynb b/src/notebooks/pycnocline_depth_mom6.ipynb → book/notebooks/pycnocline_depth_mom6.ipynb
diff --git a/src/notebooks/xarray_intro.ipynb → book/notebooks/xarray_intro.ipynb b/src/notebooks/xarray_intro.ipynb → book/notebooks/xarray_intro.ipynb
diff --git a/src/notebooks/xgcm_intro.ipynb → book/notebooks/xgcm_intro.ipynb b/src/notebooks/xgcm_intro.ipynb → book/notebooks/xgcm_intro.ipynb
diff --git a/src/references.bib → book/references.bib b/src/references.bib → book/references.bib