Merge pull request #1030 from MPAS-Dev/develop

Merge develop to main for 1.12.0 release

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    assignees:
+      - "xylar"
+      - "altheaden"
+    reviewers:
+      - "xylar"
+      - "altheaden"
+

.github/pull_request_template.md

@@ -0,0 +1,21 @@
+<!--
+Thank you for your pull request.
+Please add a description of what is accomplished in the PR here at the top:
+-->
+
+<!--
+Below are a few things we ask you or your reviewers to kindly check. 
+***Remove checks that are not relevant by deleting the line(s) below.***
+-->
+Checklist
+* [ ] User's Guide has been updated
+* [ ] If this PR adds a new analysis task, it has also been added to the user's guide
+* [ ] Developer's Guide has been updated
+* [ ] API documentation in the Developer's Guide (`api.rst`) has any new or modified class, method and/or functions listed
+* [ ] Documentation has been [built locally](https://mpas-dev.github.io/MPAS-Analysis/latest/users_guide/quick_start.html#generating-documentation) and changes look as expected
+* [ ] `Testing` comment in the PR documents testing used to verify the changes
+
+<!--
+Please note any issues this fixes using closing keywords: https://help.github.com/articles/closing-issues-using-keywords
+-->
+

.github/workflows/build_workflow.yml

@@ -0,0 +1,92 @@
+name: CI/CD Build Workflow
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+  pull_request:
+    branches:
+      - main
+      - develop
+
+  workflow_dispatch:
+
+env:
+  CANCEL_OTHERS: false
+  PATHS_IGNORE: '["**/README.md", "**/docs/**"]'
+
+jobs:
+  build:
+    name: test mpas_analysis - python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          cancel_others: ${{ env.CANCEL_OTHERS }}
+          paths_ignore: ${{ env.PATHS_IGNORE }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        uses: actions/checkout@v4
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Cache Conda
+        uses: actions/cache@v4
+        env:
+          # Increase this value to reset cache if conda-dev-spec.template has not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-${{ matrix.python-version }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('dev-spec.txt,setup.py') }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Set up Conda Environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: "mpas_analysis_ci"
+          miniforge-version: latest
+          channels: conda-forge
+          channel-priority: strict
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Install mpas_analysis
+        run: |
+          conda create -n mpas_analysis_dev --file dev-spec.txt \
+              python=${{ matrix.python-version }}
+          conda activate mpas_analysis_dev
+          python -m pip install --no-deps --no-build-isolation -vv -e .
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Run Tests
+        env:
+           CHECK_IMAGES: False
+        run: |
+          set -e
+          conda activate mpas_analysis_dev
+          pip check
+          pytest --pyargs mpas_analysis
+          mpas_analysis --help
+          download_analysis_data --help
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Build Sphinx Docs
+        run: |
+          conda activate mpas_analysis_dev
+          # sphinx-multiversion expects at least a "main" branch
+          git branch main || echo "branch main already exists."
+          cd docs
+          sphinx-multiversion . _build/html
+

.github/workflows/docs_workflow.yml

@@ -0,0 +1,96 @@
+name: CI/CD Release Workflow
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+
+  release:
+    types: [published]
+
+jobs:
+  publish-docs:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+
+      - name: Cache Conda
+        uses: actions/cache@v4
+        env:
+          # Increase this value to reset cache if deploy/conda-dev-spec.template has not changed in the workflow
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('dev-spec.txt') }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Set up Conda Environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: "mpas_analysis_ci"
+          miniforge-version: latest
+          channels: conda-forge
+          channel-priority: strict
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+
+      - if: ${{ steps.skip_check.outputs.should_skip != 'true' }}
+        name: Install mpas_analysis
+        run: |
+          git config --global url."https://github.com/".insteadOf "git@github.com:"
+          conda create -n mpas_analysis_dev --file dev-spec.txt \
+            python=${{ matrix.python-version }}
+          conda activate mpas_analysis_dev
+          python -m pip install -vv --no-deps --no-build-isolation -e .
+
+      - name: Build Sphinx Docs
+        run: |
+          set -e
+          conda activate mpas_analysis_dev
+          pip check
+          mpas_analysis sync diags --help
+          cd docs
+          sphinx-multiversion . _build/html
+      - name: Copy Docs and Commit
+        run: |
+          set -e
+          conda activate mpas_analysis_dev
+          pip check
+          mpas_analysis sync diags --help
+          cd docs
+          # gh-pages branch must already exist
+          git clone https://github.com/MPAS-Dev/MPAS-Analysis.git --branch gh-pages --single-branch gh-pages
+          # Make sure we're in the gh-pages directory.
+          cd gh-pages
+          # Create `.nojekyll` (if it doesn't already exist) for proper GH Pages configuration.
+          touch .nojekyll
+          # Add `index.html` to point to the `develop` branch automatically.
+          printf '<meta http-equiv="refresh" content="0; url=./develop/index.html" />' > index.html
+          # Only replace docs in a directory with the destination branch name with latest changes. Docs for
+          # releases should be untouched.
+          rm -rf ${{ github.head_ref || github.ref_name }}
+          # don't clobber existing release versions (in case we retroactively fixed them)
+          cp -r -n ../_build/html/* .
+          # Configure git using GitHub Actions credentials.
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          # The second command will fail if no changes were present, so we ignore it
+          git add .
+          git commit -m "Update documentation" -a || true
+      - name: Push Changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: docs/gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          force: true
+

README.md

@@ -1,5 +1,4 @@
 # MPAS-Analysis
-[![Build Status](https://dev.azure.com/MPAS-Dev/MPAS-Analysis%20testing/_apis/build/status/MPAS-Dev.MPAS-Analysis?branchName=develop)](https://dev.azure.com/MPAS-Dev/MPAS-Analysis%20testing/_build/latest?definitionId=2&branchName=develop)
 
 Analysis for simulations produced with Model for Prediction Across Scales
 (MPAS) components and the Energy Exascale Earth System Model (E3SM), which
@@ -28,7 +27,7 @@ used those components.
 
 ## Documentation
 
-[https://mpas-dev.github.io/MPAS-Analysis/latest/](https://mpas-dev.github.io/MPAS-Analysis/latest/)
+[https://mpas-dev.github.io/MPAS-Analysis/develop/](https://mpas-dev.github.io/MPAS-Analysis/develop/)
 
 ## Installation for users
 
@@ -57,7 +56,7 @@ conda config --add channels conda-forge
 conda config --set channel_priority strict
 conda create -y -n mpas_dev --file dev-spec.txt
 conda activate mpas_dev
-python -m pip install -e .
+python -m pip install --no-deps --no-build-isolation -e .
 ```
 
 If you are developing another conda package at the same time (this is common
@@ -69,9 +68,9 @@ conda create -y -n mpas_dev --file tools/MPAS-Tools/conda_package/dev-spec.txt \
     --file analysis/MPAS-Analysis/dev-spec.txt
 conda activate mpas_dev
 cd tools/MPAS-Tools/conda_package
-python -m pip install -e .
+python -m pip install --no-deps --no-build-isolation -e .
 cd ../../../analysis/MPAS-Analysis
-python -m pip install -e .
+python -m pip install --no-deps --no-build-isolation -e .
 ```
 Obviously, the paths to the repos may be different in your local clones.  With
 the `mpas_dev` environment as defined above, you can make changes to both
@@ -290,7 +289,7 @@ to be generated and is set up properly.
 
 ## Generating Documentation
 
-Create a development environment as described above in "Installation for 
+Create a development environment as described above in "Installation for
 developers".  Then run:
 To generate the `sphinx` documentation, run:
 ```
@@ -301,4 +300,4 @@ make html
 The results can be viewed in your web browser by opening:
 ```
 _build/html/index.html
-```
+```