Merge branch 'main' into moist_thermal_sw

.github/workflows/build.yml

@@ -35,23 +35,14 @@ jobs:
           . /home/firedrake/firedrake/bin/activate
           python -m pip install -r requirements.txt
           python -m pip install -e .
-      - name: Gusto unit-tests
+          python -m pip install  \
+            pytest-cov pytest-timeout pytest-xdist
+      - name: Gusto tests
         run: |
           . /home/firedrake/firedrake/bin/activate
-          python $(which firedrake-clean)
-          python -m pytest -n 12 -v unit-tests
-      - name: Gusto integration-tests
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python $(which firedrake-clean)
-          python -m pytest -n 12 -v integration-tests
-      - name: Gusto examples
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          python $(which firedrake-clean)
-          python -m pytest -n 12 -v examples
-      - name: Lint
-        if: ${{ always() }}
-        run: |
-          . /home/firedrake/firedrake/bin/activate
-          make lint
+          which firedrake-clean
+          python -m pytest \
+            -n 12 --dist worksteal \
+            --durations=100 \
+            --cov gusto \
+            -v unit-tests integration-tests examples

.github/workflows/docs.yml

@@ -0,0 +1,57 @@
+name: Check docs build cleanly
+
+on:
+  # Run on pushes to master
+  push:
+    branches:
+      - master
+  # And all pull requests
+  pull_request:
+
+concurrency:
+  # Cancels jobs running if new commits are pushed
+  group: >
+    ${{ github.workflow }}-
+    ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_docs:
+    name: Run doc build
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    # The docker container to use.
+    container:
+      image: firedrakeproject/firedrake-docdeps:latest
+      options: --user root
+      volumes:
+        - ${{ github.workspace }}:/home/firedrake/output
+    # Steps represent a sequence of tasks that will be executed as
+    # part of the jobs
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install checkedout Gusto
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python -m pip install -e .
+      - name: Install Read the Docs theme
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python -m pip install sphinx_rtd_theme
+      - name: Check documentation links
+        if: ${{ github.ref == 'refs/heads/master' }}
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          cd docs
+          make linkcheck
+      - name: Build docs
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          cd docs
+          make html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          name: github-pages
+          path: /__w/gusto/gusto/docs/build/html
+          retention-days: 1

.github/workflows/lint.yml

@@ -0,0 +1,40 @@
+name: Run lint
+
+on:
+  # Push to master or PR
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  linter:
+    name: "Run linter"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
+      - name: Install linter
+        run: |
+          pip install flake8 pylint
+      - name: Lint codebase
+        run: |
+          make lint GITHUB_ACTIONS_FORMATTING=1
+  actionlint:
+    name: "Lint Github actions YAML files"
+    # There's a way to add error formatting so GH actions adds messages to code,
+    # but I can't work out the right number of quotes to get it to work
+    # https://github.com/rhysd/actionlint/blob/main/docs/usage.md
+    # #example-error-annotation-on-github-actions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Check workflow files
+        uses: docker://rhysd/actionlint:latest
+        with:
+          args: -color

.github/workflows/website.yml

@@ -0,0 +1,53 @@
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll with GitHub Pages dependencies preinstalled
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./docs
+          destination: ./docs/_site
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: ./docs/_site/
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

Makefile

@@ -1,14 +1,22 @@
+# Adds file annotations to Github Actions (only useful on CI)
+GITHUB_ACTIONS_FORMATTING=0
+ifeq ($(GITHUB_ACTIONS_FORMATTING), 1)
+	FLAKE8_FORMAT=--format='::error file=%(path)s,line=%(row)d,col=%(col)d,title=%(code)s::%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
+else
+	FLAKE8_FORMAT=
+endif
+
 lint:
 	@echo "    Linting gusto codebase"
-	@python3 -m flake8 gusto
+	@python3 -m flake8 $(FLAKE8_FORMAT) gusto
 	@echo "    Linting gusto examples"
-	@python3 -m flake8 examples
+	@python3 -m flake8 $(FLAKE8_FORMAT) examples
 	@echo "    Linting gusto unit-tests"
-	@python3 -m flake8 unit-tests
+	@python3 -m flake8 $(FLAKE8_FORMAT) unit-tests
 	@echo "    Linting gusto integration-tests"
-	@python3 -m flake8 integration-tests
+	@python3 -m flake8 $(FLAKE8_FORMAT) integration-tests
 	@echo "    Linting gusto plotting scripts"
-	@python3 -m flake8 plotting
+	@python3 -m flake8 $(FLAKE8_FORMAT) plotting
 
 test:
 	@echo "    Running all tests"
@@ -24,4 +32,4 @@ integration_test:
 
 example:
 	@echo "    Running all examples"
-	@python3 -m pytest examples $(PYTEST_ARGS)
+	@python3 -m pytest examples $(PYTEST_ARGS)

docs/_includes/navbar.html

@@ -4,7 +4,7 @@
       <ul>
     <li class="logo" style="float:left""><a href="{{ site.url }}/gusto/" style="padding-bottom:0px"><img id="navbarimg" src="{{'assets/images/gusto_navbar.png'}}" style="max-width:160px; max-height:60px; height:auto; width:auto; padding-top:10px" /></a></li>
     <li class="page_item" style="float:right"><a href="https://github.com/firedrakeproject/gusto">Github</a></li>
-    <li class="page_item" style="float:right"><a href="https://firedrakeproject.org/gusto/">Docs</a></li>
+    <li class="page_item" style="float:right"><a href="https://firedrakeproject.org/gusto-docs">Docs</a></li>
     <li class="page_item" style="float:right"><a href="{{ site.url }}/gusto/about_gusto.html">About</a>
       <ul id="dropdown" style="padding-top:20px;">
         <li><a href="{{ site.url }}/gusto/about_gusto.html#download">Download</a></li>