Merge pull request #13 from scientificcomputing/dokken/update-workflows

Try updating example paper workflows

Author: jorgensd

.github/workflows/build_docs.yml

@@ -1,29 +1,16 @@
-name: Github Pages
+name: Build documentation
 
 on:
   push:
     branches:
       - "**"
-
-  # 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 one concurrent deployment
-concurrency:
-  group: "pages"
-  cancel-in-progress: true
+  workflow_call:
 
 jobs:
   build:
     runs-on: ubuntu-22.04
     container:
-      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2024-02-19
 
     env:
       # Directory that will be published on github pages
@@ -38,10 +25,9 @@ jobs:
       - name: Build docs
         run: jupyter book build -W .
 
-
       - name: Cache
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/pip
@@ -57,28 +43,7 @@ jobs:
         run: jupyter book build .
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           path: ${{ env.PUBLISH_DIR }}
-
-  # Single deploy job since we're just deploying
-  deploy:
-    if: github.ref == 'refs/heads/main'
-    needs: build
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Setup Pages
-        uses: actions/configure-pages@v3
-
-
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+          name: documentation

.github/workflows/deploy_pages.yml

@@ -0,0 +1,49 @@
+name: Deploy pages
+on:
+  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 one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    uses: ./.github/workflows/build_docs.yml
+
+  build:
+    runs-on: ubuntu-22.04
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Download docs artifact
+        # docs artifact is uploaded by build-docs job
+        uses: actions/download-artifact@v4
+        with:
+          name: documentation
+          path: "./public"
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "./public"
+
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/docker-image.yml

@@ -6,9 +6,9 @@
 name: Create and publish a Docker image
 
 on:
+  pull_request:
+    branches: ["main"]
   push:
-    branches:
-      - "!*"
     tags:
       - "v*"
 
@@ -25,29 +25,41 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v2
+        uses: docker/setup-qemu-action@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
+        uses: docker/setup-buildx-action@v3
 
       - name: Log in to the Container registry
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v3
+      - name: Build local docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: false
+          load: true
+          platforms: linux/amd64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          file: docker/Dockerfile
+
+      - name: Build and push Docker image (on tagged version)
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true

.github/workflows/reproduce_results.yml

@@ -6,24 +6,24 @@ on:
     branches: ["main"]
   pull_request:
     branches: ["main"]
-
+  schedule:
+    - cron: "30 9 * * 1"
     # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
   workflow_call:
 
-
 jobs:
   run:
     runs-on: ubuntu-22.04
     container:
-      image: ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
+      image: ghcr.io/scientificcomputing/fenics-gmsh:2024-02-19
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Cache
         id: cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ~/.cache/pip
@@ -48,7 +48,7 @@ jobs:
 
       - name: Upload artifact
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           path: |
             ./data/mesh

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/scientificcomputing/fenics-gmsh:2023-08-16
+FROM ghcr.io/scientificcomputing/fenics-gmsh:2024-02-19
 
 ARG REPO_BRANCH="main"
 

pyproject.toml

@@ -4,9 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "my-fenics-paper"
-version = "0.3.0"
+version = "0.4.0"
 dependencies = [
-    "h5py==3.9.0",                # Pin to same version that is allready installed in the docker image
+    "h5py==3.10.0",               # Same as in docker image to avoid compilation issues with HDF5
     "cardiac-geometries>=0.11.0",
     "ldrb",
     "requests",

requirements-docs.txt

@@ -22,7 +22,7 @@ babel==2.13.1
 beautifulsoup4==4.12.2
     # via pydata-sphinx-theme
 cardiac-geometries==0.11.0
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 certifi==2023.7.22
     # via requests
 charset-normalizer==3.3.2
@@ -56,10 +56,10 @@ fastjsonschema==2.18.1
     # via nbformat
 greenlet==3.0.1
     # via sqlalchemy
-h5py==3.9.0
+h5py==3.10.0
     # via
     #   ldrb
-    #   my-paper (pyproject.toml)
+    #   my-fenics-paper (pyproject.toml)
 idna==3.4
     # via requests
 imagesize==1.4.1
@@ -88,7 +88,7 @@ jsonschema==4.19.2
 jsonschema-specifications==2023.7.1
     # via jsonschema
 jupyter-book==0.15.1
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 jupyter-cache==0.6.1
     # via myst-nb
 jupyter-client==8.6.0
@@ -102,11 +102,11 @@ jupyter-core==5.5.0
     #   nbclient
     #   nbformat
 jupytext==1.15.2
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 latexcodec==2.0.1
     # via pybtex
 ldrb==2023.4.0
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 linkify-it-py==2.0.2
     # via jupyter-book
 llvmlite==0.40.1
@@ -211,7 +211,7 @@ referencing==0.30.2
     #   jsonschema-specifications
 requests==2.31.0
     # via
-    #   my-paper (pyproject.toml)
+    #   my-fenics-paper (pyproject.toml)
     #   sphinx
 rich==13.6.0
     # via
@@ -277,7 +277,7 @@ sphinxcontrib-applehelp==1.0.7
 sphinxcontrib-bibtex==2.5.0
     # via
     #   jupyter-book
-    #   my-paper (pyproject.toml)
+    #   my-fenics-paper (pyproject.toml)
 sphinxcontrib-devhelp==1.0.5
     # via sphinx
 sphinxcontrib-htmlhelp==2.0.4
@@ -301,7 +301,7 @@ tornado==6.3.3
     #   ipykernel
     #   jupyter-client
 tqdm==4.66.1
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 traitlets==5.13.0
     # via
     #   comm

requirements.txt

@@ -5,7 +5,7 @@
 #    pip-compile --output-file=requirements.txt pyproject.toml
 #
 cardiac-geometries==0.11.0
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 certifi==2023.7.22
     # via requests
 charset-normalizer==3.3.2
@@ -14,14 +14,14 @@ click==8.1.3
     # via rich-click
 commonmark==0.9.1
     # via rich
-h5py==3.9.0
+h5py==3.10.0
     # via
     #   ldrb
-    #   my-paper (pyproject.toml)
+    #   my-fenics-paper (pyproject.toml)
 idna==3.4
     # via requests
 ldrb==2023.4.0
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 llvmlite==0.40.1
     # via numba
 meshio==5.3.4
@@ -38,14 +38,14 @@ numpy==1.21.6
 pygments==2.13.0
     # via rich
 requests==2.31.0
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 rich==12.6.0
     # via
     #   meshio
     #   rich-click
 rich-click==1.5.2
     # via cardiac-geometries
 tqdm==4.66.1
-    # via my-paper (pyproject.toml)
+    # via my-fenics-paper (pyproject.toml)
 urllib3==2.0.7
     # via requests