Merge pull request #267 from NBISweden/devel

Merge GitHub Pages changes to `main`

.github/workflows/build-and-deploy-website.yml

@@ -0,0 +1,50 @@
+name: Build and deploy site
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - "README.md"
+      - "LICENCE.md"
+      - "env/"
+      - "pages/tools-for-reproducible-research.md"
+      - "tutorials/"
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    container: ghcr.io/nbisweden/workshop-reproducible-research/build-website:specky
+    steps:
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build website with Quarto
+        uses: quarto-dev/quarto-actions/render@v2
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/'
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/build-and-publish-images.yml

@@ -0,0 +1,78 @@
+name: Build and publish Docker images
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "env/*/Dockerfile"
+      - "env/*/environment.yml"
+
+env:
+  REGISTRY: ghcr.io
+  INCLUDE_DIR: "env/"
+  REPOSITORY: ${{ github.repository }}
+
+jobs:
+  changed-directories:
+    name: Get last directory name of changed files
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.changed-files.outputs.all_changed_files }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Get changed files
+        uses: tj-actions/changed-files@v45
+        id: changed-files
+        with:
+          matrix: true
+          dir_names: true
+          path: ${{ env.INCLUDE_DIR }}
+          dir_names_include_files: ${{ env.INCLUDE_DIR }}
+          dir_names_exclude_current_dir: true
+
+  build-and-push-image:
+    name: Build and push Docker images
+    runs-on: ubuntu-latest
+    needs: changed-directories
+    strategy:
+      fail-fast: false
+      matrix:
+        name: ${{ fromJSON(needs.changed-directories.outputs.matrix) }}
+        platform: [linux/amd64]
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Extract metadata for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.REPOSITORY }}/${{ matrix.name }}
+          tags: |
+            type=raw,value=latest,enable=${{ endsWith(github.ref, github.event.repository.default_branch) }}
+            type=ref,event=branch,enable=${{ !endsWith(github.ref, github.event.repository.default_branch) }}
+          flavor: |
+            latest=false
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: ${{ env.INCLUDE_DIR }}/${{ matrix.name }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          platforms: ${{ matrix.platform }}

.github/workflows/setup.yml → .github/workflows/test-conda-environments.yml

@@ -1,20 +1,35 @@
-name: setup
+name: Test Conda environments
 
 on:
   workflow_dispatch:
     branches:
       - main
-      - devel
   pull_request:
     branches:
       - main
+    paths:
+      - 'tutorials/snakemake/snakefile_mrsa.smk'
+      - 'tutorials/snakemake/environment.yml'
+      - 'tutorials/nextflow/environment.yml'
+      - 'tutorials/nextflow/main_mrsa.yml'
+      - 'tutorials/nextflow/samplesheet.csv'
+      - 'tutorials/jupyter/environment.yml'
+      - 'tutorials/jupyter/references.bib'
+      - 'tutorials/jupyter/supplementary_material.ipynb'
+      - 'tutorials/quarto/environment.yml'
+      - 'tutorials/quarto/quarto-tutorial-example.qmd'
+
+concurrency:
+  group: conda-env-test
+  cancel-in-progress: true
 
 jobs:
-  install:
+  test:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [ macos-latest, ubuntu-latest ]
+        os: [macos-latest, ubuntu-latest]
         env: [snakemake, nextflow, jupyter, quarto]
         include:
           - env: snakemake
@@ -24,18 +39,25 @@ jobs:
           - env: jupyter
             cmd: jupyter nbconvert --to HTML tutorials/jupyter/supplementary_material.ipynb
           - env: quarto
-            cmd: mamba install -c conda-forge quarto && mamba install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html
+            cmd: conda install -c conda-forge quarto && conda install -c conda-forge deno && export QUARTO_DENO=$(which deno) && quarto render tutorials/quarto/quarto-tutorial-example.qmd --to html
+        exclude:
+          - os: macos-latest
+            env: snakemake
+          - os: macos-latest
+            env: nextflow
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2.2.0
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Conda setup
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: ${{ matrix.env }}-env
           environment-file: tutorials/${{ matrix.env }}/environment.yml
-          use-mamba: true
           channel-priority: strict
-      - name: Test ${{ matrix.env }}
+
+      - name: Test ${{ matrix.env }} environment
         shell: bash -l {0}
         run: |
           conda list

.github/workflows/docker-run.yml → .github/workflows/test-mrsa-image.yml

@@ -1,26 +1,27 @@
-name: docker
+name: Test MRSA image
 
 on:
   workflow_dispatch:
     branches:
       - main
-      - devel
   pull_request:
+    branches:
+      - main
     paths:
       - 'tutorials/containers/Dockerfile'
       - 'tutorials/containers/environment.yml'
       - 'tutorials/containers/Snakefile'
       - 'tutorials/containers/config.yml'
       - 'tutorials/containers/code/*'
-    branches:
-      - main
 
 jobs:
   docker-build-and-run:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Docker build
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Build and test Docker image
         run: |
           docker build -t my_docker_project -f tutorials/containers/Dockerfile tutorials/containers/
-          docker run --rm my_docker_project
+          docker run --rm my_docker_project

.github/workflows/upload-to-canvas.yml

@@ -0,0 +1,28 @@
+name: Upload landing page to Canvas
+
+on:
+  workflow_dispatch:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+    paths:
+      - 'pages/tools-for-reproducible-research.md'
+      - 'pages/upload-page-to-canvas.sh'
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    container: pandoc/latex
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Upload to Canvas
+        env:
+          API_TOKEN: ${{ secrets.CANVAS_API_TOKEN }}
+        run: |
+          bash pages/upload-page-to-canvas.sh pages/tools-for-reproducible-research.md $API_TOKEN

.gitignore

@@ -28,6 +28,10 @@ snakemake/*tsv
 # Quarto-related files
 .quarto/
 **/*_files
+_freeze/
+docs/
 
 # VScode
 .vscode
+
+/.quarto/

404.md

@@ -0,0 +1,21 @@
+---
+pagetitle: "404: Page not found"
+date: ""
+toc: false
+sidebar: false
+number-sections: false
+format: html
+execute:
+  freeze: false
+---
+
+::: {style="text-align: center;"}
+
+[404]{.fourofour}
+
+# 404: Page not found
+
+It seems like you have stumbled upon a page that doesn't exist.
+Please check your URL again.
+
+:::