Update versioning strategy and doc

.github/workflows/ci.yml

@@ -1,12 +1,9 @@
 name: CI
 
 on:
-  schedule:
-    - cron: '0 10 * * 0'  # every Sunday at 10am
   push:
     branches:
       - main
-      - develop
     tags:
       - '*.*.*'
   pull_request:
@@ -19,39 +16,10 @@ env:
   default_branch: main
 
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-    - name: Lint Dockerfiles
-      uses: docker://hadolint/hadolint:latest
-      with:
-        entrypoint: hadolint
-        args: Dockerfile
-    - name: Check that packages in requirements.txt files are in asc order
-      run: |
-        sort -f --check conda/sage-bionetworks/requirements.txt
-
-  test:
-    needs: [lint]
+  configure:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set environment variables
-      run: |
-        cp .env.example .env
-        export $(grep -v '^#' .env | xargs -d '\n')
-    - name: Validate docker-compose.yml
-      run: docker-compose -f docker-compose.yml config >/dev/null
-
-  build-and-publish:
-    needs: [test]
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: Prepare build
-      id: prep
+    - name: Create configuration
       run: |
         DOCKER_IMAGE=${{ env.docker_repository }}
         VERSION=noop
@@ -62,8 +30,7 @@ jobs:
           PUSH_IMAGE=true
           PUSH_NOTEBOOKS=true
         elif [[ $GITHUB_REF == refs/tags/* ]]; then
-          # VERSION=${GITHUB_REF#refs/tags/}
-          VERSION=$(cat RSTUDIO_VERSION)
+          VERSION=${GITHUB_REF#refs/tags/}
         elif [[ $GITHUB_REF == refs/heads/* ]]; then
           VERSION=$(echo ${GITHUB_REF#refs/heads/} | sed -r 's#/+#-#g')
           if [ "${{ github.event.repository.default_branch }}" = "$VERSION" ]; then
@@ -77,25 +44,70 @@ jobs:
           PUSH_NOTEBOOKS=true
         fi
         TAGS="${DOCKER_IMAGE}:${VERSION}"
-        if [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
+        if [[ $VERSION == "edge" ]]; then
+          TAGS="$TAGS,${DOCKER_IMAGE}:edge-${GITHUB_SHA::8}"
+        elif [[ $VERSION =~ ^[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}$ ]]; then
           MINOR=${VERSION%.*}
           MAJOR=${MINOR%.*}
-          TAGS="$TAGS,${DOCKER_IMAGE}:${MINOR}"
-          TAGS="$TAGS,${DOCKER_IMAGE}:${MAJOR}"
           TAGS="$TAGS,${DOCKER_IMAGE}:latest"
-          TAGS="$TAGS,${DOCKER_IMAGE}:${VERSION}-${GITHUB_SHA::8}"
           PUSH_IMAGE=true
           PUSH_NOTEBOOKS=true
-        # elif [ "${{ github.event_name }}" = "push" ]; then
-        #   TAGS="$TAGS,${DOCKER_IMAGE}:sha-${GITHUB_SHA::8}"
         fi
-        echo ::set-output name=version::${VERSION}
-        echo ::set-output name=version_major::${MAJOR}
-        echo ::set-output name=version_minor::${MINOR}
-        echo ::set-output name=tags::${TAGS}
-        echo ::set-output name=created::$(date -u +'%Y-%m-%dT%H:%M:%SZ')
-        echo ::set-output name=push_image::${PUSH_IMAGE}
-        echo ::set-output name=push_notebooks::${PUSH_NOTEBOOKS}
+        printf "%s\n" \
+          "version=${VERSION}" \
+          "version_major=${MAJOR}" \
+          "version_minor=${MINOR}" \
+          "tags=${TAGS}" \
+          "created=$(date -u +'%Y-%m-%dT%H:%M:%SZ')" \
+          "push_image=${PUSH_IMAGE}" \
+          "push_notebooks=${PUSH_NOTEBOOKS}" | tee -a .github_env
+
+    - name: Upload .github_env
+      uses: actions/upload-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .github_env
+
+  lint:
+    needs: [configure]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Lint Dockerfiles
+      uses: docker://hadolint/hadolint:latest
+      with:
+        entrypoint: hadolint
+        args: Dockerfile
+    - name: Check that packages in requirements.txt files are in asc order
+      run: |
+        sort -f --check conda/sage-bionetworks/requirements.txt
+
+  test:
+    needs: [lint]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set environment variables
+      run: |
+        cp .env.example .env
+        export $(grep -v '^#' .env | xargs -d '\n')
+    - name: Validate docker-compose.yml
+      run: docker-compose -f docker-compose.yml config >/dev/null
+
+  build-and-publish:
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Download .github_env
+      uses: actions/download-artifact@v2
+      with:
+        name: GITHUB_ENV
+        path: .
+
+    - name: Restore $GITHUB_ENV
+      run: cat .github_env >> $GITHUB_ENV
 
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v1
@@ -128,8 +140,6 @@ jobs:
         push: false
         platforms: linux/amd64
         tags: rstudio-cached:latest
-        cache-from: type=local,src=/tmp/.buildx-cache
-        cache-to: type=local,dest=/tmp/.buildx-cache-new
 
     - name: Create .env
       run: |
@@ -144,69 +154,59 @@ jobs:
       run: |
         docker run --rm \
           --env-file .env \
-          -v $(pwd)/notebooks:/data \
+          -v $(pwd):/project \
           rstudio-cached:latest \
-          render /data/examples/*.Rmd
+          render /project/notebooks/*.Rmd
 
     - name: Push image
-      if: steps.prep.outputs.push_image == 'true'
+      if: env.push_image == 'true'
       id: docker_push
       uses: docker/build-push-action@v2
       with:
         context: .
         file: Dockerfile
         builder: ${{ steps.buildx.outputs.name }}
         push: true
-        platforms: linux/amd64,linux/arm64
-        tags: ${{ steps.prep.outputs.tags }}
+        platforms: linux/amd64
+        tags: ${{ env.tags }}
         labels: |
-          org.opencontainers.image.created=${{ steps.prep.outputs.created }}
+          org.opencontainers.image.created=${{ env.created }}
           org.opencontainers.image.source=${{ github.repositoryUrl }}
-          org.opencontainers.image.version=${{ steps.prep.outputs.version }}
+          org.opencontainers.image.version=${{ env.version }}
           org.opencontainers.image.revision=${{ github.sha }}
           org.opencontainers.image.licenses=${{ github.event.repository.license.name }}
-        cache-from: type=local,src=/tmp/.buildx-cache
-        cache-to: type=local,dest=/tmp/.buildx-cache-new
-
-    - name: Update Docker Hub repository description
-      if: steps.prep.outputs.push_image == 'true'
-      uses: peter-evans/dockerhub-description@v2
-      with:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_PASSWORD }}
-        repository: ${{ env.docker_repository }}
 
     - name: Prepare to publish HTML notebooks to GH Pages
-      if: steps.prep.outputs.push_notebooks == 'true'
+      if: env.push_notebooks == 'true'
       run: |
         git clone ${{ env.clone_url }} \
           --branch gh-pages --single-branch gh-pages
 
         # Update gh-pages: version specified
-        NOTEBOOKS_TARGET_DIR=gh-pages/${{ steps.prep.outputs.version }}/notebooks
+        NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version }}/notebooks
         rm -fr ${NOTEBOOKS_TARGET_DIR}
         mkdir -p ${NOTEBOOKS_TARGET_DIR}
-        cp -R notebooks/examples/*.html ${NOTEBOOKS_TARGET_DIR}
+        cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}
 
         # Update gh-pages: latest, major, and minor versions
-        if [ ! -z "${{ steps.prep.outputs.version_major }}" ]; then
+        if [ ! -z "${{ env.version_major }}" ]; then
           # Update latest (e.g. "1.2.3" => "latest")
           NOTEBOOKS_TARGET_DIR=gh-pages/latest/notebooks
           rm -fr ${NOTEBOOKS_TARGET_DIR}
           mkdir -p ${NOTEBOOKS_TARGET_DIR}
-          cp -R notebooks/examples/*.html ${NOTEBOOKS_TARGET_DIR}
+          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}
 
           # Update major version (e.g. "1.2.3" => "1")
-          NOTEBOOKS_TARGET_DIR=gh-pages/${{ steps.prep.outputs.version_major }}/notebooks
+          NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version_major }}/notebooks
           rm -fr ${NOTEBOOKS_TARGET_DIR}
           mkdir -p ${NOTEBOOKS_TARGET_DIR}
-          cp -R notebooks/examples/*.html ${NOTEBOOKS_TARGET_DIR}
+          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}
 
           # Update minor version (e.g. "1.2.3" => "1.2")
-          NOTEBOOKS_TARGET_DIR=gh-pages/${{ steps.prep.outputs.version_minor }}/notebooks
+          NOTEBOOKS_TARGET_DIR=gh-pages/${{ env.version_minor }}/notebooks
           rm -fr ${NOTEBOOKS_TARGET_DIR}
           mkdir -p ${NOTEBOOKS_TARGET_DIR}
-          cp -R notebooks/examples/*.html ${NOTEBOOKS_TARGET_DIR}
+          cp -R notebooks/*.html ${NOTEBOOKS_TARGET_DIR}
         fi
         cd gh-pages
         git config --local user.email "[email protected]"
@@ -217,7 +217,7 @@ jobs:
         # that.
 
     - name: Push to gh-pages
-      if: steps.prep.outputs.push_notebooks == 'true'
+      if: env.push_notebooks == 'true'
       uses: ad-m/github-push-action@master
       with:
         branch: gh-pages

README.md

@@ -1,12 +1,10 @@
-# RStudio
+# Sage Bionetworks Docker image for RStudio
 
 [![GitHub Release](https://img.shields.io/github/release/Sage-Bionetworks/docker-rstudio.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/docker-rstudio/releases)
 [![GitHub CI](https://img.shields.io/github/workflow/status/Sage-Bionetworks/docker-rstudio/CI.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/docker-rstudio)
 [![GitHub License](https://img.shields.io/github/license/Sage-Bionetworks/docker-rstudio.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://github.com/Sage-Bionetworks/docker-rstudio/blob/main/LICENSE)
 [![Docker Pulls](https://img.shields.io/docker/pulls/sagebionetworks/rstudio.svg?color=94398d&labelColor=555555&logoColor=ffffff&style=for-the-badge&label=pulls&logo=docker)](https://hub.docker.com/r/sagebionetworks/rstudio)
 
-Docker image for analyses using RStudio and Python-Conda
-
 ## Introduction
 
 The motivation for this project is to encourage the use of portable development
@@ -58,10 +56,10 @@ by the [CI/CD workflow of this repository](.github/workflows/ci.yml).
 
 Rmd Notebook | Description | HTML Notebook
 -------- | ----------- | -------------
-[notebook.Rmd](notebooks/examples/notebook.Rmd)         | Default RStudio notebook.                                | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/rstudio/latest/notebooks/notebook.html)
-[r-and-python.Rmd](notebooks/examples/r-and-python.Rmd) | Shows how to use R and Python together.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/rstudio/latest/notebooks/r-and-python.html)
-[sagethemes.Rmd](notebooks/examples/sagethemes.Rmd)     | Example notebook provided by the R library [sagethemes]. | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/rstudio/latest/notebooks/sagethemes.html)
-[synapse.Rmd](notebooks/examples/synapse.Rmd)           | Shows how to interact with Synapse API.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/rstudio/latest/notebooks/synapse.html)
+[notebook.Rmd](notebooks/notebook.Rmd)         | Default RStudio notebook.                                | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/docker-rstudio/latest/notebooks/notebook.html)
+[r-and-python.Rmd](notebooks/r-and-python.Rmd) | Shows how to use R and Python together.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/docker-rstudio/latest/notebooks/r-and-python.html)
+[sagethemes.Rmd](notebooks/sagethemes.Rmd)     | Example notebook provided by the R library [sagethemes]. | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/docker-rstudio/latest/notebooks/sagethemes.html)
+[synapse.Rmd](notebooks/synapse.Rmd)           | Shows how to interact with Synapse API.                  | [![HTML notebook](https://img.shields.io/badge/latest-blue.svg?color=1283c3&labelColor=555555&logoColor=ffffff&style=for-the-badge&logo=github)](https://sage-bionetworks.github.io/docker-rstudio/latest/notebooks/synapse.html)
 
 > Important: Please make sure when you write your own notebooks that no
 > sensitive information ends up being publicly available. Please check with the
@@ -70,15 +68,19 @@ Rmd Notebook | Description | HTML Notebook
 
 ## Usage
 
-1. Create and edit the configuration file. You can initially start RStudio using
+1. Clone this GitHub repository.
+2. Create and edit the configuration file. You can initially start RStudio using
    this configuration as-is.
 
        cp .env.example .env
 
-2. Start RStudio. Add the option `-d` or `--detach` to run in the background.
+3. Start RStudio. Add the option `-d` or `--detach` to run in the background.
 
        docker compose up
 
+> If the command `docker compose` is not available for your system, [install
+> docker-compose] and use the command `docker-compose`.
+
 RStudio is now available at http://localhost. On the login page, enter the
 default username (`rstudio`) and the password specified in `.env`.
 
@@ -214,9 +216,9 @@ HTML notebook that will be saved to the same directory with the extension
 ```console
 docker run --rm \
     --env-file .env \
-    -v $(pwd)/notebooks:/data \
+    -v $(pwd):/project \
     sagebionetworks/rstudio:4.1.0 \
-    render /data/examples/*.Rmd
+    render /project/notebooks/*.Rmd
 ```
 
 ## Versioning
@@ -227,23 +229,20 @@ This repository uses [semantic versioning] to track the releases of this
 project. This repository uses "non-moving" GitHub tags, that is, a tag will
 always point to the same git commit once it has been created.
 
-### Docker tags
+### Docker and GitHub Pages tags
 
-The artifact published by this repository is the Docker image
-[sagebionetworks/rstudio]. The versions of the image are aligned with the
-versions of R/RStudio, not the GitHub tags of this repository.
+The artifact published by this repository are HTML notebooks published to GitHub
+Pages and the Docker image [sagebionetworks/rstudio]. The tags of these
+artifacts are aligned with the GitHub tags.
 
 The table below describes the image tags available.
 
-| Tag name                        | Moving | Description
-|---------------------------------|--------|------------
-| `latest`                        | Yes    | Latest stable release.
-| `edge`                          | Yes    | Lastest commit made to the default branch.
-| `weekly`                        | Yes    | Weekly release from the default branch.
-| `<major>`                       | Yes    | Latest stable major release of R/RStudio.
-| `<major>.<minor>`               | Yes    | Latest stable minor release of R/RStudio.
-| `<major>.<minor>.<patch>`       | Yes    | Latest stable patch release of R/RStudio.
-| `<major>.<minor>.<patch>-<sha>` | No     | Same as above but with the reference to the git commit.
+| Tag name                        | Description                                            | Moving
+|---------------------------------|--------------------------------------------------------|-------
+| `latest`                        | Latest stable release.                                 | Yes
+| `edge`                          | Lastest commit made to the default branch.             | Yes
+| `edge-<sha>`                    | Same as above with the reference to the git commit.    | No
+| `<major>.<minor>.<patch>`       | Latest stable patch release `<major>.<minor>.<patch>`. | No
 
 You should avoid using a moving tag like `latest` when deploying containers in
 production, because this makes it hard to track which version of the image is
@@ -283,4 +282,4 @@ Thinking about contributing to this project? Get started by reading our
 [Sage-Bionetworks-Challenges/challenge-analysis]: https://github.com/Sage-Bionetworks-Challenges/challenge-analysis
 [Sage-Bionetworks/docker-rstudio]: https://github.com/Sage-Bionetworks/docker-rstudio
 [Docker Engine]: https://docs.docker.com/engine/install/
-[Docker Compose]: https://docs.docker.com/compose/install/
+[install docker-compose]: https://docs.docker.com/compose/install/