build.yml

# build and test synapser. Additionally deploys to  S3 RAN server on GitHub release.

name: build

on:
  push:
    # we build/test all pushed branches, but not tags.
    # we only push tags with releases, and we handle releases explicitly
    branches:
      - '**'
    tags-ignore:
      - '**'

  pull_request:

  release:
    types:
      - 'published'

jobs:
  build:

    runs-on: ${{ matrix.os }}
    outputs:
      package_version: ${{ steps.shared-env.outputs.package_version }}
      r_minor_version: ${{ steps.shared-env.outputs.r_minor_version }}

    strategy:
      matrix:
        os: [ubuntu-22.04, macos-13, windows-2022]
        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]

    steps:
      - name: checkout
        uses: actions/checkout@v4

      - name: Set up Python Version
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'

      - name: setup-r
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r }}
          architecture: 'x64'

      - name: shared-env
        id: shared-env
        shell: bash
        run: |
          PACKAGE_NAME=synapser
          echo "PACKAGE_NAME=$PACKAGE_NAME" >> $GITHUB_ENV

          PACKAGE_VERSION=$(grep "Version: " DESCRIPTION | awk '{print $2'})

          # if this was triggered by a release and the release tag
          # looks like semver then we use that for the package version.
          RELEASE_TAG=${{ github.event.release.tag_name }}
          if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then
            RELEASE_VERSION="${BASH_REMATCH[1]}.$GITHUB_RUN_NUMBER"

            # a release version overrides the package version
            # for purposes of creating artifacts
            PACKAGE_VERSION=$RELEASE_VERSION

            DATE=`date +%Y-%m-%d`
            # replace DESCRIPTION with $VERSION & $DATE
            # sed -i not portable on OSX so we wash through some temp files instead
            sed "s|^Version: .*$|Version: $PACKAGE_VERSION|g" DESCRIPTION > DESCRIPTION.temp
            sed "s|^Date: .*$|Date: $DATE|g" DESCRIPTION.temp > DESCRIPTION2.temp

            rm DESCRIPTION
            mv DESCRIPTION2.temp DESCRIPTION
            rm DESCRIPTION.temp
          fi

          echo "BRANCH_VERSION=$BRANCH_VERSION" >> $GITHUB_ENV
          echo "PACKAGE_VERSION=$PACKAGE_VERSION" >> $GITHUB_ENV

          R_VERSION=${{matrix.r}}
          R_MAJOR_VERSION=$(echo $R_VERSION | cut -f1 -d".")
          R_MINOR_VERSION=$R_MAJOR_VERSION.$(echo $R_VERSION | cut -f2 -d".")
          echo "R_VERSION=$R_VERSION" >> $GITHUB_ENV
          echo "R_MAJOR_VERSION=$R_MAJOR_VERSION" >> $GITHUB_ENV
          echo "R_MINOR_VERSION=$R_MINOR_VERSION" >> $GITHUB_ENV

          # replace backslashes with forward slashes for windows.
          # windows bash will handle forward slashes fine and this
          # makes it easier to unify the path handling.
          R_LIBS_USER_SANITIZED=$(echo $R_LIBS_USER | sed 's/\\/\//g')
          echo "R_LIBS_USER=$R_LIBS_USER_SANITIZED" >> $GITHUB_ENV

          # echo "::set-output name=package_version::$PACKAGE_VERSION"
          # echo "::set-output name=r_minor_version::$R_MINOR_VERSION"
          echo "package_version=$PACKAGE_VERSION" >> $GITHUB_OUTPUT
          echo "r_minor_version=$R_MINOR_VERSION" >> $GITHUB_OUTPUT

      - name: setup-r-mac-13
        if: ${{matrix.os == 'macos-13'}}
        run: |
          R_LIBS_USER=${GITHUB_WORKSPACE}/R_LIBS
          rm -rf R_LIBS_USER
          mkdir -p $R_LIBS_USER
          echo "R_LIBS_USER=$R_LIBS_USER" >> $GITHUB_ENV

          echo "R=R" >> $GITHUB_ENV


      - name: install-test-config
        shell: bash
        run: |
          if [ -z "${{ secrets.encrypted_d17283647768_key }}" ]  || [ -z "${{ secrets.encrypted_d17283647768_key }}" ]; then
            echo "No test configuration decryption keys available, skipping integration tests"
            exit 1
          fi

          # decrypt the encrypted test synapse configuration
          openssl aes-256-cbc -K ${{ secrets.encrypted_d17283647768_key }} -iv ${{ secrets.encrypted_d17283647768_iv }} -in test.synapseConfig.enc -out test.synapseConfig -d
          mv test.synapseConfig ~/.synapseConfig

      - name: install-pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: install-python-dependencies
        shell: bash
        if: ${{runner.os == 'Windows'}}
        run: |
          pip install 'synapseclient[pandas]'

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache: true
          cache-version: 2
          architecture: 'x64'

      - name: linux-build-package
        if: ${{runner.os == 'linux'}}
        run: |
          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
          Rscript -e "reticulate::install_miniconda()"
          echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
          Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
          R CMD build ./
          R CMD INSTALL ./ --library=$R_LIBS_USER --no-test-load

          echo "ARTIFACT_EXTENSION=tar.gz" >> $GITHUB_ENV

      - name: mac-build-package
        if: ${{runner.os == 'macOS'}}
        run: |
            Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
            Rscript -e "reticulate::install_miniconda()"
            echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
            Rscript -e "reticulate::conda_create('r-reticulate', packages = c('python==3.10'))"
            R CMD build ./
            R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load

            echo "ARTIFACT_EXTENSION=tgz" >> $GITHUB_ENV

      - name: windows-build-package
        if: ${{runner.os == 'Windows'}}
        shell: bash
        run: |
          echo "options(repos = c(CRAN = 'https://cloud.r-project.org'))" >> .Rprofile
          Rscript -e "install.packages('remotes'); remotes::install_version('reticulate', version = '1.28')"
          Rscript -e "reticulate::install_python(version = '3.10.11')"
          Rscript -e "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')"
          Rscript -e "reticulate::use_virtualenv('r-reticulate')"
          R CMD build ./
          R CMD INSTALL --build ${PACKAGE_NAME}_${PACKAGE_VERSION}.tar.gz --library=$R_LIBS_USER --no-test-load --no-multiarch

          echo "ARTIFACT_EXTENSION=zip" >> $GITHUB_ENV

      - name: run-tests
        shell: bash
        run: |
          echo ".libPaths(c('$R_LIBS_USER', .libPaths()));" > runTests.R
          echo "setwd(sprintf('%s/tests', getwd()));" >> runTests.R
          echo "source('testthat.R')" >> runTests.R
          echo "library(synapser);" >> runTests.R
          echo "detach(\"package:synapser\", unload=TRUE);" >> runTests.R
          echo "library(synapser)" >> runTests.R
          R --vanilla < runTests.R
          rm runTests.R

      - name: artifact-name
        shell: bash
        run: |
          # we format our artifact names so we align to the same pattern
          # used by the deploy gist written to work with jenkins.

          ARTIFACT_NAME="${PACKAGE_NAME}_${PACKAGE_VERSION}.${ARTIFACT_EXTENSION}"

          OS_LABEL=$(echo ${{runner.os}} | tr '[:upper:]' '[:lower:]')
          if [[ "$OS_LABEL" == "macos" ]]; then
            OS_LABEL="mac"
          fi

          UPLOAD_NAME="label=${OS_LABEL}-RVERS-${{ steps.shared-env.outputs.r_minor_version }}"
          echo "ARTIFACT_NAME=$ARTIFACT_NAME" >> $GITHUB_ENV
          echo "UPLOAD_NAME=$UPLOAD_NAME" >> $GITHUB_ENV

      - name: upload-artifact
        uses: actions/upload-artifact@v4
        with:
          name: ${{env.UPLOAD_NAME}}
          path: ${{env.ARTIFACT_NAME}}

  deploy:
    runs-on: ubuntu-22.04
    needs: build
    permissions:
      id-token: write
      contents: read
    if: github.event_name == 'release'
    outputs:
      s3_ran: ${{ steps.deploy-to-target.outputs.s3_ran }}

    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: check-deployment-target
        id: check-deployment-target
        if: ${{github.event.action == 'published'}}
        shell: bash
        run: |
          DEPLOY_TARGET=""
          RELEASE_VERSION=""
          RELEASE_TAG=${{ github.event.release.tag_name }}
          if [[ $RELEASE_TAG =~ ^v?([[:digit:]\.]+)(-rc)? ]]; then
            RELEASE_VERSION="${BASH_REMATCH[1]}"
            echo $RELEASE_VERSION
            if [[ -n "$RELEASE_VERSION" ]]; then
              if [[ "${{ github.event.release.prerelease }}" == "true" ]]; then
                DEPLOY_TARGET="staging"
              else
                DEPLOY_TARGET="prod"
              fi
            fi
          fi

          echo "DEPLOY_TARGET=$DEPLOY_TARGET" >> $GITHUB_ENV
          # echo "::set-output name=deploy_target::$DEPLOY_TARGET"
          echo "deploy_target=$DEPLOY_TARGET" >> $GITHUB_OUTPUT

      - name: download-artifacts
        uses: actions/download-artifact@v4
        if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
        with:
          path: deploy_artifacts

        # Before deoloying to RAN (which is an S3 bucket), authenticate to AWS using GitHub OIDC
      - name: Assume AWS Role
        uses: aws-actions/configure-aws-credentials@v3
        with:
          aws-region: us-east-1
          role-to-assume: arn:aws:iam::325565585839:role/sagebase-github-oidc-sage-bionetworks-synapser
          role-session-name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }}
          role-duration-seconds: 1200
          
      - name: deploy-to-target
        id: deploy-to-target
        if: ${{steps.check-deployment-target.outputs.deploy_target != ''}}
        shell: bash
        run: |
          # we use a gist to upload and the gist internally uses R so we need R on this runner.
          # TODO maybe create a docker image to run this with R preloaded (and/or an action).
          sudo apt-get -y update && sudo apt-get -y install r-base

          export ARTIFACTS_DIR=deploy_artifacts
          if [[ "$DEPLOY_TARGET" == "staging" ]]; then
            export S3_RAN=staging-ran.synapse.org
          elif [[ "$DEPLOY_TARGET" == "prod" ]]; then
            export S3_RAN=ran.synapse.org
          fi

          bash tools/deploy.sh
          # echo "::set-output name=s3_ran::$S3_RAN"
          echo "s3_ran=$S3_RAN" >> $GITHUB_OUTPUT

  # on each of our matrix platforms, download the newly uploaded package from RAN
  check-deploy:
    needs:
      [build, deploy]

    strategy:
      matrix:
        os: [ubuntu-22.04, windows-2022, macos-13]
        r: [4.1.3, 4.2.3, 4.3.1, 4.4.1]

    runs-on: ${{ matrix.os }}

    steps:
      - name: checkout
        uses: actions/checkout@v4

      - name: setup-r
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r }}
          
      - name: setup-r-dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache: true
          cache-version: 2
          architecture: 'x64'
          
      - name: check-install
        shell: bash
        run: |
          RAN="http://${{ needs.deploy.outputs.s3_ran }}"
          VERSION_TO_CHECK="${{ needs.build.outputs.package_version }}"
          PACKAGE="synapser"
          echo "if (available.packages(repos='$RAN')['$PACKAGE','Version'] != '$VERSION_TO_CHECK') { quit(save = 'no', status = 1) }" > test.R
          echo "try(remove.packages('$PACKAGE'), silent=T)" >> test.R
          echo "install.packages('remotes', repos = 'https://cloud.r-project.org'); remotes::install_version('reticulate', version = '1.28', repos = 'https://cloud.r-project.org')" >> test.R
          echo "reticulate::install_python(version = '3.10.11')" >> test.R
          echo "reticulate::virtualenv_create(envname='r-reticulate',version = '3.10.11')" >> test.R
          echo "reticulate::use_virtualenv('r-reticulate')" >> test.R
          echo "install.packages('$PACKAGE', repos=c('$RAN', 'https://cloud.r-project.org/'))" >> test.R
          echo "library('$PACKAGE')" >> test.R
          R --vanilla < test.R