Update Variables for leaf_phenology data extraction
#6322
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| name: Docker GHA | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| tags: | |
| - "v*.*.*" | |
| pull_request: | |
| merge_group: | |
| workflow_dispatch: | |
| inputs: | |
| r_version: | |
| description: 'R version to use' | |
| required: true | |
| type: choice | |
| default: "4.1" | |
| options: | |
| - 4.1 | |
| - 4.2 | |
| - 4.3 | |
| - 4.4 | |
| - devel | |
| schedule: | |
| # 1:30 AM UTC, different R version each day | |
| - cron: '30 1 * * 1' # Rdevel | |
| - cron: '30 1 * * 2' # R4.4 | |
| - cron: '30 1 * * 3' # R4.3 | |
| - cron: '30 1 * * 4' # R4.2 | |
| - cron: '30 1 * * 5' # R4.1 | |
| jobs: | |
| # ---------------------------------------------------------------------- | |
| # Set R version. | |
| # This is a hack: We really just want a global env var here, but it seems | |
| # `env:` values can't be passed into a `jobs.<jobid>.with` context | |
| # (see https://github.com/actions/runner/issues/2372). | |
| # As an ugly workaround, we assign it to a job output instead. | |
| # ---------------------------------------------------------------------- | |
| rversion: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: mon | |
| if: github.event.schedule == '30 1 * * 1' | |
| run: echo "R_VERSION=devel" >> "$GITHUB_OUTPUT" | |
| - id: tue | |
| if: github.event.schedule == '30 1 * * 2' | |
| run: echo "R_VERSION=4.4" >> "$GITHUB_OUTPUT" | |
| - id: wed | |
| if: github.event.schedule == '30 1 * * 3' | |
| run: echo "R_VERSION=4.3" >> "$GITHUB_OUTPUT" | |
| - id: thu | |
| if: github.event.schedule == '30 1 * * 4' | |
| run: echo "R_VERSION=4.2" >> "$GITHUB_OUTPUT" | |
| - id: fri | |
| if: github.event.schedule == '30 1 * * 5' | |
| run: echo "R_VERSION=4.1" >> "$GITHUB_OUTPUT" | |
| - id: default | |
| if: github.event_name != 'schedule' | |
| run: echo "R_VERSION=${{ github.event.inputs.r_version || '4.1' }}" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| # Note: "steps.*" seems to mean "all step ids", not "all steps" | |
| # If seeing weird results here, check that all steps above have an id set. | |
| R_VERSION: ${{ join(steps.*.outputs.R_VERSION, '') }} | |
| # ---------------------------------------------------------------------- | |
| # depends image has all the dependencies installed | |
| # ---------------------------------------------------------------------- | |
| depends: | |
| permissions: | |
| packages: write | |
| needs: rversion | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: depends | |
| build-context: docker/depends | |
| dockerfile: docker/depends/Dockerfile | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| platforms: "linux/amd64" | |
| secrets: inherit | |
| # ---------------------------------------------------------------------- | |
| # base image has PEcAn compiled and installed, and depends on depends | |
| # ---------------------------------------------------------------------- | |
| base: | |
| needs: [rversion, depends] | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: base | |
| build-context: . | |
| dockerfile: docker/base/Dockerfile | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| parent-image: "depends" | |
| platforms: "linux/amd64" | |
| secrets: inherit | |
| # ---------------------------------------------------------------------- | |
| # models image has some python installed to run models, depends on base | |
| # ---------------------------------------------------------------------- | |
| models: | |
| needs: [rversion, base] | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: models | |
| build-context: docker/models | |
| dockerfile: docker/models/Dockerfile | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| parent-image: "base" | |
| secrets: inherit | |
| # ---------------------------------------------------------------------- | |
| # Next are images that have models installed | |
| # ---------------------------------------------------------------------- | |
| modelsbinary: | |
| needs: [rversion, models] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| name: | |
| - basgra | |
| - biocro | |
| # - ed2_2.2.0 | |
| - ed2_git | |
| - maespa | |
| - sipnet | |
| include: | |
| - name: basgra | |
| CONTEXT: models/basgra | |
| DOCKERFILE: models/basgra/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| MODEL: basgra | |
| VERSION: BASGRA_N_v1 | |
| - name: biocro | |
| CONTEXT: models/biocro | |
| DOCKERFILE: models/biocro/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| MODEL: biocro | |
| VERSION: "0.95" | |
| # - name: ed2_2.2.0 | |
| # CONTEXT: models/ed | |
| # DOCKERFILE: models/ed/Dockerfile | |
| # PLATFORM: "linux/amd64" | |
| # MODEL: ed2 | |
| # VERSION: "2.2.0" | |
| - name: ed2_git | |
| CONTEXT: models/ed | |
| DOCKERFILE: models/ed/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| MODEL: ed2 | |
| VERSION: "git" | |
| - name: maespa | |
| CONTEXT: models/maespa | |
| DOCKERFILE: models/maespa/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| MODEL: maespa | |
| VERSION: "git" | |
| - name: sipnet | |
| CONTEXT: models/sipnet | |
| DOCKERFILE: models/sipnet/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| MODEL: sipnet | |
| VERSION: "git" | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: model-${{ matrix.MODEL }}-${{ matrix.VERSION }} | |
| build-context: ${{ matrix.CONTEXT }} | |
| dockerfile: ${{ matrix.DOCKERFILE }} | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| parent-image: "models" | |
| model-version: ${{ matrix.VERSION }} | |
| platforms: ${{ matrix.PLATFORM }} | |
| secrets: inherit | |
| # ---------------------------------------------------------------------- | |
| # Next are images that depend on base image | |
| # ---------------------------------------------------------------------- | |
| baseplus: | |
| needs: [rversion, base] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| name: | |
| - docs | |
| - executor | |
| - api | |
| include: | |
| - name: docs | |
| CONTEXT: . | |
| DOCKERFILE: docker/docs/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| - name: executor | |
| CONTEXT: docker/executor | |
| DOCKERFILE: docker/executor/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| - name: api | |
| CONTEXT: apps/api | |
| DOCKERFILE: apps/api/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: ${{ matrix.name }} | |
| build-context: ${{ matrix.CONTEXT }} | |
| dockerfile: ${{ matrix.DOCKERFILE }} | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| platforms: ${{ matrix.PLATFORM }} | |
| secrets: inherit | |
| # ---------------------------------------------------------------------- | |
| # Next are images that do not depend on either depends or base image | |
| # ---------------------------------------------------------------------- | |
| extras: | |
| needs: rversion | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| name: | |
| - web | |
| - shiny-dbsync | |
| - data | |
| - monitor | |
| - rstudio-nginx | |
| include: | |
| - name: web | |
| CONTEXT: . | |
| DOCKERFILE: docker/web/Dockerfile | |
| PLATFORM: "linux/amd64,linux/arm64" | |
| - name: shiny-dbsync | |
| CONTEXT: . | |
| DOCKERFILE: shiny/dbsync/Dockerfile | |
| PLATFORM: "linux/amd64" | |
| - name: data | |
| CONTEXT: docker/data | |
| DOCKERFILE: docker/data/Dockerfile | |
| PLATFORM: "linux/amd64,linux/arm64" | |
| - name: monitor | |
| CONTEXT: docker/monitor | |
| DOCKERFILE: docker/monitor/Dockerfile | |
| PLATFORM: "linux/amd64,linux/arm64" | |
| - name: rstudio-nginx | |
| CONTEXT: docker/rstudio-nginx | |
| DOCKERFILE: docker/rstudio-nginx/Dockerfile | |
| PLATFORM: "linux/amd64,linux/arm64" | |
| uses: ./.github/workflows/docker-build-image.yml | |
| with: | |
| image-name: ${{ matrix.name }} | |
| build-context: ${{ matrix.CONTEXT }} | |
| dockerfile: ${{ matrix.DOCKERFILE }} | |
| platforms: ${{ matrix.PLATFORM }} | |
| r-version: ${{ needs.rversion.outputs.R_VERSION }} | |
| secrets: inherit |