initial commit

.dockerignore

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+# ignore everything
+**
+
+# except what we need
+!/pm25_iweek_startdate.csv
+!/habre.tif
+!/renv.lock
+!/entrypoint.R

.github/workflows/build-deploy-pr.yaml

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+name: build-deploy-pr
+on:
+  pull_request:
+jobs:
+  deploy-images:
+    runs-on: ubuntu-latest
+    env:
+      registry: ghcr.io
+      username: degauss-org
+      repository: habre_pm
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: create latest tag variable
+        run: |
+          container="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:latest"
+          echo "container=${container}" >> $GITHUB_ENV
+      - name: create pull request tag variable based on name of associated branch
+        if: github.event_name == 'pull_request'
+        run: |
+          versioned="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:${GITHUB_HEAD_REF}"
+          echo "versioned=${versioned}" >> $GITHUB_ENV
+      - name: build container
+        run: |
+          docker build -t ${{ env.container }} .
+      - name: test run container
+        run: |
+          docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} my_address_file_geocoded.csv
+      - name: login to ghcr
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.registry }}
+          username: ${{ env.username }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: deploy pull request container
+        run: |
+          docker tag ${{ env.container }} ${{ env.versioned }}
+          docker push ${{ env.versioned }}

.github/workflows/build-deploy-release.yaml

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+name: build-deploy-release
+on:
+  release:
+    types: [published]
+jobs:
+  deploy-images:
+    runs-on: ubuntu-latest
+    env:
+      registry: ghcr.io
+      username: degauss-org
+      repository: habre_pm
+    strategy:
+      fail-fast: false
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: create latest tag variable
+        run: |
+          container="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:latest"
+          echo "container=${container}" >> $GITHUB_ENV
+      - name: create release tag variable
+        if: github.event_name == 'release'
+        run: |
+          versioned="${{ env.registry }}/${{ env.username}}/${{ env.repository }}:${GITHUB_REF##*/}"
+          echo "versioned=${versioned}" >> $GITHUB_ENV
+      - name: build container
+        run: |
+          docker build -t ${{ env.container }} .
+      - name: test container
+        run: |
+          docker run --rm -v "${PWD}/test":/tmp ${{ env.container }} my_address_file_geocoded.csv
+      - name: login to ghcr
+        uses: docker/login-action@v1
+        with:
+          registry: ${{ env.registry }}
+          username: ${{ env.username }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: deploy release (and latest) container
+        run: |
+          docker tag ${{ env.container }} ${{ env.versioned }}
+          docker push ${{ env.versioned }}
+          docker push ${{ env.container }}

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

Dockerfile

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+FROM rocker/r-ver:4.2.2
+
+# DeGAUSS container metadata
+ENV degauss_name="habre_pm"
+ENV degauss_version="0.1.0"
+ENV degauss_description="weekly pm2.5 for California (Habre)"
+
+# add OCI labels based on environment variables too
+LABEL "org.degauss.name"="${degauss_name}"
+LABEL "org.degauss.version"="${degauss_version}"
+LABEL "org.degauss.description"="${degauss_description}"
+
+RUN R --quiet -e "install.packages('remotes', repos = c(CRAN = 'https://packagemanager.rstudio.com/all/__linux__/focal/latest'))"
+
+RUN R --quiet -e "remotes::install_github('rstudio/[email protected]')"
+
+WORKDIR /app
+
+RUN apt-get update \
+    && apt-get install -yqq --no-install-recommends \
+    libgdal-dev \
+    libgeos-dev \
+    libudunits2-dev \
+    libproj-dev \
+    && apt-get clean
+
+COPY renv.lock .
+
+RUN R --quiet -e "renv::restore()"
+
+COPY habre.tif .
+COPY pm25_iweek_startdate.csv .
+COPY entrypoint.R .
+
+WORKDIR /tmp
+
+ENTRYPOINT ["/app/entrypoint.R"]