combine update combined_metadata and data-raw actions (#208)

waldronlab · Apr 23, 2021 · 2421d2b · 2421d2b
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commit 2421d2b
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diff --git a/.github/workflows/data-raw.yaml b/.github/workflows/data-raw.yaml
diff --git a/.github/workflows/update-curation.yml b/.github/workflows/update-curation.yml
@@ -0,0 +1,92 @@
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+  push:
+    branches:
+      - main
+      - master
+  schedule:
+    - cron: "0 5 * * 6"
+
+name: Update curation
+
+jobs:
+  update-curation:
+    runs-on: ubuntu-latest
+    container: bioconductor/bioconductor_docker:devel
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: /usr/local/lib/R/site-library
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Update curation
+        run: |
+          Rscript data-raw/sysdata.R
+          Rscript data-raw/sampleMetadata.R
+
+      - name: Test curation
+        id: update_curation
+        run: |
+          library("curatedMetagenomicData")
+          library("curatedMetagenomicDataCuration")
+          message(paste("\n****", Sys.time(), "Check curation ****"))
+          status <- "passing"
+          data(sampleMetadata)
+          tryCatch(curatedMetagenomicDataCuration::checkCuration(sampleMetadata),
+               warning = function(w) {
+                   status <<- "failing"
+                   message(paste(w, "\n"))
+          })
+          color = if (status == "passing") "brightgreen" else "red"
+          message(paste("::set-output name=status::", status, sep=""))
+          message(paste("::set-output name=color::", color, sep=""))
+        shell: Rscript {0}
+
+      - name: Get actions URL
+        id: actions_url
+        run: echo "::set-output name=url::${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
+
+      - name: Update documentation
+        run: roxygen2::roxygenize()
+        shell: Rscript {0}
+
+      - name: Commit and create pull request for updated curation
+        uses: peter-evans/create-pull-request@v3
+        with:
+          commit-message: Update curation
+          committer: GitHub Actions <[email protected]>
+          signoff: false
+          branch: update-curation
+          delete-branch: true
+          title: 'Update curation'
+          body: |
+            Update curation.
+
+            [![Curation Status](https://img.shields.io/badge/Curation-${{ steps.update_curation.outputs.status }}-${{ steps.update_curation.outputs.color }})](${{ steps.actions_url.outputs.url }})
+
+            Auto-generated by [create-pull-request][1].
+
+            [1]: https://github.com/peter-evans/create-pull-request
+          labels: automated pr
+          team-reviewers: |
+            owners
+            maintainers
+          draft: false
+          base: master