Merge pull request #17 from jiajic/dev

Edit workflows

.github/workflows/covr.yml

@@ -0,0 +1,63 @@
+
+
+name: code coverage
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    types: closed
+    branches: [ "main" ]
+  schedule:
+    - cron: '16 20 * * 2'
+
+jobs:
+  test-coverage:
+    name: Code coverage
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up dependencies (general)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
+          needs: coverage
+
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
+
+      - name: Generate coverage report
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: 4c596b03-f583-4114-8c3a-f89ed373c53b
+          fail_ci_if_error: false
+          flags: unittests
+          verbose: true

.github/workflows/dev_check.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+#
+# See https://github.com/r-lib/actions/tree/master/examples#readme for
+# additional example workflows available for the R community.
+
+
+name: Dev Workflow - Test and check
+on:
+  push:
+    branches: [ "dev" ]
+
+permissions:
+  contents: read
+
+jobs:
+  R-CMD-check:
+    name: R CMD Check
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - name: Remove vignettes dir
+        run: rm -rf 'vignettes/'
+        shell: bash
+
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up dependencies (general)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes
+
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
+
+      - name: Run R CMD check
+        uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          error-on: '"error"' # workflow errors on error only, can change to include warnings
+
+      # show testthat output for ease of access
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+
+

.github/workflows/lintr.yml

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+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# lintr provides static code analysis for R.
+# It checks for adherence to a given style,
+# identifying syntax errors and possible semantic issues,
+# then reports them to you so you can take action.
+# More details at https://lintr.r-lib.org/
+
+name: lintr
+
+on:
+  push:
+    branches: [ "dev" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "dev" ]
+  schedule:
+    - cron: '16 20 * * 2'
+
+permissions:
+  contents: read
+
+jobs:
+  lintr:
+    name: Run lintr scanning
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read # for checkout to fetch code
+      security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
+      actions: read # only required for a private repository by github/codeql-action/upload-sarif to get the Action run status
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          _R_CHECK_FORCE_SUGGESTS: false
+          _R_CHECK_RD_XREFS: false
+        with:
+          dependencies: '"hard"' # do not use suggested dependencies
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Run lintr
+        run: lintr::sarif_output(lintr::lint_dir("."), "lintr-results.sarif")
+        shell: Rscript {0}
+        continue-on-error: true
+
+      - name: Upload analysis results to GitHub
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: lintr-results.sarif
+          wait-for-processing: true