Merge pull request #12 from jiajic/dev

Update checks and gh-actions
drieslab · Sep 6, 2023 · 802e369 · 802e369
2 parents 3da6900 + 73ae625
commit 802e369
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diff --git a/.github/workflows/dev_workflow.yml b/.github/workflows/dev_workflow.yml
@@ -0,0 +1,146 @@
+# 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.WORKFLOW_PAT }}
+    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
+
+
+  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: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      # add code cov
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+
+
+  lint:
+    runs-on: ubuntu-latest
+    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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: false
+
+
+
diff --git a/.github/workflows/github_workflow.yml → .github/workflows/prod_workflow.yml b/.github/workflows/github_workflow.yml → .github/workflows/prod_workflow.yml
@@ -7,19 +7,21 @@
 # additional example workflows available for the R community.
 
 
+name: Master Workflow - Deploy to production
+
 on:
-  push:
-    branches: [ "main" ]
   pull_request:
+    types: closed
     branches: [ "main" ]
 
 permissions:
   contents: read
 
-name: github_workflow
 
 jobs:
   R-CMD-check:
+    env:
+      GITHUB_PAT: ${{ secrets.WORKFLOW_PAT }}
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -35,32 +37,46 @@ jobs:
           - {os: ubuntu-latest,   r: 'oldrel-1'}
 
     steps:
-      # remove vignettes dir
+
       - name: Remove vignettes dir
         run: rm -rf 'vignettes/'
         shell: bash
 
-      # checkout repo for workflow access
-      - uses: actions/checkout@v2
+      - name: Checkout repo for workflow access
+        uses: actions/checkout@v3
 
-      # setup R
-      - uses: r-lib/actions/setup-r@v2
+      - name: Set up R environment
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      # setup dependencies
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - 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::data.table
+          extra-packages: any::rcmdcheck, any::testthat, any::rlang, any::R.utils, any::remotes, any::covr
+
+      - name: Set up dependencies (GiottoData)
+        run: |
+          suppressWarnings({
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
+          })
+        shell: Rscript {0}
 
-      # run R CMD check
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Test python env build
+        run: |
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
+        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
@@ -71,35 +87,40 @@ jobs:
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
+
   test-coverage:
+    name: Code coverage
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v2
+      - 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
 
-      # install extra dependencies
-      - name: Install GiottoData
+      - 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({
-            if(!require(remotes)){
-              install.packages('R.utils', repos = 'http://cran.us.r-project.org')
-              install.packages('remotes', repos = 'http://cran.us.r-project.org')
-            }
-            remotes::install_github('drieslab/GiottoData', build = FALSE)
+            remotes::install_github('drieslab/GiottoData@suite_modular', build = FALSE)
           })
         shell: Rscript {0}
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr
-          needs: coverage
-
       - name: Test coverage
         run: |
           covr::codecov(
@@ -109,15 +130,14 @@ jobs:
           )
         shell: Rscript {0}
 
-      # add code cov
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-
   # lint:
   #   runs-on: ubuntu-latest
+  #   needs: R-CMD-check
   #   env:
   #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   #   steps:
@@ -139,29 +159,31 @@ jobs:
   #         LINTR_ERROR_ON_LINT: true
 
 
-  # render-rmarkdown:
-  #   runs-on: ubuntu-latest
-  #   env:
-  #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-  #   steps:
-  #     - name: Checkout repo
-  #       uses: actions/checkout@v3
-  #       with:
-  #         fetch-depth: 0
-  #
-  #     - uses: r-lib/actions/setup-pandoc@v2
-  #
-  #     - uses: r-lib/actions/setup-r@v2
-  #
-  #     - uses: r-lib/actions/setup-renv@v2
-  #
-  #     - name: Install rmarkdown
-  #       run: Rscript -e 'install.packages("rmarkdown")'
-  #
-  #     - name: Render README
-  #       run: Rscript -e 'rmarkdown::render("README.Rmd")'
-  #
-  #     - name: Commit results
-  #       run: |
-  #         git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
-  #         git push origin || echo "No changes to commit"
+  render-rmarkdown:
+    name: Update README.Rmd
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install rmarkdown
+        run: Rscript -e 'install.packages("rmarkdown")'
+
+      - name: Render README
+        run: Rscript -e 'rmarkdown::render("README.Rmd")'
+
+      - name: Commit results
+        run: |
+          git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
+          git push origin || echo "No changes to commit"
+
+
+
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -52,6 +52,7 @@ Suggests:
     HDF5Array (>= 1.18.1),
     remotes,
     rhdf5,
+    rlang,
     RTriangle (>= 1.6-0.10),
     S4Vectors,
     scattermore,

diff --git a/NAMESPACE b/NAMESPACE
@@ -32,6 +32,7 @@ export(calculateOverlapParallel)
 export(calculateOverlapPolygonImages)
 export(calculateOverlapRaster)
 export(calculateOverlapSerial)
+export(calculateSpatCellMetadataProportions)
 export(changeGiottoInstructions)
 export(changeImageBg)
 export(checkGiottoEnvironment)
@@ -44,6 +45,7 @@ export(combineFeatureOverlapData)
 export(combineMetadata)
 export(combineSpatialCellFeatureInfo)
 export(combineSpatialCellMetadataInfo)
+export(compatible_spatial_network)
 export(convertGiottoLargeImageToMG)
 export(convert_mgImage_to_array_DT)
 export(convert_to_full_spatial_network)