Merge pull request #223 from drieslab/dev2

chore: GHA updates
drieslab · Aug 28, 2024 · 7b9f80e · 7b9f80e
2 parents 7456cd1 + 9674e00
commit 7b9f80e
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Showing 3 changed files with 86 additions and 7 deletions.
diff --git a/.github/workflows/covr.yml b/.github/workflows/covr.yml
@@ -4,7 +4,7 @@ name: code coverage
 
 on:
   push:
-    branches: [ "dev2 " ]
+    branches: [ "dev2" ]
   schedule:
     - cron: '16 20 * * 2'
 
@@ -37,19 +37,66 @@ jobs:
           install-pandoc: false
           extra-packages: |
             github::drieslab/GiottoData
+            any::covr
             any::rcmdcheck
             any::testthat
             any::rlang
             any::R.utils
+            any::knitr
+            any::rmarkdown
+            any::qs
             any::sp
             any::stars
             any::raster
             any::sf
+            any::scattermore
+            any::exactextractr
             any::RTriangle
             any::geometry
-            any::covr
+            any::qs
+            any::future.apply
+            any::Biobase
+            any::chihaya
+            any::DelayedArray
+            any::DelayedMatrixStats
+            any::HDF5Array
+            any::plotly
+            any::rgl
+            any::rhdf5
+            any::S4Vectors
+            any::ScaledMatrix
+            any::XML
+            any::Seurat
+            any::SeuratObject
+            any::SingleCellExperiment
+            any::SpatialExperiment
+            any::STexampleData
+            any::SummarizedExperiment
+
           needs: coverage
 
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: setup giotto_env
+        shell: Rscript {0}
+        run: |
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
+          
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
+
       - name: Generate coverage report
         run: |
           covr::codecov(

diff --git a/.github/workflows/dev_check.yml b/.github/workflows/dev_check.yml
@@ -87,7 +87,7 @@ jobs:
       - name: setup giotto_env
         shell: Rscript {0}
         run: |
-          if (!GiottoClass::checkGiottoEnvironment(envname = "giotto_env")) {
+          if (!GiottoClass::checkGiottoEnvironment()) {
             GiottoClass::installGiottoEnvironment()
           }
 

diff --git a/.github/workflows/main_check.yml b/.github/workflows/main_check.yml
@@ -11,7 +11,7 @@ name: R-CMD-check
 
 on:
   pull_request:
-    types: closed
+    types: opened
     branches: [ "main" ]
 
 permissions:
@@ -64,9 +64,9 @@ jobs:
             any::testthat
             any::rlang
             any::R.utils
-            any::remotes
             any::knitr
             any::rmarkdown
+            any::qs
             any::sp
             any::stars
             any::raster
@@ -77,14 +77,46 @@ jobs:
             any::geometry
             any::qs
             any::future.apply
+            any::Biobase
+            any::chihaya
+            any::DelayedArray
+            any::DelayedMatrixStats
+            any::HDF5Array
+            any::plotly
+            any::rgl
+            any::rhdf5
+            any::S4Vectors
+            any::ScaledMatrix
+            any::XML
+            any::Seurat
+            any::SeuratObject
+            any::SingleCellExperiment
+            any::SpatialExperiment
+            any::STexampleData
+            any::SummarizedExperiment
             github::drieslab/GiottoData
 
-      - name: Test python env build
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: setup giotto_env
+        shell: Rscript {0}
         run: |
           if (!GiottoClass::checkGiottoEnvironment()) {
             GiottoClass::installGiottoEnvironment()
           }
-        shell: Rscript {0}
+          
+          reticulate::conda_install(
+            envname = 'giotto_env',
+            packages = 'scanpy',
+            pip = TRUE
+          )
+          
+          path_to_python <- GiottoClass::set_giotto_python_path()
+          
+          writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
+                     Sys.getenv("GITHUB_ENV"))
 
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2