Merge pull request #10 from jiajic/dev

fix main check workflow

.github/workflows/main_check.yml

@@ -7,19 +7,21 @@
 # additional example workflows available for the R community.
 
 
+name: R-CMD-check
+
 on:
-  push:
-    branches: [ "main" ]
   pull_request:
+    types: closed
     branches: [ "main" ]
 
 permissions:
   contents: read
 
-name: github_workflow
 
 jobs:
   R-CMD-check:
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -35,32 +37,39 @@ 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
 
-      # run R CMD check
-      - uses: r-lib/actions/check-r-package@v2
+      - 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
@@ -71,66 +80,11 @@ jobs:
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
-  test-coverage:
-    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::covr
-          needs: coverage
-
-      - 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
-  #   env:
-  #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-  #   steps:
-  #     - uses: actions/checkout@v3
-  #
-  #     - uses: r-lib/actions/setup-r@v2
-  #       with:
-  #         use-public-rspm: true
-  #
-  #     - uses: r-lib/actions/setup-r-dependencies@v2
-  #       with:
-  #         extra-packages: any::lintr, local::.
-  #         needs: lint
-  #
-  #     - name: Lint
-  #       run: lintr::lint_package()
-  #       shell: Rscript {0}
-  #       env:
-  #         LINTR_ERROR_ON_LINT: true
 
 
   # render-rmarkdown:
+  #   name: Update README.Rmd
   #   runs-on: ubuntu-latest
-  #   env:
-  #     GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
   #   steps:
   #     - name: Checkout repo
   #       uses: actions/checkout@v3
@@ -153,3 +107,6 @@ jobs:
   #       run: |
   #         git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
   #         git push origin || echo "No changes to commit"
+
+
+

README.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 ![Version](https://img.shields.io/github/r-package/v/drieslab/GiottoVisuals)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![Codecov test coverage](https://codecov.io/gh/jiajic/GiottoVisuals/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jiajic/GiottoVisuals?branch=main)
+[![codecov](https://codecov.io/github/drieslab/GiottoVisuals/graph/badge.svg?token=F4ga1Ahbhw)](https://codecov.io/github/drieslab/GiottoVisuals)
 [![R-CMD-check](https://github.com/drieslab/GiottoVisuals/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/drieslab/GiottoVisuals/actions/workflows/R-CMD-check.yml)
 [![GitHub issues](https://img.shields.io/github/issues/drieslab/Giotto)](https://github.com/drieslab/Giotto/issues)
 [![GitHub pulls](https://img.shields.io/github/issues-pr/drieslab/GiottoVisuals)](https://github.com/drieslab/GiottoVisuals/pulls)

README.md

@@ -8,8 +8,7 @@
 ![Version](https://img.shields.io/github/r-package/v/drieslab/GiottoVisuals)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![Codecov test
-coverage](https://codecov.io/gh/jiajic/GiottoVisuals/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jiajic/GiottoVisuals?branch=main)
+[![codecov](https://codecov.io/github/drieslab/GiottoVisuals/graph/badge.svg?token=F4ga1Ahbhw)](https://codecov.io/github/drieslab/GiottoVisuals)
 [![R-CMD-check](https://github.com/drieslab/GiottoVisuals/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/drieslab/GiottoVisuals/actions/workflows/R-CMD-check.yml)
 [![GitHub
 issues](https://img.shields.io/github/issues/drieslab/Giotto)](https://github.com/drieslab/Giotto/issues)