Merge pull request #338 from Olink-Proteomics/optimization_develop_st…

…rict_ci_workflow Update CI workflows
Olink-Proteomics · Mar 15, 2024 · a601f46 · a601f46
2 parents 052c9cb + 1ad3dbe
commit a601f46
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -12,22 +12,22 @@ jobs:
       matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
       # Required as the JSON input file needs to be read
-      - uses: actions/checkout@v2      
+      - uses: actions/checkout@v2
       - id: set-matrix
-        uses: JoshuaTheMiller/conditional-build-matrix@main        
+        uses: JoshuaTheMiller/conditional-build-matrix@main
         with:
-          inputFile: '.github/workflows/matrix_config_check.json' 
+          inputFile: '.github/workflows/matrix_config_check.json'
           filter: '[?runOn==`${{ github.event_name }}` || runOn==`always`]'
           # addInclude: true
 
   R-CMD-check:
     needs: matrix_prep
-    strategy:      
-      fail-fast: false    
-      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}  
+    strategy:
+      fail-fast: false
+      matrix: ${{fromJson(needs.matrix_prep.outputs.matrix)}}
 
     runs-on: ${{ matrix.os }}
-    timeout-minutes: 120       
+    timeout-minutes: 120
 
     name: ${{ matrix.os }} (${{ matrix.r }})
 
@@ -37,30 +37,27 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
-          use-public-rspm: true            
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-pandoc@v2
-        with:
-          pandoc-version: '2.18'      
-
+
       - name: Set BioC version
         run: |
           install.packages("remotes")
           forenv <- paste("R_BIOC_VERSION=", as.character(remotes::bioc_version()), sep = "")
-          write(forenv, file = Sys.getenv("GITHUB_ENV"), append = TRUE) # Store current value to ENV          
+          write(forenv, file = Sys.getenv("GITHUB_ENV"), append = TRUE) # Store current value to ENV
         shell: Rscript {0}
 
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           working-directory: OlinkAnalyze
-          extra-packages: any::rcmdcheck, pillar
+          extra-packages: any::rcmdcheck
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          working-directory: OlinkAnalyze     
+          working-directory: OlinkAnalyze
diff --git a/.github/workflows/R-CMD-check_no-suggests.yaml b/.github/workflows/R-CMD-check_no-suggests.yaml
@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  push:
+    branches: [main, develop, optimization_develop]
+  pull_request:
+    branches: [main, develop, optimization_develop]
+
+name: R-CMD-check-hard
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: OlinkAnalyze
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: OlinkAnalyze
diff --git a/OlinkAnalyze/tests/testthat/helper-get_wide_synthetic_data.R b/OlinkAnalyze/tests/testthat/helper-get_wide_synthetic_data.R
@@ -50,8 +50,15 @@ get_wide_synthetic_data <- function(olink_platform,
   return(df_synthetic)
 }
 
-## Compute num of rows of output df ----
+# function to get the format specifications for wide files
+get_format_spec <- function(data_type) {
+  format_spec <- olink_wide_spec |>
+    dplyr::filter(.data[["data_type"]] == .env[["data_type"]])
 
+  return(format_spec)
+}
+
+# Compute num of rows of output df
 olink_wide2long_rows <- function(n_panels,
                                  n_assays,
                                  n_samples,

diff --git a/OlinkAnalyze/tests/testthat/test-read_npx.R b/OlinkAnalyze/tests/testthat/test-read_npx.R
@@ -137,6 +137,8 @@ test_that(
 test_that(
   "data loads correctly - long - zip",
   {
+    skip_if_not_installed("zip")
+
     withr::with_tempfile(
       new = "tmp_long_csv_zip",
       pattern = "csv-zip-long-",
@@ -205,6 +207,8 @@ test_that(
 test_that(
   "data loads correctly - long - extended v1 - zip",
   {
+    skip_if_not_installed("zip")
+
     withr::with_tempfile(
       new = "tmp_long_csv_ext_v1_zip",
       pattern = "csv-ext_v1-zip-long-",
@@ -279,6 +283,8 @@ test_that(
 test_that(
   "data loads correctly - long - extended v2 - zip",
   {
+    skip_if_not_installed("zip")
+
     withr::with_tempfile(
       new = "tmp_long_csv_ext_v2_zip",
       pattern = "csv-ext_v2-zip-long-",

diff --git a/OlinkAnalyze/tests/testthat/test-read_npx_delim.R b/OlinkAnalyze/tests/testthat/test-read_npx_delim.R
@@ -429,6 +429,7 @@ test_that(
 test_that(
   "check_field_separator - error - sep not a scalar string",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "cfile_test",
@@ -473,6 +474,7 @@ test_that(
 test_that(
   "check_field_separator - error - sep is scalar string but not accepted",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "cfile_test",
@@ -517,6 +519,7 @@ test_that(
 test_that(
   "check_field_separator - works - long format - sep is NULL",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = c("cdfile_test", "scdfile_test"),
@@ -604,6 +607,7 @@ test_that(
 test_that(
   "check_field_separator - works - wide format - sep is NULL",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = c("cdfile_test", "scdfile_test"),
@@ -689,6 +693,7 @@ test_that(
 test_that(
   "check_field_separator - works - long format - sep is correct",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = c("cdfile_test", "scdfile_test"),
@@ -776,6 +781,7 @@ test_that(
 test_that(
   "check_field_separator - works - wide format - sep is correct",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = c("cdfile_test", "scdfile_test"),
@@ -863,6 +869,7 @@ test_that(
 test_that(
   "get_field_separator - error - empty header or file",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "tfile_empty",
@@ -891,6 +898,7 @@ test_that(
 test_that(
   "get_field_separator - works - semicolon",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "tfile_semicolon",
@@ -919,6 +927,7 @@ test_that(
 test_that(
   "get_field_separator - works - comma",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "tfile_comma",
@@ -947,6 +956,7 @@ test_that(
 test_that(
   "get_field_separator - error - wrong sep",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "tfile_hashtag",
@@ -975,6 +985,7 @@ test_that(
 test_that(
   "get_field_separator - error - both comma and semicolon",
   {
+    skip_on_cran()
 
     withr::with_tempfile(
       new = "tfile_mixed",

diff --git a/OlinkAnalyze/tests/testthat/test-read_npx_excel.R b/OlinkAnalyze/tests/testthat/test-read_npx_excel.R
@@ -1,6 +1,8 @@
 test_that(
   "read_npx_excel - works - wide format",
   {
+    skip_if_not_installed("writexl")
+
     # get wide synthetic data
     df_synthetic <- get_wide_synthetic_data(olink_platform = "Target 96",
                                             data_type = "NPX",
@@ -91,6 +93,8 @@ test_that(
 test_that(
   "read_npx_excel - works - long format",
   {
+    skip_if_not_installed("writexl")
+
     # get wide synthetic data
     df_synthetic <- get_wide_synthetic_data(olink_platform = "Target 96",
                                             data_type = "NPX",
@@ -219,6 +223,8 @@ test_that(
 test_that(
   "read_npx_excel - error - df has one column only",
   {
+    skip_if_not_installed("writexl")
+
     withr::with_tempfile(
       new = "excel_file",
       pattern = "excel-file-test",