neurogenomics · HDash · Mar 12, 2025 · Mar 12, 2025 · Mar 12, 2025 · Mar 12, 2025
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -25,7 +25,7 @@ jobs:
         - os: ubuntu-latest
           r: auto
           bioc: release
-          cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_19
+          cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_20
           python-version: 3.11
         - os: macOS-latest
           r: latest
@@ -50,7 +50,9 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
         DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1
+        ncpus: 2
         # free_diskspace: ${{ true }}
         # miniforge_variant: false
diff --git a/.github/workflows/rworkflows_static.yml b/.github/workflows/rworkflows_static.yml
@@ -121,7 +121,7 @@ jobs:
     - name: "\U0001F3E6 Restore R package cache"
       if: |
         !contains(github.event.head_commit.message, '[nocache]') && runner.os != 'Linux'
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc
@@ -131,7 +131,7 @@ jobs:
     - name: "\U0001F3E6 Cache R packages on Linux"
       if: |
         !contains(github.event.head_commit.message, '[nocache]') && runner.os == 'Linux'
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: /home/runner/work/_temp/Library
         key: ${{ env.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 1.0.6
+Version: 1.0.7
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -17,8 +17,12 @@ Authors@R:
              family = "Skene",
              role = c("aut"),
              email = "[email protected]",
-             comment = c(ORCID = "0000-0002-6807-3180")) 
-             ) 
+             comment = c(ORCID = "0000-0002-6807-3180")),
+      person(given = "Hiranyamaya (Hiru)",
+           family = "Dash",
+           role = c("ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0009-0005-5514-505X"))) 
 Description: Reproducibility is essential to the progress of research, 
   yet achieving it remains elusive even in computational fields. 
   Continuous Integration (CI) platforms offer a powerful way to launch automated workflows 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+# rworkflows 1.0.7
+
+## New features
+
+* New arg for number of cores to use for R package installation (`ncpus`).
+* Add `CODECOV_TOKEN` and `ncpus` to `rworkflows.yml` template.
+* Update to `actions/cache@v4` as v3 is marked for deprecation.
+## Documentation
+* Mention `CODECOV_TOKEN` in GitHub Secrets section.
+
+
 # rworkflows 1.0.6
 
 ## Bug fixes

diff --git a/README.Rmd b/README.Rmd
@@ -134,7 +134,11 @@ To use certain features of `rworkflows`, you may need to set up one or more
     repos on GitHub Actions. You can generate your very own Personal
     Authentication Token with `usethis::create_github_token()`. See the [GitHub docs](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token) for details.   
 * `DOCKER_TOKEN` [Optional]: Allows GitHub Actions to push to a
-    [DockerHub](https://hub.docker.com) account. 
+    [DockerHub](https://hub.docker.com) account.  
+* `CODECOV_TOKEN` [Optional]: Codecov repository token to upload coverage
+      reports. Providing this token helps prevent report upload failures by
+      bypassing Codecov's GitHub API rate limits. See the [Codecov documentation](https://docs.codecov.com/docs/adding-the-codecov-token)
+      for details.   
 
 ## Acknowledgments
 `rworkflows` builds upon the work of many others, especially the following:

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3)
 [![](https://img.shields.io/badge/doi-https://doi.org/10.5281/zenodo.10048573-blue.svg)](https://doi.org/https://doi.org/10.5281/zenodo.10048573)
 <br>
-[![](https://img.shields.io/badge/devel%20version-1.0.5-black.svg)](https://github.com/neurogenomics/rworkflows)
+[![](https://img.shields.io/badge/devel%20version-1.0.7-black.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/languages/code-size/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows)
 [![](https://img.shields.io/github/last-commit/neurogenomics/rworkflows.svg)](https://github.com/neurogenomics/rworkflows/commits/master)
 <br> [![R build
@@ -19,10 +19,11 @@ status](https://github.com/neurogenomics/rworkflows/workflows/rworkflows_dev/bad
 <br>
 <a href='https://app.codecov.io/gh/neurogenomics/rworkflows/tree/master' target='_blank'><img src='https://codecov.io/gh/neurogenomics/rworkflows/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
 <h4>  
-Authors: <i>Brian Schilder, Alan Murphy, Nathan Skene</i>  
+Authors: <i>Brian Schilder, Alan Murphy, Nathan Skene, Hiranyamaya
+(Hiru) Dash</i>  
 </h4>
 <h4>  
-README updated: <i>Dec-18-2024</i>  
+README updated: <i>Mar-17-2025</i>  
 </h4>
 
 [![CRAN
@@ -190,7 +191,13 @@ Secrets](https://docs.github.com/en/actions/security-guides/encrypted-secrets):
   docs](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token)
   for details.  
 - `DOCKER_TOKEN` \[Optional\]: Allows GitHub Actions to push to a
-  [DockerHub](https://hub.docker.com) account.
+  [DockerHub](https://hub.docker.com) account.  
+- `CODECOV_TOKEN` \[Optional\]: Codecov repository token to upload
+  coverage reports. Providing this token helps prevent report upload
+  failures by bypassing Codecov’s GitHub API rate limits. See the
+  [Codecov
+  documentation](https://docs.codecov.com/docs/adding-the-codecov-token)
+  for details.
 
 ## Acknowledgments
 
@@ -287,9 +294,9 @@ GitHub Action to setup Miniconda and conda environments.
 utils::sessionInfo()
 ```
 
-    ## R version 4.4.1 (2024-06-14)
+    ## R version 4.4.2 (2024-10-31)
     ## Platform: aarch64-apple-darwin20
-    ## Running under: macOS 15.1
+    ## Running under: macOS Sequoia 15.3.1
     ## 
     ## Matrix products: default
     ## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
@@ -305,21 +312,20 @@ utils::sessionInfo()
     ## [1] stats     graphics  grDevices utils     datasets  methods   base     
     ## 
     ## loaded via a namespace (and not attached):
-    ##  [1] gtable_0.3.6        jsonlite_1.8.9      renv_1.0.11        
-    ##  [4] dplyr_1.1.4         compiler_4.4.1      BiocManager_1.30.25
+    ##  [1] gtable_0.3.6        jsonlite_1.9.1      renv_1.1.2         
+    ##  [4] dplyr_1.1.4         compiler_4.4.2      BiocManager_1.30.25
     ##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.3.0       
     ## [10] yaml_2.3.10         fastmap_1.2.0       here_1.0.1         
-    ## [13] ggplot2_3.5.1       R6_2.5.1            generics_0.1.3     
-    ## [16] knitr_1.48          yulab.utils_0.1.7   tibble_3.2.1       
-    ## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
-    ## [22] munsell_0.5.1       pillar_1.9.0        RColorBrewer_1.1-3 
-    ## [25] rlang_1.1.4         utf8_1.2.4          badger_0.2.4       
-    ## [28] xfun_0.49           fs_1.6.5            cli_3.6.3          
-    ## [31] magrittr_2.0.3      rworkflows_1.0.4    digest_0.6.37      
-    ## [34] grid_4.4.1          rstudioapi_0.17.1   lifecycle_1.0.4    
-    ## [37] vctrs_0.6.5         evaluate_1.0.1      glue_1.8.0         
-    ## [40] data.table_1.16.2   fansi_1.0.6         colorspace_2.1-1   
-    ## [43] rmarkdown_2.29      tools_4.4.1         pkgconfig_2.0.3    
-    ## [46] htmltools_0.5.8.1
+    ## [13] ggplot2_3.5.1       R6_2.6.1            generics_0.1.3     
+    ## [16] knitr_1.49          yulab.utils_0.2.0   tibble_3.2.1       
+    ## [19] desc_1.4.3          dlstats_0.1.7       munsell_0.5.1      
+    ## [22] rprojroot_2.0.4     pillar_1.10.1       RColorBrewer_1.1-3 
+    ## [25] rlang_1.1.5         badger_0.2.4        xfun_0.51          
+    ## [28] fs_1.6.5            cli_3.6.4           magrittr_2.0.3     
+    ## [31] rworkflows_1.0.7    digest_0.6.37       grid_4.4.2         
+    ## [34] rstudioapi_0.17.1   lifecycle_1.0.4     vctrs_0.6.5        
+    ## [37] evaluate_1.0.3      glue_1.8.0          data.table_1.17.0  
+    ## [40] colorspace_2.1-1    rmarkdown_2.29      tools_4.4.2        
+    ## [43] pkgconfig_2.0.3     htmltools_0.5.8.1
 
 </details>
diff --git a/action.yml b/action.yml
@@ -176,6 +176,12 @@ inputs:
       Recommended to set to `true` when pushing changes without updating R
       package version, such as during pre-release phase of developement.
     default: false
+  ncpus:
+    description: >
+      Number of CPUs to use for R package installation. Higher values can speed
+      up the dependency installation process but may result in spurious errors.
+      Default is 2.
+    default: 2
 
 runs:
   using: 'composite'
@@ -257,7 +263,7 @@ runs:
     - name: 🏦 Restore R package cache 
       if: |
         !contains(github.event.head_commit.message, '[nocache]') && runner.os != 'Linux'
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
@@ -266,7 +272,7 @@ runs:
     - name: 🏦 Cache R packages on Linux 
       if: |
         !contains(github.event.head_commit.message, '[nocache]') && runner.os == 'Linux'
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: /home/runner/work/_temp/Library
         key: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
@@ -343,12 +349,14 @@ runs:
         timeout: ${{ inputs.timeout }}
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
         force_install: ${{ inputs.force_install }}
+        ncpus: ${{ inputs.ncpus }}
       run: |
-         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
+         options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"), Ncpus=as.integer(Sys.getenv("ncpus")))
          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck ****'))
          install.packages(c("rmarkdown","BiocManager"), dependencies = TRUE)
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies****'))
+         message(paste('**** Using', Sys.getenv("ncpus"), 'cores for installation.'))
          repos <- BiocManager::repositories()
          remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=Sys.getenv("force_install"))
       continue-on-error: true
@@ -358,8 +366,9 @@ runs:
       env:
         timeout: ${{ inputs.timeout }}
         GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}
+        ncpus: ${{ inputs.ncpus }}
       run: |
-        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"))
+        options(crayon.enabled = TRUE, timeout=Sys.getenv("timeout"), Ncpus=as.integer(Sys.getenv("ncpus")))
         message(paste('****', Sys.time(), 'pass number 2 at installing dependencies****'))
         repos <- BiocManager::repositories()
         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=FALSE)

diff --git a/inst/templates/rworkflows_template.yml b/inst/templates/rworkflows_template.yml
@@ -43,5 +43,7 @@
           docker_user: 'bschilder'
           docker_org: 'neurogenomicslab'
           DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} 
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} 
           runner_os: ${{ runner.os }} 
           cache_version: cache-master
+          ncpus: 2
diff --git a/tests/testthat/test-get_authors.R b/tests/testthat/test-get_authors.R
@@ -1,6 +1,6 @@
 test_that("get_authors works", {
 
-  true_auths <- "Brian Schilder, Alan Murphy, Nathan Skene"
+  true_auths <- "Brian Schilder, Alan Murphy, Nathan Skene, Hiranyamaya (Hiru) Dash"
   #### ref is NULL ####
   auths1 <- get_authors(ref = NULL)
   testthat::expect_null(auths1)

diff --git a/vignettes/rworkflows.Rmd b/vignettes/rworkflows.Rmd
@@ -30,7 +30,11 @@ Before pushing changes to your new R package, you may want to set up one or more
     Authentication Token using [these
     instructions](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token).   
 * `DOCKER_TOKEN` [Optional]: Allows GitHub Actions to push to a
-    [DockerHub](https://hub.docker.com) account. 
+    [DockerHub](https://hub.docker.com) account.   
+* `CODECOV_TOKEN` [Optional]: Codecov repository token to upload coverage
+      reports. Providing this token helps prevent report upload failures by
+      bypassing Codecov's GitHub API rate limits. See the [Codecov documentation](https://docs.codecov.com/docs/adding-the-codecov-token)
+      for details.   
 
 # `use_workflow`