diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 00000000..94be2898 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,22 @@ +--- +name: R CMD check +'on': + workflow_dispatch: + pull_request: + push: + branches: + - main + schedule: + - cron: '0 0 * * MON' +jobs: + R-CMD-check: + runs-on: ubuntu-latest + steps: + - name: Install system dependencies + run: | + sudo apt-get update + sudo apt-get install -y \ + libjpeg-dev \ + libpng-dev + - uses: r-lib/actions/setup-tinytex@v2 + - uses: uclahs-cds/tool-R-CMD-check-action@v2 diff --git a/.github/workflows/r-lib-check.yaml b/.github/workflows/r-lib-check.yaml deleted file mode 100644 index 184c71c1..00000000 --- a/.github/workflows/r-lib-check.yaml +++ /dev/null @@ -1,16 +0,0 @@ ---- -name: R-CMD-check (r-lib) -'on': - workflow_dispatch: - pull_request: - push: - branches: - - main - schedule: - - cron: '0 0 * * MON' -jobs: - R-CMD-check: - runs-on: ubuntu-latest - steps: - - uses: r-lib/actions/setup-tinytex@v2 - - uses: uclahs-cds/tool-R-CMD-check-action@CEV diff --git a/DESCRIPTION b/DESCRIPTION index f95f394c..788c30c3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: CancerEvolutionVisualization Title: Publication Quality Phylogenetic Tree Plots Version: 3.0.0 -Date: 2025-04-09 +Date: 2025-06-13 Authors@R: c( person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"), person("Adriana Salcedo", role = "aut"), @@ -24,6 +24,7 @@ Imports: BoutrosLab.plotting.general Suggests: testthat, + rmarkdown, knitr VignetteBuilder: knitr LazyLoad: yes diff --git a/NEWS.md b/NEWS.md index 82b8f3d7..8ececee4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# CancerEvolutionVisualization 3.0.0 (2025-04-09) +# CancerEvolutionVisualization 3.0.0 (2025-06-13) ## Added * Dendrogram mode @@ -17,6 +17,7 @@ * Add support for 1xn and 1x1 heatmaps. * Add `get.colours.in.order` function to get a list of colours and corresponding clone ID order. * Add `sample.order` and `clone.order` as input parameters to `create.cluster.heatmap` +* Suggest rmarkdown dependency for rendering vignettes ## Update * Fixed angle calculation bug where child angles do not follow @@ -33,6 +34,7 @@ * Updated the user guide to reflect new features. * Fix bug where the x-axis only renders when y-axis is also rendered. * Fix issue when creating polygons with more than 2 siblings +* Use updated `R CMD check` CI/CD action ## Bug * Resolved issue where the spread parameter was not applied in dendrogram mode.