diff --git a/.github/workflows/make-live.yml b/.github/workflows/make-live.yml index 093b0912..d10d0a2c 100644 --- a/.github/workflows/make-live.yml +++ b/.github/workflows/make-live.yml @@ -8,14 +8,14 @@ on: rendering: description: Should rendering be completed? TRUE or FALSE required: true - default: 'TRUE' + default: "TRUE" jobs: make-live: # The type of runner that the job will run on runs-on: ubuntu-latest container: - image: ccdl/training_dev:latest + image: ccdl/training_rstudio:edge steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it @@ -59,7 +59,7 @@ jobs: signoff: false branch: auto_render_live delete-branch: true - title: 'GHA: Automated live (rendered) versions of the notebooks' + title: "GHA: Automated live (rendered) versions of the notebooks" body: | ### Description: This PR auto-generated from github actions running make-live.R with: @@ -73,7 +73,6 @@ jobs: automated reviewers: $GITHUB_ACTOR - # Write PR info - name: Check outputs run: | diff --git a/.github/workflows/render-rmds.yml b/.github/workflows/render-rmds.yml index 0cae09e7..3b3cd56c 100644 --- a/.github/workflows/render-rmds.yml +++ b/.github/workflows/render-rmds.yml @@ -17,7 +17,7 @@ jobs: test-render: runs-on: ubuntu-latest container: - image: ccdl/training_dev:latest + image: ccdl/training_rstudio:edge steps: - name: Checkout code diff --git a/.github/workflows/spell-check.yml b/.github/workflows/spell-check.yml index 739b6739..9b313fb3 100644 --- a/.github/workflows/spell-check.yml +++ b/.github/workflows/spell-check.yml @@ -1,42 +1,43 @@ - name: Spell check R Markdown and Markdown files -# Controls when the action will run. -# Pull requests to master only. on: pull_request: branches: - master -# A workflow run is made up of one or more jobs that can run sequentially or in parallel +concurrency: + # only one run per branch at a time + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + jobs: - # This workflow contains a single job called "spell check" - spell-check: + spellcheck: runs-on: ubuntu-latest - container: - image: rocker/tidyverse:4.2.3 + name: Spell check files + permissions: + contents: read + issues: write - # Steps represent a sequence of tasks that will be executed as part of the job steps: - - uses: actions/checkout@v3 - - - name: Install packages - run: Rscript --vanilla -e "install.packages(c('spelling'), repos = c(CRAN = '$CRAN'))" + - name: Checkout + uses: actions/checkout@v4 - - name: Run spell check - id: spell_check_run - run: | - results=$(Rscript --vanilla "scripts/spell-check.R") - echo "sp_chk_results=$results" >> $GITHUB_OUTPUT - cat spell_check_errors.tsv + - name: Spell check action + uses: alexslemonade/spellcheck@v0 + id: spell + with: + dictionary: components/dictionary.txt - - name: Archive spelling errors - uses: actions/upload-artifact@v3 + - name: Upload spell check errors + uses: actions/upload-artifact@v4 + id: artifact-upload-step with: - name: spell-check-results + name: spell_check_errors path: spell_check_errors.tsv - # If there are too many spelling errors, this will stop the workflow - - name: Check spell check results - fail if too many errors - if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }} - run: exit 1 + - name: Fail if there are spelling errors + if: steps.spell.outputs.error_count > 0 + run: | + echo "There were ${{ steps.spell.outputs.error_count }} errors" + column -t spell_check_errors.tsv + exit 1 diff --git a/components/dictionary.txt b/components/dictionary.txt index 27e678ff..3379690a 100644 --- a/components/dictionary.txt +++ b/components/dictionary.txt @@ -1,4 +1,5 @@ ʹ +⚠️ Adelie ADT ADTs @@ -80,9 +81,9 @@ Danio Darmanis DataFrames dataset +de deconvolution deconvolved -de dendritic DESeq DESeq2 @@ -92,6 +93,7 @@ DGE digoxin DIPG directionality +discoverable dispersions displaystyle DocToc @@ -109,6 +111,7 @@ embryonal emptyDrops ENA endothelium +enforceability Enricher Ensdb Ensembl @@ -145,6 +148,7 @@ GBM GC GeneCard GeneCards +generis geo GG ggplot @@ -185,10 +189,12 @@ HPCA https HVGs ICb +ies IgG IgSF Illumina imap +immunities immunohistochemical immunophenotypic immunostaining @@ -218,6 +224,9 @@ Lafzi LFC LGLs Liberzon +licensor +licensor's +licensors linkedTxome lncRNAs loadings @@ -243,6 +252,7 @@ medulloblastoma MEK Menyhárt mer +merchantability mesenchymal mesoderm metacell @@ -353,6 +363,7 @@ RAS rds Reactome README +redistributions redux relevel renv @@ -415,7 +426,8 @@ summarization SummarizedExperiment symlinked symlinks -Τ +synched +T Tabula Tamayo TBD @@ -465,6 +477,7 @@ VST Wattenberg Wickham Wickham's +WIPO WNT xenograft Yu