diff --git a/.Rbuildignore b/.Rbuildignore index 360db7d..aa91b24 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -11,3 +11,4 @@ ^\.prettierrc$ ^data-raw$ ^Dockerfile$ +^CITATION\.cff$ diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml new file mode 100644 index 0000000..4cdc07a --- /dev/null +++ b/.github/workflows/update-citation-cff.yaml @@ -0,0 +1,55 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# The action runs when: +# - A new release is published +# - The DESCRIPTION or inst/CITATION are modified +# - Can be run manually +# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows +on: + release: + types: [published] + push: + branches: [master, main] + paths: + - DESCRIPTION + - inst/CITATION + workflow_dispatch: + +name: Update CITATION.cff + +jobs: + update-citation-cff: + runs-on: macos-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: | + any::cffr + any::V8 + + - name: Update CITATION.cff + run: | + + library(cffr) + + # Customize with your own code + # See https://docs.ropensci.org/cffr/articles/cffr.html + + # Write your own keys + mykeys <- list() + + # Create your CITATION.cff file + cff_write(keys = mykeys) + + shell: Rscript {0} + + - name: Commit results + run: | + git config --local user.name "github-actions[bot]" + git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com" + git add CITATION.cff + git commit -m 'chore: update CITATION.cff' || echo "No changes to commit" + git push origin || echo "No changes to commit" diff --git a/.prettierrc b/.prettierrc index df71f4f..6385d00 100644 --- a/.prettierrc +++ b/.prettierrc @@ -1,4 +1,7 @@ overrides: - - files: "*.md" + - files: + - "*.md" + - "citation.cff" + - ".prettierrc" options: tabWidth: 2 diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..99d9a2b --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,156 @@ +# ----------------------------------------------------------- +# CITATION file created with {cffr} R package, v0.5.0 +# See also: https://docs.ropensci.org/cffr/ +# ----------------------------------------------------------- + +cff-version: 1.2.0 +message: 'To cite package "reneeTools" in publications use:' +type: software +license: MIT +title: "reneeTools: Helper functions for RENEE" +version: 0.0.0.9000 +abstract: TODO What the package does (one paragraph). +authors: + - family-names: Koparde + given-names: Vishal + email: vishal.koparde@nih.gov + orcid: https://orcid.org/0000-0001-8978-8495 + - family-names: Sovacool + given-names: Kelly + email: kelly.sovacool@nih.gov + orcid: https://orcid.org/0000-0003-3283-829X +repository-code: https://github.com/CCBR/reneeTools +url: https://ccbr.github.io/reneeTools/ +contact: + - family-names: Koparde + given-names: Vishal + email: vishal.koparde@nih.gov + orcid: https://orcid.org/0000-0001-8978-8495 +references: + - type: software + title: "R: A Language and Environment for Statistical Computing" + notes: Depends + url: https://www.R-project.org/ + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: "2024" + institution: + name: R Foundation for Statistical Computing + version: ">= 2.10" + - type: software + title: DESeq2 + abstract: + "DESeq2: Differential gene expression analysis based on the negative binomial + distribution" + notes: Imports + url: https://github.com/thelovelab/DESeq2 + repository: https://bioconductor.org/ + authors: + - family-names: Love + given-names: Michael + email: michaelisaiahlove@gmail.com + - family-names: Anders + given-names: Simon + - family-names: Huber + given-names: Wolfgang + year: "2024" + doi: 10.18129/B9.bioc.DESeq2 + - type: software + title: dplyr + abstract: "dplyr: A Grammar of Data Manipulation" + notes: Imports + url: https://dplyr.tidyverse.org + repository: https://CRAN.R-project.org/package=dplyr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + - family-names: François + given-names: Romain + orcid: https://orcid.org/0000-0002-2444-4226 + - family-names: Henry + given-names: Lionel + - family-names: Müller + given-names: Kirill + orcid: https://orcid.org/0000-0002-1416-3412 + - family-names: Vaughan + given-names: Davis + email: davis@posit.co + orcid: https://orcid.org/0000-0003-4777-038X + year: "2024" + - type: software + title: S7 + abstract: "S7: An Object Oriented System Meant to Become a Successor to S3 and S4" + notes: Imports + url: https://github.com/rconsortium/S7/ + repository: https://CRAN.R-project.org/package=S7 + authors: + - family-names: Vaughan + given-names: Davis + - family-names: Hester + given-names: Jim + orcid: https://orcid.org/0000-0002-2739-7082 + - family-names: Kalinowski + given-names: Tomasz + - family-names: Landau + given-names: Will + - family-names: Lawrence + given-names: Michael + - family-names: Maechler + given-names: Martin + orcid: https://orcid.org/0000-0002-8685-9910 + - family-names: Tierney + given-names: Luke + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + orcid: https://orcid.org/0000-0003-4757-117X + year: "2024" + - type: software + title: tidyr + abstract: "tidyr: Tidy Messy Data" + notes: Imports + url: https://tidyr.tidyverse.org + repository: https://CRAN.R-project.org/package=tidyr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Vaughan + given-names: Davis + email: davis@posit.co + - family-names: Girlich + given-names: Maximilian + year: "2024" + - type: software + title: readr + abstract: "readr: Read Rectangular Text Data" + notes: Suggests + url: https://readr.tidyverse.org + repository: https://CRAN.R-project.org/package=readr + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + - family-names: Hester + given-names: Jim + - family-names: Bryan + given-names: Jennifer + email: jenny@posit.co + orcid: https://orcid.org/0000-0002-6983-2759 + year: "2024" + - type: software + title: testthat + abstract: "testthat: Unit Testing for R" + notes: Suggests + url: https://testthat.r-lib.org + repository: https://CRAN.R-project.org/package=testthat + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@posit.co + year: "2024" + version: ">= 3.0.0"