diff --git a/.Rbuildignore b/.Rbuildignore index d9c6d28..a0b4d5f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -8,3 +8,6 @@ CONDUCT.md CONTRIBUTING.md ^\.github$ data-raw/ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..bfc9f4d --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,49 @@ +# 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 +on: + push: + branches: [main, master] + pull_request: + release: + types: [published] + workflow_dispatch: + +name: pkgdown.yaml + +permissions: read-all + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.gitignore b/.gitignore index 9ee2175..3261c13 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,4 @@ doc Meta /doc/ /Meta/ +docs diff --git a/DESCRIPTION b/DESCRIPTION index a4203bd..cbe39eb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,12 +3,16 @@ Package: VISCfunctions Title: VISC STP/SRA functions Version: 1.3.0.9000 Authors@R: c( - person("Bryan", "Mayer", , "bmayer@fredhutch.org", role = "aut"), - person("Monica", "Gerber", , "mgerber@fredhutch.org", role = "aut"), - person("Celia", "Mahoney", , "cmahoney@fredhutch.org", role = "aut"), - person("Ellis", "Hughes", , "ehhughes@fredhutch.org", role = "aut"), - person("Heather", "Bouzek", , "hbouzek@fredhutch.org", role = "aut"), - person("Jimmy", "Fulp", , "wfulp@fredhutch.org", role = c("aut", "cre")) + person("Bryan", "Mayer", , "bmayer@fredhutch.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2258-5276")), + person("Dave", "Slager", , "dslager@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0003-2525-2039")), + person("Kellie", "MacPhee", , "kmacphee@fredhutch.org", role = "aut", comment = c(ORCID = "0009-0008-0993-4009")), + person("Gabrielle", "Lemire", , "glemire@fredhutch.org", role = "aut"), + person("Claudio", "Yurdadon", , "cyurdado@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0002-4928-2737")), + person("Monica", "Gerber", , , role = "aut"), + person("Celia", "Mahoney", , , role = "aut"), + person("Ellis", "Hughes", , , role = "aut", comment = c(ORCID = "0000-0003-0637-4436")), + person("Heather", "Bouzek", , , role = "aut"), + person("Jimmy", "Fulp", , , role = "aut") ) Description: Statistical, data processing, and annotation functions for VISC. @@ -37,3 +41,4 @@ Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.3 +URL: https://fredhutch.github.io/VISCfunctions/ diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..2062931 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: https://fredhutch.github.io/VISCfunctions/ +template: + bootstrap: 5 + diff --git a/man/VISCfunctions-package.Rd b/man/VISCfunctions-package.Rd index 7cd87e6..b82ff73 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -6,17 +6,28 @@ \title{VISCfunctions: VISC STP/SRA functions} \description{ Statistical, data processing, and annotation functions for VISC. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://fredhutch.github.io/VISCfunctions/} +} + } \author{ -\strong{Maintainer}: Jimmy Fulp \email{wfulp@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} (\href{https://orcid.org/0000-0003-2258-5276}{ORCID}) Authors: \itemize{ - \item Bryan Mayer \email{bmayer@fredhutch.org} - \item Monica Gerber \email{mgerber@fredhutch.org} - \item Celia Mahoney \email{cmahoney@fredhutch.org} - \item Ellis Hughes \email{ehhughes@fredhutch.org} - \item Heather Bouzek \email{hbouzek@fredhutch.org} + \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) + \item Kellie MacPhee \email{kmacphee@fredhutch.org} (\href{https://orcid.org/0009-0008-0993-4009}{ORCID}) + \item Gabrielle Lemire \email{glemire@fredhutch.org} + \item Claudio Yurdadon \email{cyurdado@fredhutch.org} (\href{https://orcid.org/0000-0002-4928-2737}{ORCID}) + \item Monica Gerber + \item Celia Mahoney + \item Ellis Hughes (\href{https://orcid.org/0000-0003-0637-4436}{ORCID}) + \item Heather Bouzek + \item Jimmy Fulp } } diff --git a/man/VISCfunctions.Rd b/man/VISCfunctions.Rd index 190cbca..d9ad4ff 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -6,17 +6,28 @@ \title{VISCfunctions: VISC STP/SRA functions} \description{ Statistical, data processing, and annotation functions for VISC. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://fredhutch.github.io/VISCfunctions/} +} + } \author{ -\strong{Maintainer}: Jimmy Fulp \email{wfulp@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} (\href{https://orcid.org/0000-0003-2258-5276}{ORCID}) Authors: \itemize{ - \item Bryan Mayer \email{bmayer@fredhutch.org} - \item Monica Gerber \email{mgerber@fredhutch.org} - \item Celia Mahoney \email{cmahoney@fredhutch.org} - \item Ellis Hughes \email{ehhughes@fredhutch.org} - \item Heather Bouzek \email{hbouzek@fredhutch.org} + \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) + \item Kellie MacPhee \email{kmacphee@fredhutch.org} (\href{https://orcid.org/0009-0008-0993-4009}{ORCID}) + \item Gabrielle Lemire \email{glemire@fredhutch.org} + \item Claudio Yurdadon \email{cyurdado@fredhutch.org} (\href{https://orcid.org/0000-0002-4928-2737}{ORCID}) + \item Monica Gerber + \item Celia Mahoney + \item Ellis Hughes (\href{https://orcid.org/0000-0003-0637-4436}{ORCID}) + \item Heather Bouzek + \item Jimmy Fulp } }