From 06feedd5ca0f67462f7dce44acbdfb7d3568b26f Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Thu, 18 Sep 2025 10:24:34 -0700 Subject: [PATCH 1/5] use_pkgdown_github_pages() --- .Rbuildignore | 3 +++ .github/workflows/pkgdown.yaml | 49 ++++++++++++++++++++++++++++++++++ .gitignore | 1 + DESCRIPTION | 3 ++- _pkgdown.yml | 4 +++ man/VISCfunctions-package.Rd | 7 +++++ man/VISCfunctions.Rd | 7 +++++ 7 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/pkgdown.yaml create mode 100644 _pkgdown.yml 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 7fc7586..48f75dd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -36,4 +36,5 @@ VignetteBuilder: Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +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..f4c6df1 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -6,6 +6,13 @@ \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} diff --git a/man/VISCfunctions.Rd b/man/VISCfunctions.Rd index 190cbca..0e74e54 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -6,6 +6,13 @@ \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} From d4a42771c614c1331b0d24b8de99a92be64c8da5 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 2 Dec 2025 13:43:55 -0800 Subject: [PATCH 2/5] update authors --- DESCRIPTION | 16 ++++++++++------ man/VISCfunctions-package.Rd | 16 ++++++++++------ man/VISCfunctions.Rd | 16 ++++++++++------ 3 files changed, 30 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 48f75dd..5f39026 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")), + person("Dave", "Slager", , "dslager@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0003-2525-2039")), + person("Kellie", "MacPhee", , "kmacphee@fredhutch.org", role = "aut"), + person("Gabrielle", "Lemire", , "glemire@fredhutch.org", role = "aut"), + person("Claudio", "Yurdadon", , "cyurdado@fredhutch.org", role = "aut"), + 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. diff --git a/man/VISCfunctions-package.Rd b/man/VISCfunctions-package.Rd index f4c6df1..d6a91db 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -15,15 +15,19 @@ Useful links: } \author{ -\strong{Maintainer}: Jimmy Fulp \email{wfulp@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} 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} + \item Gabrielle Lemire \email{glemire@fredhutch.org} + \item Claudio Yurdadon \email{cyurdado@fredhutch.org} + \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 0e74e54..11afd32 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -15,15 +15,19 @@ Useful links: } \author{ -\strong{Maintainer}: Jimmy Fulp \email{wfulp@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} 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} + \item Gabrielle Lemire \email{glemire@fredhutch.org} + \item Claudio Yurdadon \email{cyurdado@fredhutch.org} + \item Monica Gerber + \item Celia Mahoney + \item Ellis Hughes (\href{https://orcid.org/0000-0003-0637-4436}{ORCID}) + \item Heather Bouzek + \item Jimmy Fulp } } From 36338529191b726fac7a48df2a2e3a80c5a4f069 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 2 Dec 2025 13:48:13 -0800 Subject: [PATCH 3/5] bryan orcid and document() --- DESCRIPTION | 2 +- man/VISCfunctions-package.Rd | 2 +- man/VISCfunctions.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5f39026..8362ada 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Package: VISCfunctions Title: VISC STP/SRA functions Version: 1.3.0.9000 Authors@R: c( - person("Bryan", "Mayer", , "bmayer@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"), person("Gabrielle", "Lemire", , "glemire@fredhutch.org", role = "aut"), diff --git a/man/VISCfunctions-package.Rd b/man/VISCfunctions-package.Rd index d6a91db..450f73e 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -15,7 +15,7 @@ Useful links: } \author{ -\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} (\href{https://orcid.org/0000-0003-2258-5276}{ORCID}) Authors: \itemize{ diff --git a/man/VISCfunctions.Rd b/man/VISCfunctions.Rd index 11afd32..8b68b44 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -15,7 +15,7 @@ Useful links: } \author{ -\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} +\strong{Maintainer}: Bryan Mayer \email{bmayer@fredhutch.org} (\href{https://orcid.org/0000-0003-2258-5276}{ORCID}) Authors: \itemize{ From 55d72198ce1aad05f6e7d7811c5f376ec4525844 Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 2 Dec 2025 13:50:08 -0800 Subject: [PATCH 4/5] add claudio orcid --- DESCRIPTION | 2 +- man/VISCfunctions-package.Rd | 2 +- man/VISCfunctions.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8362ada..39918b0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,7 @@ Authors@R: c( person("Dave", "Slager", , "dslager@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0003-2525-2039")), person("Kellie", "MacPhee", , "kmacphee@fredhutch.org", role = "aut"), person("Gabrielle", "Lemire", , "glemire@fredhutch.org", role = "aut"), - person("Claudio", "Yurdadon", , "cyurdado@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")), diff --git a/man/VISCfunctions-package.Rd b/man/VISCfunctions-package.Rd index 450f73e..76f66ce 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -22,7 +22,7 @@ Authors: \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) \item Kellie MacPhee \email{kmacphee@fredhutch.org} \item Gabrielle Lemire \email{glemire@fredhutch.org} - \item Claudio Yurdadon \email{cyurdado@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}) diff --git a/man/VISCfunctions.Rd b/man/VISCfunctions.Rd index 8b68b44..e922334 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -22,7 +22,7 @@ Authors: \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) \item Kellie MacPhee \email{kmacphee@fredhutch.org} \item Gabrielle Lemire \email{glemire@fredhutch.org} - \item Claudio Yurdadon \email{cyurdado@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}) From 0e43b1173d354239dbb1fe9297ef30a55e92810f Mon Sep 17 00:00:00 2001 From: Dave Slager Date: Tue, 2 Dec 2025 14:05:20 -0800 Subject: [PATCH 5/5] kellie orcid & document --- DESCRIPTION | 2 +- man/VISCfunctions-package.Rd | 2 +- man/VISCfunctions.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 39918b0..cbe39eb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Version: 1.3.0.9000 Authors@R: c( 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"), + 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"), diff --git a/man/VISCfunctions-package.Rd b/man/VISCfunctions-package.Rd index 76f66ce..b82ff73 100644 --- a/man/VISCfunctions-package.Rd +++ b/man/VISCfunctions-package.Rd @@ -20,7 +20,7 @@ Useful links: Authors: \itemize{ \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) - \item Kellie MacPhee \email{kmacphee@fredhutch.org} + \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 diff --git a/man/VISCfunctions.Rd b/man/VISCfunctions.Rd index e922334..d9ad4ff 100644 --- a/man/VISCfunctions.Rd +++ b/man/VISCfunctions.Rd @@ -20,7 +20,7 @@ Useful links: Authors: \itemize{ \item Dave Slager \email{dslager@fredhutch.org} (\href{https://orcid.org/0000-0003-2525-2039}{ORCID}) - \item Kellie MacPhee \email{kmacphee@fredhutch.org} + \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