From 598f9f2ce041bad62dd6e9276fbf05f106bbe670 Mon Sep 17 00:00:00 2001 From: SkylarMarvel <57526164+SkylarMarvel@users.noreply.github.com> Date: Tue, 29 Oct 2024 17:06:03 -0600 Subject: [PATCH] Updated GHA (#68) * Changed GHA R-CMD-check from release to standard * Updated GHA pkgdown * Required R version >= 4.4.0 * Updated title case, separate URLs with comma * Updated medrxiv urls * Increment version number to 0.1.3 * Removed old empty news entries * Regenerated docs after fixing urls * Removed 'oldrel-1' ubuntu rcmdcheck until R 4.5.0 * Added .DS_Store to .Rbuildignore --- .Rbuildignore | 1 + .github/workflows/R-CMD-check.yaml | 52 ++++++++++++++++++++++++++++ .github/workflows/check-release.yaml | 31 ----------------- .github/workflows/pkgdown.yaml | 8 +++-- DESCRIPTION | 8 ++--- NEWS.md | 8 ++--- README.Rmd | 7 ++-- README.md | 8 ++--- inst/CITATION | 4 +-- man/GeoTox-package.Rd | 5 +-- 10 files changed, 74 insertions(+), 58 deletions(-) create mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .github/workflows/check-release.yaml diff --git a/.Rbuildignore b/.Rbuildignore index 83da26f..92c734a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,6 +1,7 @@ ^renv$ ^renv\.lock$ ^\.Rprofile$ +^\.DS_Store$ ^GeoTox\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..c93888e --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,52 @@ +# 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: + branches: [main, master] + +name: R-CMD-check.yaml + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + #- {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/check-release.yaml b/.github/workflows/check-release.yaml deleted file mode 100644 index 88e15c5..0000000 --- a/.github/workflows/check-release.yaml +++ /dev/null @@ -1,31 +0,0 @@ -# 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: - branches: [main, master] - -name: R-CMD-check - -jobs: - R-CMD-check: - runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes - steps: - - uses: actions/checkout@v3 - - - uses: r-lib/actions/setup-r@v2 - with: - use-public-rspm: true - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::rcmdcheck - needs: check - - - uses: r-lib/actions/check-r-package@v2 - with: - upload-snapshots: true diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index ed7650c..4bbce75 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -9,7 +9,9 @@ on: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -22,7 +24,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/DESCRIPTION b/DESCRIPTION index 636c9da..52709ec 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: GeoTox -Title: Spatiotemporal mixture risk assessment -Version: 0.1.2 +Title: Spatiotemporal Mixture Risk Assessment +Version: 0.1.3 Authors@R: c( person("Skylar", "Marvel", , "skylar.marvel@nih.gov", role = c("aut", "ctb"), comment = c(ORCID = "0000-0002-2971-9743")), person("David", "Reif", , "david.reif@nih.gov", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-7815-6767")), @@ -8,9 +8,9 @@ Authors@R: c( ) Description: Connecting spatiotemporal exposure to individual and population-level risk via source-to-outcome continuum modeling. License: MIT + file LICENSE -URL: https://niehs.github.io/GeoTox/ https://github.com/NIEHS/GeoTox +URL: https://niehs.github.io/GeoTox/, https://github.com/NIEHS/GeoTox Depends: - R (>= 4.1.0) + R (>= 4.4.0) Imports: dplyr, ggplot2, diff --git a/NEWS.md b/NEWS.md index 3287740..109c05a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,10 +1,6 @@ -# GeoTox 0.1.2 +# GeoTox 0.1.3 -# GeoTox 0.1.1 - -# GeoTox 0.1.0 - -# 0.0.1 +# GeoTox 0.0.1 - Adding supporting documents to the `GeoTox` repository such as this news.md, issue templates, and contributor's guide - NC areal level analysis vignette is complete - Key developments on the object oriented approach: simulate and sensitivity wrappers diff --git a/README.Rmd b/README.Rmd index a9a3e66..f30d800 100644 --- a/README.Rmd +++ b/README.Rmd @@ -18,11 +18,10 @@ knitr::opts_chunk$set( [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![R-CMD-check](https://github.com/NIEHS/GeoTox/actions/workflows/check-release.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/check-release.yaml) +[![R-CMD-check](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml) [![pkgdown](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml) [![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions) [![CRAN status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox) - @@ -37,9 +36,7 @@ The package will be on CRAN in the near future - please stay tuned. You can inst [GitHub](https://github.com/NIEHS/GeoTox) with: ```{r, eval=FALSE} -if (!require("pak", quietly = TRUE)) { - install.packages("pak") -} +install.packages("pak") pak::pkg_install("NIEHS/GeoTox") ``` diff --git a/README.md b/README.md index 792809f..12a950b 100644 --- a/README.md +++ b/README.md @@ -8,12 +8,11 @@ [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![R-CMD-check](https://github.com/NIEHS/GeoTox/actions/workflows/check-release.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/check-release.yaml) +[![R-CMD-check](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml) [![pkgdown](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml) [![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions) [![CRAN status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox) - `GeoTox` open-source R software package for characterizing the risk of @@ -36,9 +35,7 @@ can install the development version of GeoTox from [GitHub](https://github.com/NIEHS/GeoTox) with: ``` r -if (!require("pak", quietly = TRUE)) { - install.packages("pak") -} +install.packages("pak") pak::pkg_install("NIEHS/GeoTox") ``` @@ -55,6 +52,7 @@ the information required to run the analysis including tracking exposure, assays, dose-response, and geospatial referencing.

+ GeoTox-Workflow
Figure 1: Overview of the steps in the GeoTox framework

diff --git a/inst/CITATION b/inst/CITATION index 371b29d..537c1ea 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -8,8 +8,8 @@ bibentry( year = "2024", doi = "10.1101/2024.09.23.24314096", elocationid = "2024.09.23.24314096", - url = "https://www.medrxiv.org/content/early/2024/09/24/2024.09.23.24314096", - eprint = "https://www.medrxiv.org/content/early/2024/09/24/2024.09.23.24314096.full.pdf" + url = "https://www.medrxiv.org/content/10.1101/2024.09.23.24314096v1", + eprint = "https://www.medrxiv.org/content/10.1101/2024.09.23.24314096v1.full.pdf" ) bibentry( diff --git a/man/GeoTox-package.Rd b/man/GeoTox-package.Rd index af8065f..edff2be 100644 --- a/man/GeoTox-package.Rd +++ b/man/GeoTox-package.Rd @@ -3,7 +3,7 @@ \docType{package} \name{GeoTox-package} \alias{GeoTox-package} -\title{GeoTox: Spatiotemporal mixture risk assessment} +\title{GeoTox: Spatiotemporal Mixture Risk Assessment} \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} @@ -12,7 +12,8 @@ Connecting spatiotemporal exposure to individual and population-level risk via s \seealso{ Useful links: \itemize{ - \item \url{https://niehs.github.io/GeoTox/ https://github.com/NIEHS/GeoTox} + \item \url{https://niehs.github.io/GeoTox/} + \item \url{https://github.com/NIEHS/GeoTox} } }