fixing issues with ncd2, improving documentation, making website

.Rbuildignore

@@ -1,10 +1,46 @@
-^renv$
-^renv\.lock$
+LICENSE
+README\.[R]?md
+README\.html
+\.Renviron$
+\.pyc$
+\.travis\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^data-raw$
-^LICENSE\.md$
-^BalSelTools\.Rproj$
-^README\.Rmd$
 ^\.github$
+^_pkgdown\.yml$
+^appveyor\.yml$
+^derby\.log$
+^docs$
+^images$
+^index\.Rmd$
+^internal$
+^issues$
+^log$
+^logs$
+^pkgdown$
+^revdep$
+^tags$
+^tests/testthat/resources/.*\.html$
+^tests/testthat/resources/.*_files
+^vignettes/images/code_completion\.png$
+^vignettes/images/help\.png$
+^vignettes/images/repl_python\.png$
+^vignettes/images/rmarkdown_reticulate\.png$
+^vignettes/images/rmarkdown_reticulate_matplotlib\.png$
+^vignettes/images/source_python\.png$
+^vignettes/rstudio_ide\.Rmd$
+^vignettes/rstudio_ide\.html$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^\.vscode$
+^Dockerfile$
+^\.dockerignore$
+^\.git-blame-ignore-revs$
+^rchk$
 ^\.library$
+^renv*
+^LICENSE\.md$
+^codecov\.yml$
+^inst/balselr_win_test\.R$
+^README\.Rmd$
+^data-raw$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+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/[email protected]
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs

.github/workflows/pr-commands.yaml

@@ -0,0 +1,79 @@
+# 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:
+ issue_comment:
+ types: [created]
+
+name: Commands
+
+jobs:
+ document:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+ name: document
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::roxygen2
+ needs: pr-document
+
+ - name: Document
+ run: roxygen2::roxygenise()
+ shell: Rscript {0}
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "[email protected]"
+ git add man/\* NAMESPACE
+ git commit -m 'Document'
+
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ style:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+ name: style
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+
+ - name: Install dependencies
+ run: install.packages("styler")
+ shell: Rscript {0}
+
+ - name: Style
+ run: styler::style_pkg()
+ shell: Rscript {0}
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "[email protected]"
+ git add \*.R
+ git commit -m 'Style'
+
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -8,3 +8,4 @@
 local_only/
 inst/doc
 .quarto
+docs

DESCRIPTION

@@ -1,29 +1,35 @@
 Package: balselr
 Title: Balancing Selection in R
-Version: 0.0.0.1000
+Version: 0.0.0.9000
 Authors@R: 
- person("Bárbara", "Bitarello", , "[email protected]", role = c("aut", "cre"),
-  comment = c(ORCID = "0000-0001-7676-9367"))
+ c(person("Bárbara", "Bitarello", , "[email protected]", role = c("cre","aut", "cre"),comment = c(ORCID = "0000-0001-7676-9367")),
+ person(give="Daphne",family="Hansell",role=c("ctb","aut")))
 Description: Run NCD statistics on population-level genomic data.
-License: MIT + file LICENSE
+License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 LazyData: true
 Imports: 
+ assertthat,
  data.table,
  dplyr,
  glue,
  magrittr,
- stringr
+ stringr,
+ tibble
 Depends: 
  R (>= 2.10)
 Config/testthat/edition: 3
 Suggests: 
+ devtools,
  knitr,
  withr,
  testthat,
  DT,
  rmarkdown,
- roxygen2
+ roxygen2,
+ rcmdcheck,
+ remotes
 VignetteBuilder: knitr
+URL: https://bitarellolab.github.io/balselr/