Merge pull request #141 from R-Computing-Lab/dev_main

Dev main

Author: smasongarrison

.Rbuildignore

@@ -1,26 +1,38 @@
+CITATION.cff$
+^.*\.Rproj$
 ^BGmisc\.Rproj$
-^\.Rproj\.user$
+^BGmisc\.code-workspace$
+^BGmisc_main\.code-workspace$
+^CITATION\.cff$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+^CRAN-SUBMISSION$
+^LICENSE.md$
 ^LICENSE\.md$
+^Meta$
 ^R/\.Rhistory$
 ^R/paper$
-^checkParents\.X
-^test-clean\.X
-CITATION.cff$
-^doc$
-^data-raw$
-^Meta$
-^vignettes/articles$
 ^README\.Rmd$
+^\.Rproj\.user$
 ^\.github$
-^cran-comments\.md$
-^CRAN-SUBMISSION$
-^BGmisc\.code-workspace$
+^\.httr-oauth$
 ^\.lintr$
-^CODE_OF_CONDUCT\.md$
-^CONTRIBUTING\.md$
+^\.vscode$
+^\.zenodo\.json$
+^_pkgdown.yml$
 ^_pkgdown\.yml$
+^checkParents\.X
+^checklist.yml$
+^codecov\.yml$
+^codecov\.xaml$
+^cran-comments\.md$
+^data-raw$
+^doc$
 ^docs$
+^man-roxygen$
+^organisation.yml$
 ^pkgdown$
-^\.vscode$
-^BGmisc_main\.code-workspace$
 ^revdep$
+^test-clean\.X
+^vignettes/articles$
+^.claude$

.github/workflows/check_on_branch.xml

@@ -0,0 +1,20 @@
+on:
+  push:
+    branches-ignore:
+      - main
+      - master
+      - ghpages
+
+name: "check package with checklist"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
+    steps:
+      - uses: inbo/actions/check_pkg@main

.github/workflows/check_on_different_r_os.xml

@@ -0,0 +1,51 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check-OS
+
+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-24.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-24.04,   r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      _R_CHECK_SYSTEM_CLOCK_: false
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          extra-repositories: https://inbo.r-universe.dev
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"error"'

.github/workflows/check_on_main.xml

@@ -0,0 +1,19 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+permissions:
+  contents: write
+
+name: "check package on main with checklist"
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    name: "check package"
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: inbo/actions/check_pkg@main

.github/workflows/release.xml

@@ -0,0 +1,30 @@
+name: Releases
+
+on:
+  push:
+    tags:
+      - v*
+  workflow_run:
+    workflows: ["check package on main with checklist"]
+    types:
+      - completed
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Get tag
+        run: |
+          git fetch --tags --force
+          TAG=$(git tag --contains $(git rev-parse HEAD))
+          TAG_BODY=$(git tag --contains $(git rev-parse HEAD) --format='%(contents)')
+          echo "tag=$TAG" >> $GITHUB_ENV
+          echo "$TAG_BODY" > body.md
+      - uses: ncipollo/release-action@v1
+        with:
+          name: Release ${{ env.tag }}
+          tag: ${{ env.tag }}
+          bodyFile: body.md

.gitignore

@@ -1,27 +1,56 @@
+!source/**/_extensions/**
 *.ASOIAF.ged
 *.Rproj
+*.[rR][dD]ata
+*.[rR]ds
+*.dbf
+*.doc*
+*.eps
+*.gddoc
+*.gdsheet
+*.gpkg
+*.html
 *.knit.md
+*.mdb
+*.pdf
+*.shp*
+*.shx
+*.sty
+*.tex
+*.xls*
+*_cache
+*_files
+*_freeze
+*_libs
 .DS_Store
+.RData
 .Rdata
+.Renviron
 .Rhistory
 .Rproj.user
+.Ruserdata
 .httr-oauth
 .quarto
 .vscode/launch.json
+.vscode/settings.json
+/.claude
 /Meta/
 BGmisc.code-workspace
 R/.Rhistory
 benchmark_results.csv
+data-raw/Landers-Wilson-Garrison Tree.ged
+data-raw/logo_orange.png
 dataRelatedPairs.csv
 dataRelatedPairs_new2.csv
+docs
+libs
+output
 paper/paper.html
+renv/library
+revdep/
 tests/testthat/Rplots.pdf
 vignettes/articles/paper.html
-.vscode/settings.json
-data-raw/logo_orange.png
-data-raw/Landers-Wilson-Garrison Tree.ged
-vignettes/understanding_relatedness.Rmd
 vignettes/rewritten_relatedness_vignette.Rmd
-vignettes/understanding_relatedness.Xmd
 vignettes/rewritten_relatedness_vignette.Xmd
-revdep/
+vignettes/understanding_relatedness.Rmd
+vignettes/understanding_relatedness.Xmd

DESCRIPTION

@@ -14,13 +14,17 @@ Authors@R: c(
     person(c("S.", "Alexandra"), "Burt", role = "aut",
            comment = c(ORCID = "0000-0001-5538-7431"))
   )
-Description: Provides functions for behavior genetics analysis, 
-    including variance component model identification [Hunter et al. (2021) <doi:10.1007/s10519-021-10055-x>],
-    calculation of relatedness coefficients using path-tracing methods 
-    [Wright (1922) <doi:10.1086/279872>; McArdle & McDonald (1984) <doi:10.1111/j.2044-8317.1984.tb00802.x>], 
-    inference of relatedness, pedigree conversion, and simulation of multi-generational family data 
-    [Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full overview, 
-    see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For a big data application see [Burt et al. (2025) <doi: 10.1016/j.ebiom.2025.105911>.
+Description: Provides functions for behavior genetics analysis, including
+    variance component model identification [Hunter et al. (2021)
+    <doi:10.1007/s10519-021-10055-x>], calculation of relatedness
+    coefficients using path-tracing methods [Wright (1922)
+    <doi:10.1086/279872>; McArdle & McDonald (1984)
+    <doi:10.1111/j.2044-8317.1984.tb00802.x>], inference of relatedness,
+    pedigree conversion, and simulation of multi-generational family data
+    [Lyu et al. (2025) <doi:10.1007/s10519-025-10225-1>]. For a full
+    overview, see [Garrison et al. (2024) <doi:10.21105/joss.06203>]. For
+    a big data application see [Burt et al. (2025) <doi:
+    10.1016/j.ebiom.2025.105911>].
 License: GPL-3
 URL: https://github.com/R-Computing-Lab/BGmisc/,
     https://r-computing-lab.github.io/BGmisc/
@@ -31,9 +35,9 @@ Imports:
     data.table,
     igraph,
     Matrix,
+    methods,
     stats,
-    stringr,
-    methods
+    stringr
 Suggests: 
     corrplot,
     discord,
@@ -43,11 +47,11 @@ Suggests:
     ggplot2,
     kinship2,
     knitr,
+    mvtnorm,
     OpenMx,
     rmarkdown,
     testthat (>= 3.0.0),
     tidyverse,
-    mvtnorm,
     withr
 VignetteBuilder: 
     knitr

NEWS.md

@@ -1,5 +1,12 @@
 # BGmisc NEWS
 
+# Development version:
+* Fixed bug in parList
+* Moved wrappers of ped2com to own .R file
+* Fixed missing checkpoint for ram_checkpoint
+* Try a chunk_size argument for ped2com to reduce memory usage during transpose
+* Try filter method for whose relatedness to return by individual ID
+
 # BGmisc 1.6.0.1
 ## CRAN submission
 * Add OpenMx pedigree model builders and docs