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Using RcppTskit + GitHub actions
1 parent 56e68ef commit 22c13a9

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‎.github/workflows/R-CMD-check.yaml‎

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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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branches: [main, master, devel]
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pull_request:
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branches: [main, master]
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branches: [main, master, devel]
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name: R-CMD-check
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- { os: macOS-latest, r: "release" }
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- { os: windows-latest, r: "release" }
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- { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
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- { os: ubuntu-latest, r: "release" }
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- { os: ubuntu-latest, r: "oldrel-1" }
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-tinytex@v2
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- uses: r-lib/actions/setup-r@v2

‎.github/workflows/document.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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paths: ["R/**"]
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name: document.yaml
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permissions: read-all
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jobs:
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document:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::roxygen2
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needs: roxygen2
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- name: Document
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run: roxygen2::roxygenise()
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shell: Rscript {0}
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- name: Commit and push changes
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
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git add man/\* NAMESPACE DESCRIPTION
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git commit -m "Update documentation" || echo "No changes to commit"
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git pull --ff-only
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git push origin

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master, devel]
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: "release" }
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# - { os: macos-latest, r: "release" }
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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# fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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fail_ci_if_error: false
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config: codecov.yaml
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files: cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎DESCRIPTION‎

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@@ -40,9 +40,9 @@ URL: https://github.com/gaynorr/AlphaSimR,
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https://www.edx.org/learn/animal-breeding/the-university-of-edinburgh-breeding-programme-modelling-with-alphasimr
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Encoding: UTF-8
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Depends: R (>= 4.0.0)
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Imports: Rcpp (>= 0.12.7), Rdpack, methods, R6, tskitr
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Imports: Rcpp (>= 0.12.7), Rdpack, methods, R6, RcppTskit (>= 0.2.0)
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RdMacros: Rdpack
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LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH, tskitr
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LinkingTo: Rcpp, RcppArmadillo (>= 0.7.500.0.0), BH, RcppTskit (>= 0.2.0)
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RoxygenNote: 7.3.3
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Suggests: knitr, rmarkdown, testthat
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VignetteBuilder: knitr

‎NAMESPACE‎

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export(solveRRBLUP_EM2)
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export(solveRRBLUP_EM3)
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export(solveUVM)
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export(ts_num_individuals2)
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export(tc_ptr_summary2)
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export(usefulness)
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export(varA)
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export(varAA)
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exportClasses(TraitAG)
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import(Rcpp)
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importFrom(R6,R6Class)
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importFrom(RcppTskit,TableCollection)
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importFrom(RcppTskit,TreeSequence)
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importFrom(Rdpack,reprompt)
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importFrom(methods,.hasSlot)
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importFrom(methods,classLabel)
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importFrom(stats,rnorm)
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importFrom(stats,runif)
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importFrom(stats,var)
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importFrom(tskitr,ts_load)
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importFrom(tskitr,ts_num_individuals)
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importFrom(utils,combn)
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importFrom(utils,packageDescription)
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importFrom(utils,read.table)

‎R/AlphaSimR.R‎

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#' @importFrom utils combn read.table write.table packageDescription
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#' @importFrom R6 R6Class
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#' @importFrom Rdpack reprompt
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#' @importFrom tskitr ts_load ts_num_individuals
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#' @importFrom RcppTskit TableCollection TreeSequence
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#' @description
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#' The successor to the 'AlphaSim' software for breeding program

‎R/RcppExports.R‎

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.Call(`_AlphaSimR_MaCS`, args, maxSites, inbred, ploidy, nThreads, seed)
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}
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#' @title Get number of individuals in tree sequence
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#' @description Get number of individuals in tree sequence
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#' @param ts an external pointer to a \code{tsk_treeseq_t} object.
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#' @return integer number of individuals
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#' @title Summarise `tskit` table collection
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#' @param tc an external pointer to a \code{tsk_table_collection_t} object.
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#' @return A list.
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#' @examples
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#' ts_file <- system.file("examples", "test.trees", package = "tskitr")
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#' ts <- tskitr::ts_load(ts_file) # slendr also has ts_load()!
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#' tskitr::ts_num_individuals(ts)
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#' AlphaSimR::ts_num_individuals2(ts)
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#' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
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#' tc <- RcppTskit:::tc_ptr_load(ts_file)
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#' RcppTskit:::tc_ptr_summary(tc)
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#' AlphaSimR:::tc_ptr_summary2(tc) # a bit simpler at this stage ...
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#' tc <- RcppTskit::TableCollection$new(ts_file)
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#' RcppTskit:::tc_ptr_summary(tc$pointer)
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#' AlphaSimR:::tc_ptr_summary2(tc$pointer) # a bit simpler at this stage ...
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#' @export
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ts_num_individuals2 <- function(ts) {
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.Call(`_AlphaSimR_ts_num_individuals2`, ts)
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tc_ptr_summary2 <- function(tc) {
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.Call(`_AlphaSimR_tc_ptr_summary2`, tc)
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}
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‎configure.win‎

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#!/bin/sh
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"${R_HOME}/bin/Rscript" tools/configure.R
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# TODO: The R Extensions manual suggest using "${R_HOME}/bin${R_ARCH_BIN}/Rscript" on Windows
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# https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Configure-and-cleanup
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"${R_HOME}/bin${R_ARCH_BIN}/Rscript" tools/configure.R

‎man/tc_ptr_summary2.Rd‎

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‎man/ts_num_individuals2.Rd‎

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