From 80f403fc37d508538be7e0368129965e72f9d49e Mon Sep 17 00:00:00 2001 From: Louis Aslett Date: Fri, 8 Mar 2024 00:40:13 +0000 Subject: [PATCH] Paper accepted in BMC Bioinformatics: version bump to 1.0.0, add citation info, Github Actions for website --- .Rbuildignore | 7 ++++- .github/.gitignore | 1 + .github/workflows/pkgdown.yaml | 48 ++++++++++++++++++++++++++++++++++ .gitignore | 1 + CITATION.cff | 28 ++++++++++++++++++++ DESCRIPTION | 4 +-- README.md | 23 +++++++++++++++- _pkgdown.yml | 4 +-- inst/CITATION | 11 ++++++++ 9 files changed, 121 insertions(+), 6 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/pkgdown.yaml create mode 100644 CITATION.cff create mode 100644 inst/CITATION diff --git a/.Rbuildignore b/.Rbuildignore index 1f06e6c..cc002ef 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,8 @@ ^.*\.Rproj$ ^\.Rproj\.user$ -README.md +^README\.md$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ +^\.github$ +^CITATION\.cff$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..a7276e8 --- /dev/null +++ b/.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/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.gitignore b/.gitignore index a10a60d..da8caf8 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ src/*.o src/*.so src/*.dll inst/doc +docs diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..5249efd --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,28 @@ +message: "If you use this software, please cite it as below." +authors: +- family-names: Aslett + given-names: L. J. M. + orcid: "https://orcid.org/0000-0003-2211-233X" +- family-names: Christ + given-names: R. R. + orcid: "https://orcid.org/0000-0002-2049-3389" +title: "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R" +version: 1.0.0 +url: "https://github.com/louisaslett/kalis" +preferred-citation: + type: article + title: "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R" + authors: + - family-names: "Aslett" + given-names: "L. J. M." + orcid: "https://orcid.org/0000-0003-2211-233X" + - family-names: "Christ" + given-names: "R. R." + orcid: "https://orcid.org/0000-0002-2049-3389" + journal: "BMC Bioinformatics" + year: 2024 + volume: 25 + issue: 1 + doi: "10.1186/s12859-024-05688-8" + start: 1 + end: 18 diff --git a/DESCRIPTION b/DESCRIPTION index da8a526..21354e7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: kalis Type: Package Title: High Performance Li & Stephens Local Ancestry Inference -Version: 0.92.0 +Version: 1.0.0 Authors@R: c(person("Louis", "Aslett", role = c("aut", "cre"), email = "louis.aslett@durham.ac.uk"), person("Ryan", "Christ", role = "aut", @@ -37,7 +37,7 @@ Imports: RColorBrewer, lobstr, prettyunits -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Roxygen: list(markdown = TRUE) Suggests: rhdf5, diff --git a/README.md b/README.md index c81be30..5a65285 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # kalis: High Performance Li & Stephens Local Ancestry Inference -kalis provides a high performance implementation of the Li & Stephens model (doi: [10.1093/genetics/165.4.2213](https://doi.org/10.1093/genetics/165.4.2213)) for local ancestry inference (local referring to a region of the genome). +kalis (doi: [10.1186/s12859-024-05688-8](https://doi.org/10.1186/s12859-024-05688-8)) provides a high performance implementation of the Li & Stephens model (doi: [10.1093/genetics/165.4.2213](https://doi.org/10.1093/genetics/165.4.2213)) for local ancestry inference (local referring to a region of the genome). For a set of N phased haplotypes, kalis computes the posterior marginal probability of each haplotype copying every other haplotype by running N hidden Markov models in parallel. This yields an N x N matrix that summarizes the recent local ancestry at each variant of interest. The package provides functionality for specifying a recombination map, site-specific mutation rates, and differing prior copying probabilities for each recipient haplotype. @@ -25,3 +25,24 @@ remotes::install_github("louisaslett/kalis", ``` If you do not have the correct flags set, kalis will fall back to an implementation which does not use the special vector instruction set architecture of your CPU and will provide a warning when you load the package in your R session. + +## Citation + +If you make use of this software, please cite: + +> Aslett L. J. M., Christ R. R. (2024). "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R." _BMC Bioinformatics_, *25*(1), 1-18. [doi:10.1186/s12859-024-05688-8](https://doi.org/10.1186/s12859-024-05688-8>). + +bibTeX: + +``` +@Article{, + title = {kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R}, + author = {Aslett, L. J. M. and Christ, R. R.}, + journal = {BMC Bioinformatics}, + year = {2024}, + volume = {25}, + number = {1}, + pages = {1--18}, + doi = {10.1186/s12859-024-05688-8} +} +``` diff --git a/_pkgdown.yml b/_pkgdown.yml index 3c0acec..0199daf 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -11,5 +11,5 @@ navbar: left: [reference,articles,paper] components: paper: - text: Paper - href: https://arxiv.org/abs/2212.11403 + text: BMC Bioinformatics Paper + href: https://doi.org/10.1186/s12859-024-05688-8 diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..7dc63fd --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,11 @@ +bibentry( + bibtype = "Article", + title = "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R", + author = c(person(c("Louis", "J.", "M."), "Aslett"), person(c("Ryan", "R."), "Christ")), + journal = "BMC Bioinformatics", + year = "2024", + volume = "25", + number = "1", + pages = "1--18", + doi = "10.1186/s12859-024-05688-8" +)