Paper accepted in BMC Bioinformatics: version bump to 1.0.0, add cita…

…tion info, Github Actions for website

.Rbuildignore

@@ -1,3 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-README.md
+^README\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^CITATION\.cff$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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

.gitignore

@@ -8,3 +8,4 @@ src/*.o
 src/*.so
 src/*.dll
 inst/doc
+docs

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

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 = "[email protected]"),
              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,

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}
+}
+```

_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

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"
+)