diff --git a/.github/workflows/test-coverage-pkgdown.yaml b/.github/workflows/test-coverage-pkgdown.yaml new file mode 100644 index 0000000..913ebd6 --- /dev/null +++ b/.github/workflows/test-coverage-pkgdown.yaml @@ -0,0 +1,94 @@ +# 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: + test-covr: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: | + any::pak + any::covr + any::devtools + any::DT + any::htmltools + needs: coverage + + - name: Cache C++ and R dependencies + uses: actions/cache@v4 + with: + path: | + ~/.cache/R + ~/.local/share/R + key: dependencies-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION') }} + restore-keys: | + dependencies-${{ runner.os }}- + + - name: Run tests and generate covr report + run: | + Rscript -e 'covr::report(file = "coverage_report.html")' + + - name: Upload covr report as artifact + uses: actions/upload-artifact@v4 + with: + name: covr-report + path: coverage_report.html + + pkgdown: + needs: test-covr + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write + steps: + - uses: actions/checkout@v4 + + - name: Download covr report + uses: actions/download-artifact@v4 + with: + name: covr-report + path: . + + - 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@v4.6.1 + with: + clean: false + branch: gh-pages + folder: docs \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 4e0ba76..0c3d4e9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,6 +8,6 @@ Description: A package for computing spatially enhanced and entropy-derived matr License: MIT License Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 LinkingTo: Rcpp, RcppArmadillo -Imports: Rcpp, sf, dplyr, nngeo, spdep, testthat (>= 3.0.0), covr, ggplot2, withr +Imports: Rcpp, sf, dplyr, nngeo, spdep, testthat (>= 3.0.0), covr, ggplot2, withr, pkgdown diff --git a/NAMESPACE b/NAMESPACE index e865972..a361178 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ export(cppJSD) export(distJSD) export(distJSD2) export(plot_dists) +export(scale_minmax) export(speedmat) export(speedmat.coord) export(speedmat.jsdist) diff --git a/R/speedmat.r b/R/speedmat.r index cc8b5ef..c0feaf8 100644 --- a/R/speedmat.r +++ b/R/speedmat.r @@ -110,8 +110,11 @@ speedmat_legacy <- function(sf, } - -scale_minmax = function(x) {(x - min(x)) / (max(x) - min(x))} +#' Max-Min scaling +#' @param x numeric vector +#' @returns numeric vector +#' @export +scale_minmax <- function(x) {(x - min(x)) / (max(x) - min(x))} #' @title SpEED matrix for matching analysis diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..a7a6248 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,27 @@ +url: https://niehs.github.io/amadeus/ +template: + bootstrap: 5 + bootswatch: minty + +navbar: + structure: + left: [reference, search] + right: [github] + +home: + links: + - text: Coverage + href: /coverage_report.html + +references: + - subtitle: Core functions + - contents: + - starts_with("speedmat_") + + - subtitle: Low-level functions + - contents: + - includes("JSD") + + - subtitle: Helpers + - contents: + - \ No newline at end of file diff --git a/man/scale_minmax.Rd b/man/scale_minmax.Rd new file mode 100644 index 0000000..72683b8 --- /dev/null +++ b/man/scale_minmax.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/speedmat.r +\name{scale_minmax} +\alias{scale_minmax} +\title{Max-Min scaling} +\usage{ +scale_minmax(x) +} +\arguments{ +\item{x}{numeric vector} +} +\value{ +numeric vector +} +\description{ +Max-Min scaling +} diff --git a/src/RcppExports.o b/src/RcppExports.o new file mode 100644 index 0000000..0cf443d Binary files /dev/null and b/src/RcppExports.o differ diff --git a/src/distJSD.o b/src/distJSD.o index aa47fde..dc47fc6 100644 Binary files a/src/distJSD.o and b/src/distJSD.o differ diff --git a/src/speedmat.so b/src/speedmat.so index f9031e5..5739eb4 100755 Binary files a/src/speedmat.so and b/src/speedmat.so differ