Merge pull request #33 from jefferislab/dev/actions

.Rbuildignore

@@ -6,8 +6,8 @@
 ^test$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^cran-comments\.md$
 ^cran-comments-l1\.md$
 ^revdep$
-^tic\.R$
+^\.github$
+^pkgdown$

.github/.gitignore

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

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# 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]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+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-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# 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.yaml
+
+permissions: read-all
+
+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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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]
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -4,3 +4,4 @@ src/*.so
 .Rhistory
 revdep/
 test/
+docs

DESCRIPTION

@@ -12,7 +12,7 @@ Description: Finds the k nearest neighbours for every point in a
     computed using the L2 (Euclidean) metric. Please see package 'RANN.L1'
     for the same functionality using the L1 (Manhattan, taxicab) metric.
 License: GPL (>=3)
-URL: https://github.com/jefferislab/RANN
+URL: https://github.com/jefferislab/RANN, http://jefferislab.github.io/RANN/
 BugReports: https://github.com/jefferislab/RANN/issues
 Suggests:
     testthat

README.md

@@ -1,8 +1,9 @@
 # RANN 
 [![Release Version](https://img.shields.io/github/release/jefferislab/RANN.svg)](https://github.com/jefferislab/RANN/releases/latest) 
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/RANN)](https://CRAN.R-project.org/package=RANN) 
-[![Build Status](https://travis-ci.org/jefferislab/RANN.svg)](https://travis-ci.org/jefferislab/RANN)
- [![Downloads](http://cranlogs.r-pkg.org/badges/RANN?color=brightgreen)](http://www.r-pkg.org/pkg/RANN)
+[![R-CMD-check](https://github.com/jefferis/RANN/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jefferislab/RANN/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/jefferislab/RANN/graph/badge.svg)](https://app.codecov.io/gh/jefferislab/RANN)
+[![Downloads](http://cranlogs.r-pkg.org/badges/RANN?color=brightgreen)](http://www.r-pkg.org/pkg/RANN)
 
 Finds the k nearest neighbours for every point in a given dataset
 in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: http://jefferislab.github.io/RANN/
+template:
+  bootstrap: 5
+