add actions, update readme

.Rbuildignore

@@ -4,3 +4,7 @@
 ^\.git$
 ^README\.Rmd$
 cran-comments.md
+^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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

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

@@ -0,0 +1,49 @@
+# 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
+
+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@v3
+
+      - 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

.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@v3
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.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]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 .DS_Store
+docs

README.Rmd

@@ -3,7 +3,9 @@ title: "lmds"
 output: github_document
 ---
 
-[![Build Status](https://travis-ci.org/dynverse/lmds.svg?branch=master)](https://travis-ci.org/dynverse/lmds) 
+  <!-- badges: start -->
+  [![R-CMD-check](https://github.com/dynverse/lmds/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/lmds/actions/workflows/R-CMD-check.yaml)
+  <!-- badges: end -->
 
 
 ```{r setup, include = FALSE}

README.md

@@ -1,8 +1,9 @@
 lmds
 ================
 
-[![Build
-Status](https://travis-ci.org/dynverse/lmds.svg?branch=master)](https://travis-ci.org/dynverse/lmds)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/dynverse/lmds/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dynverse/lmds/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
 
 # `lmds`: Landmark Multi-Dimensional Scaling
 
@@ -17,12 +18,14 @@ library(lmds)
 x <- as.matrix(iris[,1:4])
 dimred <- lmds(x, ndim = 2)
 qplot(dimred[,1], dimred[,2]) + labs(title = "lmds()") + theme_classic()
+#> Warning: `qplot()` was deprecated in ggplot2 3.4.0.
+#> This warning is displayed once every 8 hours.
+#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
 ```
 
 <img src="man/figures/compare-1.png" width="100%" />
 
 ``` r
-
 dimred <- cmdscale(dist(x))
 qplot(dimred[,1], dimred[,2]) + labs(title = "cmdscale()") + theme_classic()
 ```
@@ -37,16 +40,15 @@ dataset size. <img src="man/figures/timings-1.png" width="100%" />
 ## Latest changes
 
 Check out `news(package = "lmds")` or [NEWS.md](NEWS.md) for a full list
-of
-changes.
+of changes.
 
 <!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
 
 ### Recent changes in lmds 0.1.0
 
 Initial release of lmds.
 
-  - A fast dimensionality reduction method scaleable to large numbers of
+-   A fast dimensionality reduction method scaleable to large numbers of
     samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension
     of classical Torgerson MDS, but rather than calculating a complete
     distance matrix between all pairs of samples, only the distances

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+