Add updated actions with usethis::use_tidy_github_actions() (do not o…

…verride standard check)

.Rbuildignore

@@ -12,3 +12,4 @@
 ^tic\.R$
 ^README\.Rmd$
 ^\.httr-oauth$
+^codecov\.yml$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/pr-commands.yaml

@@ -0,0 +1,55 @@
+on:
+  issue_comment:
+    types: [created]
+name: Commands
+jobs:
+  document:
+    if: startsWith(github.event.comment.body, '/document')
+    name: document
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  style:
+    if: startsWith(github.event.comment.body, '/style')
+    name: style
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+      - name: commit
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@v1
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -40,5 +40,6 @@ Suggests:
     knitr,
     rmarkdown,
     ceramic,
-    bookdown
+    bookdown,
+    covr
 VignetteBuilder: knitr

README.Rmd

@@ -17,6 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/itsleeds/slopes/workflows/R-CMD-check/badge.svg)](https://github.com/itsleeds/slopes/actions)
+[![Codecov test coverage](https://codecov.io/gh/itsleeds/slopes/branch/master/graph/badge.svg)](https://codecov.io/gh/itsleeds/slopes?branch=master)
 <!-- badges: end -->
 
 The goal of slopes is to enable fast, accurate and user friendly calculation longitudinal steepness of linear features such as roads and rivers, based on commonly available input datasets such as road geometries and digital elevation model (DEM) datasets.

README.md

@@ -6,6 +6,8 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/itsleeds/slopes/workflows/R-CMD-check/badge.svg)](https://github.com/itsleeds/slopes/actions)
+[![Codecov test
+coverage](https://codecov.io/gh/itsleeds/slopes/branch/master/graph/badge.svg)](https://codecov.io/gh/itsleeds/slopes?branch=master)
 <!-- badges: end -->
 
 The goal of slopes is to enable fast, accurate and user friendly
@@ -181,15 +183,15 @@ res
 #> # A tibble: 2 x 6
 #>   expression        min   median `itr/sec` mem_alloc `gc/sec`
 #>   <bch:expr>   <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
-#> 1 slope_raster   37.9ms   39.7ms      25.2    32.7MB     7.57
-#> 2 slope_terra    60.6ms   62.4ms      15.2    29.1MB     5.05
+#> 1 slope_raster   47.3ms   49.3ms      20.0    32.7MB     5.01
+#> 2 slope_terra      74ms   78.1ms      11.8    29.1MB     2.37
 ```
 
 That is approximately
 
 ``` r
 round(res$`itr/sec` * nrow(r))
-#> [1] 6834 4106
+#> [1] 5426 3206
 ```
 
 routes per second using the `raster` and `terra` (the default if
@@ -218,10 +220,10 @@ res
 #> # A tibble: 4 x 6
 #>   expression      min   median `itr/sec` mem_alloc `gc/sec`
 #>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
-#> 1 bilinear1    38.7ms   39.7ms      25.1    32.7MB     8.35
-#> 2 bilinear2    61.4ms   62.4ms      15.9      29MB     5.29
-#> 3 simple1      30.4ms   32.1ms      31.3      29MB     7.22
-#> 4 simple2        60ms   61.5ms      16.2      29MB     5.40
+#> 1 bilinear1    47.9ms   52.3ms      19.3    32.7MB     4.81
+#> 2 bilinear2      75ms   84.4ms      12.0      29MB     2.41
+#> 3 simple1        32ms     38ms      26.4      29MB     7.93
+#> 4 simple2      74.9ms   80.8ms      12.4      29MB     2.06
 ```
 
 The equivalent benchmark with the `raster` package is as follows:
@@ -240,8 +242,6 @@ res
 #> # A tibble: 2 x 6
 #>   expression      min   median `itr/sec` mem_alloc `gc/sec`
 #>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
-#> 1 bilinear     38.4ms   40.2ms      24.9    32.7MB     4.53
-#> 2 simple       30.6ms     31ms      31.8      29MB     7.34
+#> 1 bilinear     49.8ms   53.2ms      18.8    32.7MB     2.36
+#> 2 simple       38.1ms     41ms      24.3      29MB     4.85
 ```
-
-<!-- That is sufficient for our needs but we plan to speed-up the calculation, e.g. using the new `terra` package, as outlined this [thread](https://github.com/rspatial/terra/issues/29#issuecomment-619444555). -->

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true