Enable GH Actions CI/CD testing (#99)

Merging to start use of tests during CD. No changes to `rgrass` itself were made. This PR squashes several individual commits: * Add initial testthat suite * Setup test helper for mac and linux * Add gisBase to initGRASS * Use grassdb at /tmp * Add read_VECT test * Expand initGRASS tests to include gmeta * Add test for getLocationProj * Use GISBASE for MacOS helper * Update CRAN badge * Use ignore.stderr = TRUE in vector related tests * Add test coverage * Use r-lib/actions/setup-r@v2 in releasebranch * Use RSPM but build terra from source due to conflict with version from ubuntugis PPA * Expand matrix of grass docker images used in tests * Separate read_VECT and write_VECT in tests * Use SpatRaster instead of SGDF to test initGRASS * Add basic tests for execGRASS * Expanded initGRASS tests for locking * Unlink .gislock at end of test * Add tests for gmeta options * Add test for legacyExecOption * Add test for useInternOption * Add test for stop_on_no_flags_parasOption * Disable sp related tests until issue resolved in terms of sp::CRS on the GRASS GIS Docker release branch
OSGeo · Jan 1, 2025 · 4b86ba8 · 4b86ba8
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,3 +5,4 @@ _pkgdown.yml
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/R-CMD-check.yaml b/.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:
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    strategy:
+          matrix:
+            os: [ubuntu-22.04, ubuntu-24.04]
+
+    runs-on: ${{ matrix.os }}
+
+    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:
+          use-public-rspm: true
+
+      - name: Install common system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y grass-dev libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
+
+      - name: Download test dataset
+        run: |
+          wget https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip -O /tmp/nc_basic_spm_grass7.zip
+          unzip /tmp/nc_basic_spm_grass7.zip -d /tmp/grassdb
+          rm /tmp/nc_basic_spm_grass7.zip
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::terra
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/check-releasebranch.yaml b/.github/workflows/check-releasebranch.yaml
@@ -0,0 +1,74 @@
+# 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:
+
+name: releasebranch_8_4-ubuntu
+
+permissions: read-all
+
+jobs:
+  R-CMD-check-releasebranch:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix: 
+        container: [
+          "osgeo/grass-gis:releasebranch_8_4-ubuntu",
+          "osgeo/grass-gis:main-ubuntu"
+        ]
+
+    container:
+      image: ${{ matrix.container }}
+      options: --privileged
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install system deps
+      run: |
+        apt-get update
+        apt-get install -y \
+          libudunits2-dev \
+          libharfbuzz-dev \
+          libfribidi-dev \
+          gdal-bin \
+          libmysqlclient-dev \
+          libfontconfig1-dev \
+          qpdf \
+          pandoc \
+          pandoc-citeproc
+
+    - name: Install R
+      run: |
+        wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+        echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" | tee -a /etc/apt/sources.list
+        apt-get update
+        apt-get install -y r-base-dev
+
+    - name: Configure RSPM in .Renviron
+      run: |
+        echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))' >> ~/.Rprofile
+        echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version["platform"], R.version["arch"], R.version["os"])))' >> ~/.Rprofile
+        echo 'options(Ncpus=parallel::detectCores())' >> ~/.Rprofile
+
+    - name: Install R dependencies
+      run: |
+        R -e "install.packages(c('remotes', 'rcmdcheck'))"
+        R -e "remotes::install_deps(dependencies = TRUE)"
+        R -e "install.packages('terra', repos = 'https://cloud.r-project.org/', type = 'source')"
+
+    - name: Download test dataset
+      run: |
+        wget https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip -O /tmp/nc_basic_spm_grass7.zip
+        unzip /tmp/nc_basic_spm_grass7.zip -d /tmp/grassdb
+        rm /tmp/nc_basic_spm_grass7.zip
+      
+    # - name: Run R CMD check
+    #   run: |
+    #     R -e "rcmdcheck::rcmdcheck(args = c('--no-manual', '--no-build-vignettes'), error_on = 'error', check_dir = 'check')"
+
+    - uses: r-lib/actions/check-r-package@v2
+      with:
+        upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,66 @@
+# 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:
+
+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
+
+      - name: Install common system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y grass-dev libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2, any::terra
+          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 if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,7 +13,16 @@ Authors@R: c(
 Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
 Depends: R (>= 3.5.0)
 Imports: stats, utils, methods, xml2
-Suggests: terra (>= 1.6-16), sp (>= 0.9), knitr, rmarkdown, sf, stars, raster (>= 3.6-3), codetools
+Suggests: 
+    terra (>= 1.6-16),
+    sp (>= 0.9),
+    knitr,
+    rmarkdown,
+    sf,
+    stars,
+    raster (>= 3.6-3),
+    codetools,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 SystemRequirements: GRASS (>= 7)
 License: GPL (>= 2)
@@ -22,3 +31,4 @@ BugReports: https://github.com/osgeo/rgrass/issues/
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
+Config/testthat/edition: 3
diff --git a/R/gmeta.R b/R/gmeta.R
@@ -188,10 +188,9 @@ getLocationProj <- function(ignore.stderr = FALSE, g.proj_WKT = NULL) {
     if (!g.proj_WKT) WKT2 <- FALSE
   }
   if (WKT2 && !old_proj) {
-    res <- paste(execGRASS("g.proj",
-      flags = c("w"), intern = TRUE,
-      ignore.stderr = ignore.stderr
-    ), collapse = "\n")
+    res <- execGRASS("g.proj", flags = c("w"), intern = TRUE, ignore.stderr = TRUE)
+    res <- paste(res, collapse = "\n")
+
     if (substr(res, 1, 5) != "ERROR") {
       if (nchar(res) == 0L) {
         res <- paste(execGRASS("g.proj",

diff --git a/R/vect_link.R b/R/vect_link.R
@@ -171,24 +171,26 @@ vDataCount <- function(vname, layer, ignore.stderr = NULL) {
 vect2neigh <- function(
     vname, ID = NULL, ignore.stderr = NULL, remove = TRUE,
     vname2 = NULL, units = "k") {
+
   if (get.suppressEchoCmdInFuncOption()) {
     inEchoCmd <- get.echoCmdOption()
     tull <- set.echoCmdOption(FALSE)
   }
+
   if (is.null(ignore.stderr)) {
     ignore.stderr <- get("ignore.stderr", envir = .GRASS_CACHE)
   }
   stopifnot(is.logical(ignore.stderr))
 
   vinfo <- vInfo(vname)
   types <- names(vinfo)[which(vinfo > 0)]
+
   if (length(grep("areas", types)) == 0) {
     stop("Vector object not of area type")
   }
 
   n <- vDataCount(vname, ignore.stderr = ignore.stderr)
 
-
   if (!is.null(ID)) {
     if (!is.character(ID)) stop("ID not character string")
     # 		cmd <- paste(paste("v.info", .addexe(), sep=""),
@@ -222,9 +224,11 @@ vect2neigh <- function(
     }
   }
   vname2_was_null <- FALSE
+
   if (is.null(vname2)) {
     pid <- as.integer(round(runif(1, 1, 1000)))
     vname2 <- paste(vname, pid, sep = "")
+
     tull <- execGRASS("g.remove",
       type = "vector", name = vname2, flags = "f",
       intern = TRUE, ignore.stderr = ignore.stderr
@@ -326,7 +330,7 @@ vect2neigh <- function(
   if (remove) {
     tull <- execGRASS("g.remove",
       name = paste(vname2, vname2a, sep = ","), type = "vector",
-      intern = TRUE, ignore.stderr = ignore.stderr
+      intern = TRUE, ignore.stderr = ignore.stderr, flags = "f"
     )
   }
 

diff --git a/R/vect_link_ng.R b/R/vect_link_ng.R
@@ -222,16 +222,21 @@ write_VECT <- function(x, vname, flags = "overwrite",
   if (!(requireNamespace("terra", quietly = TRUE))) {
     stop("terra required for SpatVector input")
   }
+
   stopifnot(is.logical(ignore.stderr), !is.na(ignore.stderr))
+
   if (get.suppressEchoCmdInFuncOption()) {
     inEchoCmd <- set.echoCmdOption(FALSE)
   }
+
   srcs <- getMethod("sources", "SpatVector")(x)
+
   if (length(srcs) == 1L) {
     tf <- srcs
   } else {
     tf <- ""
   }
+
   # exit when the source is a GRASS database layer already:
   if (grepl("[/\\\\]head::[^/\\\\]+$", tf)) {
     grass_layername <- regmatches(
@@ -254,7 +259,7 @@ write_VECT <- function(x, vname, flags = "overwrite",
   if (!file.exists(tf)) {
     tf <- tempfile(fileext = ".gpkg")
     getMethod("writeVector", c("SpatVector", "character"))(x, filename = tf,
-    filetype = "GPKG", overwrite = TRUE)
+      filetype = "GPKG", options = NULL, overwrite = TRUE)
   }
 
   type <- NULL
@@ -267,6 +272,7 @@ write_VECT <- function(x, vname, flags = "overwrite",
     flags = flags, input = tf, output = vname, type = type,
     ignore.stderr = ignore.stderr
   )
+
   if (get.suppressEchoCmdInFuncOption()) {
     tull <- set.echoCmdOption(inEchoCmd)
   }

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 # rgrass
 
-[![CRAN](http://www.r-pkg.org/badges/version/rgrass)](https://cran.r-project.org/package=rgrass)
+[![CRAN status](https://www.r-pkg.org/badges/version/rgrass)](https://CRAN.R-project.org/package=rgrass)
+[![Codecov test coverage](https://codecov.io/gh/stevenpawley/rgrass/graph/badge.svg)](https://app.codecov.io/gh/stevenpawley/rgrass)
 
 ### Interface Between GRASS Geographical Information System and R
 

diff --git a/codecov.yml b/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
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(rgrass)
+
+test_check("rgrass")