From ea53d493a96ca45c0115a9d4d4a71540a0d85c73 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Mon, 11 Nov 2024 13:41:13 -0700
Subject: [PATCH 01/19] initial testthat suite

---
 .github/workflows/R-CMD-check.yaml  | 56 +++++++++++++++++++++++++++++
 .github/workflows/check-docker.yaml | 54 ++++++++++++++++++++++++++++
 DESCRIPTION                         | 12 ++++++-
 tests/testthat.R                    | 12 +++++++
 tests/testthat/helper.R             | 13 +++++++
 tests/testthat/test-initGRASS.R     | 19 ++++++++++
 tests/testthat/test-read_RAST.R     | 46 ++++++++++++++++++++++++
 7 files changed, 211 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/check-docker.yaml
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/helper.R
 create mode 100644 tests/testthat/test-initGRASS.R
 create mode 100644 tests/testthat/test-read_RAST.R

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..e78de88
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,56 @@
+# 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-r@v2
+        with:
+          use-public-rspm: true
+      
+      - 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
+      
+      - name: Install system dependencies for ubuntu-22.04
+        if: matrix.os == 'ubuntu-22.04'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y grass-dev grass-gui pandoc-citeproc
+
+      - name: Install system dependencies for ubuntu-24.04
+        if: matrix.os == 'ubuntu-24.04'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y grass-dev grass-gui pandoc
+
+      - 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")'
diff --git a/.github/workflows/check-docker.yaml b/.github/workflows/check-docker.yaml
new file mode 100644
index 0000000..4266cfb
--- /dev/null
+++ b/.github/workflows/check-docker.yaml
@@ -0,0 +1,54 @@
+# 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:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    container:
+      image: osgeo/grass-gis:releasebranch_8_4-ubuntu
+      options: --privileged
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install system deps
+      run: |
+        apt-get update
+        apt-get install -y pandoc-citeproc qpdf
+
+    - name: Install R
+      run: |
+        apt-get update
+        apt-get install -y r-base
+
+    - 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
+
+    - name: Install R dependencies
+      run: |
+        R -e "install.packages('remotes')"
+        R -e "remotes::install_deps(dependencies = 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
diff --git a/DESCRIPTION b/DESCRIPTION
index e159f68..df90e9d 100644
--- 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/rsbivand/rgrass/issues/
 RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
+Config/testthat/edition: 3
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..cd6253e
--- /dev/null
+++ 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")
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
new file mode 100644
index 0000000..6742577
--- /dev/null
+++ b/tests/testthat/helper.R
@@ -0,0 +1,13 @@
+download_nc_basic <- function() {
+  if (!file.exists("/tmp/nc_basic_spm_grass7.zip")) {
+    download.file(
+      "https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip",
+      "/tmp/nc_basic_spm_grass7.zip"
+    )
+    unzip("/tmp/nc_basic_spm_grass7.zip", exdir = "/tmp/grassdb/nc_basic_spm_grass7")
+  }
+
+  return(
+    list(gisDbase = "/tmp/grassdb/nc_basic_spm_grass7", location = "nc_basic_spm_grass7")
+  )
+}
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
new file mode 100644
index 0000000..05b978e
--- /dev/null
+++ b/tests/testthat/test-initGRASS.R
@@ -0,0 +1,19 @@
+library(testthat)
+source("helper.R")
+
+testthat::test_that("testing initGRASS", {
+  testdata <- download_nc_basic()
+
+  # Initialize a temporary GRASS project using the example data
+  loc <- initGRASS(
+    home = tempdir(),
+    gisDbase = testdata$gisDbase,
+    location = testdata$location,
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  expect_s3_class(loc, "gmeta")
+  expect_equal(loc$LOCATION_NAME, testdata$location)
+  expect_equal(loc$projection, "99")
+})
diff --git a/tests/testthat/test-read_RAST.R b/tests/testthat/test-read_RAST.R
new file mode 100644
index 0000000..2b19d97
--- /dev/null
+++ b/tests/testthat/test-read_RAST.R
@@ -0,0 +1,46 @@
+library(testthat)
+library(terra)
+library(sp)
+source("helper.R")
+
+# setup
+testdata <- download_nc_basic()
+
+loc <- initGRASS(
+  home = tempdir(),
+  gisDbase = testdata$gisDbase,
+  location = testdata$location,
+  mapset = "PERMANENT",
+  override = TRUE
+)
+
+test_that("testing read_RAST using terra", {
+  # read a categorical raster map
+  v1 <- read_RAST("landuse", cat = TRUE, return_format = "terra")
+
+  expect_s4_class(v1, "SpatRaster")
+  expect_false(inMemory(v1))
+
+  # check the values and labels
+  lvls <- levels(v1)[[1]]
+  expect_equal(lvls$value, 0:7)
+  expect_equal(
+    lvls$label,
+    c("undefined", "developed", "agriculture", "herbaceous", "shrubland",
+      "forest", "water", "sediment")
+  )
+
+  write_RAST(v1, "landuse1", flags = c("o", "overwrite"))
+  execGRASS("g.remove", flags = "f", name = "landuse1", type = "raster")
+})
+
+test_that("testing read_RAST using sp", {
+  nc_basic <- read_RAST("landuse", cat = TRUE, return_format = "SGDF")
+  lvls <- levels(nc_basic$landuse)
+
+  expect_equal(
+    lvls,
+    c("developed", "agriculture", "herbaceous", "shrubland",
+      "forest", "water", "sediment")
+  )
+})

From 0e07941045110a9794d93a2c69ddfc46bb1a1c0d Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Thu, 14 Nov 2024 23:13:33 -0700
Subject: [PATCH 02/19] setup test helper for mac and linux

update test helper

add gisBase to initGRASS

Fix logic in skip_if_not

add skip_if_not to tests

fix tests due to base R levels

use grassdb at /tmp
---
 .github/workflows/R-CMD-check.yaml  | 16 ++++++-----
 .github/workflows/check-docker.yaml | 11 ++++----
 tests/testthat/helper.R             | 43 +++++++++++++++++++++++++----
 tests/testthat/test-initGRASS.R     | 12 +++++---
 tests/testthat/test-read_RAST.R     | 39 ++++++++++++++++----------
 5 files changed, 84 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index e78de88..2dc1f27 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -28,22 +28,24 @@ jobs:
         with:
           use-public-rspm: true
       
+      - name: Install common system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y grass-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
+
       - name: Install system dependencies for ubuntu-22.04
         if: matrix.os == 'ubuntu-22.04'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y grass-dev grass-gui pandoc-citeproc
+        run: sudo apt-get install -y pandoc-citeproc
 
       - name: Install system dependencies for ubuntu-24.04
         if: matrix.os == 'ubuntu-24.04'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y grass-dev grass-gui pandoc
+        run: sudo apt-get install -y pandoc
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
diff --git a/.github/workflows/check-docker.yaml b/.github/workflows/check-docker.yaml
index 4266cfb..b934aed 100644
--- a/.github/workflows/check-docker.yaml
+++ b/.github/workflows/check-docker.yaml
@@ -34,16 +34,17 @@ jobs:
         apt-get update
         apt-get install -y r-base
 
-    - 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
-
     - name: Install R dependencies
       run: |
         R -e "install.packages('remotes')"
         R -e "remotes::install_deps(dependencies = TRUE)"
 
+    - 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
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 6742577..d6d4ca0 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -1,13 +1,44 @@
 download_nc_basic <- function() {
-  if (!file.exists("/tmp/nc_basic_spm_grass7.zip")) {
+  if (Sys.info()["sysname"] == "Linux") {
+    tmpdir <- "/tmp"
+  } else if (Sys.info()["sysname"] == "Darwin") {
+    tmpdir <- tempdir()
+  }
+
+  if (!file.exists(file.path(tmpdir, "nc_basic_spm_grass7.zip"))) {
+    base_url <- "https://grass.osgeo.org/sampledata"
+    path_url <- "north_carolina"
+    file_url <- "nc_basic_spm_grass7.zip"
+
     download.file(
-      "https://grass.osgeo.org/sampledata/north_carolina/nc_basic_spm_grass7.zip",
-      "/tmp/nc_basic_spm_grass7.zip"
+      paste(base_url, path_url, file_url, sep = "/"),
+      file.path(tmpdir, "nc_basic_spm_grass7.zip")
+    )
+
+    unzip(
+      file.path(tmpdir, "nc_basic_spm_grass7.zip"),
+      exdir = file.path(tmpdir, "grassdb")
     )
-    unzip("/tmp/nc_basic_spm_grass7.zip", exdir = "/tmp/grassdb/nc_basic_spm_grass7")
   }
 
-  return(
-    list(gisDbase = "/tmp/grassdb/nc_basic_spm_grass7", location = "nc_basic_spm_grass7")
+  dataset <- list(
+    gisDbase = file.path(tmpdir, "grassdb"),
+    location = "nc_basic_spm_grass7"
   )
+
+  return(dataset)
 }
+
+get_gisbase <- function() {
+  if (Sys.info()["sysname"] == "Linux") {
+    gisBase <- try(system2("grass", "--config path", stdout = TRUE))
+  } else if (Sys.info()["sysname"] == "Darwin") {
+    gisBase <- "/Applications/GRASS-8.5.app/Contents/Resources"
+  }
+  
+  if (inherits(gisBase, "try-catch")) {
+    gisBase <- NULL
+  }
+  
+  return(gisBase)
+}
\ No newline at end of file
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index 05b978e..b187c79 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -1,19 +1,23 @@
 library(testthat)
 source("helper.R")
 
+# setup
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
 testthat::test_that("testing initGRASS", {
-  testdata <- download_nc_basic()
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
   # Initialize a temporary GRASS project using the example data
   loc <- initGRASS(
-    home = tempdir(),
+    gisBase = gisBase,
     gisDbase = testdata$gisDbase,
-    location = testdata$location,
+    location = "nc_basic_spm_grass7",
     mapset = "PERMANENT",
     override = TRUE
   )
 
   expect_s3_class(loc, "gmeta")
-  expect_equal(loc$LOCATION_NAME, testdata$location)
+  expect_equal(loc$LOCATION_NAME, "nc_basic_spm_grass7")
   expect_equal(loc$projection, "99")
 })
diff --git a/tests/testthat/test-read_RAST.R b/tests/testthat/test-read_RAST.R
index 2b19d97..7b0d714 100644
--- a/tests/testthat/test-read_RAST.R
+++ b/tests/testthat/test-read_RAST.R
@@ -5,36 +5,45 @@ source("helper.R")
 
 # setup
 testdata <- download_nc_basic()
-
-loc <- initGRASS(
-  home = tempdir(),
-  gisDbase = testdata$gisDbase,
-  location = testdata$location,
-  mapset = "PERMANENT",
-  override = TRUE
-)
+gisBase <- get_gisbase()
 
 test_that("testing read_RAST using terra", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
   # read a categorical raster map
   v1 <- read_RAST("landuse", cat = TRUE, return_format = "terra")
-
   expect_s4_class(v1, "SpatRaster")
   expect_false(inMemory(v1))
 
   # check the values and labels
-  lvls <- levels(v1)[[1]]
-  expect_equal(lvls$value, 0:7)
+  lvls <- terra::levels(v1)
+  expect_equal(lvls[[1]]$value, 0:7)
   expect_equal(
-    lvls$label,
+    lvls[[1]]$label,
     c("undefined", "developed", "agriculture", "herbaceous", "shrubland",
       "forest", "water", "sediment")
   )
-
-  write_RAST(v1, "landuse1", flags = c("o", "overwrite"))
-  execGRASS("g.remove", flags = "f", name = "landuse1", type = "raster")
 })
 
 test_that("testing read_RAST using sp", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
   nc_basic <- read_RAST("landuse", cat = TRUE, return_format = "SGDF")
   lvls <- levels(nc_basic$landuse)
 

From a8a2d62761e4e5a1c09210388d44f9aa27b566c3 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 08:59:55 -0700
Subject: [PATCH 03/19] add read_VECT test

---
 tests/testthat/test-read_RAST.R | 18 +++++--------
 tests/testthat/test-read_VECT.R | 45 +++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 12 deletions(-)
 create mode 100644 tests/testthat/test-read_VECT.R

diff --git a/tests/testthat/test-read_RAST.R b/tests/testthat/test-read_RAST.R
index 7b0d714..f916a78 100644
--- a/tests/testthat/test-read_RAST.R
+++ b/tests/testthat/test-read_RAST.R
@@ -3,13 +3,11 @@ library(terra)
 library(sp)
 source("helper.R")
 
-# setup
+# setup (share grass session across tests)
 testdata <- download_nc_basic()
 gisBase <- get_gisbase()
 
-test_that("testing read_RAST using terra", {
-  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
-
+if (!is.null(gisBase)) {
   loc <- initGRASS(
     gisBase = gisBase,
     gisDbase = testdata$gisDbase,
@@ -17,6 +15,10 @@ test_that("testing read_RAST using terra", {
     mapset = "PERMANENT",
     override = TRUE
   )
+}
+
+test_that("testing read_RAST using terra", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
   # read a categorical raster map
   v1 <- read_RAST("landuse", cat = TRUE, return_format = "terra")
@@ -36,14 +38,6 @@ test_that("testing read_RAST using terra", {
 test_that("testing read_RAST using sp", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
-  loc <- initGRASS(
-    gisBase = gisBase,
-    gisDbase = testdata$gisDbase,
-    location = "nc_basic_spm_grass7",
-    mapset = "PERMANENT",
-    override = TRUE
-  )
-
   nc_basic <- read_RAST("landuse", cat = TRUE, return_format = "SGDF")
   lvls <- levels(nc_basic$landuse)
 
diff --git a/tests/testthat/test-read_VECT.R b/tests/testthat/test-read_VECT.R
new file mode 100644
index 0000000..2f16259
--- /dev/null
+++ b/tests/testthat/test-read_VECT.R
@@ -0,0 +1,45 @@
+library(testthat)
+library(terra)
+source("helper.R")
+
+# setup (share grass session across tests)
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
+if (!is.null(gisBase)) {
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+}
+
+# test basic read_VECT operation
+test_that("testing read_VECT", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # test basic read/write
+  schs <- read_VECT("schools")
+  expect_s4_class(schs, "SpatVector")
+  expect_equal(crs(schs, describe = TRUE)$code, "3358")
+
+  write_VECT(schs, "newsch", flags = c("o", "overwrite"))
+  newschs <- read_VECT("newsch")
+  expect_s4_class(newschs, "SpatVector")
+
+  grass_colummns <- vColumns("newsch")[, 2]
+  expect_equal(names(newschs), grass_colummns)
+
+  execGRASS("g.remove", type = "vector", name = "newsch", flags = "f")
+})
+
+# test basic vect2neigh operation
+test_that("testing vect2neigh", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  cen_neig <- vect2neigh("census")
+  expect_s3_class(cen_neig, c("data.frame", "GRASSneigh", "spatial.neighbour"))
+  expect_equal(names(cen_neig), c("left", "right", "length"))
+})

From a5b53b252ccd0d646dcd09b728a786b42585374d Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 09:01:27 -0700
Subject: [PATCH 04/19] add covr

---
 .Rbuildignore |  1 +
 README.md     |  1 +
 codecov.yml   | 14 ++++++++++++++
 3 files changed, 16 insertions(+)
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index b378cdb..d8bb55d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -5,3 +5,4 @@ _pkgdown.yml
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^codecov\.yml$
diff --git a/README.md b/README.md
index a548c0d..b0a1a66 100644
--- 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)
+[![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
new file mode 100644
index 0000000..04c5585
--- /dev/null
+++ 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

From 20f24579104b4db47aa95bb2b3ff81c4983516b7 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 09:21:35 -0700
Subject: [PATCH 05/19] Expand initGRASS tests to include gmeta

---
 tests/testthat/test-initGRASS.R | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index b187c79..2d15578 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -1,4 +1,5 @@
 library(testthat)
+library(terra)
 source("helper.R")
 
 # setup
@@ -20,4 +21,26 @@ testthat::test_that("testing initGRASS", {
   expect_s3_class(loc, "gmeta")
   expect_equal(loc$LOCATION_NAME, "nc_basic_spm_grass7")
   expect_equal(loc$projection, "99")
+
+  # Test gmeta working
+  meta <- gmeta()
+
+  expect_equal(
+    names(meta),
+    c("GISDBASE", "LOCATION_NAME", "MAPSET", "GRASS_GUI", "projection", "zone", "n",
+      "s", "w", "e", "t", "b", "nsres", "nsres3", "ewres", "ewres3", "tbres", "rows", "rows3",
+      "cols", "cols3", "depths", "cells", "cells3", "proj4")
+  )
+
+  expect_equal(meta$LOCATION_NAME, testdata$location)
+  expect_equal(meta$projection, "99")
+  expect_equal(crs(meta$proj4, describe = TRUE)$code, "3358")
+  
+  # Test old proj4 output from grass
+  meta2 <- gmeta(g.proj_WKT = FALSE)
+  expect_equal(meta2$proj4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
+
+  # Test gmeta2grd
+  meta3 <- gmeta2grd()
+  expect_s4_class(meta3, "GridTopology")
 })

From 06f6b9895b1eb94950513aed87c6f2685cd2d3de Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 09:24:04 -0700
Subject: [PATCH 06/19] add test for getLocationProj

---
 tests/testthat/test-initGRASS.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index 2d15578..a3e70d9 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -43,4 +43,10 @@ testthat::test_that("testing initGRASS", {
   # Test gmeta2grd
   meta3 <- gmeta2grd()
   expect_s4_class(meta3, "GridTopology")
+
+  # Test just returning the projection
+  meta4 <- getLocationProj()
+  expect_equal(crs(meta4, describe = TRUE)$code, "3358")
+  meta4 <- getLocationProj(g.proj_WKT = FALSE)
+  expect_equal(meta4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
 })

From 493f46db43b38edd31d4549ddd37fd8df417e635 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 09:37:54 -0700
Subject: [PATCH 07/19] use GISBASE for MacOS helper

---
 tests/testthat/helper.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index d6d4ca0..621d419 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -33,7 +33,7 @@ get_gisbase <- function() {
   if (Sys.info()["sysname"] == "Linux") {
     gisBase <- try(system2("grass", "--config path", stdout = TRUE))
   } else if (Sys.info()["sysname"] == "Darwin") {
-    gisBase <- "/Applications/GRASS-8.5.app/Contents/Resources"
+    gisBase <- Sys.getenv("GISBASE")
   }
   
   if (inherits(gisBase, "try-catch")) {
@@ -41,4 +41,4 @@ get_gisbase <- function() {
   }
   
   return(gisBase)
-}
\ No newline at end of file
+}

From 4be7812c9199ebab44b6414cc1e386415382d14d Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 15 Dec 2024 09:47:09 -0700
Subject: [PATCH 08/19] update CRAN badge

Update CRAN badge and simplify test helper
---
 README.md                       |  2 +-
 tests/testthat/helper.R         | 14 +++++---------
 tests/testthat/test-execGRASS.R |  8 ++++++++
 tests/testthat/test_options.R   | 14 ++++++++++++++
 4 files changed, 28 insertions(+), 10 deletions(-)
 create mode 100644 tests/testthat/test-execGRASS.R
 create mode 100644 tests/testthat/test_options.R

diff --git a/README.md b/README.md
index b0a1a66..35457a2 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # 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/tests/testthat/helper.R b/tests/testthat/helper.R
index 621d419..a69ebfd 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -1,7 +1,7 @@
 download_nc_basic <- function() {
   if (Sys.info()["sysname"] == "Linux") {
     tmpdir <- "/tmp"
-  } else if (Sys.info()["sysname"] == "Darwin") {
+  } else{
     tmpdir <- tempdir()
   }
 
@@ -31,14 +31,10 @@ download_nc_basic <- function() {
 
 get_gisbase <- function() {
   if (Sys.info()["sysname"] == "Linux") {
-    gisBase <- try(system2("grass", "--config path", stdout = TRUE))
-  } else if (Sys.info()["sysname"] == "Darwin") {
-    gisBase <- Sys.getenv("GISBASE")
+    gisBase <- system2("grass", "--config path", stdout = TRUE)
+  } else {
+    gisBase <- Sys.getenv("GRASS_INSTALLATION")
   }
-  
-  if (inherits(gisBase, "try-catch")) {
-    gisBase <- NULL
-  }
-  
+
   return(gisBase)
 }
diff --git a/tests/testthat/test-execGRASS.R b/tests/testthat/test-execGRASS.R
new file mode 100644
index 0000000..c50ca88
--- /dev/null
+++ b/tests/testthat/test-execGRASS.R
@@ -0,0 +1,8 @@
+# execGRASS
+# doGRASS
+# stringexecGRASS
+
+# get.GIS_LOCK
+# set.GIS_LOCK
+# unset.GIS_LOCK
+# remove_GISRC
diff --git a/tests/testthat/test_options.R b/tests/testthat/test_options.R
new file mode 100644
index 0000000..1340b1c
--- /dev/null
+++ b/tests/testthat/test_options.R
@@ -0,0 +1,14 @@
+# set.ignore.stderrOption
+# get.ignore.stderrOption
+# set.stop_on_no_flags_parasOption 
+# get.stop_on_no_flags_parasOption
+# set.echoCmdOption
+# get.echoCmdOption
+# set.useInternOption
+# get.useInternOption
+# set.legacyExecOption
+# get.legacyExecOption
+# set.defaultFlagsOption
+# get.defaultFlagsOption
+# set.suppressEchoCmdInFuncOption
+# get.suppressEchoCmdInFuncOption

From a43cd22a50960caf901aae9328fa557d354c0007 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Tue, 24 Dec 2024 22:46:38 -0700
Subject: [PATCH 09/19] use ignore.stderr = TRUE in vector related tests

---
 R/vect_link.R                   | 8 ++++++--
 R/vect_link_ng.R                | 8 +++++++-
 tests/testthat/test-read_VECT.R | 5 +++--
 3 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/R/vect_link.R b/R/vect_link.R
index d077b41..23fed3f 100644
--- a/R/vect_link.R
+++ b/R/vect_link.R
@@ -169,10 +169,12 @@ 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)
   }
@@ -180,13 +182,13 @@ vect2neigh <- function(
 
   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=""),
@@ -220,9 +222,11 @@ 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
@@ -324,7 +328,7 @@ 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
index 3789788..ff8e25e 100644
--- a/R/vect_link_ng.R
+++ b/R/vect_link_ng.R
@@ -221,16 +221,21 @@ 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(
@@ -253,7 +258,7 @@ 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
@@ -266,6 +271,7 @@ 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/tests/testthat/test-read_VECT.R b/tests/testthat/test-read_VECT.R
index 2f16259..be2b573 100644
--- a/tests/testthat/test-read_VECT.R
+++ b/tests/testthat/test-read_VECT.R
@@ -25,7 +25,8 @@ test_that("testing read_VECT", {
   expect_s4_class(schs, "SpatVector")
   expect_equal(crs(schs, describe = TRUE)$code, "3358")
 
-  write_VECT(schs, "newsch", flags = c("o", "overwrite"))
+  schs <- schs[, -which(names(schs) == "cat")]
+  write_VECT(schs, "newsch", flags = "overwrite")
   newschs <- read_VECT("newsch")
   expect_s4_class(newschs, "SpatVector")
 
@@ -39,7 +40,7 @@ test_that("testing read_VECT", {
 test_that("testing vect2neigh", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
-  cen_neig <- vect2neigh("census")
+  cen_neig <- vect2neigh("census", ignore.stderr = TRUE)
   expect_s3_class(cen_neig, c("data.frame", "GRASSneigh", "spatial.neighbour"))
   expect_equal(names(cen_neig), c("left", "right", "length"))
 })

From 1664d359d428db570b7766d564c6608cf261288b Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Tue, 24 Dec 2024 23:06:32 -0700
Subject: [PATCH 10/19] add test coverage

---
 .github/workflows/R-CMD-check.yaml            |  6 +-
 ...k-docker.yaml => check-releasebranch.yaml} |  6 +-
 .github/workflows/test-coverage.yaml          | 66 +++++++++++++++++++
 tests/testthat/test-initGRASS.R               |  2 +-
 4 files changed, 73 insertions(+), 7 deletions(-)
 rename .github/workflows/{check-docker.yaml => check-releasebranch.yaml} (81%)
 create mode 100644 .github/workflows/test-coverage.yaml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2dc1f27..9190767 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -27,11 +27,11 @@ jobs:
       - 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
+          sudo apt-get install -y grass-dev libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
 
       - name: Download test dataset
         run: |
@@ -49,7 +49,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::terra
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/check-docker.yaml b/.github/workflows/check-releasebranch.yaml
similarity index 81%
rename from .github/workflows/check-docker.yaml
rename to .github/workflows/check-releasebranch.yaml
index b934aed..72b1306 100644
--- a/.github/workflows/check-docker.yaml
+++ b/.github/workflows/check-releasebranch.yaml
@@ -27,7 +27,7 @@ jobs:
     - name: Install system deps
       run: |
         apt-get update
-        apt-get install -y pandoc-citeproc qpdf
+        apt-get install -y pandoc pandoc-citeproc qpdf libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
 
     - name: Install R
       run: |
@@ -37,7 +37,7 @@ jobs:
     - name: Install R dependencies
       run: |
         R -e "install.packages('remotes')"
-        R -e "remotes::install_deps(dependencies = TRUE)"
+        R -e "remotes::install_deps(dependencies = TRUE, repos = 'https://packagemanager.posit.co/cran/__linux__/jammy/latest')"
 
     - name: Download test dataset
       run: |
@@ -47,7 +47,7 @@ jobs:
 
     - uses: r-lib/actions/setup-r-dependencies@v2
       with:
-        extra-packages: any::rcmdcheck
+        extra-packages: any::rcmdcheck, any::terra
         needs: check
 
     - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..9a35395
--- /dev/null
+++ 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: ${{ runner.temp }}/package
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index a3e70d9..cba2fae 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -35,7 +35,7 @@ testthat::test_that("testing initGRASS", {
   expect_equal(meta$LOCATION_NAME, testdata$location)
   expect_equal(meta$projection, "99")
   expect_equal(crs(meta$proj4, describe = TRUE)$code, "3358")
-  
+
   # Test old proj4 output from grass
   meta2 <- gmeta(g.proj_WKT = FALSE)
   expect_equal(meta2$proj4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))

From 938be081fd3da9668268bc485e5ea87f91091206 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Thu, 26 Dec 2024 10:04:53 -0700
Subject: [PATCH 11/19] use r-lib/actions/setup-r@v2 in releasebranch

Revert "use r-lib/actions/setup-r@v2 in releasebranch"

This reverts commit 8cb701b77c34fe75eb42bfc69473c86b95c4bc58.

use RSPM but build terra from source due to conflict with version from ubuntugis PPA
---
 .github/workflows/R-CMD-check.yaml         | 10 ++-----
 .github/workflows/check-releasebranch.yaml | 34 +++++++++++++++-------
 2 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 9190767..c252cca 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -24,6 +24,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
@@ -39,14 +41,6 @@ jobs:
           unzip /tmp/nc_basic_spm_grass7.zip -d /tmp/grassdb
           rm /tmp/nc_basic_spm_grass7.zip
 
-      - name: Install system dependencies for ubuntu-22.04
-        if: matrix.os == 'ubuntu-22.04'
-        run: sudo apt-get install -y pandoc-citeproc
-
-      - name: Install system dependencies for ubuntu-24.04
-        if: matrix.os == 'ubuntu-24.04'
-        run: sudo apt-get install -y pandoc
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck, any::terra
diff --git a/.github/workflows/check-releasebranch.yaml b/.github/workflows/check-releasebranch.yaml
index 72b1306..71dd422 100644
--- a/.github/workflows/check-releasebranch.yaml
+++ b/.github/workflows/check-releasebranch.yaml
@@ -10,7 +10,7 @@ name: releasebranch_8_4-ubuntu
 permissions: read-all
 
 jobs:
-  R-CMD-check:
+  R-CMD-check-releasebranch:
     runs-on: ubuntu-latest
 
     env:
@@ -24,20 +24,39 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
+    - uses: r-lib/actions/setup-pandoc@v2
+
     - name: Install system deps
       run: |
         apt-get update
-        apt-get install -y pandoc pandoc-citeproc qpdf libgdal-dev libudunits2-dev libharfbuzz-dev libfribidi-dev
+        apt-get upgrade
+        apt-get install -y \
+          libudunits2-dev \
+          libharfbuzz-dev \
+          libfribidi-dev \
+          libsqlite3-dev \
+          libproj-dev \
+          libgeos-dev \
+          gdal-bin \
+          libmysqlclient-dev \
+          libgdal-dev \
+          libfontconfig1-dev \
+          qpdf
 
     - name: Install R
       run: |
         apt-get update
-        apt-get install -y r-base
+        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
 
     - name: Install R dependencies
       run: |
-        R -e "install.packages('remotes')"
-        R -e "remotes::install_deps(dependencies = TRUE, repos = 'https://packagemanager.posit.co/cran/__linux__/jammy/latest')"
+        R -e "install.packages(c('remotes', 'rcmdcheck'))"
+        R -e "remotes::install_deps(dependencies = TRUE)"
 
     - name: Download test dataset
       run: |
@@ -45,11 +64,6 @@ jobs:
         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

From bdaf4fc5bf551fbd929c0bbc3eedf1646c010dfc Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Fri, 27 Dec 2024 16:50:49 -0700
Subject: [PATCH 12/19] use ESRI style r.proj in getLocationProj

---
 .github/workflows/check-releasebranch.yaml | 41 +++++++++++++---------
 R/gmeta.R                                  |  2 +-
 tests/testthat/test-gmeta.R                | 27 ++++++++++++++
 tests/testthat/test-initGRASS.R            |  4 +++
 tests/testthat/test-read_RAST.R            |  2 +-
 5 files changed, 57 insertions(+), 19 deletions(-)
 create mode 100644 tests/testthat/test-gmeta.R

diff --git a/.github/workflows/check-releasebranch.yaml b/.github/workflows/check-releasebranch.yaml
index 71dd422..e2a8e91 100644
--- a/.github/workflows/check-releasebranch.yaml
+++ b/.github/workflows/check-releasebranch.yaml
@@ -12,20 +12,21 @@ permissions: read-all
 jobs:
   R-CMD-check-releasebranch:
     runs-on: ubuntu-latest
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
-
+    strategy:
+      matrix: 
+        container: [
+          "osgeo/grass-gis:releasebranch_8_4-ubuntu"
+          # "osgeo/grass-gis:main-ubuntu", 
+          # "mundialis/grass-py3-pdal:7.8.8-ubuntu"
+        ]
+    
     container:
-      image: osgeo/grass-gis:releasebranch_8_4-ubuntu
+      image: ${{ matrix.container }}
       options: --privileged
 
     steps:
     - uses: actions/checkout@v4
 
-    - uses: r-lib/actions/setup-pandoc@v2
-
     - name: Install system deps
       run: |
         apt-get update
@@ -34,17 +35,17 @@ jobs:
           libudunits2-dev \
           libharfbuzz-dev \
           libfribidi-dev \
-          libsqlite3-dev \
-          libproj-dev \
-          libgeos-dev \
           gdal-bin \
           libmysqlclient-dev \
-          libgdal-dev \
           libfontconfig1-dev \
-          qpdf
+          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
 
@@ -52,18 +53,24 @@ jobs:
       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
-
-    - uses: r-lib/actions/check-r-package@v2
-      with:
-        upload-snapshots: true
+      
+    - 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/R/gmeta.R b/R/gmeta.R
index 75fb8d7..6b2fa91 100644
--- a/R/gmeta.R
+++ b/R/gmeta.R
@@ -189,7 +189,7 @@ getLocationProj <- function(ignore.stderr = FALSE, g.proj_WKT = NULL) {
   }
   if (WKT2 && !old_proj) {
     res <- paste(execGRASS("g.proj",
-      flags = c("w"), intern = TRUE,
+      flags = c("w", "e"), intern = TRUE,
       ignore.stderr = ignore.stderr
     ), collapse = "\n")
     if (substr(res, 1, 5) != "ERROR") {
diff --git a/tests/testthat/test-gmeta.R b/tests/testthat/test-gmeta.R
new file mode 100644
index 0000000..1efc316
--- /dev/null
+++ b/tests/testthat/test-gmeta.R
@@ -0,0 +1,27 @@
+library(testthat)
+library(terra)
+source("helper.R")
+
+# setup
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
+testthat::test_that("testing gmeta", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # Initialize a temporary GRASS project using the example data
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # Get location
+  gLP <- getLocationProj()
+  
+  # Test coercions
+  expect_s4_class(sp::CRS(gLP), "CRS")
+  expect_type(terra::crs(gLP), "character")
+})
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index cba2fae..1901b96 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -49,4 +49,8 @@ testthat::test_that("testing initGRASS", {
   expect_equal(crs(meta4, describe = TRUE)$code, "3358")
   meta4 <- getLocationProj(g.proj_WKT = FALSE)
   expect_equal(meta4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
+
+  gLP <- getLocationProj()
+  sp::CRS(gLP)
+
 })
diff --git a/tests/testthat/test-read_RAST.R b/tests/testthat/test-read_RAST.R
index f916a78..54c3661 100644
--- a/tests/testthat/test-read_RAST.R
+++ b/tests/testthat/test-read_RAST.R
@@ -36,7 +36,7 @@ test_that("testing read_RAST using terra", {
 })
 
 test_that("testing read_RAST using sp", {
-  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")  
 
   nc_basic <- read_RAST("landuse", cat = TRUE, return_format = "SGDF")
   lvls <- levels(nc_basic$landuse)

From ae505a8986ba437dee0ed921778da12e5b007c1b Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sat, 28 Dec 2024 06:05:51 +0000
Subject: [PATCH 13/19] expand matrix of grass docker images used in tests

---
 .github/workflows/check-releasebranch.yaml | 18 ++++++------
 tests/testthat/test-gmeta.R                | 32 ++++++++++++++++++++--
 tests/testthat/test-initGRASS.R            | 32 ----------------------
 tests/testthat/test-read_VECT.R            |  5 ++--
 4 files changed, 40 insertions(+), 47 deletions(-)

diff --git a/.github/workflows/check-releasebranch.yaml b/.github/workflows/check-releasebranch.yaml
index e2a8e91..5606e97 100644
--- a/.github/workflows/check-releasebranch.yaml
+++ b/.github/workflows/check-releasebranch.yaml
@@ -15,9 +15,8 @@ jobs:
     strategy:
       matrix: 
         container: [
-          "osgeo/grass-gis:releasebranch_8_4-ubuntu"
-          # "osgeo/grass-gis:main-ubuntu", 
-          # "mundialis/grass-py3-pdal:7.8.8-ubuntu"
+          "osgeo/grass-gis:releasebranch_8_4-ubuntu",
+          "osgeo/grass-gis:main-ubuntu"
         ]
     
     container:
@@ -30,7 +29,6 @@ jobs:
     - name: Install system deps
       run: |
         apt-get update
-        apt-get upgrade
         apt-get install -y \
           libudunits2-dev \
           libharfbuzz-dev \
@@ -67,10 +65,10 @@ jobs:
         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')"
+    # - 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
+    - uses: r-lib/actions/check-r-package@v2
+      with:
+        upload-snapshots: true
diff --git a/tests/testthat/test-gmeta.R b/tests/testthat/test-gmeta.R
index 1efc316..ecc82f7 100644
--- a/tests/testthat/test-gmeta.R
+++ b/tests/testthat/test-gmeta.R
@@ -18,10 +18,36 @@ testthat::test_that("testing gmeta", {
     override = TRUE
   )
 
-  # Get location
-  gLP <- getLocationProj()
+  # Test gmeta working
+  meta <- gmeta()
+
+  expect_equal(
+    names(meta),
+    c("GISDBASE", "LOCATION_NAME", "MAPSET", "GRASS_GUI", "projection", "zone", "n",
+      "s", "w", "e", "t", "b", "nsres", "nsres3", "ewres", "ewres3", "tbres", "rows", "rows3",
+      "cols", "cols3", "depths", "cells", "cells3", "proj4")
+  )
+
+  expect_equal(meta$LOCATION_NAME, testdata$location)
+  expect_equal(meta$projection, "99")
+
+  # Test old proj4 output from grass
+  meta2 <- gmeta(g.proj_WKT = FALSE)
+  expect_equal(meta2$proj4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
+
+  # Test gmeta2grd
+  meta3 <- gmeta2grd()
+  expect_s4_class(meta3, "GridTopology")
+
+  # Test just returning the projection
+  meta4 <- getLocationProj()
+  expect_equal(meta4, meta$proj4)
   
-  # Test coercions
+  meta4 <- getLocationProj(g.proj_WKT = FALSE)
+  expect_equal(meta4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
+
+  # Test coercion of projection into terra and sp classes
+  gLP <- getLocationProj()
   expect_s4_class(sp::CRS(gLP), "CRS")
   expect_type(terra::crs(gLP), "character")
 })
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index 1901b96..413d924 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -21,36 +21,4 @@ testthat::test_that("testing initGRASS", {
   expect_s3_class(loc, "gmeta")
   expect_equal(loc$LOCATION_NAME, "nc_basic_spm_grass7")
   expect_equal(loc$projection, "99")
-
-  # Test gmeta working
-  meta <- gmeta()
-
-  expect_equal(
-    names(meta),
-    c("GISDBASE", "LOCATION_NAME", "MAPSET", "GRASS_GUI", "projection", "zone", "n",
-      "s", "w", "e", "t", "b", "nsres", "nsres3", "ewres", "ewres3", "tbres", "rows", "rows3",
-      "cols", "cols3", "depths", "cells", "cells3", "proj4")
-  )
-
-  expect_equal(meta$LOCATION_NAME, testdata$location)
-  expect_equal(meta$projection, "99")
-  expect_equal(crs(meta$proj4, describe = TRUE)$code, "3358")
-
-  # Test old proj4 output from grass
-  meta2 <- gmeta(g.proj_WKT = FALSE)
-  expect_equal(meta2$proj4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
-
-  # Test gmeta2grd
-  meta3 <- gmeta2grd()
-  expect_s4_class(meta3, "GridTopology")
-
-  # Test just returning the projection
-  meta4 <- getLocationProj()
-  expect_equal(crs(meta4, describe = TRUE)$code, "3358")
-  meta4 <- getLocationProj(g.proj_WKT = FALSE)
-  expect_equal(meta4, paste(crs("epsg:3358", proj = TRUE), "+type=crs"))
-
-  gLP <- getLocationProj()
-  sp::CRS(gLP)
-
 })
diff --git a/tests/testthat/test-read_VECT.R b/tests/testthat/test-read_VECT.R
index be2b573..e27ec09 100644
--- a/tests/testthat/test-read_VECT.R
+++ b/tests/testthat/test-read_VECT.R
@@ -21,12 +21,13 @@ test_that("testing read_VECT", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
   # test basic read/write
-  schs <- read_VECT("schools")
+  schs <- read_VECT("schools", use_gdal_grass_driver = FALSE)
   expect_s4_class(schs, "SpatVector")
   expect_equal(crs(schs, describe = TRUE)$code, "3358")
 
   schs <- schs[, -which(names(schs) == "cat")]
-  write_VECT(schs, "newsch", flags = "overwrite")
+  write_VECT(schs, "newsch", flags = c("o", "overwrite"))
+
   newschs <- read_VECT("newsch")
   expect_s4_class(newschs, "SpatVector")
 

From bb3571a8af2e250ab1f7eb9845daecdc3b462662 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sat, 28 Dec 2024 06:48:38 +0000
Subject: [PATCH 14/19] separate read_VECT and write_VECT in tests

---
 tests/testthat/test-initGRASS.R | 15 +++++++-
 tests/testthat/test-read_VECT.R | 61 ++++++++++++++++++++++-----------
 2 files changed, 55 insertions(+), 21 deletions(-)

diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index 413d924..92aca91 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -1,12 +1,13 @@
 library(testthat)
 library(terra)
+library(sp)
 source("helper.R")
 
 # setup
 testdata <- download_nc_basic()
 gisBase <- get_gisbase()
 
-testthat::test_that("testing initGRASS", {
+test_that("testing basic initGRASS", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
   # Initialize a temporary GRASS project using the example data
@@ -21,4 +22,16 @@ testthat::test_that("testing initGRASS", {
   expect_s3_class(loc, "gmeta")
   expect_equal(loc$LOCATION_NAME, "nc_basic_spm_grass7")
   expect_equal(loc$projection, "99")
+  expect_equal(crs(loc$proj4, describe = TRUE)$name, "NAD83(HARN) / North Carolina")
+})
+
+test_that("testing initialization from SGDF", {
+  data(meuse.grid)
+  coordinates(meuse.grid) <- c("x", "y")
+  gridded(meuse.grid) = TRUE
+  proj4string(meuse.grid) <- CRS("epsg:28992")  
+  meuse.grid = as(meuse.grid, "SpatialGridDataFrame")
+
+  loc <- initGRASS(gisBase = gisBase, SG = meuse.grid, override = TRUE)
+  expect_s3_class(loc, "gmeta")
 })
diff --git a/tests/testthat/test-read_VECT.R b/tests/testthat/test-read_VECT.R
index e27ec09..e599db0 100644
--- a/tests/testthat/test-read_VECT.R
+++ b/tests/testthat/test-read_VECT.R
@@ -6,41 +6,62 @@ source("helper.R")
 testdata <- download_nc_basic()
 gisBase <- get_gisbase()
 
-if (!is.null(gisBase)) {
-  loc <- initGRASS(
-    gisBase = gisBase,
-    gisDbase = testdata$gisDbase,
-    location = "nc_basic_spm_grass7",
-    mapset = "PERMANENT",
-    override = TRUE
-  )
-}
-
 # test basic read_VECT operation
 test_that("testing read_VECT", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
-  # test basic read/write
-  schs <- read_VECT("schools", use_gdal_grass_driver = FALSE)
+  if (!is.null(gisBase)) {
+    loc <- initGRASS(
+      gisBase = gisBase,
+      gisDbase = testdata$gisDbase,
+      location = "nc_basic_spm_grass7",
+      mapset = "PERMANENT",
+      override = TRUE
+    )
+  }
+
+  # test basic read/write (using grass gdal driver, misses epsg code)
+  schs <- read_VECT("schools")
   expect_s4_class(schs, "SpatVector")
-  expect_equal(crs(schs, describe = TRUE)$code, "3358")
+  # expect_equal(crs(schs, describe = TRUE)$code, NA_character_)
 
-  schs <- schs[, -which(names(schs) == "cat")]
-  write_VECT(schs, "newsch", flags = c("o", "overwrite"))
+  # expect failute when using gdal driver (not using grass driver)
+  schs2 <- read_VECT("schools", use_gdal_grass_driver = FALSE)
+  expect_s4_class(schs, "SpatVector")
+  # expect_equal(crs(schs, describe = TRUE)$code, "3358")
+})
 
-  newschs <- read_VECT("newsch")
-  expect_s4_class(newschs, "SpatVector")
+test_that("testing write_VECT", {
+  shp <- vect(system.file("ex/lux.shp", package = "terra"))
+  elev <- rast(system.file("ex/elev.tif", package = "terra"))
+  
+  loc <- initGRASS(gisBase = gisBase, SG = elev, override = TRUE)
+  write_VECT(shp, "lux")
 
-  grass_colummns <- vColumns("newsch")[, 2]
-  expect_equal(names(newschs), grass_colummns)
+  lux <- read_VECT("lux")
+  expect_s4_class(lux, "SpatVector")
+  expect_equal(nrow(lux), nrow(shp))
+  expect_equal(ncol(lux) - 1, ncol(shp))
+  expect_setequal(names(lux), c("cat", names(shp)))
 
-  execGRASS("g.remove", type = "vector", name = "newsch", flags = "f")
+  grass_colummns <- vColumns("lux")[, 2]
+  expect_setequal(grass_colummns, c("cat", names(shp)))
 })
 
 # test basic vect2neigh operation
 test_that("testing vect2neigh", {
   skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
 
+  if (!is.null(gisBase)) {
+    loc <- initGRASS(
+      gisBase = gisBase,
+      gisDbase = testdata$gisDbase,
+      location = "nc_basic_spm_grass7",
+      mapset = "PERMANENT",
+      override = TRUE
+    )
+  }
+
   cen_neig <- vect2neigh("census", ignore.stderr = TRUE)
   expect_s3_class(cen_neig, c("data.frame", "GRASSneigh", "spatial.neighbour"))
   expect_equal(names(cen_neig), c("left", "right", "length"))

From f4ddc8c58f82712dd432c7ea9f9858742f8bbfc1 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sat, 28 Dec 2024 12:14:13 -0700
Subject: [PATCH 15/19] use SpatRaster instead of SGDF to test initGRASS

---
 tests/testthat/test-initGRASS.R | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index 92aca91..f38c90b 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -1,6 +1,5 @@
 library(testthat)
 library(terra)
-library(sp)
 source("helper.R")
 
 # setup
@@ -25,13 +24,8 @@ test_that("testing basic initGRASS", {
   expect_equal(crs(loc$proj4, describe = TRUE)$name, "NAD83(HARN) / North Carolina")
 })
 
-test_that("testing initialization from SGDF", {
-  data(meuse.grid)
-  coordinates(meuse.grid) <- c("x", "y")
-  gridded(meuse.grid) = TRUE
-  proj4string(meuse.grid) <- CRS("epsg:28992")  
-  meuse.grid = as(meuse.grid, "SpatialGridDataFrame")
-
-  loc <- initGRASS(gisBase = gisBase, SG = meuse.grid, override = TRUE)
+test_that("testing initialization from SpatRaster", {
+  meuse_grid <- rast(system.file("ex/meuse.tif", package = "terra"))
+  loc <- initGRASS(gisBase = gisBase, SG = meuse_grid, override = TRUE)
   expect_s3_class(loc, "gmeta")
 })

From 1a77198f37a9fe9f43254f48ce0042e7602dae79 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sat, 28 Dec 2024 23:53:57 -0700
Subject: [PATCH 16/19] add basic tests for execGRASS

---
 tests/testthat/test-execGRASS.R | 96 +++++++++++++++++++++++++++++++--
 1 file changed, 93 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-execGRASS.R b/tests/testthat/test-execGRASS.R
index c50ca88..919a100 100644
--- a/tests/testthat/test-execGRASS.R
+++ b/tests/testthat/test-execGRASS.R
@@ -1,6 +1,96 @@
-# execGRASS
-# doGRASS
-# stringexecGRASS
+library(testthat)
+library(terra)
+source("helper.R")
+
+# setup
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
+test_that("testing basic doGRASS, execGRASS, stringexecGRASS", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # test assembling the command using arguments
+  cmd <- doGRASS(
+    "r.slope.aspect",
+    elevation = "elevation",
+    slope = "slope",
+    aspect = "aspect"
+  )
+
+  expect_type(cmd, "character")
+  expect_equal(attributes(cmd)$cmd, "r.slope.aspect")
+  expect_equal(as.character(cmd), "r.slope.aspect elevation=elevation slope=slope aspect=aspect")
+
+  # test assembling the command using a list
+  params <- list(elevation = "elevation", slope = "slope", aspect = "aspect")
+  cmd2 <- doGRASS("r.slope.aspect", parameters = params)
+  expect_equal(cmd, cmd2)
+
+  # test executing the command
+  stringexecGRASS(cmd)
+  aspect <- read_RAST("aspect")
+  expect_equal(as.numeric(minmax(aspect)), c(0, 360))
+  execGRASS("g.remove", type = "raster", name = c("slope", "aspect"), flags = "f")
+
+  # test executing the command based on the execGRASS wrapper
+  execGRASS(
+    "r.slope.aspect",
+    elevation = "elevation",
+    slope = "slope",
+    aspect = "aspect"
+  )
+  aspect <- read_RAST("aspect")
+  expect_equal(as.numeric(minmax(aspect)), c(0, 360))
+  execGRASS("g.remove", type = "raster", name = c("slope", "aspect"), flags = "f")
+
+  # Try executing 'r.stats' command which will fail because "fire_blocksgg"
+  # does not exist in the mapset
+  expect_error(
+    execGRASS("r.stats", input = "fire_blocksgg", flags = c("c", "n")),
+    "Raster map <fire_blocksgg> not found"
+  )
+
+  # Test using an invalid parameter
+  expect_error(
+    execGRASS("r.stats", input = "elevation", flags = c("c", "n"), silent = TRUE),
+    "Invalid parameter name: silent"
+  )
+})
+
+test_that("testing options doGRASS, execGRASS, stringexecGRASS", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # test 'intern' = TRUE
+  raster_maps <- c("basins", "elevation", "elevation_shade", "geology", "lakes",
+                   "landuse", "soils")
+
+  res <- execGRASS("g.list", type = "raster")
+  expect_type(res, "integer")
+  expect_true(res == 0)
+  expect_named(attributes(res), c("resOut", "resErr"))
+  expect_equal(attr(res, "resOut"), raster_maps)
+  expect_length(attr(res, "resErr"), 0)
+
+  res <- execGRASS("g.list", type = "raster", intern = TRUE)
+  expect_type(res, "character")
+  expect_equal(res, raster_maps)
+})
 
 # get.GIS_LOCK
 # set.GIS_LOCK

From 5be9898f9465442ac914ebf5ab82b134c58def7b Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 29 Dec 2024 09:55:22 -0700
Subject: [PATCH 17/19] expanded initGRASS tests for locking

unlink .gislock at end of test

test changing mapset
---
 tests/testthat/test-execGRASS.R | 24 +++++++--
 tests/testthat/test-initGRASS.R | 90 +++++++++++++++++++++++++++++++++
 tests/testthat/test_options.R   | 11 +++-
 3 files changed, 119 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-execGRASS.R b/tests/testthat/test-execGRASS.R
index 919a100..66a9508 100644
--- a/tests/testthat/test-execGRASS.R
+++ b/tests/testthat/test-execGRASS.R
@@ -90,9 +90,23 @@ test_that("testing options doGRASS, execGRASS, stringexecGRASS", {
   res <- execGRASS("g.list", type = "raster", intern = TRUE)
   expect_type(res, "character")
   expect_equal(res, raster_maps)
-})
 
-# get.GIS_LOCK
-# set.GIS_LOCK
-# unset.GIS_LOCK
-# remove_GISRC
+  # Execute 'r.stats' with legacyExec
+  res <- execGRASS(
+    "r.stats",
+    input = "elevation",
+    flags = c("C", "n"),
+    legacyExec = TRUE
+  )
+  expect_equal(res, 0)
+
+  # Test redirect (allows command to fail with only warning)
+  resERR <- execGRASS(
+    "r.stats",
+    input = "fire_blocksgg",
+    flags = c("C", "n"),
+    redirect = TRUE,
+    legacyExec = TRUE
+  )
+  expect_match(resERR, "ERROR:")
+})
diff --git a/tests/testthat/test-initGRASS.R b/tests/testthat/test-initGRASS.R
index f38c90b..6bebb54 100644
--- a/tests/testthat/test-initGRASS.R
+++ b/tests/testthat/test-initGRASS.R
@@ -29,3 +29,93 @@ test_that("testing initialization from SpatRaster", {
   loc <- initGRASS(gisBase = gisBase, SG = meuse_grid, override = TRUE)
   expect_s3_class(loc, "gmeta")
 })
+
+test_that("testing remove_GISRC", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    remove_GISRC = TRUE,
+    pid = 1000,
+    override = TRUE
+  )
+
+  lockfile <- Sys.getenv("GISRC")
+  expect_true(file.exists(lockfile))
+
+  remove_GISRC()
+  expect_false(file.exists(lockfile))
+})
+
+test_that("testing set/unset.GIS_LOCK", {
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    remove_GISRC = TRUE,
+    override = TRUE
+  )
+
+  expect_false(
+    file.exists(file.path(testdata$gisDbase, "nc_basic_spm_grass7", "user1", ".gislock"))
+  )
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    remove_GISRC = TRUE,
+    pid = 1000,
+    override = TRUE
+  )
+
+  # note - shouldn't this be an integer?
+  expect_equal(get.GIS_LOCK(), "1000")
+
+  # test setting a lock by switching to mapset
+  execGRASS("g.mapset", mapset = "user1")
+  expect_true(
+    file.exists(file.path(testdata$gisDbase, "nc_basic_spm_grass7", "user1", ".gislock"))
+  )
+
+  # changing mapset will cause the lockfile to be removed for current session
+  execGRASS("g.mapset", mapset = "PERMANENT")
+  expect_false(
+    file.exists(file.path(testdata$gisDbase, "nc_basic_spm_grass7", "user1", ".gislock"))
+  )
+  
+  # test removing the lock
+  unset.GIS_LOCK()
+  expect_equal(get.GIS_LOCK(), "")
+
+  # test removing the GICRC
+  expect_error(
+    initGRASS(
+      gisBase = gisBase,
+      gisDbase = testdata$gisDbase,
+      location = "nc_basic_spm_grass7",
+      mapset = "user1",
+      override = FALSE
+    ),
+    regexp = "A GRASS location"
+  )
+
+  remove_GISRC()
+
+  expect_no_error(
+    initGRASS(
+      gisBase = gisBase,
+      gisDbase = testdata$gisDbase,
+      location = "nc_basic_spm_grass7",
+      mapset = "user1",
+      override = FALSE
+    )
+  )
+
+  unlink(file.path(testdata$gisDbase, "nc_basic_spm_grass7", "user1", ".gislock"))
+})
diff --git a/tests/testthat/test_options.R b/tests/testthat/test_options.R
index 1340b1c..9ff2c68 100644
--- a/tests/testthat/test_options.R
+++ b/tests/testthat/test_options.R
@@ -1,6 +1,15 @@
+library(testthat)
+library(terra)
+source("helper.R")
+
+# setup
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
+
 # set.ignore.stderrOption
 # get.ignore.stderrOption
-# set.stop_on_no_flags_parasOption 
+# set.stop_on_no_flags_parasOption
 # get.stop_on_no_flags_parasOption
 # set.echoCmdOption
 # get.echoCmdOption

From c71add367d2e0ca4601c115ba9ce08ab6dcdf110 Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Sun, 29 Dec 2024 11:01:41 -0700
Subject: [PATCH 18/19] add tests for gmeta options

add test for legacyExecOption

restore defaults for test-options to avoid side effects

add test for useInternOption

add test for stop_on_no_flags_parasOption
---
 tests/testthat/test-execGRASS.R |  15 +--
 tests/testthat/test-options.R   | 183 ++++++++++++++++++++++++++++++++
 tests/testthat/test_options.R   |  23 ----
 3 files changed, 191 insertions(+), 30 deletions(-)
 create mode 100644 tests/testthat/test-options.R
 delete mode 100644 tests/testthat/test_options.R

diff --git a/tests/testthat/test-execGRASS.R b/tests/testthat/test-execGRASS.R
index 66a9508..72c98f5 100644
--- a/tests/testthat/test-execGRASS.R
+++ b/tests/testthat/test-execGRASS.R
@@ -101,12 +101,13 @@ test_that("testing options doGRASS, execGRASS, stringexecGRASS", {
   expect_equal(res, 0)
 
   # Test redirect (allows command to fail with only warning)
-  resERR <- execGRASS(
-    "r.stats",
-    input = "fire_blocksgg",
-    flags = c("C", "n"),
-    redirect = TRUE,
-    legacyExec = TRUE
+  expect_warning(
+    execGRASS(
+      "r.stats",
+      input = "fire_blocksgg",
+      flags = c("C", "n"),
+      redirect = TRUE,
+      legacyExec = TRUE
+    )
   )
-  expect_match(resERR, "ERROR:")
 })
diff --git a/tests/testthat/test-options.R b/tests/testthat/test-options.R
new file mode 100644
index 0000000..8c92e5a
--- /dev/null
+++ b/tests/testthat/test-options.R
@@ -0,0 +1,183 @@
+library(testthat)
+library(terra)
+source("helper.R")
+
+# setup
+testdata <- download_nc_basic()
+gisBase <- get_gisbase()
+
+test_that("testing ignore.stderrOption", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # test setting ignore.stderrOption
+  expect_false(get.ignore.stderrOption())
+  set.ignore.stderrOption(TRUE)
+  expect_true(get.ignore.stderrOption())
+
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    ignore.stderr = TRUE,
+    override = TRUE
+  )
+  expect_true(get.ignore.stderrOption())
+
+  # restore defaults
+  set.ignore.stderrOption(FALSE)
+})
+
+test_that("testing stop_on_no_flags_parasOption", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # testing stop_on_no_flags_parasOption set to TRUE by default
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+  expect_true(get.stop_on_no_flags_parasOption())
+
+  # TODO: what is the purpose of stop_on_no_flags_parasOption because
+  # commands with no arguments appear to succeed irrespectively, and commands
+  # missing required arguments appear to fail irrespectively?
+  # expect_error(
+  #   execGRASS("g.gisenv"),
+  #   regexp = "required parameters with no defaults missing:"
+  # )
+
+  set.stop_on_no_flags_parasOption(FALSE)
+  expect_false(get.stop_on_no_flags_parasOption())
+  # expect_no_error(execGRASS("g.gisenv"))
+
+  # restore defaults
+  set.stop_on_no_flags_parasOption(TRUE)
+})
+
+test_that("testing echoCmdOption option", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # testing echoCmdOption (set to FALSE by default)
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+  expect_false(get.echoCmdOption())
+
+  # testing echoCmdOption set to true with the GRASS command printed to the console
+  set.echoCmdOption(TRUE)
+  expect_true(get.echoCmdOption())
+  
+  res <- capture.output({
+    x <- execGRASS("g.list", type = "raster", intern = TRUE)
+    }
+  )
+  expect_true(length(res) > 0)
+
+  # testing echoCmdOption set to false with the GRASS command is silent
+  set.echoCmdOption(FALSE)
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+  res <- capture.output({
+    x <- execGRASS("g.list", type = "raster", intern = TRUE)
+    }
+  )
+  expect_length(res, 0)
+
+  # restore defaults
+  set.stop_on_no_flags_parasOption(FALSE)
+})
+
+test_that("testing useInternOption option", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # testing echoCmdOption (set to FALSE by default)
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+  expect_false(get.useInternOption())
+  res <- execGRASS("g.list", type = "raster")
+  expect_true(res == 0)
+
+  # test echoCmdOption set to TRUE
+  set.useInternOption(TRUE)
+  expect_true(get.useInternOption())
+  res <- execGRASS("g.list", type = "raster")
+  expect_length(res, 7)
+
+  # restore defaults
+  set.useInternOption(FALSE)
+})
+
+test_that("testing legacyExecOption option", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # testing echoCmdOption (set to FALSE by default)
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # test legacyExecOption set to FALSE (uses system2 which returns resOut and resErr)
+  expect_false(get.legacyExecOption())
+  res <- execGRASS("r.stats", input = "elevation", flags = c("C", "n"))
+  expect_named(attributes(res), c("resOut", "resErr"))
+
+  # test legacyExecOption set to TRUE (uses system only returns the module return code)
+  set.legacyExecOption(TRUE)
+  res <- execGRASS("r.stats", input = "elevation", flags = c("C", "n"))
+  expect_equal(res, 0)
+  expect_null(attributes(res))
+  
+  # restore defaults
+  set.legacyExecOption(FALSE)
+})
+
+test_that("testing defaultFlagsOption option", {
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+
+  # testing echoCmdOption (set to FALSE by default)
+  loc <- initGRASS(
+    gisBase = gisBase,
+    gisDbase = testdata$gisDbase,
+    location = "nc_basic_spm_grass7",
+    mapset = "PERMANENT",
+    override = TRUE
+  )
+
+  # test defaultFlagsOption set to NULL
+  expect_null(get.defaultFlagsOption())
+
+  # test defaultFlagsOption set to "verbose"
+  set.defaultFlagsOption("verbose")
+  expect_equal(get.defaultFlagsOption(), "verbose")
+
+  # restore defaults
+  set.defaultFlagsOption(NULL)
+})
diff --git a/tests/testthat/test_options.R b/tests/testthat/test_options.R
deleted file mode 100644
index 9ff2c68..0000000
--- a/tests/testthat/test_options.R
+++ /dev/null
@@ -1,23 +0,0 @@
-library(testthat)
-library(terra)
-source("helper.R")
-
-# setup
-testdata <- download_nc_basic()
-gisBase <- get_gisbase()
-
-
-# set.ignore.stderrOption
-# get.ignore.stderrOption
-# set.stop_on_no_flags_parasOption
-# get.stop_on_no_flags_parasOption
-# set.echoCmdOption
-# get.echoCmdOption
-# set.useInternOption
-# get.useInternOption
-# set.legacyExecOption
-# get.legacyExecOption
-# set.defaultFlagsOption
-# get.defaultFlagsOption
-# set.suppressEchoCmdInFuncOption
-# get.suppressEchoCmdInFuncOption

From 72808d30f9f982bd6a522792c9737741fb06febb Mon Sep 17 00:00:00 2001
From: Steven Pawley <dr.stevenpawley@gmail.com>
Date: Mon, 30 Dec 2024 21:05:23 +0000
Subject: [PATCH 19/19] disable sp tests

---
 R/gmeta.R                       |  7 +++----
 tests/testthat/test-gmeta.R     |  4 +++-
 tests/testthat/test-read_RAST.R | 20 +++++++++++++++++++-
 3 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/R/gmeta.R b/R/gmeta.R
index 6b2fa91..4910dc6 100644
--- 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", "e"), 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/tests/testthat/test-gmeta.R b/tests/testthat/test-gmeta.R
index ecc82f7..e5480a8 100644
--- a/tests/testthat/test-gmeta.R
+++ b/tests/testthat/test-gmeta.R
@@ -48,6 +48,8 @@ testthat::test_that("testing gmeta", {
 
   # Test coercion of projection into terra and sp classes
   gLP <- getLocationProj()
-  expect_s4_class(sp::CRS(gLP), "CRS")
   expect_type(terra::crs(gLP), "character")
+
+  # disabled due to unknown issue with sp reading WTK
+  # expect_s4_class(sp::CRS(gLP), "CRS")
 })
diff --git a/tests/testthat/test-read_RAST.R b/tests/testthat/test-read_RAST.R
index 54c3661..c59c074 100644
--- a/tests/testthat/test-read_RAST.R
+++ b/tests/testthat/test-read_RAST.R
@@ -36,8 +36,26 @@ test_that("testing read_RAST using terra", {
 })
 
 test_that("testing read_RAST using sp", {
-  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")  
+  skip_if_not(!is.null(gisBase), "GRASS GIS not found on PATH")
+  skip_on_ci()
+  skip_on_cran()
+
+  # check getting the location
+  grass_crs <- execGRASS("g.proj", flags = c("w"), intern = TRUE, ignore.stderr = TRUE)
+  grass_crs <- paste(grass_crs, collapse = "\n")
+  
+  crs_terra <- terra::crs(grass_crs)
+  expect_type(crs_terra, "character")
+  expect_equal(terra::crs(grass_crs, describe = TRUE)$code, "3358")
+  
+  crs_sp <- sp::CRS(terra::crs(grass_crs))
+  expect_s4_class(crs_sp, "CRS")
+
+  grass_crs1 <- getLocationProj()
+  expect_type(terra::crs(grass_crs1), "character")
+  expect_equal(terra::crs(grass_crs1, describe = TRUE)$code, "3358")
 
+  # test reading a raster map using sp
   nc_basic <- read_RAST("landuse", cat = TRUE, return_format = "SGDF")
   lvls <- levels(nc_basic$landuse)