Merge pull request #15 from DrylandEcology/release/v0.2.0

Release/v0.2.0

* Github Actions are triggered for `release/**` branches in addition to `main`.
* `r-lib` Github Actions updated to `v2` (#6; @dschlaep).
* `get_data_dims()` now returns consistently an integer vector.
* Linting updated to `lintr` >= 3 and
  lint workflow switched from package tests to Github Action (#5; @dschlaep).
* `isoline_from_raster()` is now based on the `stars` and `sf` packages
  (removing a dependency on `rgeos`; addressing #3; @dschlaep).
* `variogram_range()` is now based on the `stars` and `sf` packages
  (removing a dependency on `rgdal`; addressing #3; @dschlaep).
* `read_netCDF_as_array()` gains arguments `"time_name"` and `"vertical_name"`
  with previous hard-coded values as defaults ("time" and "vertical")
  (#14; @dschlaep)
* New `get_nc_type()` identifies a suitable netCDF data type from an R object.
* `read_netCDF()` gains argument `"verbose_read"` which, if set to `"FALSE"`,
  attempts to silence communication (messages, warnings, and print statements)
  generated from reading a `netCDF` (#9; @dschlaep).

.github/workflows/check-standard.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, release/**]
+  pull_request:
+    branches: [main, release/**]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# 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, release/**]
+  pull_request:
+    branches: [main, release/**]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, release/**]
+  pull_request:
+    branches: [main, release/**]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.lintr

@@ -0,0 +1,12 @@
+linters: lintr::linters_with_tags(
+  tags = NULL,
+  #--- Change arguments of linters:
+  line_length_linter = lintr::line_length_linter(length = 80L),
+  #--- Turn off linters:
+  cyclocomp_linter = NULL,
+  implicit_integer_linter = NULL,
+  object_name_linter = NULL,
+  todo_comment_linter = NULL,
+  yoda_test_linter = NULL)
+error_on_lint: TRUE
+encoding: "UTF-8"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rSW2st
 Title: Spatiotemporal Tools for SOILWAT2 and STEPWAT2 Simulation Experiments
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
   person(
     "Daniel", "Schlaepfer",
@@ -17,7 +17,6 @@ Imports:
     abind (>= 1.4.5),
     sf (>= 0.9.8),
     sp (>= 1.4.5),
-    rgdal (>= 1.5.23),
     raster (>= 3.4.5),
     stars (>= 0.4.3)
 Suggests:
@@ -27,16 +26,16 @@ Suggests:
     ggplot2,
     ncdf4 (>= 1.17),
     ncmeta (>= 0.3.0),
-    rgeos,
+    RNetCDF (>= 2.6.2),
     testthat (>= 3.0.0),
+    terra (>= 1.4.22),
     spelling,
-    lintr,
+    lintr (>= 3.0.0),
     covr
 License: GPL-3
 URL: https://github.com/DrylandEcology/rSW2st
 BugReports: https://github.com/DrylandEcology/rSW2st/issues
 Encoding: UTF-8
-LazyData: true
 Language: en-US
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NAMESPACE

@@ -10,6 +10,7 @@ export(create_raster_from_variables)
 export(crs_units)
 export(epsg_for_utm)
 export(get_data_dims)
+export(get_nc_type)
 export(get_xyspace)
 export(is_netCDF_gridded)
 export(isoline_from_raster)

NEWS.md

@@ -0,0 +1,22 @@
+# rSW2st v0.2.0
+
+* Github Actions are triggered for `release/**` branches in addition to `main`.
+* `r-lib` Github Actions updated to `v2` (#6; @dschlaep).
+* `get_data_dims()` now returns consistently an integer vector.
+* Linting updated to `lintr` >= 3 and
+  lint workflow switched from package tests to Github Action (#5; @dschlaep).
+* `isoline_from_raster()` is now based on the `stars` and `sf` packages
+  (removing a dependency on `rgeos`; addressing #3; @dschlaep).
+* `variogram_range()` is now based on the `stars` and `sf` packages
+  (removing a dependency on `rgdal`; addressing #3; @dschlaep).
+* `read_netCDF_as_array()` gains arguments `"time_name"` and `"vertical_name"`
+  with previous hard-coded values as defaults ("time" and "vertical")
+  (#14; @dschlaep)
+* New `get_nc_type()` identifies a suitable netCDF data type from an R object.
+* `read_netCDF()` gains argument `"verbose_read"` which, if set to `"FALSE"`,
+  attempts to silence communication (messages, warnings, and print statements)
+  generated from reading a `netCDF` (#9; @dschlaep).
+
+
+# rSW2st v0.1.0
+Initial release

R/conversions.R

@@ -92,7 +92,7 @@ as_points <- function(
       x <- matrix(x, nrow = 1, ncol = 2)
     }
 
-    if (missing(crs)) {
+    if (missing(crs) || is.null(crs)) {
       stop("`crs` is missing and `x` is not a spatial object.")
     }
 
@@ -104,7 +104,7 @@ as_points <- function(
         coords = unname(x),
         proj4string = as(crs, "CRS")
       ),
-      sf = , # nolint
+      sf = ,
       sfc = sf::st_cast(
         x = sf::st_sfc(
           sf::st_multipoint(

R/crs.R

@@ -29,7 +29,7 @@ NULL
 #'
 #' @export
 crs_units <- function(crs) {
-  sf::st_crs(crs)$units_gdal
+  sf::st_crs(crs)$units_gdal # nolint: extraction_operator_linter.
 }
 
 
@@ -49,7 +49,7 @@ crs_units <- function(crs) {
 #' }
 #'
 #' @references Convert Latitude/Longitude to UTM
-# nolint start
+# nolint start: line_length_linter.
 #'   \url{https://www.wavemetrics.com/code-snippet/convert-latitudelongitude-utm}
 # nolint end
 #'   (attributed to Chuck Gantz).
@@ -72,16 +72,16 @@ utm_zone <- function(x, crs = 4326) {
   mxy <- colMeans(xy)
 
   # Make sure longitude is between -180.00 .. 179.9
-  long <- mxy[1] - floor((mxy[1] + 180) / 360) * 360
+  long <- mxy[[1L]] - floor((mxy[[1L]] + 180) / 360) * 360
 
   utm_zone <- floor((long + 180) / 6) + 1
 
-  if (mxy[2] >= 56 && mxy[2] < 64 && long >= 3 && long < 12) {
+  if (mxy[[2L]] >= 56 && mxy[[2L]] < 64 && long >= 3 && long < 12) {
     utm_zone <- 32
   }
 
   # Special zones for Svalbard
-  if (mxy[2] >= 72 && mxy[2] < 84) {
+  if (mxy[[2L]] >= 72 && mxy[[2L]] < 84) {
     if (long >= 0 && long < 9) {
       utm_zone <- 31
     } else if (long >= 9 && long < 21) {
@@ -95,7 +95,7 @@ utm_zone <- function(x, crs = 4326) {
 
   list(
     utm_zone = as.integer(unname(utm_zone)),
-    utm_NS = if (mxy[2] > 0) "N" else "S"
+    utm_NS = if (mxy[[2L]] > 0) "N" else "S"
   )
 }