Merge pull request #8 from DrylandEcology/release/v0.2.0

Release v0.2.0

- Replace rgdal/rgeos with sf/terra/stars #4
- Updating linting to lintr >= v3.0.0 #5
- Update github actions to use r-lib actions v2 #6

.github/workflows/check-standard.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, 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
+
+    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 +1,13 @@
+linters: lintr::linters_with_tags(
+  tags = NULL,
+  #--- Change arguments of linters:
+  line_length_linter = lintr::line_length_linter(length = 80L),
+  #--- Turn off linters:
+  implicit_integer_linter = NULL,
+  object_length_linter = NULL,
+  object_name_linter = NULL,
+  todo_comment_linter = NULL,
+  cyclocomp_linter = NULL,
+  yoda_test_linter = NULL)
+error_on_lint: TRUE
+encoding: "UTF-8"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rSW2exter
 Title: Access External Data as Input for SOILWAT2 and STEPWAT2 Simulations
-Version: 0.1.1
+Version: 0.2.0
 Authors@R: c(
   person(
     "Daniel", "Schlaepfer",
@@ -17,17 +17,18 @@ Imports:
     rSW2utils (>= 0.1.0),
     rSW2st (>= 0.1.0),
     rSW2data (>= 0.1.0),
+    terra,
     raster,
     reshape2,
-    sf,
-    sp
+    sf
 Suggests:
-    FedData,
+    FedData (>= 3.0.2),
     soilDB (>= 2.5.7),
+    sp,
     utils,
     testthat (>= 3.0.0),
     spelling,
-    lintr,
+    lintr (>= 3.0.0),
     covr
 Remotes:
     github::DrylandEcology/rSW2utils,
@@ -37,7 +38,6 @@ License: GPL-3
 URL: https://github.com/DrylandEcology/rSW2exter
 BugReports: https://github.com/DrylandEcology/rSW2exter/issues
 Encoding: UTF-8
-LazyData: true
 Config/testthat/edition: 3
 Language: en-US
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3

NEWS.md

@@ -0,0 +1,15 @@
+# rSW2exter v0.2.0
+* `fetch_mukeys_spatially_NRCS_SDA()` now handles versions of "soilDB"
+  from `2.5.7` to at least `2.6.14`.
+* `extract_soils_NRCS_SDA()` queries include now `localphase`;
+  this should improve the ability to identify a component of a soil map unit
+  across NRCS data releases by a combination of
+  `compname`, `comppct_r`, `localphase`.
+* `extract_soils_NRCS_SDA()` gains argument `only_soilcomp` which excludes
+  non-soil components, i.e., those that are not "Miscellaneous areas" and
+  are not "NOTCOM" (not completed).
+* Linting updated to `lintr` >= 3 and
+  lint workflow switched from package tests to Github Action (#5).
+
+# rSW2exter v0.1.0
+Initial release

R/extract_soils_Miller1998_CONUSSoils.R

@@ -32,7 +32,7 @@ create_reference_for_Miller1998_CONUSSoil <- function() {
     "Miller, D. A., and R. A. White. 1998. A conterminous United States ",
     "multilayer soil characteristics dataset for regional climate and ",
     "hydrology modeling. Earth Interactions 2:1-26. ",
-    "https://doi.org/10.1175%2F1087-3562%281998%29002%3C0001%3AACUSMS%3E2.3.CO%3B2 ", # nolint
+    "https://doi.org/10.1175%2F1087-3562%281998%29002%3C0001%3AACUSMS%3E2.3.CO%3B2 ", # nolint: line_length_linter
     "Data accessed [",
     format(as.POSIXlt(Sys.Date()), "%Y-%b-%e"),
     "]"
@@ -106,7 +106,7 @@ prepare_script_for_Miller1998_CONUSSoil <- function(
 #'
 #' @export
 create_conditioned_Miller1998_CONUSSoil <- function(
-  path,
+  path = ".",
   vars = c("rockdepm", "rockvol", "bd", "sand", "clay", "silt"),
   lower_limits_by_vars = c(
     rockdepm = 0, rockvol = 0, bd = 30, sand = 0, clay = 0, silt = 0
@@ -215,15 +215,16 @@ check_Miller1998_CONUSSoil <- function(
   )
 ) {
 
-  sapply(
+  vapply(
     vars,
     function(var) {
       file.exists(filepath_Miller1998_CONUSSoil(
         path = path,
         var = var,
         lower_limit = lower_limits_by_vars[var]
       ))
-    }
+    },
+    FUN.VALUE = NA
   )
 }
 
@@ -253,8 +254,8 @@ fetch_soils_from_Miller1998_CONUSSoil <- function(
   # Align with data crs
   ftmp <- filepath_Miller1998_CONUSSoil(
     path = path,
-    var = vars[1],
-    lower_limit = lower_limits_by_vars[vars[1]]
+    var = vars[[1L]],
+    lower_limit = lower_limits_by_vars[vars[[1L]]]
   )
 
   tmp_crs <- sf::st_crs(raster::brick(ftmp))
@@ -292,7 +293,7 @@ fetch_soils_from_Miller1998_CONUSSoil <- function(
         method = "simple"
       )
 
-      # nolint start
+      # nolint start: commented_code_linter
       # tmp <- do.call(
       #   "extract_rSFSW2",
       #   args = list(
@@ -312,7 +313,9 @@ fetch_soils_from_Miller1998_CONUSSoil <- function(
       }
 
     } else {
-      stop("Miller1998/CONUSSoil data ", shQuote(basename(ftmp)), " not found.")
+      stop(
+        "Miller1998 (CONUSSoil) data ", shQuote(basename(ftmp)), " not found."
+      )
     }
   }
 
@@ -377,7 +380,7 @@ fetch_soils_from_Miller1998_CONUSSoil <- function(
 extract_soils_Miller1998_CONUSSoil <- function(
   x,
   crs = 4326,
-  path,
+  path = ".",
   vars = c("bd", "rockvol", "sand", "clay", "silt"),
   lower_limits_by_vars = c(bd = 30, rockvol = 0, sand = 0, clay = 0, silt = 0),
   replace_missing_fragvol_with_zero = c("none", "all", "at_surface"),
@@ -410,7 +413,7 @@ extract_soils_Miller1998_CONUSSoil <- function(
     verbose = verbose
   )
 
-  N_layers <- dim(res)[3]
+  N_layers <- dim(res)[[3L]]
 
 
   # Calculate restriction depth by >99% rock volume
@@ -595,9 +598,10 @@ extract_soils_Miller1998_CONUSSoil <- function(
     formula = id ~ Horizon_No + variable
   )
 
-  colnames(locs_table_texture) <- sapply(
-    X = strsplit(colnames(locs_table_texture), split = "_"),
-    FUN = function(x) paste0(x[2], "_L", x[1])
+  colnames(locs_table_texture) <- vapply(
+    X = strsplit(colnames(locs_table_texture), split = "_", fixed = TRUE),
+    FUN = function(x) paste0(x[[2L]], "_L", x[[1L]]),
+    FUN.VALUE = NA_character_
   )