Merge pull request #104 from inbo/dev_nextrelease

Release version 0.4.2
inbo · Sep 15, 2023 · d35e7b4 · d35e7b4
2 parents 5da5ed8 + 5daa3aa
commit d35e7b4
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diff --git a/.github/workflows/R-CMD-check-latest.yaml b/.github/workflows/R-CMD-check-latest.yaml
@@ -23,10 +23,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release'}
-          - {os: ubuntu-20.04, r: 'devel'}
-          - {os: ubuntu-18.04, r: 'release'}
-          - {os: ubuntu-18.04, r: 'devel'}
+          # - {os: ubuntu-22.04, r: 'release'}
+          # - {os: ubuntu-22.04, r: 'devel'}
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
 
@@ -35,13 +33,15 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: false
 
       - name: Query dependencies
         run: |
@@ -89,7 +89,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,6 +2,8 @@
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
   push:
+    branches:
+      - '*'
 
 name: R-CMD-check
 
@@ -15,71 +17,30 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: ubuntu-22.04,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore (or define new) R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
+          cache-version: ${{ secrets.CACHE_VERSION }}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install system dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install udunits
-          brew install gdal
-          brew install proj
-
-      - name: Install package dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: |
-          options(rmarkdown.html_vignette.check_title = FALSE)
-          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/site-deploy.yaml b/.github/workflows/site-deploy.yaml
@@ -8,53 +8,23 @@ name: site-deploy
 
 jobs:
   site-deploy:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    strategy:
-      matrix:
-        config:
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+    runs-on: ubuntu-22.04
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore (or define new) R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          use-public-rspm: true
 
-      - name: Install system dependencies (Linux)
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
-          sudo apt-get install -y libfribidi-dev libharfbuzz-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: ${{ secrets.CACHE_VERSION }}
+          extra-packages: local::., [email protected]
+          needs: website
 
       - name: Deploy package
         run: |

diff --git a/.github/workflows/site-devel.yaml b/.github/workflows/site-devel.yaml
@@ -8,60 +8,30 @@ name: site-devel
 
 jobs:
   site-devel:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    strategy:
-      matrix:
-        config:
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+    runs-on: ubuntu-22.04
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore (or define new) R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          use-public-rspm: true
 
-      - name: Install system dependencies (Linux)
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
-          sudo apt-get install -y libfribidi-dev libharfbuzz-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown")
-        shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: ${{ secrets.CACHE_VERSION }}
+          extra-packages: local::., [email protected]
+          needs: website
 
       - name: Build site
         run: |
           Rscript -e 'options(rmarkdown.html_vignette.check_title = FALSE); pkgdown::build_site()'
 
       - name: Upload pkgdown-site as artifact
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v3
         with:
           name: pkgdown-site
           path: docs
diff --git a/.zenodo.json b/.zenodo.json
@@ -4,7 +4,7 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.4.1",
+    "version": "0.4.2",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: watina
 Title: Querying and Processing Data from the INBO Watina Database
-Version: 0.4.1
+Version: 0.4.2
 Description: The R-package watina contains functions to query
     and process data from the Watina database at the Research Institute for
     Nature and Forest (INBO). This database primarily provides
@@ -23,7 +23,6 @@ Imports:
     assertthat,
     dplyr,
     inbodb,
-    KSgeneral,
     lubridate,
     rlang,
     stringr,
@@ -32,6 +31,7 @@ Imports:
 Suggests:
     DBI,
     knitr,
+    KSgeneral,
     purrr,
     rmarkdown,
     sf,
@@ -41,5 +41,5 @@ Remotes:
     inbo/inbodb
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -13,7 +13,6 @@ export(get_locs)
 export(get_xg3)
 export(selectlocs_chem)
 export(selectlocs_xg3)
-importFrom(KSgeneral,disc_ks_test)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_args)
 importFrom(assertthat,has_name)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# watina 0.4.2 (2023-09-15)
+
+- Move package {KSgeneral} to `Suggests` (#103).
+This avoids package breaking when {KSgeneral} is not available on CRAN.
+For the moment not taking further measures to protect against it, as the package is currently back on CRAN.
+
 # watina 0.4.1 (2021-06-11)
 
 - Fixed non-working `get_xg3()` and `get_chem()` for dataframe input, by avoiding the currently defunct `dbplyr::db_drop_table()` (#89, [08bc66d](https://github.com/inbo/watina/commit/08bc66d)).

diff --git a/R/eval.R b/R/eval.R
@@ -354,8 +354,6 @@ qualify_xg3 <- function(data,
 #' @importFrom rlang .data
 #' @importFrom assertthat
 #' assert_that
-#' @importFrom KSgeneral
-#' disc_ks_test
 #' @importFrom stringr
 #' str_detect
 #' @importFrom stats
@@ -382,6 +380,8 @@ eval_xg3_series <- function(data,
                             max_gap,
                             min_dur) {
 
+    require_pkgs("KSgeneral")
+
     if (missing(xg3_type)) {
         xg3_type <- match.arg(xg3_type)} else {
             assert_that(all(xg3_type %in%
@@ -410,11 +410,13 @@ eval_xg3_series <- function(data,
             ser_rel_nryears = .data$ser_nryears / .data$ser_length,
             ser_firstyear = min(.data$hydroyear),
             ser_lastyear = max(.data$hydroyear),
-            ser_pval_uniform = disc_ks_test(.data$hydroyear,
-                                            ecdf(seq(.data$ser_firstyear,
-                                                     .data$ser_lastyear)),
-                                            exact = TRUE) %>%
-                                .$p.value
+            ser_pval_uniform = KSgeneral::disc_ks_test(
+                .data$hydroyear,
+                ecdf(seq(.data$ser_firstyear,
+                         .data$ser_lastyear)),
+                exact = TRUE
+            ) %>%
+                .$p.value
         ) %>%
         ungroup
     },
@@ -650,6 +652,8 @@ eval_chem <- function(data,
                       type = c("avail", "num", "both"),
                       uniformity_test = FALSE) {
 
+    require_pkgs("KSgeneral")
+
     type <- match.arg(type)
 
     assert_that(inherits(data, what = c("tbl_lazy", "data.frame")),
@@ -774,13 +778,15 @@ date, lab_sample_id, chem_variable, value, unit, below_loq."
                 df %>%
                 summarise(
                     nryears = sum(.data$available),
-                    pval_uniform_totalspan = ifelse(.data$nryears > 0,
-                                            disc_ks_test(.data$year[.data$available],
-                                                        ecdf(seq(firstyear,
-                                                                 lastyear)),
-                                                        exact = TRUE) %>%
-                                                .$p.value,
-                                            NA)
+                    pval_uniform_totalspan = ifelse(
+                        .data$nryears > 0,
+                        KSgeneral::disc_ks_test(.data$year[.data$available],
+                                                ecdf(seq(firstyear,
+                                                         lastyear)),
+                                                exact = TRUE) %>%
+                            .$p.value,
+                        NA
+                    )
                 ) %>%
                 select(-.data$nryears) %>%
                 ungroup