Merge pull request #171 from inbo/dev_nextrelease

Release version 0.9.0
inbo · Nov 22, 2023 · ca6f60e · ca6f60e
2 parents 956ff81 + dc7dd7e
commit ca6f60e
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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'}
 
@@ -35,61 +33,29 @@ jobs:
       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@v2
 
-      - 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@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: false
 
-      - name: Install system dependencies (Linux)
+      - name: Add ubuntugis-unstable PPA (Linux)
         if: runner.os == 'Linux'
         run: |
-          sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
-          sudo apt-get update
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
+          # Add ubuntugis-unstable PPA
+          sudo mkdir -p /root/.gnupg
+          sudo chmod 700 /root/.gnupg
+          sudo gpg --no-default-keyring --keyring /etc/apt/keyrings/ubuntugis-unstable-archive-keyring.gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 6B827C12C2D425E227EDCA75089EBE08314DF160
+          sudo sh -c 'echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/ubuntugis-unstable-archive-keyring.gpg] http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu `lsb_release -c -s` main" > /etc/apt/sources.list.d/ubuntugis-unstable.list'
 
-      - name: Install system dependencies (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          brew install pkg-config
-          brew install udunits
-          brew install gdal
-
-      - 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
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
+          cache-version: ${{ secrets.CACHE_VERSION }}
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -17,8 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
+          - {os: ubuntu-22.04,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest,   r: 'release'}
 
@@ -28,7 +27,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

diff --git a/.github/workflows/site-deploy.yaml b/.github/workflows/site-deploy.yaml
@@ -8,11 +8,11 @@ name: site-deploy
 
 jobs:
   site-deploy:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,14 +23,9 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache-version: ${{ secrets.CACHE_VERSION }}
-          extra-packages: local::.
+          extra-packages: local::., [email protected]
           needs: website
 
-      - name: Install pkgdown version
-        run: |
-          remotes::install_version("pkgdown", "1.6.1")
-        shell: Rscript {0}
-
       - name: Deploy package
         run: |
           git config --local user.email "[email protected]"

diff --git a/.github/workflows/site-devel.yaml b/.github/workflows/site-devel.yaml
@@ -8,11 +8,11 @@ name: site-devel
 
 jobs:
   site-devel:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,20 +23,15 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           cache-version: ${{ secrets.CACHE_VERSION }}
-          extra-packages: local::.
+          extra-packages: local::., [email protected]
           needs: website
 
-      - name: Install pkgdown version
-        run: |
-          remotes::install_version("pkgdown", "1.6.1")
-        shell: Rscript {0}
-
       - 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": "0.8.0",
+    "version": "0.9.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: n2khab
 Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
-Version: 0.8.0
+Version: 0.9.0
 Authors@R: c(
     person("Floris", "Vanderhaeghe", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6378-6229")), 
     person("Toon", "Westra", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0003-2478-9459")), 
@@ -14,6 +14,7 @@ Authors@R: c(
     person("Luc", "Denys", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0002-1841-6579")), 
     person("An", "Leyssen", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0003-3537-286X")), 
     person("Patrik", "Oosterlynck", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0002-5712-0770")), 
+    person("Jeroen", "Vanden Borre", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0002-0153-7243")), 
     person("Nathalie", "Cools", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0002-7059-2318")), 
     person("Bruno", "De Vos", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0001-9523-3453")), 
     person("Suzanna", "Lettens", email = "[email protected]", role = c("ctb"), comment = c(ORCID = "0000-0001-5032-495X")), 
@@ -30,38 +31,38 @@ Depends:
     R (>= 3.5.0)
 Imports:
     assertthat,
+    curl,
     dplyr,
     forcats,
     git2rdata (>= 0.4.0),
     magrittr,
     plyr,
     purrr,
+    remotes,
     rlang,
     rprojroot,
     sf,
     stringr,
-    tibble,
     tidyr (>= 1.0.0),
-    withr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests: 
     bib2df,
-    curl,
     digest,
     googledrive,
     jsonlite,
     knitr,
     mapview,
     openssl,
-    parallel,
-    raster (>= 3.3-16),
+    raster (>= 3.6-3),
     readxl,
-    remotes,
     rmarkdown,
+    testthat (>= 3.0.0),
     tidyverse,
     tools,
     units,
-    utils
+    utils,
+    withr
 VignetteBuilder: knitr
+Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -36,6 +36,7 @@ importFrom(assertthat,assert_that)
 importFrom(assertthat,is.flag)
 importFrom(assertthat,is.string)
 importFrom(assertthat,noNA)
+importFrom(curl,nslookup)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,anti_join)
@@ -85,6 +86,8 @@ importFrom(sf,"st_crs<-")
 importFrom(sf,read_sf)
 importFrom(sf,st_centroid)
 importFrom(sf,st_drop_geometry)
+importFrom(sf,st_is_valid)
+importFrom(sf,st_make_valid)
 importFrom(sf,st_transform)
 importFrom(stats,setNames)
 importFrom(stringr,fixed)
@@ -102,5 +105,5 @@ importFrom(tidyr,gather)
 importFrom(tidyr,nest)
 importFrom(tidyr,spread)
 importFrom(tidyr,unnest)
+importFrom(utils,packageDescription)
 importFrom(utils,packageVersion)
-importFrom(withr,with_options)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,18 @@
+# n2khab 0.9.0 (2023-11-22)
+
+- `download_zenodo()` has been improved (#169):
+  - fixes in order to use the renewed Zenodo website;
+  - speedup the initiation of a multi-file download;
+  - set concurrent (parallel) downloading as default for multi-file records;
+  - add unit tests to regularly check that the function still works.
+- `read_watersurfaces()` gained extra capabilities (#168):
+  - data source version `watersurfaces_v1.2` is now supported;
+  - a new `fix_geom` argument allows to fix invalid or corrupt geometries on the fly.
+  This behaviour is turned off by default (see #60).
+- Package startup messages have been updated, including a check whether the latest release is being used (#170, [502c3a2](https://github.com/inbo/n2khab/commit/502c3a2)).
+- Internally, an update has been applied ([9691ec2](https://github.com/inbo/n2khab/commit/9691ec2)) to googlesheets authentication, used in updating the built-in textual data sources.
+These data sources have not changed since previous release.
+
 # n2khab 0.8.0 (2022-11-18)
 
 - Reference list `namelist` has been updated with improved type names (#163; thanks @jeroenvdborre).