Merging dev into main.

.github/workflows/codecov.yml

@@ -1,38 +1,30 @@
-name: R Package CI workflow that runs tests, checks coverage, and updates the Codecov badge
+name: Run tests and upload coverage report to Codecov
 
 on:
   push:
-    branches:
-      - dev
-  pull_request:
-    branches:
-      - dev
+    branches: [dev, main]
 
 jobs:
-  test:
+  coverage:
     runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
 
-    - name: Set up R
-      uses: r-lib/actions/setup-r@v2
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-    - name: Install dependencies using setup-r-dependencies
-      uses: r-lib/actions/setup-r-dependencies@v2
-      with:
-        extra-packages: |
-          devtools
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+            use-public-rspm: true
 
-    - name: Install covr
-      run: |
-        Rscript -e "install.packages('covr')"
+      - name: Install R dependencies
+        run: |
+          Rscript -e "install.packages(c('covr', 'devtools', 'remotes'))"
+          Rscript -e "devtools::install_deps(dependencies = TRUE)"
 
-    - name: Run tests, generate coverage report and upload it to Codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}  # Expose the token to the R environment
-      run: |
-        Rscript -e "library(covr)"
-        Rscript -e "covr::package_coverage()"
-        Rscript -e "covr::codecov(token = Sys.getenv('CODECOV_TOKEN'))"
+      - name: Run tests and upload coverage to Codecov
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          NOT_CRAN: "false"
+        run: |
+          Rscript -e "covr::codecov(token = Sys.getenv('CODECOV_TOKEN'))"

.github/workflows/pkgdown.yaml

@@ -1,37 +1,41 @@
-name: Build pkgdown site
+name: Build and deploy pkgdown site to GitHub Pages
 
 on:
   push:
-    branches:
-      - dev  # Trigger on push to the dev branch (commit, merge, etc.)
-  pull_request:
-    branches:
-      - dev
+    branches: [main]
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Set up Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v2
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::pkgdown, local::.
-          needs: website
+      - name: Install R dependencies
+        run: |
+            Rscript -e "install.packages(c('pkgdown', 'devtools', 'remotes'))"
+            Rscript -e "devtools::install_deps(dependencies = TRUE)"
+            Rscript -e "devtools::install_local('.')"
 
-      - name: Build site
+      - name: Build pkgdown site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy pkgdown site to dev branch
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+      - name: Deploy site to gh-pages branch
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages
-          folder: .
+          folder: docs

.gitignore

@@ -1,7 +1,6 @@
 .Rproj.user
 .Rhistory
 .RData
+.Rprofile
 .Ruserdata
-docs
-/doc/
-/Meta/
+docs

DESCRIPTION

@@ -1,14 +1,13 @@
 Package: eppoFindeR
 Type: Package
-Title: A Wrapper for 'EPPO' Codes
-Version: 1.0.0
+Title: R interface to the EPPO Database and Public APIs
+Version: 2.0.0
 Maintainer: Luca Belmonte <luca.belmonte@efsa.europa.eu>
-Authors@R: 
-  c(person(given = "Luca",
-           family = "Belmonte",
-           role = c("aut", "cre"),
-           email = "luca.belmonte@efsa.europa.eu",
-           comment = c(ORCID = "0000-0002-7977-9170")),
+Authors@R:
+  c(person(given = "Lorenzo",
+           family = "Copelli",
+           role = "aut",
+           comment = c(ORCID = "0009-0002-4305-065X")),
     person(given = "Dayana Stephanie",
            family = "Buzle",
            role = "aut",
@@ -20,41 +19,42 @@ Authors@R:
     person(given = "Agata",
            family = "Kaczmarek",
            role = "aut",
-           comment = c(ORCID = "0000-0002-7463-5821")))
-Description: A wrapper around the European and Mediterranean Plant Protection 
-    Organization ('EPPO') database public 'APIs' at <https://data.eppo.int/>. 
-    It enables users to retrieve 'EPPO'-related data through searches across 
-    the entire 'EPPO' database or by utilizing specific services, including 
-    categorization, taxonomy, and more. The package also includes a data 
-    wrangling function to integrate taxonomy and rank information, and a
-    function that returns the list of member countries for each Regional 
-    Plant Protection Organization acronym which is used in the 'EPPO' database.
-License: EUPL (>= 1.2)
-URL: https://github.com/openefsa/eppoFindeR, https://openefsa.github.io/eppoFindeR/
+           comment = c(ORCID = "0000-0002-7463-5821")),
+    person(given = "Luca",
+           family = "Belmonte",
+           role = c("aut", "cre"),
+           email = "luca.belmonte@efsa.europa.eu",
+           comment = c(ORCID = "0000-0002-7977-9170")))
+Description: The eppoFindeR package provides an interface to the public APIs 
+    of the European and Mediterranean Plant Protection Organization (EPPO) 
+    database. It enables users to retrieve EPPO data by accessing specific 
+    services and datasets. The package also includes utilities for data 
+    wrangling, including the integration of taxonomy with rank information.
+License: file LICENSE
+URL: https://openefsa.github.io/eppoFindeR
 BugReports: https://github.com/openefsa/eppoFindeR/issues
 Depends:
     R (>= 4.0.0)
 Imports:
-    httr (>= 1.4.7),
-    jsonlite (>= 1.8.7),
-    tidyr (>= 1.3.1),
+    cli (>= 3.6.5),
+    httr2 (>= 1.2.1),
+    jsonlite (>= 1.8.8),
     dplyr (>= 1.1.4),
     glue (>= 1.7.0),
     purrr (>= 1.0.2),
-    magrittr (>= 2.0.3),
     checkmate (>= 2.3.1),
-    lifecycle (>= 1.0.4)
+    tibble(>= 3.3.0)
 Suggests:
     devtools (>= 2.4.5),
-    roxygen2 (>= 7.2.1),
-    testthat (>= 3.0.0),
+    roxygen2 (>= 7.3.1),
+    testthat (>= 3.2.1),
     usethis (>= 2.2.3),
     knitr (>= 1.0),
     rmarkdown (>= 2.0),
     covr (>= 3.6.4)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Config/Needs/website: pkgdown