Abson-dev · Abson-dev · Jul 9, 2026 · Jul 9, 2026
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,106 +1,43 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 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: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.3',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
     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: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+          extra-packages: any::rcmdcheck
+          needs: check
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,48 +1,40 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request'
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Deploy to GitHub pages
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -1,48 +1,41 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,71 +1,70 @@
 Package: sdmApp
 Title: A User-Friendly Application for Species Distribution Modeling
-Version: 0.0.2
+Version: 0.0.3
 Authors@R: c(
-    person("Aboubacar", "HEMA", , "aboubacarhema94@gmail.com", role = c("aut", "cre")),
+    person("Aboubacar", "HEMA", , "aboubacarhema94@gmail.com",
+           role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0000-0000-0000")),
     person("Babacar", "NDAO", , "babacar.ndao@cse.sn", role = "aut"),
     person("Louise", "LEROUX", , "louise.leroux@cirad.fr", role = "aut"),
     person("Abdoul Aziz", "DIOUF", , "aziz.diouf@cse.sn", role = "aut")
   )
-Author: Aboubacar HEMA [aut, cre], Babacar NDAO [aut], Louise LEROUX
-    [aut], Abdoul Aziz DIOUF [aut]
-Maintainer: Aboubacar HEMA <aboubacarhema94@gmail.com>
 Description: A 'shiny' application that allows non-expert 'R' users to
     easily model species distribution. It offers a reproducible work flow
     for species distribution modeling into a single and user friendly
     environment.  'sdmApp' takes 'raster' data (in format supported by the
-    'raster package') and species occurrence data (several format
+    'raster' package) and species occurrence data (several format
     supported) as input argument.  It provides an interactive graphical
     user interface (GUI).
 License: GPL-3
-URL: https://github.com/Abson-dev/sdmApp
+URL: https://github.com/Abson-dev/sdmApp,
+    https://abson-dev.github.io/sdmApp/
 BugReports: https://github.com/Abson-dev/sdmApp/issues
-Depends: 
+Depends:
     R (>= 3.5.0)
 Imports:
-    raster (>= 2.6.7),
+    cowplot (>= 1.1.1),
+    ggplot2 (>= 3.4.0),
+    graphics,
+    grDevices,
+    raster (>= 3.6.3),
+    sf (>= 1.0.0),
     shiny (>= 0.12.2),
-    sp (>= 1.2.0)
-Suggests: 
+    sp (>= 1.6.0),
+    stats
+Suggests:
     automap (>= 1.0-14),
     blockCV (>= 2.1.1),
     covr,
-    cowplot (>= 1.1.1),
     data.table,
     dismo (>= 1.0.12),
     dplyr (>= 1.0.3),
     DT,
-    future.apply,
     ggcorrplot (>= 0.1.3),
-    ggplot2 (>= 3.1.1),
-    grDevices,
     haven (>= 2.3.1),
     kernlab (>= 0.9-29),
     knitr,
     randomForest (>= 4.6.10),
     readxl (>= 1.3.1),
-    rgdal (>= 1.5-8),
-    rgeos (>= 0.3-8),
     rhandsontable (>= 0.3.7),
     rJava (>= 0.9-13),
     rmarkdown,
-    sf,
     shinyBS (>= 0.61),
+    shinydashboard,
     shinyFiles (>= 0.7.0),
     SSDM (>= 0.2.8),
-    stats,
+    terra,
     testthat (>= 3.0.0),
-    tidyr (>= 1.1.2),
-    utils
-VignetteBuilder: 
+    tidyr (>= 1.1.2)
+Remotes:
+    rinnan/CENFA
+VignetteBuilder:
     knitr,
     rmarkdown
-BuildResaveData: no
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: no
-LazyLoad: yes
-RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
 SystemRequirements: Java (>= 8)
-ZipData: no
+Config/roxygen2/version: 8.0.0