commit the dev changes in the main

.Rbuildignore

@@ -15,3 +15,5 @@
 ^miscellaneus$
 ^.*\.zenodo.json$
 ^CITATION\.cff$
+^doc$
+^Meta$

.github/workflows/check-standard.yaml

@@ -1,95 +1,64 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
-# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+name: R-CMD-check
+
 on:
   push:
+    branches: [main, dev, dev-OggioniAle]
   pull_request:
-    branches: [main]
-
-name: R-CMD-check
+    branches: [main, dev, dev-OggioniAle]
 
 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', usgs_user: 'modistsp_ci_macos_release',   test_mode: 'FALSE'}
-          - {os: windows-latest, r: 'release', usgs_user: 'modistsp_ci_windows_release', test_mode: 'FALSE'}
-          - {os: ubuntu-20.04,   r: 'devel',   usgs_user: 'modistsp_ci_ubuntu_release',  test_mode: 'FALSE', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'release', usgs_user: 'modistsp_ci_ubuntu_devel',    test_mode: 'FALSE', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: 'oldrel',  usgs_user: 'modistsp_ci_ubuntu_oldrel',   test_mode: 'FALSE', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      USGS_USER: ${{ matrix.config.usgs_user }}
-      USGS_PASSWORD: ${{ secrets.USGS_PASSWORD }}
-      R_KEEP_PKG_SOURCE: yes
-      LOCAL_DEIMS: ${{ matrix.config.test_mode }}
-
+      LOCAL_DEIMS: false
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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
 
-      - name: Query dependencies
-        run: |
-          install.packages("remotes")
-          install.packages("rnaturalearthdata")
-          install.packages("webshot")
-          webshot::install_phantomjs()
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: "Cache R packages"
-        if: runner.os != 'Windows'
-        uses: actions/cache@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: "[Linux] Install system dependencies"
+      # Extra system deps solo su Ubuntu (le stesse del Dockerfile)
+      - 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", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          if (Sys.info()["sysname"]=="Darwin") {options("pkgType" = "binary")}
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: download system packages
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt update
-          sudo apt-get install \
-            r-base-dev \
-            build-essential \
-            gdal-bin \
-            libgdal-dev \
-            libjq-dev \
+          sudo apt-get update -y
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
             libssl-dev \
             libxml2-dev \
-            libprotobuf-dev \
-            protobuf-compiler \
+            libudunits2-dev \
+            libgdal-dev \
+            libgeos-dev \
+            libproj-dev \
+            libfontconfig1-dev \
+            libjq-dev \
             libv8-dev \
-            libssl-dev \
-            libcairo2-dev \
-            libgit2-dev
+            libgit2-dev \
+            build-essential \
+            gfortran \
+            libglpk-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck,markdown,rbibutils
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/docker-publish-on-tag.yaml

@@ -0,0 +1,28 @@
+name: Publish Docker image on tag
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          push: true
+          tags: |
+            oggioniale/relter:latest
+            oggioniale/relter:${{ github.ref_name }}

.github/workflows/test-coverage.yml

@@ -1,43 +1,55 @@
+name: test-coverage
+
 on:
   push:
-
-name: test-coverage
+    branches: [main, dev, dev-OggioniAle]
+  pull_request:
+    branches: [main, dev, dev-OggioniAle]
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      USGS_USER: 'modistsp_ci_codecov'
-      USGS_PASSWORD: ${{ secrets.USGS_PASSWORD }}
       LOCAL_DEIMS: false
+
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v2
-
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages("remotes")
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: "Cache R packages"
-        uses: actions/cache@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-
+          use-public-rspm: true
 
-      - name: Install dependencies
+      # Install system dependencies (come nel Dockerfile)
+      - name: Install system dependencies
         run: |
-          remotes::install_deps(dependencies = TRUE, type = "binary")
-          remotes::install_cran("rcmdcheck")
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          sudo apt-get update -y
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libudunits2-dev \
+            libgdal-dev \
+            libgeos-dev \
+            libproj-dev \
+            libfontconfig1-dev \
+            libjq-dev \
+            libv8-dev \
+            libgit2-dev \
+            build-essential \
+            gfortran \
+            libglpk-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
 
       - name: Test coverage
         run: covr::codecov(quiet = FALSE)
         shell: Rscript {0}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -12,3 +12,5 @@ rosm.cache
 submission_rOpenSci
 _pkgdown.yaml
 *.rds
+/doc/
+/Meta/

.zenodo.json

@@ -1,6 +1,6 @@
 {
-  "title": "ReLTER: An Interface for the eLTER Community (v2.1)",
-  "version": "2.1.1",
+  "title": "ReLTER: An Interface for the eLTER Community (v3.0)",
+  "version": "3.0.0",
   "creators": [
     {
       "name": "Oggioni, Alessandro",
@@ -23,5 +23,5 @@
   "license": {
     "id": "GPL-3.0-or-later"
   },
-  "publication_date": "2023-01-30"
+  "publication_date": "2025-08-20"
 }