Merge branch 'main' into species_max_length

Author: CamilleLeclerc

.github/workflows/test-coverage.yaml

@@ -0,0 +1,66 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Prepare optional ASPE data
+        run: |
+          R CMD INSTALL .
+          Rscript -e "options(timeout = 3600); fishdatabuilder::download_optional_data(); fishdatabuilder::extract_optional_data()"
+        shell: bash
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,23 +1,36 @@
 Package: fishdatabuilder
-Title: What the Package Does (One Line, Title Case)
+Title: Tools to Make Analysis of Fish Monitoring Data Easier
 Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
-           comment = c(ORCID = "YOUR-ORCID-ID"))
-Description: What the package does (one paragraph).
+Authors@R: c(
+        person("Alain", "Danet", , "alain.danet@inrae.fr", role = c("aut", "cre"),
+            comment = c(ORCID = "0000-0002-1592-9483")),
+        person("Camille", "Leclerc", role = "aut",
+            comment = c(ORCID = "0000-0001-5830-1787")),
+        person("Willem", "Bonnaffé", role = "aut",
+            comment = c(ORCID = "0000-0002-5053-8891"))
+        )
+Description: Collection of tools to clean, filter, rearrange, and augment fish monitoring data.
 License: GPL (>= 3)
-Suggests: 
+Suggests:
     covr,
     knitr,
-    mockery,
     quarto,
-    testthat (>= 3.0.0),
-    truncdist
+    testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
 Imports: 
-    pkgfilecache
+    dplyr,
+    lubridate,
+    pkgfilecache,
+    purrr,
+    rfishbase,
+    rlang,
+    sf,
+    stringr,
+    tibble,
+    tidyr,
+    truncdist
 VignetteBuilder: quarto
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(check_aspe_fish_species)
-export(check_batch)
 export(clean_description_operation_aspe)
 export(clean_fish_batch)
 export(clean_individual_measurement_aspe)
@@ -14,16 +13,16 @@ export(cleaning_ref_length_type_aspe)
 export(cleaning_species_ref_aspe)
 export(coefficients_fork2total)
 export(convert_fork_to_total)
+export(convert_length_to_weight)
 export(delete_all_optional_data)
 export(download_optional_data)
 export(extract_optional_data)
 export(filter_operation_batch_measure)
 export(filter_operation_id)
-export(gen_fish_from_batch)
 export(generate_individual_sizes)
-export(get_check_batch)
 export(get_description_operation_aspe)
 export(get_elementary_sampling_aspe)
+export(get_environmental_data_operation_aspe)
 export(get_fish_batch_aspe)
 export(get_individual_measurement_aspe)
 export(get_objective_operation_aspe)
@@ -53,7 +52,10 @@ export(species_latin_name_to_replace)
 export(vec_op_objective_to_exclude)
 importFrom(dplyr,all_of)
 importFrom(dplyr,anti_join)
+importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,case_when)
+importFrom(dplyr,coalesce)
 importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
@@ -66,20 +68,27 @@ importFrom(dplyr,recode)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
+importFrom(dplyr,right_join)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,ungroup)
 importFrom(lubridate,date)
 importFrom(lubridate,ymd_hms)
 importFrom(purrr,map2)
+importFrom(rfishbase,length_weight)
+importFrom(rfishbase,popchar)
 importFrom(rfishbase,validate_names)
 importFrom(rlang,.data)
 importFrom(sf,st_as_sf)
 importFrom(sf,st_coordinates)
 importFrom(sf,st_transform)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stringr,str_replace_all)
+importFrom(tibble,as_tibble)
+importFrom(tibble,tibble)
 importFrom(tidyr,nest)
 importFrom(tidyr,unnest)
 importFrom(truncdist,rtrunc)
 importFrom(utils,read.csv2)
+importFrom(utils,unzip)