Dev

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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@v5
+        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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
-          path: ${{ runner.temp }}/package
+          path: ${{ runner.temp }}/package

.gitignore

@@ -13,3 +13,5 @@ docs/*
 /Meta/
 docs
 SECRETS.txt
+.secure-credentials
+/TEST-SENSITIVE-DATA

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: galah
 Type: Package
 Title: Biodiversity Data from the GBIF Node Network
-Version: 2.1.2
+Version: 2.2.0
 Authors@R: 
     c(person(given = "Martin",
              family = "Westgate",
@@ -11,13 +11,13 @@ Authors@R:
              family = "Kellie",
              email = "dax.kellie@csiro.au",
              role = "aut"),
+      person(given = "Shandiya",
+             family = "Balasubramaniam",
+             email = "shandiya.balasubramaniam@csiro.au",
+             role = "ctb"),
       person(given = "Matilda",
              family = "Stevenson",
-             role = "aut"),
-      person(given = "Peggy",
-             family = "Newman",
-             email = "peggy.newman@csiro.au",
-             role = "aut"))
+             role = "ctb"))
 Description: The Global Biodiversity Information Facility 
     ('GBIF', <https://www.gbif.org>) sources data from an international network
     of data providers, known as 'nodes'. Several of these nodes - the "living 
@@ -62,6 +62,7 @@ BugReports: https://github.com/AtlasOfLivingAustralia/galah-R/issues
 Maintainer: Martin Westgate <martin.westgate@csiro.au>
 LazyLoad: yes
 VignetteBuilder: knitr
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,51 +1,86 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(add_count,data_request)
 S3method(arrange,data_request)
 S3method(arrange,metadata_request)
+S3method(capture,data_request)
+S3method(capture,files_request)
+S3method(capture,list)
+S3method(capture,metadata_request)
 S3method(collapse,data_request)
 S3method(collapse,files_request)
 S3method(collapse,metadata_request)
+S3method(collapse,prequery)
+S3method(collapse,query)
+S3method(collapse,query_set)
 S3method(collect,computed_query)
 S3method(collect,data_request)
 S3method(collect,files_request)
 S3method(collect,metadata_request)
+S3method(collect,prequery)
 S3method(collect,query)
+S3method(collect,query_set)
+S3method(compound,data_request)
+S3method(compound,files_request)
+S3method(compound,metadata_request)
+S3method(compound,prequery)
+S3method(compound,query)
+S3method(compound,query_set)
 S3method(compute,data_request)
 S3method(compute,files_request)
 S3method(compute,metadata_request)
+S3method(compute,prequery)
 S3method(compute,query)
+S3method(compute,query_set)
 S3method(count,data_request)
+S3method(distinct,data_request)
 S3method(filter,data_request)
 S3method(filter,files_request)
 S3method(filter,metadata_request)
+S3method(glimpse,data_request)
 S3method(group_by,data_request)
 S3method(identify,data_request)
 S3method(identify,metadata_request)
 S3method(print,computed_query)
+S3method(print,data_filter)
 S3method(print,data_request)
+S3method(print,files_filter)
 S3method(print,files_request)
 S3method(print,galah_config)
+S3method(print,metadata_filter)
 S3method(print,metadata_request)
+S3method(print,occurrences_glimpse)
+S3method(print,predicates_filter)
+S3method(print,prequery)
 S3method(print,query)
 S3method(print,query_set)
 S3method(select,data_request)
+S3method(select,metadata_request)
 S3method(slice_head,data_request)
 S3method(slice_head,metadata_request)
 S3method(st_crop,data_request)
+export(add_count)
 export(apply_profile)
 export(arrange)
+export(as_data_filter)
+export(as_files_filter)
+export(as_metadata_filter)
+export(as_predicates_filter)
 export(atlas_citation)
 export(atlas_counts)
 export(atlas_media)
 export(atlas_occurrences)
 export(atlas_species)
 export(atlas_taxonomy)
+export(authenticate)
+export(capture)
 export(collapse)
 export(collect)
 export(collect_media)
+export(compound)
 export(compute)
 export(count)
-export(desc)
+export(distinct)
 export(filter)
 export(galah_apply_profile)
 export(galah_bbox)
@@ -59,6 +94,7 @@ export(galah_polygon)
 export(galah_radius)
 export(galah_select)
 export(geolocate)
+export(glimpse)
 export(group_by)
 export(identify)
 export(read_zip)
@@ -75,6 +111,7 @@ export(search_fields)
 export(search_identifiers)
 export(search_licences)
 export(search_lists)
+export(search_media)
 export(search_profiles)
 export(search_providers)
 export(search_ranks)
@@ -87,6 +124,7 @@ export(show_all_apis)
 export(show_all_assertions)
 export(show_all_atlases)
 export(show_all_collections)
+export(show_all_config)
 export(show_all_datasets)
 export(show_all_fields)
 export(show_all_licences)
@@ -99,123 +137,22 @@ export(show_values)
 export(slice_head)
 export(st_crop)
 export(unnest)
-importFrom(cli,cli_div)
-importFrom(cli,cli_end)
-importFrom(cli,cli_text)
-importFrom(cli,col_magenta)
-importFrom(cli,col_yellow)
 importFrom(crayon,make_style)
-importFrom(crayon,silver)
-importFrom(dplyr,all_of)
-importFrom(dplyr,any_of)
+importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
-importFrom(dplyr,bind_cols)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,c_across)
-importFrom(dplyr,case_match)
 importFrom(dplyr,collapse)
 importFrom(dplyr,collect)
 importFrom(dplyr,compute)
 importFrom(dplyr,count)
-importFrom(dplyr,desc)
+importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
-importFrom(dplyr,full_join)
+importFrom(dplyr,glimpse)
 importFrom(dplyr,group_by)
-importFrom(dplyr,join_by)
-importFrom(dplyr,last_col)
-importFrom(dplyr,mutate)
-importFrom(dplyr,pull)
-importFrom(dplyr,relocate)
-importFrom(dplyr,rename)
-importFrom(dplyr,right_join)
-importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
-importFrom(dplyr,slice)
 importFrom(dplyr,slice_head)
-importFrom(dplyr,starts_with)
-importFrom(dplyr,ungroup)
-importFrom(glue,glue)
-importFrom(glue,glue_collapse)
-importFrom(glue,glue_data)
 importFrom(graphics,identify)
-importFrom(httr2,req_body_raw)
-importFrom(httr2,req_error)
-importFrom(httr2,req_headers)
-importFrom(httr2,req_perform)
-importFrom(httr2,req_timeout)
-importFrom(httr2,request)
-importFrom(httr2,resp_body_json)
-importFrom(httr2,resp_body_string)
-importFrom(httr2,url_build)
-importFrom(httr2,url_parse)
-importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,toJSON)
-importFrom(jsonlite,unbox)
 importFrom(lifecycle,badge)
-importFrom(lifecycle,deprecate_stop)
-importFrom(lifecycle,deprecate_warn)
-importFrom(potions,brew)
-importFrom(potions,pour)
-importFrom(purrr,list_flatten)
-importFrom(purrr,list_transpose)
-importFrom(purrr,map)
-importFrom(purrr,pluck)
-importFrom(purrr,pluck_depth)
-importFrom(purrr,rate_backoff)
-importFrom(purrr,rate_delay)
-importFrom(purrr,rate_sleep)
 importFrom(rlang,.data)
-importFrom(rlang,abort)
-importFrom(rlang,as_label)
-importFrom(rlang,as_name)
-importFrom(rlang,as_quosure)
-importFrom(rlang,as_string)
+importFrom(rlang,`:=`)
 importFrom(rlang,caller_env)
-importFrom(rlang,enquo)
-importFrom(rlang,enquos)
-importFrom(rlang,eval_tidy)
-importFrom(rlang,expr_text)
-importFrom(rlang,f_lhs)
-importFrom(rlang,f_rhs)
-importFrom(rlang,format_error_bullets)
-importFrom(rlang,get_env)
-importFrom(rlang,get_expr)
-importFrom(rlang,inform)
-importFrom(rlang,is_bare_environment)
-importFrom(rlang,is_empty)
-importFrom(rlang,is_list)
-importFrom(rlang,is_quosure)
-importFrom(rlang,is_string)
-importFrom(rlang,is_syntactic_literal)
-importFrom(rlang,new_quosure)
-importFrom(rlang,parse_expr)
-importFrom(rlang,quo_get_env)
-importFrom(rlang,quo_get_expr)
-importFrom(rlang,quo_is_call)
-importFrom(rlang,quo_is_symbol)
-importFrom(rlang,quo_squash)
-importFrom(rlang,try_fetch)
-importFrom(rlang,warn)
-importFrom(sf,st_as_sf)
-importFrom(sf,st_as_sfc)
-importFrom(sf,st_as_text)
-importFrom(sf,st_bbox)
-importFrom(sf,st_cast)
-importFrom(sf,st_coordinates)
 importFrom(sf,st_crop)
-importFrom(sf,st_crs)
-importFrom(sf,st_geometry)
-importFrom(sf,st_geometry_type)
-importFrom(sf,st_is_empty)
-importFrom(sf,st_is_simple)
-importFrom(sf,st_is_valid)
-importFrom(stringr,str_detect)
-importFrom(stringr,str_extract)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_replace)
-importFrom(stringr,str_replace_all)
-importFrom(stringr,str_split)
-importFrom(stringr,str_to_title)
-importFrom(stringr,str_trim)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)

NEWS.md

@@ -1,3 +1,35 @@
+# galah 2.2.0
+
+### Improved organisational support
+* Flemish living atlas and Kew Gardens Data Portal added (#256, #271).
+* Authentication supported for ALA users, with associated vignette (#189).
+* All GBIF data queries now use predicates. `filter()` builds predicate queries natively when atlas is set to `GBIF` using an object-oriented workflow (#272).
+* Re-downloading a file via its' DOI now supported for `GBIF` (#272).
+* `search_identifiers()` and `tibble`-based searching via `search_taxa()` now supported for `GBIF` 
+
+### New functions
+* `dplyr::distinct()` can be used to find grouped data and summaries, generalising `atlas_species()` (#284).
+* `dplyr::glimpse()` can be used to see what the resulting query will look like.
+* New functions `capture()` and `compound()` as prequels to `collapse()` (#278).
+
+## Changes to metadata functions
+* All metadata requests now accept `select()`.
+* Metadata types that support `unnest()` now also support `filter()`, even when `unnest()` is not supplied.
+* All `show_all()` and `search_all()` functions gain an `all_fields` argument.
+* Metadata now supports list-columns where the API returns nested data.
+* Metadata functions now return columns names in `snake_case` rather than `camelCase`.
+* All metadata functions support caching, and are affected by re-introduced `caching` argument in `galah_config()` (set to `TRUE` by default #282).
+* Media metadata now uses a different API to return more relevant information.
+
+### Minor improvements and bug fixes
+* `galah_call()` is now synonmous with `request_data()` rather than wrapping all `request_` functions; `method` argument is removed.
+* Move to `testthat` 3rd edition for improved test functionality.
+* Move to `{cli}` for `print()` calls, not `cat()`.
+* Reduce usage of `@importFrom` in favour of `pkg::fun()` syntax, as per R style guide.
+* `basisOfRecord` now included as default field (i.e. with `select(group = "basic")`). (#281)
+* `query` objects now have a `request` slot showing the request that generated them .
+
+
 # galah 2.1.2
 
 ### Minor improvements