taxonomic_resources: Rename tables to snake_case, add family, add structure tests - #272
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…ance structure tests - Renames `APC list (accepted)` → `APC_accepted` and `APC list (known names)` → `APC_synonyms` throughout the codebase, and updates all references in align_taxa.R, match_taxa.R, and update_taxonomy.R. - adds `family` to the columns selected in taxonomic_resources - adds tests for the structure of tables in taxonomic_resources
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Pull request overview
This PR updates the taxonomic_resources interface and downstream consumers to use simpler snake_case table names, includes family in APC-derived accepted/synonym tables, and adds structure tests to prevent regressions.
Changes:
- Renamed
resources$APC list (accepted)/resources$APC list (known names)toresources$APC_accepted/resources$APC_synonymsand updated references across alignment/matching/updating code. - Added
familyto the columns selected for APC species/infraspecific resource subsets. - Added a new test file asserting expected resource table names and key column sets.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
R/load_taxonomic_resources.R |
Adds family to APC subset selection and renames generated resource list elements to APC_accepted / APC_synonyms. |
R/align_taxa.R |
Updates APC accepted-name lookup to use resources$APC_accepted. |
R/match_taxa.R |
Updates all APC accepted/known-name matching paths to use APC_accepted / APC_synonyms. |
R/update_taxonomy.R |
Updates APC accepted/known-name references to the renamed resource tables. |
tests/testthat/test-taxonomic_resources_structure.R |
Adds tests asserting resource list names and expected columns for key tables. |
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ehwenk
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Mar 23, 2026
ehwenk
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Mar 23, 2026
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Thanks! This looks good.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
ehwenk
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Prefect! Ready to merge.
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Closes #271
APC list (accepted)→APC_accepted,APC list (known names)→APC_synonymsandAPNI names→APNI_namesthroughout the codebase, and updates all references in align_taxa.R, match_taxa.R, and update_taxonomy.R.familyto the columns selected in taxonomic_resources