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Common names tracking issue

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#38 コメント 0 件 リアクション 0 件 担当者 0 名 GitHub で見る

まだ誰も着手していません。

評価

難易度
4/5
見積もり時間
3〜5日
初心者へのやさしさ
45/100
issue の種類
機能追加
明瞭さ
おおむね明確
活発さ
活発
技術スタック
postgresql, python
領域
backend, databases

調査の方向性

Review the history in the issue body and linked PRs #6, #14, #26, #36, #37. Understand the current common-names handling in the codebase, likely in a module like common_names.py. Examine the GBIF Backbone and Catalogue of Life data sources. The work involves fixing homonym lookups, cache handling, and deciding on rerun behavior. A newcomer must first understand the project's taxonomic resolution flow and the existing Polars-based data processing.

索引モデルが issue の本文から書いたものです。

説明

enhancement

Issue text drafted with the help of Opus 5.5.

Common-name handling has gone through several iterations across releases, PRs, and branches. This issue collects that history in one place and gathers the open work that should inform the next iteration.

History

Stage Where Released? Behavior
Original retrieval #6 (merged 2025-05-01) v0.1.0 Merges GBIF Backbone vernacular names into resolved output. Input common names could pass through.
Deterministic rewrite #14 (open, branch feat/deterministic-common-names) never merged Backbone-only names, Polars rewrite, higher-rank coverage, tests. The review discussion there (usefulness of higher-rank names such as "Orchid" for many species; recording the source rank) directly shaped later work.
Hierarchical fallback #26 v0.2.0 Always climbs species → kingdom. Prefers the first English name, then any language. Input common names always replaced.
Optional fallback + rank column #36 → #37 unreleased (on main only) --no-higher-rank-fallback disables climbing. New common_name_rank column records the rank the name came from. Default output matches v0.2.0 plus the new column.

Note: #37's behavior has not shipped in any tagged release. If the next iteration lands before the next tag, release notes should describe the net change from v0.2.0.

Open items

  • #10: input common names must not pass through. The literal request is addressed since v0.2.0 (the input common_name column is always dropped before lookup). Its broader goal, a uniform one-to-one mapping between taxonomy and vernacular, is affected by the homonym item below.
  • Homonym-blind taxon lookup (new). Each rank's name is mapped to a backbone taxonID by canonicalName alone, ignoring kingdom and taxonomicStatus. Duplicates are dropped with Polars unique(subset=[rank]), which keeps an arbitrary row (stable in practice, not guaranteed). In the GBIF Backbone: 44,403 duplicated genus names (11,520 spanning more than one kingdom), 248,587 duplicated species names, 194 duplicated family names. Example: genus Laelia maps to taxonID 7562880 (Plantae, doubtful) for every row, so animal Laelia can receive a plant's common name.
  • #35: dead cache_dir handling in the standalone common-names parser.
  • #34 (last bullet): --full-rerun does not apply to common-names, although the command writes its own manifest. Decide whether it should, or document that it is resolve-only.

Related branches (kept for reference)

  • feat/deterministic-common-names: #14's branch.

Next iteration

Should include fixes required by the above notes.
Before common names updates are added to a tagged release, the strategy should shift to use Catalogue of Life vernacular data retrieved from here.

Furthermore, a vernacular assignment strategy for TaxonoPy-resolved entries should be agreed upon. Default behavior can be unfiltered retrieval of all vernacular data, enabling a user to apply custom strategy of their design. Additionally, we can provide reasonable prioritization/filtering strategies that serve our own use-cases.

主要言語
Python
スター
19
フォーク
0
30日以内にマージされた PR はありません

環境構築

このプロジェクトの環境構築ファイルはまだ確認していません。まず README を読み、一般的な手順ははじめてのコントリビューションガイドを参照してください。

はじめの一歩

  1. issue を最後まで読み、次にプロジェクトのコントリビューションガイドを読みます。
  2. 着手することを issue にコメントします — 二人が同じ作業をするのを防げます。
  3. リポジトリをフォークし、ブランチを切って変更します。
  4. issue 番号を参照したプルリクエストを送ります。

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