perf(pmid): derive abstract from the single article-XML fetch

[caufieldjh]

Follow-up to #57, addressing the review's deferred note 2 ("still two efetch calls per PMID").

What changed

PMIDSource.fetch() used to make two NCBI efetch calls per PMID:

1. rettype="abstract", retmode="text" → the abstract
2. rettype="xml" → the article XML (MeSH terms + publication types)

The article XML already contains the abstract, so this parses it from there and drops the second call (and its rate_limit_delay sleep). One fewer round-trip to NCBI per PMID.

• New _parse_abstract(soup) reconstructs the abstract prose from Abstract/AbstractText, preserving structured-section labels (e.g. METHODS:, RESULTS:), mirroring how PubMed renders structured abstracts as text. Replaces the now-removed _fetch_abstract.

Behavior note (why this was deferred, and why it's safe)

content is now the abstract prose only, without the citation-header boilerplate (title/authors/journal/PMID/DOI) that the old text-mode fetch prepended. This is safe — and arguably cleaner:

• Supporting-text validation (supporting_text_validator.py) fuzzy-matches claim text against abstract / full-text prose, never against citation headers. Verified no code or test relies on header text in content; the real/e2e validation tests use cached fixtures, not live fetches.
• A record with no abstract now correctly yields no content (content_type "unavailable"/"summary") instead of a header-only stub that was misleadingly tagged abstract_only.

Live verification

lookup PMID:33301246 now reconstructs the structured abstract from a single efetch:

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 ...

METHODS: In an ongoing multinational, placebo-controlled ...

Testing

New unit tests: structured / unstructured / absent / empty abstract parsing, plus a fetch() test asserting exactly one Entrez.efetch call backs all three fields (abstract, MeSH, publication types). Doctests on _parse_abstract.

Full just test green: 625 passed, mypy + ruff clean.

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Review: perf(pmid): derive abstract from the single article-XML fetch

• Read PR diff
• Review pmid.py changes (abstract parsing, single fetch)
• Review test coverage
• Post review feedback

Nice, focused change. It cleanly resolves note 2 from #57 — dropping one efetch round-trip and one rate_limit_delay sleep per PMID by reconstructing the abstract from the article XML that was already being fetched for MeSH terms and publication types. The behavior-change reasoning in the PR body is sound, and I confirmed there are no dangling references to the removed _fetch_abstract in the source tree (only historical mentions in docs/).

Strengths

• _parse_abstract correctly targets <Abstract> (not <OtherAbstract>), preserves structured-section Labels, and skips empty nodes.
• Test coverage is good: structured / unstructured / absent / empty, plus the test_fetch_uses_single_efetch assertion that mock_efetch.call_count == 1 — that call-count assertion is exactly what pins the perf win in place. Doctests double as docs. 👍
• Removing the header-only stub so a record with no abstract yields unavailable/summary instead of a misleading abstract_only is a genuine correctness improvement.

Minor observations (non-blocking)

1. Structured abstracts that use NlmCategory without Label (pmid.py:229). Some PubMed records label sections only via NlmCategory="METHODS" and omit the human-readable Label attribute. For those, the current code produces unlabelled prose (sections still joined, just no METHODS: prefix). Not a correctness bug for fuzzy matching — the prose is preserved — but if you want to mirror PubMed's text rendering more faithfully, consider falling back to NlmCategory when Label is absent:

   label = node.get("Label") or node.get("NlmCategory")

   (PubMed suppresses the UNLABELLED category, so you'd want to guard against emitting UNLABELLED:.)

2. Records with only <OtherAbstract> (author-manuscript / non-English abstracts). soup.find("Abstract") returns None for these, so content is now empty where the old text-mode efetch might have surfaced that text. Likely rare and arguably fine to skip, but worth a mention as a behavioral nuance since it's a subtle difference from the old path.

3. Inline markup spacing (node.get_text(), pmid.py:226). get_text() concatenates nested <sub>/<sup>/<i> content with no separator (e.g. H<sub>2</sub>O → H2O, usually desirable; but adjacent inline tags without whitespace can merge words). Minor and consistent with _parse_mesh_terms; only flagging for awareness.

None of these block merging — the change is correct and well-tested as written. If you'd like, I'm happy to add the NlmCategory fallback (item 1) in a follow-up.

I was not able to run just test in this review pass, but the CI on this PR should cover the 625-test suite the description references.
• feat/abstract-from-article-xml