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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[0.1.1] - 2026-04-17

Maintenance release focused on aligning the abstract-retrieval semantics across code, templates, docs, tests, and metadata. No breaking public-API changes; the one renamed kwarg keeps its old name as a deprecated alias for this release cycle.

Added

  • Abstract retrieval now falls back through a DOI-only cascade when CrossRef does not return an abstract: Semantic Scholar (/paper/DOI:{doi}?fields=abstract) → PubMed (ESearch DOI→PMID, then EFetch PMID→abstract). The cascade is only invoked when the user's original raw input carried a DOI; DOIs inferred by fuzzy search do not trigger it, so that a possibly-wrong candidate does not cost extra roundtrips. In particular, a local BibTeX entry with no DOI field — regardless of whether other stages would later resolve one — does not trigger the abstract cascade.
  • Semantic Scholar search results now carry the abstract field, which propagates through _convert_search_metadata into the final BibTeX output whenever the identification stage already resolved the entry through SS.
  • EnricherModule._get_semantic_scholar_abstract(doi) helper for DOI-based Semantic Scholar abstract retrieval. Handles 404 / 429 gracefully by returning None.
  • _complete_fields gained an allow_abstract_fallback kwarg (default False) that gates the new cascade. _enrich_single_entry passes True only when the raw entry contributed a DOI.
  • Default journal_article_full template now lists abstract as an optional field, so the template declaration matches what the enricher emits. The older journal_article_with_abstract template is retained as a compatibility alias and will stay available for at least one release cycle.
  • Regression test test_enrich_single_entry_no_doi_in_raw_skips_abstract_fallback pinning the "no-DOI-in raw ⇒ no Semantic-Scholar / PubMed network call" guarantee at the _enrich_single_entry layer, so a future refactor of the raw_has_doi gate cannot silently start leaking network calls for local-only inputs.

Changed

  • _get_pubmed_abstract now requires a DOI and no longer falls back to PubMed title search. The removed title-based path empirically returned the abstract of an unrelated paper (e.g., the Zhang 2020 AI Review DOI 10.1007/s10462-019-09792-7 pulled the abstract of a different RSI segmentation paper), which is strictly worse than returning None for downstream semantic cross-checks such as the sci skill.
  • Abstract coverage on an internal 10-DOI cross-publisher spot-check (Nature, Science, PLOS, Cell, IEEE CVPR, Frontiers, arXiv, Springer, ACM, plus one deliberately invalid DOI) rose from 4/9 to 8/9. This number is a local indicator, not a release gate: reproducing it requires a live network and the probe scripts are no longer in the repository.

Deprecated

  • _complete_fields(..., allow_pubmed_fallback=...) is deprecated in favour of allow_abstract_fallback. The old name still works for one release cycle and emits DeprecationWarning. It was renamed because the flag actually gates the entire Semantic-Scholar + PubMed cascade, not PubMed alone.

Removed

  • IdentifierModule._check_doi_content_consistency and the consistency_score / low_consistency warning path. A fuzzy string-similarity score on bibliographic fields is not a reliable signal for detecting fabricated references, and it was only emitted as a logger.warning that downstream tools could not act on. Citation-authenticity verification belongs at the abstract-vs-claim semantic layer in the consuming tool, not at the bibliographic-string layer here.

[0.1.0] - 2026-04-17

First formal PyPI release since 0.0.12.

Added

  • RST documentation using Sphinx
  • Full API reference documentation
  • FAQ section with common questions
  • Contributing guidelines
  • Pre-commit hooks configuration
  • Google-style docstrings with Args/Returns for all public API functions
  • Auto-deploy documentation to GitHub Pages via CI

Changed

  • Split monolithic pipeline.py (~3000 lines) into a proper onecite/pipeline/ package with one module per stage (parser.py / identifier.py / enricher.py / formatter.py) plus a _utils.py for shared helpers. Public imports (from onecite.pipeline import IdentifierModule) and mocking targets (patch("onecite.pipeline.requests.get", ...)) continue to work unchanged because __init__.py re-exports every public symbol and keeps requests at the package level.
  • Unify CrossRef request and parsing methods; all CrossRef calls now go through a single helper with a proper User-Agent header and mailto query-string parameter.
  • Rewrite fuzzy-search scoring as a weighted title / author / year / venue model with three confidence tiers (auto-adopt / interactive / cautious) and a unified low-confidence threshold.
  • Simplify identifier routing; CrossRef and Semantic Scholar are always consulted for text queries, with signal-based additional queries to PubMed / Google Books / OpenAIRE / BASE.
  • Use bibtexparser.dumps() for BibTeX rendering.
  • Expose use_google_scholar as a real CLI flag and API parameter instead of a hard-coded False.
  • Clarify that templates define metadata-field requirements and a fallback BibTeX entry type, not output formatting.
  • Refactored exception hierarchy
  • Added type hints to Python API
  • Updated README examples
  • Bumped minimum Python version declaration in docs to 3.10
  • Updated CI actions to latest versions (checkout v4, setup-python v5)
  • Updated copyright year to 2024-2025
  • Fixed Documentation URL in pyproject.toml to point to GitHub Pages

Removed

  • APA and MLA output renderers; they produced inconsistent output and the CLI now rejects anything other than --output-format bibtex. Users wanting APA/MLA should post-process the BibTeX through pandoc or citeproc-py.
  • Hard-coded "well-known paper" shortcut that masked failures on the main example input.
  • MCP integration page and all related references
  • .readthedocs.yml (docs now hosted on GitHub Pages)
  • docs/_build/ build artifacts from repository

Fixed

  • README / docs/index.rst / docs/faq.rst no longer advertise OpenAlex or dblp as data sources — they were never wired into the code.
  • README quick-start example now shows booktitle (NeurIPS) instead of journal = "arXiv preprint" for the @inproceedings sample.
  • docs/api/pipeline.rst rewritten to match the actual module structure; removed references to classes and methods that never existed (Validator / Identifier / Completer / Formatter, set_source_priority, set_timeout, add_template_path).
  • docs/output_formats.rst, docs/faq.rst, docs/quick_start.rst, docs/python_api.rst, docs/templates.rst, docs/index.rst and docstrings in core.py / formatter.py no longer advertise APA / MLA output.
  • Crossref author names parsed as given family instead of mangled concatenations.
  • Semantic Scholar HTTP 429 responses return an empty candidate list cleanly instead of bubbling up.
  • Previously-unused exception classes (ParseError, ValidationError, FormatError) are now actually raised in the right places.
  • CONTRIBUTING.md no longer tells developers to use a requirements.txt that does not exist; the documented install is pip install -e .[dev].
  • black formatting is enforced via pyproject.toml [tool.black] plus a pre-commit hook.
  • URL-bearing entries are no longer queried twice.
  • Fallback paths mark entries as identification_failed rather than fabricating plausible-looking but invented metadata.
  • CrossRef and Semantic Scholar response parsing edge cases
  • API documentation using incorrect return value fields (output_content -> results)
  • Version number inconsistencies across metadata files
  • Python version requirement inconsistencies in docs (3.7 -> 3.10)

[0.0.11] - 2024-10-19

Added

  • Custom YAML-based template system
  • Support for multiple output formats (BibTeX, APA, MLA)
  • Interactive mode for ambiguous reference selection
  • Support for DOI, arXiv, PMID, ISBN, and GitHub identifiers
  • Integration with 9 major academic data sources
  • Test suite

Changed

  • Refactored core processing pipeline
  • Reordered data source priority (CrossRef first for DOI queries)
  • Clearer error messages on failed lookups

Fixed

  • Encoding issues with non-ASCII characters in author names
  • DOI parsing for URLs with trailing query strings
  • Python 3.10 compatibility issues

[0.0.10] - 2024-10-01

Added

  • Initial Python API
  • Basic citation processing
  • Support for journal articles and conference papers

Changed

  • Better title matching for fuzzy searches

Fixed

  • PubMed API response handling
  • Semantic Scholar rate limit handling

[0.0.9] and Earlier

See GitHub Releases for details on older versions.