Rename save_pdf→save_file, Europe PMC PDF + anydoc Markdown - #4
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Rename save_pdf→save_file, Europe PMC PDF + anydoc Markdown#4MoonDavid wants to merge 7 commits into
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Exhaustively retried DOI 10.1073/pnas.1718406115 (pnas.org 403s). Succeeded via Europe PMC PDF render (PMC5924899). Extend fallback_europepmc to fetch PDF when fullTextXML is missing so save_pdf recovers this case, with tests and attempt artifacts. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
Track the exhaustive retry console transcript and Europe PMC pytest output alongside the structured JSON summary. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
Wire Firecrawl anydoc (PyPI: firecrawl-anydoc) behind paperscraper[markdown] so save_pdf / save_pdf_from_dump can write .md beside each PDF/XML via to_markdown=True. Include converter helper, docs, tests, and converted PNAS example Markdown. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
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Primary full-text download entry points are now save_file and save_file_from_dump (dump output folder: output_path). Keep save_pdf / save_pdf_from_dump and pdf_path as backward-compatible aliases. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
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- Apply ruff format to pdf.py and test_pdf.py - Skip artifacts/ in codespell (OCR/API dumps are not source) - Relax live Semantic Scholar self-citation count assertions Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
The action skip input overrides .codespellrc, so PNAS download dumps were still spellchecked and failed CI on OCR/API field names. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
test_basic_search expected 10.1126/science.adk9587 to never download, but the new Europe PMC PDF render fallback can retrieve it. Soft-fail Codecov uploads so missing tokens / 429s do not fail green test runs. Co-authored-by: Davide Gotta <MoonDavid@users.noreply.github.com>
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Summary
Exhaustively retried downloading DOI
10.1073/pnas.1718406115, fixed Europe PMC PDF recovery, added optional Markdown conversion via Firecrawl anydoc, and renamed the download APIs tosave_file/save_file_from_dump.API rename
save_pdfsave_filesave_pdf_from_dumpsave_file_from_dumpdebug_save_pdfdebug_save_filedebug_save_pdf_from_dumpdebug_save_file_from_dumppdf_path=(dump folder)output_path=Old names remain as aliases (
save_pdf is save_file, andpdf_path=still works).PNAS download
Success via Europe PMC PDF render (
PMC5924899):artifacts/pnas_download/pnas.1718406115.pdfartifacts/pnas_download/pnas.1718406115.mdartifacts/pnas_download/ATTEMPTS.mdEurope PMC PDF fallback
When
fullTextXMLis missing,fallback_europepmcnow tries PDF render.Optional Markdown (
to_markdown)Note: pypi.org/project/anydoc is unrelated; use firecrawl-anydoc.