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FIX: Strip PMC from ID - #58
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adelavega
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Aug 29, 2025
adelavega
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- Strip PMC from pmcid found in text
adelavega
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Sep 8, 2026
…s was wrong The patch was written against pubget 0.0.8 in ~/.local, which is what the fallback ~/.local/bin/autonima runs. That is not the interpreter this project uses: pyproject.toml pins pubget for the pixi environment, which already had 0.0.9.dev including the get_pmcid fix from neuroquery/pubget#58. So most of the "pubget discards modern PMC records" failure was an artifact of invoking the fallback CLI rather than pixi run, against a pubget predating that fix. The same applies to ACE, which pyproject.toml already installs editable from ../ACE -- the scratch-directory install used earlier was unnecessary. One real bug survived in 0.0.9.dev and is fixed properly in the pubget repo instead, on branch fix/skip-unidentifiable-article: get_pmcid raises ValueError for unresolvable records and _extract_from_articleset did not catch it, so a single such article still aborted a whole download batch. pyproject.toml now takes pubget editable from ../pubget so that fix is live here. The ~/.local patch has been reverted to its shipped state. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
adelavega
added a commit
to neurostuff/autonima-results
that referenced
this pull request
Sep 25, 2026
…s was wrong The patch was written against pubget 0.0.8 in ~/.local, which is what the fallback ~/.local/bin/autonima runs. That is not the interpreter this project uses: pyproject.toml pins pubget for the pixi environment, which already had 0.0.9.dev including the get_pmcid fix from neuroquery/pubget#58. So most of the "pubget discards modern PMC records" failure was an artifact of invoking the fallback CLI rather than pixi run, against a pubget predating that fix. The same applies to ACE, which pyproject.toml already installs editable from ../ACE -- the scratch-directory install used earlier was unnecessary. One real bug survived in 0.0.9.dev and is fixed properly in the pubget repo instead, on branch fix/skip-unidentifiable-article: get_pmcid raises ValueError for unresolvable records and _extract_from_articleset did not catch it, so a single such article still aborted a whole download batch. pyproject.toml now takes pubget editable from ../pubget so that fix is live here. The ~/.local patch has been reverted to its shipped state. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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