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v1.2.2 — PubMed and alerts fixes

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@pryndor pryndor released this 27 Sep 06:31
· 15 commits to main since this release

More complete PubMed results, friendlier NCBI outages, and alerts fixes.

Install / upgrade

pip install --upgrade "lixplore-cli[tui]"      # PyPI
brew upgrade lixplore-cli                      # Homebrew
yay -S lixplore-cli                            # Arch (AUR)

Changed

  • Python 3.9 or newer is required (3.8 reached end of life in October 2024; source builds on it
    already failed). CI now tests 3.9 to 3.13

Fixed

  • Alerts .env: when a variable appears twice, the later line now wins (as in other .env tools).
    Before, a LIXPLORE_QUERIES line added below the init template's example was silently ignored
  • Alerts test and check work before any search is set, so channels can be tested first
    (before, both stopped with "LIXPLORE_QUERIES is empty"). run and dry-run still require it
  • PubMed: DOIs were missing for many older papers (the DOI was read only from ELocationID,
    not from the article ID list), which weakened deduplication, enrichment and PDF lookup
  • PubMed: year was empty when the record only has a date range such as "2001 May 1-15"
  • PubMed: when NCBI's search backend is temporarily down, requests are retried and a clear
    "temporarily unavailable" message is shown instead of the raw server error

Full changelog: v1.2.1...v1.2.2