FLAIR Release 3.0.1

[v3.0.1] 2026-08-10

• General
  • fixed problems with some diffsplice_fishers_exact, and other
    auxiliary console script installs
  • dropped the mark_productivity console script and the bin/bam2Bed12
    and bin/mark_productivity links, which were never functional
  • supported Python versions widened from 3.12 only to 3.12 through 3.14,
    in both the pip and Conda installs. The expected files for the --help
    tests are now generated with Python 3.13, so those tests fail on 3.12
• FLAIR collapse
  • worked around --remove_internal_priming failing when applied during the
    transcriptome alignment phase (#629)
• FLAIR combine
  • error out with a clear message when the manifest contains no samples
  • added debug logging of sample, intron-chain and final isoform counts
• Documentation
  • new FLAIR pipeline figure on the main page; the compartmentalized workflow
    figure moved to the modules page
  • fixed figures mangled by the conversion to SVG and a bad margin
  • removed the obsolete FLAIR2 functions page
  • removed the stale note that the protocol applies only to a GitHub master
    checkout