All pull requests

Pull requests

• Serializable help model rebuild

  #2853·ekiefl opened Oct 10, 2026Contributor·

  ·
  1

• Use pyANI-plus for ANIb and ANIm on Python 3.13

  #2845·bcoltman opened Oct 5, 2026Contributor·

  ·

• Move the supported runtime to Python 3.13 and Snakemake 9

  #2842·bcoltman opened Oct 5, 2026Contributor·

  ·

• Fix workflow table parsing and mapped-read import reruns

  #2840·bcoltman opened Oct 5, 2026Contributor·

  ·

• Update pandas APIs and preserve missing-value handling

  #2838·bcoltman opened Oct 5, 2026Contributor·

  ·

• Correct gene coverage mask decoding and INSEQ recovery

  #2837·bcoltman opened Oct 5, 2026Contributor·

  ·

• Fix split-FASTA test output paths and invalid escape sequences

  #2833·bcoltman opened Oct 5, 2026Contributor·

  ·
  1

• Structure prediction in the contigs workflow

  #2824·FlorianTrigodet opened Oct 4, 2026Contributor·

  ·

• Add help page for pangenomics workflow

  #2807·ivagljiva opened Sep 10, 2026Contributor·

  ·

• Anvi-run-antismash and anvi-script-gen-antismash-matrix

  feature
  #2745·jessika-fuessel opened Jul 9, 2026Contributor·

  ·
  

• Add anvi-export-genome-specific-trna-modifications

  #2719·tucker4 opened Jun 8, 2026Contributor·

  ·
  1

  

• Enable metabolism framework tests

  #2713·ulgens opened Jun 7, 2026Collaborator·

  ·
  6

• Lazy snv access

  #2691·FlorianTrigodet opened May 28, 2026Contributor·

  ·
  3

  

• Port anvi'o to Python 3.13

  #2681·bcoltman opened May 24, 2026Contributor·

  ·
  27

  

• anvi-report-indels: track mobile indels

  hackathon 2026
  #2673·FlorianTrigodet opened May 22, 2026Contributor·

  ·
  5

• Add anvi-screw-you: It empathizes with the user once they are frustrated

  hackathon 2026
  #2671·sarilog opened May 22, 2026Contributor·

  ·
  2

• Add modifications parsing from MM and ML tags in BAMs during anvi-profile

  hackathon 2026
  #2663·Ge0rges opened May 21, 2026Collaborator·

  ·
  1

  10

  

• Add first-class PHROGs support via anvi-setup-phrogs and anvi-run-phrogs

  hackathon 2026
  #2649·Ge0rges with CopilotAI opened May 20, 2026·

  ·
  1

  4

  

• Profile read clipping events from BAM files

  hackathon 2026
  #2645·FlorianTrigodet opened May 20, 2026Contributor·

  ·
  

• General implementation for annotation with user-defined databases

  hackathon 2026
  #2644·l-gallucci opened May 20, 2026Contributor·

  ·
  2

• anvi-compute-functional-consensus: *FunctionalConsensus classes

  hackathon 2026
  #2633·ChiaraVanni opened May 20, 2026Contributor·

  ·
  1

• Python 3.14 support

  #2628·ulgens opened May 20, 2026Collaborator·

  ·

• Add Python 3.11 support

  #2625·ulgens opened May 20, 2026Collaborator·

  ·
  1

  

• Enrich ruff rules

  #2592·ulgens opened Apr 30, 2026Collaborator·

  ·
  1

• Don't override default ruff rules selection

  #2582·ulgens opened Apr 28, 2026Collaborator·

  ·
  3