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Commits on Nov 25, 2023

• Fix many warnings from PYTHONDEVMODE=1 (sourmash-bio#2849)

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  luizirber

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  17bc030

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• Drop 3.8 and 3.9, default to 3.10 for most CI tasks (sourmash-bio#2848)

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  luizirber

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  32d46dd

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Commits on Oct 15, 2023

• MRG: make sourmash plot labels/indices arguments make sense (sourmash-bio#2790)

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  ctb

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  9ff523e

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Commits on Sep 15, 2023

• MRG: fix exponential time explosion in sig check (sourmash-bio#2762)

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  ctb

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  94d82b1

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Commits on Sep 13, 2023

• MRG: fix duplicate md5 in picklist problem (sourmash-bio#2747)

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  ctb

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  6df0360

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Commits on Sep 7, 2023

• MRG: avoid compressing sig files in directory output twice (sourmash-bio#2752)

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  ctb

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  d4a1b45

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Commits on Aug 12, 2023

• Feat: add a sourmash.cli.parse_args([...]) function (sourmash-bio#2691)

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  ctb

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  02d2331

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• Fix: update a manifest test to use temp directory (sourmash-bio#2689)

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  ctb

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  e0a0698

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• MRG: add support for -E/--extension to sig split (sourmash-bio#2712)

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  ctb

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Commits on Apr 30, 2023

• MRG: switch dib-lab links to sourmash-bio links in .md files (sourmash-bio#2588)

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  ctb

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  7311eb5

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Commits on Apr 20, 2023

• [MRG] add optional reporting for duplicated names in sketch fromfile (sourmash-bio#2580)

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  bluegenes

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  ee69c50

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Commits on Apr 19, 2023

• [MRG] fix lineage_summary tax bug (sourmash-bio#2579)

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  bluegenes

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  7a9fed0

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Commits on Apr 13, 2023

• MRG: add --create-empty-results option to gather (sourmash-bio#2557)

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  ctb

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  252f2f2

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• MRG: fix exception error when no arguments are provided to sig intersect (sourmash-bio#2555)

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  ctb

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Commits on Apr 5, 2023

• MRG: update prefetch/gather output to be clearer (sourmash-bio#2543)

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  ctb

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  df201c3

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• MRG: modify annotate for flexibility (sourmash-bio#2518)

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  bluegenes

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  ctb

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  7e90715

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• MRG: tax genome with --lins (sourmash-bio#2519)

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  bluegenes

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  ctb

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  bd2fdcc

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• MRG: output bioboxes profile from tax metagenome (for CAMI) (sourmash-bio#2468)

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  bluegenes

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  ctb

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  fd53c50

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• MRG: Add taxonomic utilities for LINs and enable tax metagenome (sourmash-bio#2469)

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  bluegenes

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  ctb

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  827b897

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Commits on Mar 5, 2023

• Remove pkg_resources usage (sourmash-bio#2505)

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  luizirber

  authored
  e9a7f1f

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Commits on Mar 1, 2023

• MRG: add plugin support for new command-line subcommands (sourmash-bio#2438)

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  ctb

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  2fd1ae0

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Commits on Feb 13, 2023

• MRG: Use RankLineageInfo to simplify reading lineages (sourmash-bio#2467)

  bluegenes

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Commits on Feb 9, 2023

• MRG: store taxids in lineageDB (sourmash-bio#2466)

  bluegenes

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Commits on Feb 8, 2023

• Use new tax classes for taxonomic summarization (sourmash-bio#2443)

  bluegenes

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Commits on Jan 16, 2023

• add tax summarization dataclasses for safety and flexibility (sourmash-bio#2439)

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  bluegenes

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  ctb

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  145d1ad

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Commits on Jan 13, 2023

• [MRG] add --scaled to sourmash compare (sourmash-bio#2414)

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  ctb

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  bluegenes

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  ca57995

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Commits on Jan 10, 2023

• MRG: replace lca_utils.LineagePair with tax_utils.LineagePair (sourmash-bio#2441)

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  ctb

  and

  bluegenes

  authored
  f2fabef

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• Add new classes for lineage manipulation (sourmash-bio#2437)

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  bluegenes

  authored
  474e4b3

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Commits on Jan 7, 2023

• [MRG] provide an initial plugin architecture for sourmash that supports new signature saving & loading mechanisms (sourmash-bio#2428)

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  ctb

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  14d79c9

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Commits on Dec 7, 2022

• [MRG] debias all containment values (sourmash-bio#2243)

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  bluegenes

  authored
  12b5e19

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Commits on Dec 3, 2022

• [MRG] fix sourmash sketch ... -o <file>.zip bug introduced in sourmash-bio#2329 and released in v4.6.0 (sourmash-bio#2391)

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  ctb

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  724ec12

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Commits on Dec 1, 2022

• [MRG] fix return type of LCA_SqliteDatabase.select (sourmash-bio#2382)

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  ctb

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Commits on Nov 30, 2022

• [MRG] fix manifest load function to properly catch gzip.BadGzipFile (sourmash-bio#2375)

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  ctb

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  dcd035d

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• [MRG] display a better error message on attempting to write a read-only sqlite database (sourmash-bio#2376)

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  ctb

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  8a13376

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Commits on Nov 14, 2022

• add tax summarize (sourmash-bio#2333)

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  ctb

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  04a9dac

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