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CHANGELOG.md

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Change Log

Unreleased - ReleaseDate

  • Add nwr seqdb

  • Tweak nwr template shell scripts

0.7.5 - 2024-09-20

  • Rewrite nwr template --ass scripts
    • Skip unnecessary downloads
  • Rewrite nwr template --pro scripts
    • Remove unnecessary intermediate files

0.7.2 - 2024-05-28

  • Fix multiple rounds of condensing leaf nodes
  • Skip invalid lines
    • nwr append
    • nwr ardb
    • nwr pl-condense
  • Rewrite nwr template --pro scripts
  • Delete fungi61 because it takes up a lot of disk space

0.7.0 - 2023-09-15

  • Add nwr pl-condense

  • Add --column to nwr label

  • Add -I and -L to nwr replace

  • Fix --term in nwr subtree

  • Handle more tags in nwr tex

0.6.5 - 2023-09-12

  • Add nwr distance

  • Add nwr replace

  • Add nwr prune

  • Add nwr reroot

  • Enhance nwr label

    • Various filtering methods
    • --descendants - Internal nodes' descendants will automatically be included

  • Enhance nwr subtree

    • --condense - Condense the subtree with the name provided

  • Adjust template.tex and update trees

0.6.4 - 2023-09-09

  • Add nwr common
  • Add nwr subtree
  • Add nwr topo

0.6.3 - 2023-09-07

  • Add nwr indent

  • Add nwr order

  • Add nwr label

  • Add nwr rename

  • Add nwr comment

  • Add nwr stat

  • Add nwr tex

  • Add a directory tree/ to store phylogenetic trees

0.6.2 - 2023-07-18

  • Add more templates to nwr template

    • --mh for MinHash
    • --count for counting
    • --pro for collecting proteins
    • --in and --not-in to including and excluding assemblies in some steps

  • Add nwr kb to bundle HMM files

    • bac120
    • ar53
    • fungi61

0.6.0 - 2023-06-03

  • Add nwr template to replace nwr assembly and temporally existed nwr biosample
    • nwr template --ass
    • nwr template --bs
  • Add columns infraspecific_name and gbrs_paired_asm to ardb

0.5.10 - 2023-01-28

  • Add nwr assembly
  • Add -e to nwr restrict
  • Add database schema

0.5.9 - 2022-12-13

  • Bump versions of deps
    • clap v4
    • Use anyhow

0.5.7 - 2022-04-10

  • Update the CI workflows
    • Remove travis and appveyor
    • Use a container with GLIBC 2.17 according to this blog post
  • Remove old scripts

0.5.5 - 2022-03-04

  • Check organism_name with the one in txdb
  • Add column biosample to ardb

0.5.4 - 2022-03-02

  • Add nwr ardb

0.5.3 - 2022-02-24

  • Move old Perl codes here
  • Add doc/assembly.md

0.5.0 - 2022-02-22

  • Extract nwr to a standalone repo.
    • SQLite can't be built statically under musl

0.4.17 - 2022-02-21

  • Add nwr download
  • Add nwr txdb
  • Add nwr info
  • Add nwr lineage
  • Add nwr restrict
  • Add nwr member
  • Add nwr append
  • Use taxdump.tar.gz instead of taxdmp.zip to avoid the zip crate

0.4.16 - 2022-02-12

  • Switch to clap v3
  • New binary nwr