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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

[4.13.0]

Added

Recipes

  • bambi 0.16.1

[4.12.0]

Added

Recipes

  • bambi 0.16.0

[4.11.0]

Added

Recipes

  • wr 0.32.2

[4.10.0]

Added

Recipes

  • samtools 1.17
  • bcftools 1.17
  • htslib 1.17

Features

Removed

Recipes

Changed

  • GH Actions: fix conda 23.3 to cope with API changes

[4.9.0]

Added

Recipes

  • bambi 0.15.0

[4.8.0]

Added

Recipes

  • wr 0.32.1
  • baton 4.0.1

Features

  • irmdir to iRODS 4.2.11 package

Changed

CI

  • Update Docker Conda build image name
  • Move from DockerHub to GitHub hosted images
  • Fix to iRODS 4.2.11 rsPhyPathReg to resolve a compilation error

[4.7.0]

Added

Recipes

  • io_lib 1.14.14

[4.6.0]

Added

Recipes

  • samtools 1.16.1
  • bcftools 1.16
  • htslib 1.16

Removed

Recipes

  • irods 4.2.10

Changed

  • Github Actions: Move from ubuntu-18.04 to ubuntu-latest

Recipes

  • Build config with compiler version and cflags and increment build number:
    • avrocpp 1.8.2, 1.9.0
    • boost 1.73.0
  • Remove irods 4.2.10 from build config:
    • baton 3.1.0, 3.2.0, 3.3.0, 4.0.0
    • htslib-plugins 201712
  • Update release url:
    • libarchive

[4.5.0]

Added

Recipes

  • wr 0.32.0
  • baton 4.0.0

[4.4.0]

Added

Recipes

  • baton 3.3.0

Removed

Recipes

  • ml-warehouse 0.1.0

[4.3.1]

Changed

  • Gitlab CI: rsync location for prod channel build fixed

[4.3.0]

Added

Recipes

  • wr 0.30.0, 0.31.0, 0.31.1, 0.31.2
  • samtools/bcftools/htslib 1.15, 1.15.1
  • filebeat 8.1.2
  • ml-warehouse 0.1.0
  • iRODS 4.2.11

Features

  • Gitlab CI : master branch build will be pushed to prod channel

Removed

Recipes

  • iRODS 4.2.8, 4.2.9

Changed

  • build configs to use iRODS 4.2.11 and increment build numbers
    • baton 3.2.0
    • htslib-plugins 201712
    • tears 1.3.1

Recipes

  • remove spurious iRODS-dev dependency for io_lib
  • curl 7.58.0 to use Conda ca-certs
  • iRODS : pin the fmt dependency to a version <8.0

[4.2.0]

Added

Recipes

  • wr 0.28.0, 0.29.0
  • samtools/bctools/htslib 1.14
  • Build htslib-plugins for iRODS 4.2.10

Features

Removed

Recipes

  • iRODS 4.2.8

Changed

  • Python source file location moved to src
  • Use conda-build API

[4.1.0]

Added

  • wr 0.27.0

Recipes

  • baton 3.1.0, 3.2.0
  • Build variants for iRODS 4.2.7 and 4.2.10

Features

  • Add support for Conda build variants and Conda versions

Changed

  • Python source file location moved to src
  • Use conda-build API
  • find_changed_recipe_files returns relative paths
  • Add a requirement for Python >=3.9, due to the use of Path.is_relative_to
  • Add . to requirments.txt so that pip will install the local tools and their modules when pip install -r requirments is run.
  • Move Python source files to ./src and unify python files into a module structure
  • Allow tests to be run from any directory.

[4.0.0]

Added

Recipes

  • bambi 0.14.0
  • baton 3.0.0, 3.0.1
  • capnproto 0.7.0
  • gnutls 3.7.1, 3.7.2
  • hisat 2.1.0
  • iRODS
    • 4.2.10
    • 4.2.9
      • avrocpp 1.9.0
    • 4.2.8
      • avrocpp 1.8.2
      • json 3.9.1
      • krb5 1.19.1
      • libarchive 3.5.1
      • nanodbc 2.13.0
  • mash 2.3
  • samtools/htslib/bcftools 1.12, 1.13
  • seqtk 1.3
  • wr 0.23.3, 0.23.4, 0.25.0, 0.26.0

Features

  • Automatic package building on pull requests
  • Build variants for packages depending on iRODS libraries
  • --pull-build-image CLI option for build script
  • --output-packages CLI option for recipebook script

Removed

  • fastx_toolkit 0.0.14
  • iRODS 4.1.12
  • Dependencies on conda-forge and consequently the "red recipes".

Changed

  • Build host image changed from Ubuntu 12.04 to CentOS 7.
  • Update recipes to build with Conda >= 4.10.3 to use GCC 9.3 and glibc 2.17.
  • The URL for boost source code was updated.
  • The --sub-packages CLI option of the recipebook script now acts as a modifier for --output-packages to print only sub-packages.
  • krb requirement to krb-dev for irods 4.2.7
  • The default behaviour of the build script is no longer to pull the build image, but to expect to find it locally.

[3.0.0]