CHANGELOG.md

Changelog

3.4.1 (2024-10-28)

Bug Fixes

• fix image artifact regex to match GitHub Actions filename (#1013) (c1adeea)

3.4.0 (2024-10-21)

Features

• Update dependencies to latest versions - less complex (#1011) (167f348)

3.3.2 (2024-08-28)

Bug Fixes

• token for CircleCI artifacts (#1001) (a5882cc)

3.3.1 (2024-06-06)

Bug Fixes

• add missing Arm platforms to skip existing builds (#999) (bbc8758)

3.3.0 (2024-06-03)

Features

• Update pinning 2024-05 (#991) (d48d6e4)

3.2.0 (2024-06-02)

Features

• Update base-glibc-*-bash images to 3.1 (#996) (e7c6ca0)

Bug Fixes

• Pass pkg_format to container-based build (#994) (e3f23ed)

3.1.0 (2024-06-01)

Features

• Update dependencies to latest versions (#992) (8c0fe35)

3.0.0 (2024-05-17)

⚠ BREAKING CHANGES

• Separate docs-only requirements (#986)
• Remove defaults channel dependency (#985)

Miscellaneous Chores

• Remove defaults channel dependency (#985) (eb043dc)
• Separate docs-only requirements (#986) (09d108e)

2.15.1 (2024-05-08)

Bug Fixes

• test_package for .tar.bz2 and .conda (#983) (c683290)

2.15.0 (2024-05-03)

Features

• Add support for .conda format (#981) (125c9ea)
• choose worker recipes by depth level (#950) (4c51ae3)
• Update dependencies to latest versions (#972) (dc6ca07)
• Use conda/conda-build instead of mamba/conda-mambabuild (#980) (17cbc7f)

Bug Fixes

• handle PR list with no items (#975) (869577a)
• Ignore src_cache for container-built packages (125c9ea)
• Ignore Zstandard-packed repodata artifact (125c9ea)
• use circleci api v1.1 to avoid login error (#982) (ebafe92)

2.14.0 (2024-04-01)

Features

• fetch artifacts from GitHub Actions (#973) (858e1cf)
• update deployment target for osx-arm64 (#967) (a7c591e)

2.13.2 (2024-03-27)

Bug Fixes

• update anaconda-client=1.12 to fix uploads (#970) (06dcacc)

2.13.1 (2024-03-27)

Bug Fixes

• detect errors when uploading artifacts (#968) (d0a79cd)

2.13.0 (2024-03-22)

Features

• add osx-arm64 to platform checks (#965) (9f6df10)

2.12.0 (2024-03-18)

Features

• add support for excluding otherwise-selected recipes (#962) (3946732)
• bioconductor improvements (#944) (b007d34)
• Bulk build failure wiki (#948) (18f988d)

Bug Fixes

• Do not emit cython_needs_compiler if compiler("cxx") is set (#927) (8255afd)

2.11.1 (2023-12-13)

Bug Fixes

• add local channel for docker builds (#945) (de8ce00)
• Fix version number check in repodata_patches_no_version_bump() (#946) (73e69b2)

2.11.0 (2023-11-30)

Features

• make GITHUB_TOKEN optional for fetch (#942) (c0eab1d)

2.10.0 (2023-11-26)

Features

• live logs for mulled build (#939) (7f83d7f)

Bug Fixes

• specify involucro path when uploading (#941) (3086cc0)

Documentation

• run_export -> run_exports plural in help message (#928) (2c5d4ad)

2.9.0 (2023-11-05)

Features

• use new container version by default (3.0) (#935) (11d53db)

2.8.0 (2023-11-02)

Features

• Enable Live logs and add option to disable (#930) (47eaadc)

Bug Fixes

• try locale C.utf8 (#931) (584fcdd)

2.7.0 (2023-10-14)

Features

• add support to run build for recipes with linux-aarch64 additional-platforms (#923) (55671f7)

2.6.0 (2023-10-08)

Features

• download aarch64 artifacts from CircleCI (#921) (b9cddd4)

2.5.0 (2023-10-04)

Features

• add special lints for bioconda-repodata-patches recipe (#855) (11c9229)

Bug Fixes

• adding "vals" to GithubRelease changes for API and expanded assets (#912) (9e0e445)
• Remove htslib build pinning (#917) (c7efb92)
• Version constraints can start with ! as well (#919) (ee56f6e), closes #918

Documentation

• try to clarify some confusion with run_exports. (#914) (417e7da)

2.4.0 (2023-08-24)

Features

• lint missing run exports (#908) (84f5c0c)

Bug Fixes

• recover --docker-base-image feature (#906) (aa08857)
• swaps from github API to expanding the assets (#907) (2099a40)
• use package name instead of folder for build failure list dag check (#910) (11fb14f)

2.3.4 (2023-07-15)

Bug Fixes

• update pinning for libxml2 due to conda-forge migration (#903) (ee226f8)

2.3.3 (2023-07-06)

Bug Fixes

• adds alternate lookup if base lookup fails (#896) (17a1475)
• update r-base pinning (#901) (54d8702)

2.3.2 (2023-06-29)

Bug Fixes

• update to boa 0.15 which supports strict channel priorities (#887) (52f5e6d)

2.3.1 (2023-06-07)

Bug Fixes

• improved release workflow (7abe60d)
• improved release workflow (18aa50b)
• improved release workflow (62b8ebe)

2.3.0 (2023-06-07)

Features

• always add a fallback archive URL to the meta.yaml when using bioconductor-skeleton (#886) (d885495)

Bug Fixes

• various little fixes for build failure records and automatic skiplisting (#894) (715efc2)

2.2.1 (2023-05-22)

Bug Fixes

• use git cli to obtain recipe commit sha, since there seems to be no fast and correct way to do that with gitpython (#892) (a6fd713)

2.2.0 (2023-05-22)

Features

• add subcommand to skiplist a given recipe using the new recipe specific mechanism; in addition, some fixes for the new skiplisting approach, and renaming blacklist into skiplist (#890) (da7a912)

2.1.0 (2023-05-21)

Features

• add ability to store build failures as yaml next to recipe, add flag to automatically do so upon build failures, consider such files as blacklisting if they include blacklist: true. (#888) (e78c120)

2.0.0 (2023-05-18)

⚠ BREAKING CHANGES

• remove old unused bot code and simplejson dependency (#883)

Features

• remove old unused bot code and simplejson dependency (#883) (cab3df5)

1.7.1 (2023-05-11)

Bug Fixes

• support proxy settings via the usual environment variables (HTTPS_PROXY, ...) (#881) (5d21b64)

1.7.0 (2023-05-08)

Performance Improvements

• update to latest conda-forge pinnings and ditch building for Python 3.7 and 3.6 (#878) (0704708)
• update to latest conda-forge pinnings and ditch building for Python 3.7 and 3.6 (#878) (6b5e9f5)

Miscellaneous Chores

• release 1.7.0 (9bf3ba9)

1.6.2 (2023-05-04)

Bug Fixes

• fix obtaining LegacyVersion class from pkg_resources (bceae0f)

1.6.1 (2023-05-04)

Bug Fixes

• use strict channel priorities in the right order in the container image (#874) (6e6c91a)

1.6.0 (2023-05-02)

Features

• Add --mulled-conda-image (#867) (1923d24)
• add Linux aarch64/arm64 support for bioconda-utils (#866) (794ec06)

Bug Fixes

• allow lint for blacklist to see blacklisted recipes (#863) (0e63e73)
• fix autobump (#865) (b6b674c)

Performance Improvements

• upgrade to latest conda, conda-build, and boa versions (#872) (21a6452)

1.5.7 (2023-03-24)

Bug Fixes

• uploading of noarch artifacts and other small improvements to artifact uploading (#860) (da41c36)

1.5.6 (2023-03-23)

Bug Fixes

• properly handle platforms as list (0b2cf30)

1.5.5 (2023-03-23)

Bug Fixes

• improved logging for artifact upload, use QUAY_LOGIN env var (6b7a56d)

1.5.4 (2023-03-10)

Bug Fixes

• use correct ssl certs for skopeo upload (#856) (a48dcf3)

1.5.3 (2023-03-09)

Bug Fixes

• load config before instantiating repodata in artifact upload (#853) (946442f)

1.5.2 (2023-03-09)

Bug Fixes

• platform specific artifact upload and fixed file renaming for container image upload (#851) (b56e1a4)

1.5.1 (2023-03-08)

Bug Fixes

• fix skopeo based upload of container images from build artifacts by removing colons in filenames (#849) (4f2eec5)

1.5.0 (2023-03-02)

Features

• make use of BIOCONDA_LABEL if specified when calling handle-merged-pr (#845) (bc30cb5)

1.4.0 (2023-03-02)

Features

• bot-free merge handling (#841) (1122dd3)

1.3.1 (2023-03-01)

Bug Fixes

• Change logic for checking if there are missing commits in a branch vs… (#843) (836ecee)

Documentation

• remove docs (#839) (d52810c)
• support anchors in
  (#832) (2ad8b61)
• update bulk docs to include BioC updates (#828) (1301a6c)

1.3.0 (2022-11-10)

Features

• Update GLPK pin for BioC 3.16 bulk rebuild (#825) (28a4dda)

1.2.0 (2022-11-02)

Features

• switch data packages to bioconductor-data-packages (#822) (5abba86)
• Update bioconda_utils-conda_build_config.yaml (#824) (f8c609a)

Bug Fixes

• autobump cache checking on circleci (954708e)

1.1.5 (2022-10-15)

Bug Fixes

• Use newer mulled conda image (#819) (1464d18)

1.1.4 (2022-10-13)

Bug Fixes

• restore from cache on circleci (#815) (001d4f8)
• update mamba when performing mulled tests (#818) (e39cc48)

1.1.3 (2022-10-11)

Bug Fixes

• Update pyopenssl pinning (#814) (e4950b0)
• Use mamba in mulled-build (#810) (554e15b)

Documentation

• add cbrueffer to core. (#811) (cecf50c)

1.1.2 (2022-10-08)

Bug Fixes

• require a more recent pyopenssl (#809) (adaebdc)

Documentation

• Bioconductor data packages (#802) (bb84df2)
• reflect Jillians leave of the core team in the docs (#807) (3e7c12b)

1.1.1 (2022-09-13)

Bug Fixes

• autobump uses correct version from common.sh (#803) (81ba442)
• circleci yaml syntax (#806) (3315057)

1.1.0 (2022-09-11)

Features

• linter for missing space in dependency version contraints (#795) (85ccb23)
• schedule docs on GitHub actions (#800) (dde65d0)
• Update htslib and conda-forge pinnings (#797) (162d597)

Documentation

• developer documentation updates (#792) (87c16fe)

1.0.1 (2022-08-01)

Bug Fixes

• Fix pinning and networkx in_degree syntax (#793) (208d970)

1.0.0 (2022-07-31)

⚠ BREAKING CHANGES

• update pinnings to python 3.10 (#790)

Documentation

• index and faqs update (#786) (1c2714c)
• notes on updating bioconda-utils (#788) (9078ae3)

Miscellaneous Chores

• update pinnings to python 3.10 (#790) (e4998a9)

0.20.0 (2022-06-23)

Features

• update mulled-test conda to 4.12 (#780) (1934fcb)

Bug Fixes

• create missing config dir (#777) (da0a3e4)
• duplicate logging (#778) (cf36bf4)
• find_best_bioc_version test (#779) (c132758)
• wrong usage of lstrip in ellipsize_recipes (#737) (afb4006)

Documentation

• minor comment (#785) (dadf9ac)
• overhaul front page (#781) (5640a66)
• remove bot from api docs (#774) (e940def)
• update guidelines.rst to mention grayskull (#771) (cdc818e)

0.19.4 (2022-04-30)

Bug Fixes

• fix problematic docs (#769) (44d6d2d)

0.19.3 (2022-04-12)

Bug Fixes

• Don't use conda build --output for finding output file names in the docker container (#766) (bdb6c67)
• https prompts to password, ssh to the rescue (#762) (6282f2d)

0.19.2 (2022-04-07)

Bug Fixes

• don't use conda build to get the output file list (#764) (f6c7b6f)
• Use mambabuild for generating the output file list (43c22aa)

0.19.1 (2022-03-25)

Bug Fixes

• loosen jinja2 requirements to enable installation on OSX (#759) (7ebe4ae)

0.19.0 (2022-03-23)

Features

• update dependencies and switch to boa/mambabuild (#755) (81a5292)

0.18.6 (2022-03-20)

Bug Fixes

• The dependency graph should use the run-time requirements too! (#756) (c49b638)

0.18.5 (2022-02-24)

Bug Fixes

• Update to the most recent conda-build so git_url works again (#753) (4eb01c5)
• Update htslib pinning to 1.15

0.18.4 (2022-02-21)

Bug Fixes

• removing tag hard-coding and use tag_name for docker container (#749) (a8e750c)

0.18.3 (2022-02-21)

Bug Fixes

• hard-code tag to fix docker container (#747) (79946cd)

0.18.2 (2022-02-21)

Bug Fixes

• image tag is screwed up (#745) (3feb6d0)

0.18.1 (2022-02-21)

Bug Fixes

• missing container (#743) (caf6680)

0.18.1

Bug Fixes

• Sync libdeflate pinning with conda-forge

0.18.0 (2022-02-20)

Features

• update conda pinnings and build docs (xref #736) (#740) (53db163)

Bug Fixes

• allow pkg_dir to be empty by creating a real conda channel there (#738) (276873d)