3.10.2 - fixes to phasing, multiprocessing and flag lookup mode

[3.10.2]

Fixed

• Add scoring normalisation for flag lookup mode (#177)
• Fix crash on test for missing annotation key for phased mode (#178)
• Bugfixes related to multiprocessing stability and error handling (#183 and #186)
• Removed unused dependency (#182)

What's Changed

• Fix #176 - flag lookup mode by @dnil in #177
• Fix phasing? by @dnil in #178
• Compound Scoring Multiprocessing Bugfixes by @torbjorgen in #183
• Remove unused dependency vcftoolbox by @vtalos in #182
• Version 3.10.2 - bump by @dnil in #186

New Contributors

• @vtalos made their first contribution in #182

Full Changelog: 3.10.1...3.10.2

Stable sorts to help container testing

[3.10.1]

Fixed

• Documentation formatting for more modern mkdocs (pages to nav) (#168)
• Stable sort in bioconda (BusyBox sort) not recognizing long options (#170)
• Unstable Annotation= order in genmod annotate --regions (#173)

Bugfixes to sorting, chrM and empty files. Allow modern python, and uv with hatchling build system.

[3.10]

Changed

• Use uv with hatchling to build and publish (#104)
• Automation for Docker publish and mkdocs githubio (#161)

Fixed

• The optional fields Source and Version are allowed in the VCF header(#106)
• Released the constraint on Python 3.8 (collections, pkg_resources to importlib, tests) (#142)
• Update annotation examples (#144)
• Updated documentation with warning about compounds only being scored within the first family in the VCF (#151)
• Fixed sorting of variants (#152)
• genmod annotate for mitochondrial variants when using the chrM notation (#157)
• Fix linting issues (#154)
• genmod models adds headers to VCF even if it contains no variants (#160)

3.9

What's Changed

• Ensure chrX and X are treated equally by @fellen31 in #135
• Add GitHub Actions workflows for PyPI and CHANGELOG by @fellen31 in #136
• Add parameters for penalty and threshold by @Jakob37 in #138
• Update readme by @dnil in #140
• Bump version to 3.9 by @dnil in #139

New Contributors

• @Jakob37 made their first contribution in #138
• @dnil made their first contribution in #140

Full Changelog: 3.8.3...3.9

3.8.3

What's Changed

• Fix unstable variants in models output by @fellen31 in #134

New Contributors

• @fellen31 made their first contribution in #134

Full Changelog: 3.8.2...3.8.3

3.8.2

What's Changed

• setup.py: Lockdown genmod, limit compatibility to python v3.8 by @torbjorgen in #120
• Export Rankscore as Float Type by @torbjorgen in #122
• setup.py: Set version 3.8.2 by @torbjorgen in #123

Full Changelog: 3.8.1...3.8.2

3.8.1

What's Changed

• setup py uplift requirements by @torbjorgen in #117
• setup.py: Set version 3.8.1 by @torbjorgen in #118

Full Changelog: 3.8.0...3.8.1

3.8.0

What's Changed

• Rankscore normalization by @torbjorgen in #108
• CHANGELOG, setup.py changes for v3.8.0 by @torbjorgen in #114

Full Changelog: 3.7.4...3.8.0

3.7.4

What's Changed

• set abstract_sockets_supported to False by @ramprasadn in #111

New Contributors

• @ramprasadn made their first contribution in #111

Full Changelog: 3.7.3...3.7.4

Updates click dependency

Use click < 7.0