Release 0.6.0

[tomwhite]

It would be good to do a new release soon.

I'd like to include the issues in https://github.com/pystatgen/sgkit/milestone/4.

Are there any other issues we should include?

[hammer]

@benjeffery @timothymillar anything in flight from y'all?

Also @tomwhite anything with the bug tag https://github.com/pystatgen/sgkit/labels/bug that would be easy to squash? The validation tests looking a bit creaky...

[timothymillar]

Nothing new from me in the short term but there are a few variable spec issues that'd be nice to close before 0.6.0:

• Is there a diference between variables dosage and call_dosage #875 (added to milestone)
• genotype_count_spec is inconsistent with VCF spec #911
• Can variable ld_prune_index_to_drop be implimented as a boolean array  #920
• Clarify covariates variable spec in gwas_linear_regression #919

I also still need to document SGKIT_DISABLE_NUMBA_CACHE #869 (added to milestone)

[benjeffery]

Nothing in-flight here, will have a few things for 0.7.0 soon as I'm putting together a tsinfer workflow and polishing up the rough edges.

[tomwhite]

It would be nice to add #669 if we can get it working (added to milestone).

[jeromekelleher]

I think we're good to go now here @tomwhite?

[tomwhite]

I think we're good to go now here @tomwhite?

Yes - I will try to do the release today.

[tomwhite]

Release instructions are here https://github.com/pystatgen/sgkit/issues/817#issuecomment-1091634891

Updating the documentation is now a two step process:

# based on docs.yml
(cd docs; make clean html SPHINXOPTS="-W --keep-going -n")
git clone https://github.com/pystatgen/sgkit.git --branch gh-pages --single-branch gh-pages
mkdir gh-pages/$VERSION
cp -r docs/_build/html/* gh-pages/$VERSION
cd gh-pages
git add $VERSION
git commit -am "Add documentation for $VERSION"
git push origin gh-pages
# check https://pystatgen.github.io/sgkit/$VERSION/
cd ..
rm -rf gh-pages

Then, in the main branch

• Update docs/_static/switcher.json to add the new release version.
• Update docs/changelog.rst to add a date for the new release, and a new section for the next version.
• Commit and push to main

[tomwhite]

Version 0.6.0 is released!

[hammer]

Awesome thank you Tom!