Release 0.1.0a1

This is an umbrella issue for our first release.

This would be an alpha pre-release (suggested version number: 0.1.0a1), which means that users would have to opt in to use it by specifying the --pre flag: pip install --pre sgkit.

Here are some of the tasks we need to do - please suggest more (or say if they are not needed).

• cyvcf2 wheel (should we wait for this?)
• Build release artifacts locally
• Add release number to documentation URL
• Use TestPyPI to test release process
• Update installation instructions for users
• Document release process

Note that these are all about what we need to do to make a release; since it’s a pre-release, the exact set of features doesn’t matter so much.

[tomwhite]

I have built the sgkit test artifacts and released to TestPyPI: https://test.pypi.org/project/sgkit/0.1.0a1/, which should be ready for testing.

You can install the main package with

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple --pre sgkit

(The --extra-index-url is needed since some of sgkit’s dependencies are not on TestPyPI, and pip needs to be told to get them from regular PyPI.)

Extras are installed in a similar way:

pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple --pre 'sgkit[bgen]'
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple --pre 'sgkit[plink]'
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple --pre 'sgkit[vcf]'

The changes needed for the release are in #376. I’ll write up some release instructions too.

BTW I successfully picked up @horta’s cyvcf2 wheels from TestPyPi when installing sgkit[vcf] on Mac, and ran a small VCF test. Thanks for your work on this @horta!

Collecting cyvcf2; extra == "vcf" (from sgkit[vcf])
  Downloading https://test-files.pythonhosted.org/packages/44/ee/816bf6dad913a314dc4fda67f08a8077bd7e14747b2701672e5c3d24f763/cyvcf2-0.20.10-cp37-cp37m-macosx_10_9_x86_64.whl (2.9MB)

[tomwhite]

The 0.1.0.a1 release is now on PyPI and can be installed with

pip install --pre sgkit

Extras can be installed with

pip install --pre 'sgkit[bgen]'
pip install --pre 'sgkit[plink]'
pip install --pre 'sgkit[vcf]'

Documentation is at https://pystatgen.github.io/sgkit/0.1.0a1/.

I’ve updated the release instructions in this issue.