Release 0.2.1 checklist

[andrewkern]

Checklist for doing a new release, copied from the last one (#1319):

• Update Changelog for new release via PR
• Create a release using the GitHub UI. This creates the appropriate tag.
• Locally, git fetch upstream --tags, git checkout upstream/main
• python3 -m build (note: you need the build and twine modules installed)
• python3 -m twine upload dist/[stuff] for instance python -m twine upload dist/{stdpopsim-0.2.1a1.tar.gz,stdpopsim-0.2.1a1-py3-none-any.whl} (note: this now uses "API tokens" from PyPI possibly stored in ~/.pypirc to upload; see here for the ever-changing procedure)
• check on pypi that the update actually worked
• check docs build succeeded (also check the docs URL substituting the release tag where latest or stable usually is)
• upload to zenodo
• update version and DOI in CITATION.cff (once added)
• conda-forge will do an automatic PR in the stdpopsim-feedstock repo; winni2k says:

"The key things I checked were that the version number is correct, the SHA sum has changed, and that the build number is reset to zero. Any other problems should be caught by the automated build system."

Post-release:

• make copy of this issue for the next release

Reference: https://packaging.python.org/tutorials/packaging-projects/, tskit-dev/pyslim#292

[petrelharp]

Here is the list of issues to do: https://github.com/popsim-consortium/stdpopsim/milestone/4

Major topics:

• ensembl build!!: What to do about shifting ensembl build? #1521,
• move stdpopsim/ext/ to just stdpopsim/: Move contents of stdpopsim/ext into stdpopsim #1373
• DFE QC: AraTha DFE #1321, QC for AraThal DFE #1344, QC for LogNormalDFE (HomSap) #1484, QC for new DFE: "generic" human DFE #1507
• SLiM support: require SLiM version 4.0++ #1343, SLiM Support in Windows #1563
• documentation/catalog info: Various issues in the docs to be resolved by the "selection release" #1403, add ploidy line in species catalog description #1449, include parameter values in catalogue for DFEs #1509, Add detail about SLiM install to installation docs #1541
• misc bugs involving breaking changes: When using left/right, output coordinate system is relative to start of contig #1404 (which should solve No variants are simulated in zero-recombination region of chr22 #1422), bug in adding mutations to the recapitated portion of the tree sequence #1496, Restarting simulations in SLiM engine (community.allScriptBlocks.active property) #1558
• usability and testing: Error with generic StrAga contig in msprime engine, due to average GC tract length #1405, load QC models only when the tests are run #1418, CLI returning haploid samples, API diploid #1451, Add per-chromosome ploidy checks to test stubs in maintenance scripts #1467, Pandas warning: Calling int on a single element Series is deprecated and will raise a TypeError  #1493, time units mismatch warning #1549, add test that nothing is simulated outside of left-right on both msprime and slim #1577
• check in on versions of requirements

[nspope]

also #1558

[petrelharp]

Also TODO: I have dealt with #1404 and merged it, but someone else ought to review the code (whoops). Done: thanks, @nspope.

[andrewkern]

I think #1646 will deal with the ensembl issues