Jerome Kelleher

Ah, we also use this in mspms so that we have strict compatibility with ms. So, we would need to turn it on for this application.

This isn't technically feasible because of our dependency on GSL, so pip install on Windows won't be supported for the foreseeable future. This is semi mentioned in the documentation, but...

We might need to make changes in the tskit-site code, I'm not sure: https://github.com/tskit-dev/tskit-site/blob/main/.github/workflows/build-deploy.yml

I think it's important that we test on both the default dask threads-within-process and an explicit scheduler. Is there something we can do with pytest to run the full test...

To reproduce: ``` NUMBA_DISABLE_JIT=1 python3 -m pytest -v sgkit/tests/test_cohort_numba_fns.py ``` gives ``` E numba.core.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend) E No implementation of function Function() found for...

I'm happy to take your lead here @timothymillar, whatever seems like the most pragmatic way forward would be great.

We agreed this is a pragmatic way forward in the meeting today

Alternatively we could discard the "#CHROM ..." line of the VCF header, since we can reproduce it using the ``sample_id`` variable. Also, it's wrong when we do a subset operation.

As a quick aside @tomwhite, do we ever use the "#CHROM POS.." line from the vcf header? If not I think we should discard it, as there's no real information...

Things that might break: - documentation hosted on GitHub pages: https://pystatgen.github.io/sgkit/latest/ - Workflows (do a grep for pystatgen in this repo?) - Conda-package?