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Add tskit CLI #374

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benjeffery
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Here's a sketch of how the tskit CLI could look. I'll add tests once were happy with it.

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coveralls commented May 9, 2025 •
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Coverage Status

coverage: 98.088% (-0.05%) from 98.142%
when pulling 8e8bd98 on benjeffery:tskit-cli
into 6708eb1 on sgkit-dev:main.

jeromekelleher
jeromekelleher reviewed May 9, 2025
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Looks good - let's ditch ploidy though, it's not worth the complexity.

bio2zarr/cli.py Outdated
@click.command(name="convert")
@click.argument("ts_path", type=click.Path(exists=True))
@click.argument("zarr_path", type=click.Path())
@click.option(
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Let's not bother with ploidy - we only support tskit files that have individuals here. Older files can go through the tskit VCF route, or just add the appropriate individuals.

bio2zarr/cli.py Outdated
setup_logging(verbose)
check_overwrite_dir(zarr_path, force)

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So, we don't need to bother importing tskit here or specifying the individuals_nodes, we just pass in the ts_path

@benjeffery benjeffery force-pushed the tskit-cli branch 2 times, most recently from 56497d4 to c3606b2 Compare May 9, 2025 09:27
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Ok, pushed a new commit that makes individuals_nodes an optional argument to the convert function, defaulting to using ts.individuals_nodes. An error is fired if the default is used and are no individuals.

The CLI code now doesn't need to import tskit and ploidy is removed.

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Great, let's build on this

@benjeffery benjeffery force-pushed the tskit-cli branch 5 times, most recently from fca4836 to db316cf Compare May 9, 2025 13:06
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Ok, tests added and other tests modified for new individuals_nodes behaviour.

@benjeffery benjeffery marked this pull request as ready for review May 9, 2025 13:15
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Need to cover num_individuals == 0 error, good to merge after that

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Test added

@jeromekelleher jeromekelleher mentioned this pull request May 9, 2025
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jeromekelleher
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@jeromekelleher jeromekelleher enabled auto-merge May 9, 2025 16:15
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Looks like this needs a rebase, we've got a conflict

@benjeffery benjeffery force-pushed the tskit-cli branch 2 times, most recently from b3af8d0 to dcb6629 Compare May 10, 2025 23:22
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@benjeffery @coveralls @jeromekelleher