ENH allow initializing a DeseqDataSet from an AnnData object

[BorisMuzellec]

Reference Issue or PRs

Fixes #94

What does your PR implement? Be specific.

This PR provides the option to initialize an DeseqDataSet by passing an AnnData as an argument.

[grst]

You may want to make those keyword-only arguments. Also all the configuration arguments that come after are unlikely to be called by position. Making them keyword-only saves you from breaking API compatibility should you decide to add more or reorder them in the future.

For counts/clinical, another option would be to remove them entirely. After all, it's easy to do

adata = AnnData(counts, obs=clinical)

[BorisMuzellec]

Thank for this helpful suggestion. I have made all arguments keyword-only.

[maikia]

LGTM. Perhaps we could also start a CHANGELOG (it could already be included within this PR).
This change could potentially cause errors in existing scripts if the version is being updated

[BorisMuzellec]

Thanks! I'm merging this PR.

Perhaps we could also start a CHANGELOG (it could already be included within this PR).

@maikia there is already a changelog being written at each new PyPI release, accessible through the github tags. Do you think this enough, or should we create a dedicate file?