Factor out inference routines #191
Conversation
adamgayoso
requested review from
BorisMuzellec,
maikia,
arthurPignetOwkin and
mandreux-owkin
as code owners
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As an aside, it would be helpful to add https://pre-commit.ci/ as a bot so that PRs can be autofixed (and more generally, following the scverse cookiecutter https://github.com/scverse/cookiecutter-scverse) |
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Just want to again mention the pre-commit here https://github.com/scverse/cookiecutter-scverse/blob/main/%7B%7Bcookiecutter.project_name%7D%7D/.pre-commit-config.yaml Ruff is really fast and adoption is rising. It can also fix a lot of the things I'm fixing myself right now :) |
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
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@BorisMuzellec I'm not sure how strongly you feel about the test_docstrings file now that ruff should be handling everything. It's failing due to no extended summary |
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@BorisMuzellec it will probably also help the project to use readthedocs pull request builds https://docs.readthedocs.io/en/stable/guides/pull-requests.html And then building docs can be previewed per PR and removed from the tests. We had done this in scvi |
pydeseq2/inference.py
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| ndarray | ||
| Estimated mean. | ||
| """ | ||
| pass |
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Ridiculous comment: not sure pass is needed (since there is a docstring)
pydeseq2/dds.py
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| ) | ||
| for i in self.non_zero_idx | ||
| ) | ||
| MLE_lfcs_, mu_, hat_diagonals_, converged_ = self.inference.irls( |
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MLE -> mle for case convention ?
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Thanks a lot @adamgayoso for this PR, and sorry for the long wait! I'm finally merging this.
Fixes #187