add milo-edger extra
#874
add milo-edger extra
#874
Conversation
The `da_nhoods` function of `pertpy`'s `milo` implementation defaults to `solver=edger` which in turn requires `rpy2` (and the `edgeR` R package) as a dependency not listed so far in `pyproject.toml`. This commit addresses this by adding the `[milo]` target with that optional dependency. --- fixes issue #873
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #874 +/- ##
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- Coverage 73.54% 72.01% -1.54%
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Files 48 48
Lines 5613 5613
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- Hits 4128 4042 -86
- Misses 1485 1571 +86
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I'll have a look at this next week, sorry. |
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No worries. This is hardly a priority. 😉 |
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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Eieiei this PR is still open. I'll finalize and merge this in about 10 days. Sorry! |
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Like I said: No rush. This is more to make it easier for people new to pertpy that install via pip/conda and then try running the milo example. |
Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
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like this or? |
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LGTM but two test are failing. The first one looks like an unrelated network/upstream related issue. The second one concerns milo. Maybe an API change? |
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I'm looking into it. I changed the default from pydeseq2 but we're passing 'edger' explicitly as solver there. I'll figure it out and merge then. |
3 participants
PR Checklist
docsis updatedDescription of changes
The
da_nhoodsfunction ofpertpy'smiloimplementation defaults tosolver=edgerwhich in turn requiresrpy2(and theedgeRR package) as a dependency not listed so far inpyproject.toml.Technical details
This commit addresses this by adding the
[milo]target with that optional dependency.Additional context
fixes issue #873