Fix notebook bugs and dependency issues #281
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
In the original cell the following code was specified:
```
data = snap.read_dataset(
"colon.h5ads",
update_data_locations = {"colon_transverse_SM-CSSDA": "colon_transverse_SM-CSSDA.h5ad"},
)
data
```
This raises the following error:
```
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
Cell In[25], line 1
----> 1 data = snap.read_dataset(
2 "colon.h5ads",
3 update_data_locations = {"colon_transverse_SM-CSSDA": "colon_transverse_SM-CSSDA.h5ad"},
4 )
5 data
TypeError: read_dataset() got an unexpected keyword argument 'update_data_locations'
```
Looking at the `read_dataset` function definition in pyanndata-0.3.2:
https://docs.rs/pyanndata/0.3.2/pyanndata/anndata/fn.read_dataset.html
It looks like the arg `update_data_locations` should actually be
`adata_files_update`.
While running SnapAtac2 notebooks the following warning was fairly frequently encountered when running `snap.pp.scrublet()`: ``` /usr/local/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024. ``` It looks like the `anndata` project plans to deprecate and completely remove the `dtype` argument to `AnnData` instantiation somewhat soon. See: scverse/anndata@85162c7 See also: scverse/anndata#1126 This commit removes the `dtype` argument from `AnnData` instantiation as it will be removed in future versions of `AnnData`.
This commit adds some additional dependencies so that more notebooks under `docs/tutorials` can run properly when installing with `pip install snapatac2[recommend]`. In future work, it may make sense to remove dependencies like `scanorama` and `harmonypy` from `extra` `[project.optional-dependencies]` as `scanpy` already shares the exact same dependencies and it may be easier for future maintenance for `scanpy` to deal with versioning and pinning.
Codecov ReportAll modified and coverable lines are covered by tests ✅
❗ Your organization needs to install the Codecov GitHub app to enable full functionality. Additional details and impacted files@@ Coverage Diff @@
## main #281 +/- ##
=======================================
Coverage 98.23% 98.23%
=======================================
Files 4 4
Lines 227 227
=======================================
Hits 223 223
Misses 4 4 ☔ View full report in Codecov by Sentry. |
|
Thank you for the pull request! I'll address the extra package issue. |
kaizhang
pushed a commit
that referenced
this pull request
Apr 1, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR is partially in response to:
#277
Notes:
atlas.ipynbrequires a bit too much data to download for me to testQuestions:
scanorama>=1.7.3andharmonypy>=0.0.9. I see them inextraunder[project.optional-dependencies]but would it make more sense to remove them fromextraand just keep the ones I newly added underrecommend? Or would you prefer the opposite (move packages likemagic-imputetoextra)?scanpymaintainers manage these dependences? (See: https://github.com/scverse/scanpy/blob/3ceb740ba37effc44f42ecdb884cef86a38d4346/pyproject.toml#L138-L151) Or are there strong reasons to havesnapatac2manage these dependencies (even underextra)?