Comments (10)
I don't know that it's a bug to import from a private module that has optional dependencies (which are specified under anndata[test]
) and for that to error.
Seems related to why I had to pin anndata fairly high here: scverse/scanpy#2816
There really is an issue of needing a similar set of helpers, but not wanting these helpers to be public because they're not considered stable.
Also, I really think the immediate answer is to add zarr with a TODO comment to the scanpy test dependencies.
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@ilan-gold is on it. Let’s not have zarr feature-creep its way into scanpy’s minimal test deps. It’s the day of hotfixes it seems
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Once pytest 8.0 is out, we can finally tackle the whole reorganization:
- make the anndata repo use a src layout
- create the public test module (
anndata.test_utils
oranndata.testing
ortesting.anndata
) with an associatedextra
- have scanpy depend on that
- move anndata’s tests out of the package
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I'm not against doing a testing module, though I do think we have to be selective about what goes in it and probably need to test it more thoroughly.
I just don't think that this problem neccesarily needs an immediate bug fix release.
from anndata.
I'm not against doing a testing module, though I do think we have to be selective about what goes in it and probably need to test it more thoroughly.
totally! those are all reasons why we should do it!
I just don't think that this problem neccesarily needs an immediate bug fix release.
I don’t like accumulating hacks, I guess. Doing it the other way means we can forget about it, and can’t merge the minimum-deps branch before we have removed zarr again.
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Could do a .post
release?
I don’t like accumulating hacks, I guess. Doing it the other way means we can forget about it, and can’t merge the minimum-deps branch before we have removed zarr again.
I'm not sure how that PR would be more affected by this?
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I've checked the current 0.10.x branch against scanpy, I think a post
branch seems appropriate here. I can make one from 08e7b94.
Any objection?
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I think I don’t fully understand. If you just mean calling the release .post
instead of giving it a new patch version number, sure!
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Huh: https://github.com/scverse/anndata/actions/runs/7670757953
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Guess it's just flaky somehow?
https://github.com/scverse/anndata/actions/runs/7670870992/job/20907984190
Anyways, release made
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Related Issues (20)
- `to_df` docstrings
- dask.array.store but with anndata schema HOT 1
- Indexing With a Dask Array HOT 5
- adata.raw = adata HOT 1
- GPU CI tests failing HOT 2
- Add working `GroupStorageType` type annotation
- 0.10.6 - Cannot write files due to implicit conversion to str dtype. HOT 2
- Saving .h5ad with pd.Series in .uns results in IORegistryError HOT 3
- `read_elem_as_dask` HOT 8
- `FileNotFoundError: [Errno 2] No such file or directory: 'llvm-config'` on CI HOT 2
- Upcoming Scipy 1.13 incompatible with file-backed sparse matrices
- CZI files' `var` count changd
- `/` in column names makes AnnData Zarr object unreadable on windows HOT 12
- String indexes in var lead to UserWarning HOT 1
- Move tests out of the package
- Refactor `BaseCompressedSparseDataset` and subclasses to remove `backed_{csr,csc}_matrix`
- concat_on_disk should use int64 indptrs by default so that it can concatenate large files HOT 4
- TypeError: Can't implicitly convert non-string objects to strings HOT 4
- Error concatenating scRNA with visium dataset
- Error: Expected a python object, received a character HOT 1
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