Add to_scipy_sparse/from_scipy_sparse xarray accessor methods - #1621
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aroaxinping wants to merge 3 commits into
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Add to_scipy_sparse/from_scipy_sparse xarray accessor methods#1621aroaxinping wants to merge 3 commits into
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Converts between a 2-dimensional DataArray and a scipy.sparse matrix via the sparse package's COO format. Adds sparse as a new optional extra, following the same try/except pattern already used for biopython/tqdm in biology.py/chemistry.py.
CI failed because pixi.lock was out of sync with the new sparse optional-dependency entries in pyproject.toml. Regenerated the lock file, and added a dedicated pixi feature/environment for sparse (mirroring biology/chemistry/engineering/spark), since the default test environments don't install optional domain packages. Also added the same skipif guard used in tests/biology and tests/chemistry, so the new tests skip cleanly instead of erroring in environments where sparse isn't installed.
Same issue as the pytest failures: the docstring examples for to_scipy_sparse/from_scipy_sparse call sparse-backed code directly, so they fail with NameError in environments where sparse isn't installed (the default test environments, matching biopython/tqdm). Marked the affected lines +SKIP, same as join_fasta's docstring in biology.py.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## dev #1621 +/- ##
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- Coverage 87.56% 85.82% -1.74%
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Files 95 125 +30
Lines 6819 9928 +3109
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+ Hits 5971 8521 +2550
- Misses 848 1407 +559 🚀 New features to boost your workflow:
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Closes #636
What
Adds
to_scipy_sparseandfrom_scipy_sparseas xarray DataArrayaccessor methods, converting between a 2D DataArray and a
scipy.sparsematrix via thesparsepackage's COO format.Heads up: new optional dependency
This pulls in
sparseas a new optional extra (pip install pyjanitor[sparse]) — nothing changes for anyone who doesn't use it.Followed the same try/except pattern already used for biopython/tqdm
in biology.py/chemistry.py: without
sparseinstalled,import janitorstill works fine, you just get a warning, and only callingthe new functions raises an error.
Notes
from_scipy_sparsewasn't in the original issue, only theto_direction had a sketch. I built it as a thin wrapper around the
existing
clone_using, since a scipy sparse matrix generally won'tshare
da's shape — happy to change the API if you had somethingdifferent in mind.
sparseinstalled either way,import janitordoesn't break.