SingleCellExperiment 0.5.3__tar.gz → 0.5.5__tar.gz

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Files changed (50) hide show
  1. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.pre-commit-config.yaml +1 -1
  2. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/PKG-INFO +2 -2
  3. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/PKG-INFO +2 -2
  4. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/SingleCellExperiment.py +25 -1
  5. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.coveragerc +0 -0
  6. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.github/workflows/publish-pypi.yml +0 -0
  7. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.github/workflows/run-tests.yml +0 -0
  8. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.gitignore +0 -0
  9. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.readthedocs.yml +0 -0
  10. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/AUTHORS.md +0 -0
  11. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/CHANGELOG.md +0 -0
  12. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/CONTRIBUTING.md +0 -0
  13. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/LICENSE.txt +0 -0
  14. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/README.md +0 -0
  15. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/Makefile +0 -0
  16. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/_static/.gitignore +0 -0
  17. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/authors.md +0 -0
  18. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/changelog.md +0 -0
  19. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/conf.py +0 -0
  20. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/contributing.md +0 -0
  21. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/index.md +0 -0
  22. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/license.md +0 -0
  23. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/readme.md +0 -0
  24. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/requirements.txt +0 -0
  25. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/docs/tutorial.md +0 -0
  26. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/pyproject.toml +0 -0
  27. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/setup.cfg +0 -0
  28. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/setup.py +0 -0
  29. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/SOURCES.txt +0 -0
  30. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/dependency_links.txt +0 -0
  31. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/not-zip-safe +0 -0
  32. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/requires.txt +0 -0
  33. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/top_level.txt +0 -0
  34. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/__init__.py +0 -0
  35. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/_combineutils.py +0 -0
  36. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/_ioutils.py +0 -0
  37. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/io/__init__.py +0 -0
  38. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/io/h5ad.py +0 -0
  39. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/io/tenx.py +0 -0
  40. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/conftest.py +0 -0
  41. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/data/adata.h5ad +0 -0
  42. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/data/mocks.py +0 -0
  43. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/data/tenx.sub.h5 +0 -0
  44. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce.py +0 -0
  45. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce_combine_cols.py +0 -0
  46. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce_combine_rows.py +0 -0
  47. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce_io.py +0 -0
  48. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce_methods.py +0 -0
  49. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tests/test_sce_slice.py +0 -0
  50. {singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/tox.ini +0 -0
{singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/.pre-commit-config.yaml RENAMED
@@ -33,7 +33,7 @@ repos:
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  - repo: https://github.com/astral-sh/ruff-pre-commit
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  # Ruff version.
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- rev: v0.8.4
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+ rev: v0.8.6
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  hooks:
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  - id: ruff
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  args: [--fix, --exit-non-zero-on-fix]
{singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.2
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  Name: SingleCellExperiment
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- Version: 0.5.3
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+ Version: 0.5.5
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  Summary: Container class for single-cell experiments
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  Home-page: https://github.com/BiocPy/SingleCellExperiment
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  Author: jkanche
{singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/SingleCellExperiment.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.2
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  Name: SingleCellExperiment
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- Version: 0.5.3
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+ Version: 0.5.5
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  Summary: Container class for single-cell experiments
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  Home-page: https://github.com/BiocPy/SingleCellExperiment
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  Author: jkanche
{singlecellexperiment-0.5.3 → singlecellexperiment-0.5.5}/src/singlecellexperiment/SingleCellExperiment.py RENAMED
@@ -1050,8 +1050,32 @@ class SingleCellExperiment(RangedSummarizedExperiment):
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  """
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  obj = super().to_anndata()
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+ from delayedarray import (
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+ DelayedArray,
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+ is_sparse,
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+ to_dense_array,
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+ to_scipy_sparse_matrix,
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+ )
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+
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  if self.reduced_dims is not None:
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- obj.obsm = self.reduced_dims
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+ nrdims_ = OrderedDict()
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+ for dim, mat in self._reduced_dims.items():
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+ if isinstance(mat, DelayedArray) or issubclass(type(mat), DelayedArray):
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+ if is_sparse(mat):
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+ warn(
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+ "Converting delayedarray into sparse, may require more memory",
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+ RuntimeWarning,
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+ )
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+
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+ mat = to_scipy_sparse_matrix(mat)
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+ else:
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+ warn(
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+ "Converting delayedarray into dense, may require more memory",
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+ RuntimeWarning,
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+ )
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+ mat = to_dense_array(mat)
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+ nrdims_[dim] = mat
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+ obj.obsm = nrdims_
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  if self.row_pairs is not None:
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  obj.varp = self.row_pairs