Release 0.2.5
#934
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Release 0.2.5
#934
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Add test class for `scvelo/core/_anndata.py::clean_obs_names`.
* Rename input arguments from `data` to `adata`, `copy` to `inplace`, `ID_length` to `id_length`, `base` to `alphabet`. * Rename variables to something more meaningful and use snake as well as lower case, consistently. * Make use of Pandas functionality. * Use regex expression.
* Move `scvelo/core/tests` to `tests/core` Moves unit tests `scvelo/core/tests` to `tests/core`. This will, for example, prevent installation files becoming large when including data or ground truth figures. * Add `tests/__init__.py` Makes `tests/` a package. This is needed to e.g. import from `tests/core` later on. * Update pytest.ini Remove `scvelo` from testpaths.
* Add `multiply` Adds function to calculate the element-wise product of two arrays or an array and a sparse matrix. * Fix and refactor `filter_genes` The original implementation fails when `adata.layers['unspliced']` is sparse but `adata.layers['spliced']` dense. The element-wise multiplication is now performend using `multiply`.
* Fix and update docstrings Update docstrings to follow codebase style. * Add option to add columns to adata.obs * Adds `obs_col_names`, `min_obs_cols`, `max_obs_cols` to composite strategy `get_adata`. Using `obs_col_names`, the column names can be set manually, the other arguments allow setting the minimum and maximum number of columns generated. * Updates unit tests to encounter for and test changes. * Add option to add columns to adata.var * Adds `var_col_names`, `min_var_cols`, `max_var_cols` to composite strategy `get_adata`. Using `var_col_names`, the column names can be set manually, the other arguments allow setting the minimum and maximum number of columns generated. * Updates unit tests to encounter for and test changes.
* Delete `pl.py`, `pp.py` and `tl.py`. * Update `__init__.py` to no longer rely on `pl.py`, `pp.py` and `tl.py`.
* Update `get_modality` Support passing `None` for argument `modality`. In this case, `adata.X` is returned. * Add `TestGetModality::test_modality_equals_none` Add unit test to check that correct modality is extracted if `None` is passed for `modality` in `get_modality`.
* Rename `layer` to `modality` Rename argument `layer` to `modality` in `get_size`. This unifies naming convention for the argument across the code base and prepares generalizing `get_size` to arbitrary modalities. * Generalize `get_size` to arbitrary modalities This allows calculating the size per observation for any modality, from `adata.X`, `adata.layers` or `adata.obsm`. * Update docstrings
Unit tests `scvelo.core._anndata.py::obs_df`.
Unit tests `scvelo.core._anndata.py::var_df`.
The addition assert statement checks that the index of the returned data frame is correct.
Reduce maximum size of generated AnnData objects in some tests.
* Run tests on ubuntu-latest using both Python 3.7 and 3.8. * Increase verbosity of pytest. * Add timeout to tests.
Add files and directories created by `pytest-cov`.
In TestShowProportions::test_layers_not_specified, layers should not be specified but `layers=None` passed instead.
Add unit tests to `TestMakeDense` and `TestMakeSparse` when `modality` is passed as a string.
* Add `varm` to AnnData strategy Strategy can now also add entries to `adata.varm`. This is tested by extending the existing unit tests. * Set `max_obs` and `max_vars` to `5` This is an attempt to make the unit tests not in the CI on GitHub due to a time out error by Hypothesis.
* Update `ci.yml` Remove testing of dataset download from job `test`. Instead, a new job `test-dataset-downloads` is added. * Update `ci.yml` Print execution time of 25 slowest tests. * Update `test_datasets.py` Skip `test_datasets.py::TestDataSets` if Python version is not 3.8 and OS is not Linux.
* Update `requirements-dev.txt` Add `pytest-cov` to the installed libraries. * Update `ci.yml` Update how dependencies are installed in the `test` job.
To prevent test failure due to exceeding deadlines, the default deadline of Hypothesis is increased to 500 milliseconds when running the tests in the CI.
* Add `test_neighbors.py` Add file to host unit tests for `preprocessing/neighbors.py`. * Add `TestGetNeighs` * Add `TestGetNNeighs` * Add `TestGetDuplicateCells` * Add `TestRemoveDuplicateCells` * Add preprocessed adata for testing Add preprocessed versions of `dentategyrus_50obs.h5ad`, `dentategyurs_100obs.h5ad`, `pancreas_50obs.h5ad`, and `pancreas_100obs.h5ad`. * Add fixtures for preprocessed datasets Add fixtures to use preprocessed datasets in unit tests. * Add fixture `adata` The fixture `adata` is used to easily load raw or preprocessed datasets in unit tests. This allows running one and the same unit test on all available datasets. * Add `TestSelectConnectivities` Add unit tests for `select_connectivities`. * Add `TestSelectDistances` Add unit tests for `select_distances`. * Add `TestSetDiagonal` Add unit tests for `set_diagonal`. * Add `TestNeighborsToBeRecomputed` Add unit tests for `neighbors_to_be_recomputed`. * Add `TestVerifyNeighbors` Add unit tests for `verify_neighbors`. * Add `TestGetConnectivities` and accompanying files Add unit tests for `get_connectivities` and saved CSR matrices to verify results. * Add `TestGetCsrFromIndices` Add unit tests for `get_csr_from_indices`. * Add `TestComputeConnectivitiesUmap` Add unit tests for `compute_connectivities_umap` * Add `TestGetRep` Add unit tests for `_get_rep`. * Add `TestSetPCA` Add unit tests for `_set_pca`. * Add `TestGetHnswNeighbors` Add unit tests for `_get_hnsw_neighbors` and corresponding CSR matrices saved using `.npz` format. * Add `TestGetScanpyNeighbors` Add unit tests for `_get_scanpy_neighbors` and corresponding CSR matrices saved using `.npz` format. * Add `TestGetSklearnNeighbors` Add unit tests for `_get_sklearn_neighbors` and corresponding CSR matrices saved using `.npz` format. * Add `TestNeighbors` Adds unit tests for the function `neighbors`.
* Add `test_moments.py` Add file to host unit tests of functions in `moments.py`. * Add `TestGetMoments` Add unit tests for `get_moments` and corresponding ground truth moments saved using `.npy` format. * Add `TestSecondOrderMomentsU` Add unit tests for `second_order_moments_u`. * Add `TestSecondOrderMoments` Add unit tests for `second_order_moments` and corresponding moments saved using `.npy` format. * Add `TestMagicImpute` Add unit tests for `magic_imput` and corresponding imputed data saved using `.npy` format. * Add `TestMoments` Add unit tests for `moments` and corresponding first order moments saved using `.npy` format. * Update `requirements-dev.txt` Add `magic-impute` to run unit tests on CI.
* Update `DynamicsRecovery` Fix parameter inference to not fit scaling when `fit_scaling=False`.
Details workaround to issue where `pip install -e '.[dev]'` leads to errors on Windows.
* Fix missing write_key for embedding stream plot. * Set save instead of wire_key when saving embedding stream plot.
* Update `core/_anndata.py` Update how Pandas displayed precision is set. * Update `core/_anndata.py` Add TODO comment to add a unit test to test the `precision` argument.
* Update `CONTRIBUTING.rst` [ci skip] Update branch name convention. * Update `docs/requirements.txt` [ci skip] Pin `Jinja` version. * Update `docs/source/conf.py` [ci skip] Update `add_stylesheet` with `add_css_file`. The former is deprecated. * Fix typo in `index.rst` [ci skip] * Fix link to bone marrow dataset [ci skip] * Fix `velocity_embedding` docs [ci skip]
* Add `_key_contributors.rst` [ci skip] Add file with key contributors and their roles. * Show key contributors on index page [ci skip]
* Add `core/_utils.py` * Add `core/_utils.py::deprecated_arg_names` Modify wrapper from Scanpy to replace old with new keyword argument. The wrapper is modified s.t. `copy=True` corresponds to `inplace=False`, and vice versa. * Make `deprecated_arg_names` importable from `core` * Update import of `deprecated_arg_names` Import local version instead of the Scanpy version s.t. the keyword argument `copy` is handled correctly.
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FYI, @adamgayoso. |
Remove reference to `develop` branch as it will be removed in the next release.
* Fix `TestLinearRegression::test_perfect_fit` Replace `array` strategy to generate `x` with `sampled_from`. * Fix `TestLinearRegression::test_perfect_fit_2d` Replace `array` strategy to generate `x` with `sampled_from`.
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Changes
ValueErrorif necessary.get_mean_varuses the same size parameter for mean and variance.tests/module outside ofscvelo/.Bug fixes
filter_genesnow works withadata.layers['unspliced']being sparse andadata.layers['spliced']dense.show_proportionsactually considers the layer"ambiguous"if present.csr_vcorrcoef.get_mean_varto work with sparse input andignore_zeros=True.optimization.py::get_weightto work with numeric, non-integer values.fit_scaling=False.get_df.