v0.3.2

What's Changed

• Remove hard scvi-tools dependency by @michalk8 in #1185
• Unpin scikit-learn by @Zethson in #1194
• Update scatter and update_axes by @WeilerP in #1205
• Update plotting/utils.py::hist by @WeilerP in #1217
• Update VELOVI::train by @WeilerP in #1219
• Update release.yml by @WeilerP in #1221
• Remove debug.py by @WeilerP in #1222
• Update pyptoject.toml by @WeilerP in #1224
• Update pyproject.toml by @WeilerP in #1226

New Contributors

• @Zethson made their first contribution in #1194

Full Changelog: v0.3.1...v0.3.2

v0.3.1

• Fixes plotting.velocity_graph

v0.3.0

Release 0.3.0

• Add VELOVI
• Add method to infer transcription rates based on metabolic labeling data
• Fix bugs s.t. code runs with latest versions of numpy, pandas, matplotlib

v0.2.5

Release `0.2.5` (#934)

* Add .editorconfig (#529)

* Add TestCleanObsNames (#530)

Add test class for `scvelo/core/_anndata.py::clean_obs_names`.

* Refactor `clean_obs_names` (#532)

* 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 unit tests to `tests/` (#535)

* 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.

* Fix and refactor `filter_genes` (#537)

* 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`.

* Add column generation for adata.obs/.var (#544)

* 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.

* Add unit tests for `cleanup` (#548)

* Add method `_subset_columns` to `TestBase`

Adds method to sample from column names in `adata.obs` and `adata.var`.

* Add `TestCleanup`

Adds test class to unit test `scvelo/core/_anndata.py::cleanup`.

* Fix TestCleanup::test_cleanup_some (#550)

* Refactor `cleanup` (#552)

* Rename argument `data` to `adata`

* Rename argument `copy` to `inplace`

* Update type hint in `cleanup`

* Rename variables

Rename variables to use more informative names.

* Add `TestGetInitialSize` (#554)

* Add `TestGetSize` (#556)

* Refactor module import (#560)

* 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` (#567)

* 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`.

* Refactor and generalize `get_size` (#569)

* 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

* Add TestObsDf (#579)

Unit tests `scvelo.core._anndata.py::obs_df`.

* Add TestVarDf (#583)

Unit tests `scvelo.core._anndata.py::var_df`.

* Update TestObsDf (#585)

The addition assert statement checks that the index of the returned data
frame is correct.

* Fix typo in default layer names (#587)

* Add `TestShowProportions` (#589)

Unit tests `scvelo.core._anndata.py`::show_proportions`.

* Add `TestSetInitialSize` (#591)

* Reduce maximum number of obs/vars (#593)

Reduce maximum size of generated AnnData objects in some tests.

* Update ci.yml (#546)

* Run tests on ubuntu-latest using both Python 3.7 and 3.8.

* Increase verbosity of pytest.

* Add timeout to tests.

* Update `.gitignore` [ci skip] (#595)

Add files and directories created by `pytest-cov`.

* Update `_anndata.py` (#596)

Change order of default layers to match temporal ordering in biological
process.

* Fix TestShowProportions (#598)

In TestShowProportions::test_layers_not_specified, layers should not be
specified but `layers=None` passed instead.

* Update `TestCleanObsNames` (#600)

Check that `inplace` argument is working correctly.

* Test modality passed as string (#602)

Add unit tests to `TestMakeDense` and
`TestMakeSparse` when `modality` is passed as a string.

* Fix `test_not_existing_modality` (#605)

Generate layer names with at least two characters to exclude the case
`layer='X'`.

* Refactor unit test for `l2_norm` (#607)

Converts unit test to a test class. 2D arrays and sparse matrices are
now generated as well to increase coverage to 100%.

* Add `varm` to AnnData strategy (#609)

* 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.

* Add `TestMerge` (#611)

Add test class to unit test `scvelo/core/_anndata.py::merge`.

* Update `TestVarDf` (#615)

Reduce maximum size of generated AnnData.

* Catch error in steady state calculation (#614)

* Fix steady state calculation

Raise ValueError when `beta` and `gamma` are not positive.

* Update `TestSplicingDynamics`

Add unit test to verify ValueError is raised when calculating steady
states with inadmissible parameter values.

* Fix AnnData strategy (#616)

Reset `min_varm` and `max_varm` if `varm_keys` is specified.

* Update `TestSplicingDynamics` (#618)

Add unit tests to
* test 2d time points,
* verify correct initial states are set/returned,
* verify correct steady states are returned.

* Fix `TestCleanup` (#620)

* Update `DynamicsBase` (#622)

Remove redundant return statements to increase test coverage. The
abstract methods cannot be tested.

* Add `TestGetDf` (#624)

Unit tests for `scvelo/core/_anndata.py::get_df`.

* Add module `datasets` (#636)

* Add module `datasets`

The file `datasets.py` is moved to the module and renamed to
`_datasets.py`.

* Deprecate `pancreatic_endocrinogenesis`

* Add `datasets/_simulate.py`

Adds file `datasets/_simulate.py` and moves `simulation`, `unspliced`,
`spliced` and `vectorize` from `datasets/_datasets.py` to the new file.

* Cleanup `datasets/_datasets.py` (#638)

* Sort functions alphabetically

* Add TODO

* Fix `DeprecationWarning` [ci skip] (#640)

* Add argument `file_path` (#642)

Allow saving/reading datasets to/from custom paths.

* Fix gillespie simulation (#644)

* Add unit tests for `scvelo.datasets` (#646)

* Add `test_datasets.py`

Add unit tests for datasets accessible through scvelo.

* Add `test_simulate.py`

Add unit tests for `scvelo.datasets.simulation`.

* Add new datasets to `datasets/__init__.py` (#677)

* Fix `csr_vcorrcoef` (#679)

* Fix `csr_vcorrcoef`

Fixes calculation of Pearson's correlation in `csr_vcorrcoef`.

* Add `tests/preprocessing`

* Add `TestCsrVcorrcoef`

Test class for unit testing `csr_vcorrcoef`.

* Update Python versions in CI (#680)

* Run linting check in Python 3.8

* Run unit tests in Python 3.9

* Fix and unit test `get_mean_var` (#698)

* Fix passing `perc` not affecting result

Up to now, passing `perc` does not affect the output as only `data` but
not `X` is manipulated.

* Fix different size parameters

Mean and variance calculation use different size parameters instead of
one and the same.

* Fix sparse input with `ignore_zeros` or nan values

Mean and variance cannot be calculated due to a shape mismatch.

* Add `TestGetMeanVar`

Unit test `test_get_mean_var`.

* Add unit tests for `preprocessing/utils.py` (#700)

* Add `TestCheckIfValidDtype`

Unit tests `check_if_valid_dtype`.

* Add `TestFilter`

Unit tests `_filter`.

* Add `TestLog1p`

Unit tests `log1p`.

* Add `TestMaterializeAsNdarray`

Unit tests `materialize_as_ndarray`.

* Add `TestNotYetNormalized`

Unit tests `not_yet_normalized`.

* Add `TestFilterGenes`

Unit tests `filter_genes`.

* Add `TestCountsPerCellQuantile`

* Add `TestNormalizePerCell`

* Add `tests/_data/`

Add subsetted datasets to use in unit tests.

* Add `confest.py`

Add file to declare fixture for entire testing directory.

* Add `TestFilterGenesDispersion`

Unit test `filter_genes_dispersion`.

* Add `TestFilterAndNormalize`

Unit test `filter_and_normalize`.

* Add `TestRecipeVelocity`

Unit test `recipe_velocity`.

* Update AnnData generation for testing (#785)

* Update `test_base.py::get_adata`

Exclude `"X"` as key of `.layers`, `.obsm` and `.varm`.

* Update `test_base.py::TestAdataGeneration`

Check that `"X"` is not a key in `.layers`, `.obsm`, `.varm`.

* Update `test_anndata.py`

Remove redundant statements in `TestCleanup::test_cleanup_some` and
`TestSetInitialSize::test_added_columns` according to changes in AnnData
generation for tests.

* Add `pull_request_template.md` [ci skip] (#787)

Add template for pull requests.

* Speed up CI (#789)

* 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.

* Refactor `neighbors` (#795)

* Split body of `neighbors` over several functions

Split body of `neighbors` over several function for easier unit testing.

* Add type hints to arguments of `neighbors`

* Fix typo in docstrings

* Fix `_get_rep` (#797)

The variable `rep` is referenced before assignment if the if-else case
is not entered. This is fixed by adding a final `else` case. In the
following, only the variable `rep` is used.

* Refactor testing in CI (#801)

* Update `requirements-dev.txt`

Add `pytest-cov` to the installed libraries.

* Update `ci.yml`

Update how dependencies are installed in the `test` job.

* Increase Hypothesis deadline in CI (#804)

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.

* Unit test `neighbors.py` (#799)

* 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`.

* Unit test `moments.py` (#806)

* 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 `docs/` [ci skip] (#810)

Recommend `kb count` instead of `loompy fromfq`.

* Update `requirements.txt` (#838)

Excludes `pandas==1.4.0` to prevent failure as reported in #811.

* Fix `optimization.py::get_weight` (#839)

Fix `scvelo.tools.optimization.py::get_weight` to work correctly when
`perc` is numeric.

* Fix inference with `fit_scaling=False` (#848)

* Update `DynamicsRecovery`
Fix parameter inference to not fit scaling when `fit_scaling=False`.

* Update `pre-commit` setup (#855)

* Update `requirements-dev.txt`

Update versions of `black` and `isort`.

* Update `.pre-commit-config.yaml`

Update repo paths and versions.

* Run `black`

Run code formatting with latest version of `black`.

* Add argument `file_path` (#853)

Adds argument `file_path` to datasets added in `scvelo=0.2.4.`.

* Update `CONTRIBUTING.rst` [ci skip] (#911)

Details workaround to issue where `pip install -e '.[dev]'` leads to
errors on Windows.

* Fix saving stream embedding figure (#900)

* Fix missing write_key for embedding stream plot.

* Set save instead of wire_key when saving embedding stream plot.

* Fix `clean_obs_names` (#921)

* Fix bug with clean_obs_names

Switched implementation to use the previously ignored id_length
parameter. New approach finds a substring of length id_length
where each of the letters are in the alphabet

* Extend tests to cover more cases for clean_obs_names

* Fix Pandas display precision (#907)

* 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.

* Fix documentation issues [ci skip] (#929)

* 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 section [ci skip] (#930)

* Add `_key_contributors.rst` [ci skip]

Add file with key contributors and their roles.

* Show key contributors on index page [ci skip]

* Fix deprecation of keyword argument `copy` (#932)

* 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.

* Update `CONTRIBUTING.rst` [ci skip] (#938)

Remove reference to `develop` branch as it will be removed in the next
release.

* Fix linear regression unit tests (#940)

* 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`.

* Update `test_neighbors.py` (#941)

Remove failing and non-essential unit tests.
See https://github.com/theislab/scvelo/issues/922.

* Update release notes [ci skip] (#945)

* Remove trailing white spaces

* Add notes for `0.2.5` release

Co-authored-by: Isaac Virshup <[email protected]>
Co-authored-by: Oisin-M <[email protected]>
Co-authored-by: Dries Schaumont <[email protected]>