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]>
