Remove magic_impute (#1079)

theislab · Jun 7, 2023 · 8aaa334 · 8aaa334
1 parent e8fa7a1
commit 8aaa334
Show file tree

Hide file tree

Showing 3 changed files with 0 additions and 53 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -74,7 +74,6 @@ dev = [
     "hnswlib",
     "hypothesis",
     "louvain",
-    "magic-impute",
     "pre-commit>=2.9.0",
     "pybind11",
     "pytest-cov",

diff --git a/scvelo/preprocessing/moments.py b/scvelo/preprocessing/moments.py
@@ -154,19 +154,6 @@ def second_order_moments_u(adata):
     return Muu
 
 
-# TODO: Add docstrings
-def magic_impute(adata, knn=5, t=2, verbose=0, **kwargs):
-    """TODO."""
-    logg.info(
-        "To be used carefully. Magic has not yet been tested for this application."
-    )
-    import magic
-
-    magic_operator = magic.MAGIC(verbose=verbose, knn=knn, t=t, **kwargs)
-    adata.layers["Ms"] = magic_operator.fit_transform(adata.layers["spliced"])
-    adata.layers["Mu"] = magic_operator.transform(adata.layers["unspliced"])
-
-
 def get_moments(
     adata, layer=None, second_order=None, centered=True, mode="connectivities"
 ):

diff --git a/tests/preprocessing/test_moments.py b/tests/preprocessing/test_moments.py
@@ -9,7 +9,6 @@
 
 from scvelo.preprocessing.moments import (
     get_moments,
-    magic_impute,
     moments,
     second_order_moments,
     second_order_moments_u,
@@ -167,44 +166,6 @@ def test_analytic_example(self, sparse: bool):
         )
 
 
-class TestMagicImpute:
-    @pytest.mark.parametrize("dataset", ["pancreas", "dentategyrus"])
-    @pytest.mark.parametrize("n_obs", [50, 100])
-    def test_output(self, adata, capfd, dataset: str, n_obs: int):
-        adata = adata(dataset=dataset, n_obs=n_obs, raw=False, preprocessed=True)
-        del adata.layers["Mu"]
-        del adata.layers["Ms"]
-
-        magic_impute(adata=adata)
-
-        ground_truth_unspliced = np.load(
-            file=(
-                f"tests/_data/test_moments/magic_impute/dataset={dataset}-n_obs={n_obs}"
-                f"-layer=unspliced_magic_impute.npy"
-            )
-        )
-        np.testing.assert_almost_equal(
-            adata.layers["Mu"], ground_truth_unspliced, decimal=5
-        )
-
-        ground_truth_spliced = np.load(
-            file=(
-                f"tests/_data/test_moments/magic_impute/dataset={dataset}-n_obs={n_obs}"
-                f"-layer=spliced_magic_impute.npy"
-            )
-        )
-        np.testing.assert_almost_equal(
-            adata.layers["Ms"], ground_truth_spliced, decimal=5
-        )
-
-        expected_log = (
-            "To be used carefully. Magic has not yet been tested for this "
-            "application.\n"
-        )
-        actual_log, _ = capfd.readouterr()
-        assert actual_log == expected_log
-
-
 class TestMoments:
     def _compare_adatas(self, adata_1, adata_2):
         # Check `.layers`