From 2d22a2f50d89a6bc4807e87ccfd13db0db1d6e0d Mon Sep 17 00:00:00 2001
From: Michal Klein <46717574+michalk8@users.noreply.github.com>
Date: Tue, 23 May 2023 12:13:15 +0200
Subject: [PATCH] Wrap `scanpy.pp.log1p`

---
 scvelo/preprocessing/utils.py       | 14 ++++----------
 tests/preprocessing/test_moments.py |  4 +++-
 tests/preprocessing/test_utils.py   |  4 ++--
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/scvelo/preprocessing/utils.py b/scvelo/preprocessing/utils.py
index 4ff8dfd6..232a55e5 100644
--- a/scvelo/preprocessing/utils.py
+++ b/scvelo/preprocessing/utils.py
@@ -5,8 +5,6 @@
 from scipy.sparse import issparse
 from sklearn.utils import sparsefuncs
 
-from anndata import AnnData
-
 from scvelo import logging as logg
 from scvelo.core import get_initial_size, get_size, multiply, set_initial_size, sum
 
@@ -587,14 +585,10 @@ def log1p(data, copy=False):
     -------
     Returns or updates `adata` depending on `copy`.
     """
-    adata = data.copy() if copy else data
-    X = (
-        (adata.X.data if issparse(adata.X) else adata.X)
-        if isinstance(adata, AnnData)
-        else adata
-    )
-    np.log1p(X, out=X)
-    return adata if copy else None
+    from scanpy.pp import log1p as _log1p
+
+    res = _log1p(data, copy=copy)
+    return res if copy else None
 
 
 def filter_and_normalize(
diff --git a/tests/preprocessing/test_moments.py b/tests/preprocessing/test_moments.py
index 46e3e0ae..b023e4c6 100644
--- a/tests/preprocessing/test_moments.py
+++ b/tests/preprocessing/test_moments.py
@@ -159,9 +159,11 @@ def test_analytic_example(self, sparse: bool):
         )
 
         second_order_moment_centered = get_moments(adata=adata, second_order=True)
-        np.testing.assert_almost_equal(
+        np.testing.assert_allclose(
             second_order_moment_centered,
             second_order_moment_uncentered - first_order_moment_ground_truth**2,
+            rtol=1e-6,
+            atol=1e-6,
         )
 
 
diff --git a/tests/preprocessing/test_utils.py b/tests/preprocessing/test_utils.py
index 43e4708d..718aa2bd 100644
--- a/tests/preprocessing/test_utils.py
+++ b/tests/preprocessing/test_utils.py
@@ -2321,7 +2321,7 @@ def test_pancreas50obs(self, capfd, pancreas_50obs):
             )
         )
         assert pancreas_50obs.var.columns.equals(pd.Index(["gene_count_corr"]))
-        assert [*pancreas_50obs.uns] == ["pca", "neighbors"]
+        assert [*pancreas_50obs.uns] == ["log1p", "pca", "neighbors"]
         assert [*pancreas_50obs.obsm] == ["X_pca"]
         assert [*pancreas_50obs.varm] == ["PCs"]
         assert [*pancreas_50obs.layers] == ["spliced", "unspliced", "Ms", "Mu"]
@@ -2373,7 +2373,7 @@ def test_dentategyrus50obs(self, capfd, dentategyrus_50obs):
             )
         )
         assert dentategyrus_50obs.var.columns.equals(pd.Index([]))
-        assert [*dentategyrus_50obs.uns] == ["pca", "neighbors"]
+        assert [*dentategyrus_50obs.uns] == ["log1p", "pca", "neighbors"]
         assert [*dentategyrus_50obs.obsm] == ["X_pca"]
         assert [*dentategyrus_50obs.varm] == ["PCs"]
         assert [*dentategyrus_50obs.layers] == [