Fix scanpy anyrandom (#777)

* Fix scanpy anyrandom Signed-off-by: zethson <[email protected]> * Restrict numpy Signed-off-by: zethson <[email protected]> * Restrict numpy Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
theislab · Jul 17, 2024 · f71f08e · f71f08e
1 parent 2ac2a54
commit f71f08e
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/ehrapy/preprocessing/_scanpy_pp_api.py b/ehrapy/preprocessing/_scanpy_pp_api.py
@@ -5,9 +5,10 @@
 import numpy as np
 import scanpy as sc
 from anndata import AnnData
-from scanpy._utils import AnyRandom
 from scipy.sparse import spmatrix
 
+AnyRandom = Union[int, np.random.RandomState, None]
+
 
 def pca(
     data: Union[AnnData, np.ndarray, spmatrix],

diff --git a/ehrapy/tools/_scanpy_tl_api.py b/ehrapy/tools/_scanpy_tl_api.py
@@ -5,11 +5,12 @@
 import scanpy as sc
 from anndata import AnnData
 from leidenalg.VertexPartition import MutableVertexPartition
-from scanpy._utils import AnyRandom
 from scipy.sparse import spmatrix
 
 from ehrapy.tools import _method_options
 
+AnyRandom = Union[int, np.random.RandomState, None]
+
 
 def tsne(
     adata: AnnData,

diff --git a/pyproject.toml b/pyproject.toml
@@ -67,6 +67,7 @@ dependencies = [
     "fknni",
     "python-dateutil",
     "filelock",
+    "numpy<2.0.0"  # for compatiblity with lifelines
 ]
 
 [project.optional-dependencies]