1.6.1

- Comply with AnnData CSR matrix changes
- Bump Python version to <=3.13

Author: dbdimitrov

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.6.0
+current_version = 1.6.1
 commit = True
 tag = True
 

.gitignore

@@ -32,6 +32,11 @@ data/
 docs/_build/*
 docs/jupyter_execute/*
 docs/generated/*
+*.h5ad
+*.gz
+*.db
+*.pkl
+*.png
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## 1.6.1 (28.09.2025)
+
+- Comply with AnnData CSR matrix changes
+- Bump Python version to <=3.13
+
 ## 1.6.0 (09.07.2025)
 
 - Adapted and bumped requirements to decopler-py \>=2.0.0 \| PR #178 by

pyproject.toml

@@ -4,7 +4,7 @@ requires = [ "hatchling" ]
 
 [project]
 name = "liana"
-version = "1.6.0"
+version = "1.6.1"
 description = "LIANA+: a one-stop-shop framework for cell-cell communication"
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -24,7 +24,7 @@ authors = [
   { name = "Julio Saez-Rodriguez"},
 
 ]
-requires-python = ">=3.10,<3.13"
+requires-python = ">=3.10,<3.14"
 classifiers = [
   "Programming Language :: Python :: 3 :: Only",
   "Programming Language :: Python :: 3.10",
@@ -52,17 +52,18 @@ optional-dependencies.dev = [
 ]
 
 optional-dependencies.extras = [
-  "decoupler>=1.6.0",
+  "decoupler>=1.6.1",
   "omnipath>=1.0.6",
   "pydeseq2>=0.3.5",
   "cell2cell",
+  "gseapy>=1.1.0",
   "kneed>=0.7.0",
   "muon",
   "mofax",
   "mofapy2>=0.7.0",
   "requests>=2.25.1",
   "corneto==0.9.1-alpha.6",
-  "cvxpy-base>=1.6.0",
+  "cvxpy-base>=1.6.1",
   "PySCIPOpt>=5.2.1",
 ]
 
@@ -103,7 +104,7 @@ scripts.clean = "git clean -fdX -- {args:docs}"
 
 [[tool.hatch.envs.hatch-test.matrix]]
 deps = [ "stable" ]
-python = [ "3.10", "3.12" ]
+python = [ "3.10", "3.13" ]
 
 [tool.hatch.envs.hatch-test]
 features = [ "test", "extras" ]

src/liana/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '1.6.0'
+__version__ = '1.6.1'
 
 from liana import method as mt, plotting as pl, resource as rs, multi as mu, utils as ut, testing
 

src/liana/method/sp/_utils.py

@@ -1,7 +1,7 @@
 import numpy as np
 from anndata import AnnData
 from pandas import Series
-from scipy.sparse import csr_matrix, hstack, isspmatrix_csr
+from scipy.sparse import csr_matrix, hstack
 
 
 def _add_complexes_to_var(adata, entities, complex_sep='_'):
@@ -22,19 +22,16 @@ def _add_complexes_to_var(adata, entities, complex_sep='_'):
                 X = new_array
             else:
                 X = hstack((X, new_array))
+            X = csr_matrix(X)
 
-    adata = AnnData(X=hstack((adata.X, X)),
+    adata = AnnData(X=hstack((adata.X, X)).tocsr(),
                     obs=adata.obs,
                     var=adata.var,
                     obsm=adata.obsm,
                     varm = adata.varm,
                     obsp=adata.obsp,
                     uns = adata.uns,
                     )
-
-    if not isspmatrix_csr(adata.X):
-        adata.X = adata.X.tocsr()
-
     return adata
 
 

src/liana/utils/interpolate_adata.py

@@ -1,7 +1,6 @@
-import numpy as np
 from anndata import AnnData
 from scipy.interpolate import griddata
-from scipy.sparse import csr_matrix, lil_matrix
+from scipy.sparse import csr_matrix
 
 from liana._constants import DefaultValues as V
 from liana._docs import d
@@ -44,9 +43,7 @@ def interpolate_adata(target: AnnData,
     target_coords = target.obsm[spatial_key]
     reference_coords = reference.obsm[spatial_key]
 
-    X = lil_matrix((reference.shape[0], target.shape[1]), dtype=np.float32)
-
-    ad = AnnData(X=X,
+    ad = AnnData(X=None,
                  uns=reference.uns,
                  obs=reference.obs,
                  obsm=reference.obsm,

tests/test_interpolate.py

@@ -1,6 +1,7 @@
 import numpy as np
 import pytest
 from anndata import AnnData
+from scipy.sparse import csr_matrix
 
 from liana.utils.interpolate_adata import interpolate_adata
 
@@ -9,7 +10,7 @@ def create_test_adata(n_cells, n_genes, spatial_key='spatial'):
     """
     Helper function to create a test AnnData object.
     """
-    X = np.random.rand(n_cells, n_genes)
+    X = csr_matrix(np.random.rand(n_cells, n_genes))
     obsm = {spatial_key: np.random.rand(n_cells, 2)}
     adata = AnnData(X, obsm=obsm)
     adata.layers['some_layer'] = X

tests/test_multi.py

@@ -1,4 +1,3 @@
-import cell2cell as c2c
 import numpy as np
 import pandas as pd
 
@@ -12,6 +11,7 @@
 
 def test_to_tensor_c2c():
     """Test to_tensor_c2c."""
+    import cell2cell as c2c
     liana_res = sample_lrs(by_sample=True)
 
     liana_dict = to_tensor_c2c(liana_res=liana_res,

tests/test_pre.py

@@ -10,7 +10,7 @@ def test_prep_check_adata():
 
     temp = prep_check_adata(adata=adata, groupby='bulk_labels', min_cells=0,
                             use_raw=True, layer=None)
-    np.testing.assert_almost_equal(np.sum(temp.X.data), 319044.22, decimal=2)
+    np.testing.assert_almost_equal(np.sum(temp.X.data), 319044.22, decimal=1)
 
     desired = np.array([2.177, 2.177, 2.544, 2.544, 1.591, 1.591, 1.591, 1.591, 1.591, 1.591])
     np.testing.assert_almost_equal(temp.X.data[0:10], desired, decimal=3)