Merge pull request #14 from KlugerLab/12-support-for-numpy-20

support for numpy 20

Author: fra-pcmgf

gene_trajectory/extract_gene_trajectory.py

@@ -136,7 +136,7 @@ def extract_gene_trajectory(
             logger.warning(f"Early stop reached. {i - 1} gene trajectories were retrieved.")
             break
 
-        dist_to_origin[df.selected != other] = -np.infty
+        dist_to_origin[df.selected != other] = -np.inf
 
         seed_idx = np.argmax(dist_to_origin)
         logger.info(f'Generating trajectory from {gene_names[seed_idx]}')

gene_trajectory/gene_distance_shared.py

@@ -56,7 +56,7 @@ def cal_ot_mat(
     else:
         pairs = gene_pairs
         npairs = len(gene_pairs)
-    emd_mat = np.full((ngenes, ngenes), fill_value=np.NaN)
+    emd_mat = np.full((ngenes, ngenes), fill_value=np.nan)
 
     with SharedMemoryManager() as manager:
         start_time = time.perf_counter()

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "gene-trajectory"
-version = "1.0.3"
+version = "1.0.4"
 description = "Compute gene trajectories"
 license = {file = "LICENSE"}
 readme = "README.md"
@@ -30,7 +30,7 @@ requires-python = ">=3.9"
 dependencies = [
     "igraph>=0.10",
     "matplotlib>=3.6",
-    "numpy>=1.23",
+    "numpy>=1.25",
     "pandas>=1.5",
     "pot>=0.8.2",
     "scanpy>=1.9.3",

requirements.txt

@@ -1,6 +1,6 @@
 igraph>=0.10
 matplotlib>=3.6
-numpy>=1.23
+numpy>=1.25
 pandas>=1.5
 pot>=0.8.2
 scanpy>=1.9.3

tests/test_gene_distance_shared.py

@@ -29,13 +29,13 @@ def test_gene_distance_shared(self):
         np.testing.assert_almost_equal(self.expected_emd, mt, 6)
 
     def test_gene_distance_input_validation(self):
-        with self.assertRaisesRegexp(ValueError, 'Cost Matrix does not have shape.*'):
+        with self.assertRaisesRegex(ValueError, 'Cost Matrix does not have shape.*'):
             cal_ot_mat(ot_cost=self.gdm, gene_expr=np.ones(shape=(6, 3)), show_progress_bar=False)
 
-        with self.assertRaisesRegexp(ValueError, 'Cost Matrix does not have shape.*'):
+        with self.assertRaisesRegex(ValueError, 'Cost Matrix does not have shape.*'):
             cal_ot_mat(ot_cost=np.ones(shape=(6, 3)), gene_expr=self.gem.T, show_progress_bar=False)
 
-        with self.assertRaisesRegexp(ValueError, 'Gene Expression Matrix should not have values less than 0.*'):
+        with self.assertRaisesRegex(ValueError, 'Gene Expression Matrix should not have values less than 0.*'):
             cal_ot_mat(ot_cost=np.ones(shape=(6, 3)), gene_expr=self.gem.T - 1, show_progress_bar=False)
 
     def test_cal_ot_mat_gene_pairs(self):

tests/test_input_validation.py

@@ -11,17 +11,17 @@ def test_validate_matrix(self):
 
         validate_matrix(m, min_value=1, max_value=4, square=True, shape=(2, 2))
 
-        with self.assertRaisesRegexp(ValueError, '.*does not have 3 rows.*'):
+        with self.assertRaisesRegex(ValueError, '.*does not have 3 rows.*'):
             validate_matrix(m, nrows=3)
-        with self.assertRaisesRegexp(ValueError, '.*does not have 8 columns.*'):
+        with self.assertRaisesRegex(ValueError, '.*does not have 8 columns.*'):
             validate_matrix(m, ncols=8)
-        with self.assertRaisesRegexp(ValueError, '.*does not have shape \\(1, 1\\)'):
+        with self.assertRaisesRegex(ValueError, '.*does not have shape \\(1, 1\\)'):
             validate_matrix(m, shape=(1, 1))
-        with self.assertRaisesRegexp(ValueError, '.*Min_size: 3.*'):
+        with self.assertRaisesRegex(ValueError, '.*Min_size: 3.*'):
             validate_matrix(m, min_size=3)
-        with self.assertRaisesRegexp(ValueError, '.*should not have values less than 5.*'):
+        with self.assertRaisesRegex(ValueError, '.*should not have values less than 5.*'):
             validate_matrix(m, min_value=5)
-        with self.assertRaisesRegexp(ValueError, '.*should not have values greater than 1.*'):
+        with self.assertRaisesRegex(ValueError, '.*should not have values greater than 1.*'):
             validate_matrix(m, max_value=1)