added test case for command line code (#20)

src/paste/paste-cmd-line.py

@@ -80,7 +80,7 @@ def main(args):
         print("Computing center alignment.")
         initial_slice = slices[args.initial_slice - 1].copy()
         # compute center align
-        center_slice, pis = center_align(initial_slice, slices, lmbda, args.alpha, args.n_components, args.threshold, dissimilarity=args.cost, distributions=[slices[i].obsm['weights'] for i in range(n_slices)], pis_init=pis_init)
+        center_slice, pis = center_align(initial_slice, slices, lmbda, args.alpha, args.n_components, args.threshold, random_seed=args.seed, dissimilarity=args.cost, distributions=[slices[i].obsm['weights'] for i in range(n_slices)], pis_init=pis_init)
         W = pd.DataFrame(center_slice.uns['paste_W'], index = center_slice.obs.index)
         H = pd.DataFrame(center_slice.uns['paste_H'], columns = center_slice.var.index)
         W.to_csv(os.path.join(args.direc, "paste_output/W_center"))
@@ -112,5 +112,6 @@ def main(args):
     parser.add_argument("-x","--coordinates", help="output new coordinates", action='store_true', default = False)
     parser.add_argument("-w","--weights", help="path to files containing weights of spots in each slice. The format of the files is the same as the coordinate files used as input",type=str, default=[], nargs='+')
     parser.add_argument("-s","--start", help="path to files containing initial starting alignmnets. If not given the OT starts the search with uniform alignments. The format of the files is the same as the alignments files output by PASTE",type=str, default=[], nargs='+')
+    parser.add_argument("--seed", help="random seed for reproducibility",type=int,default=None)
     args = parser.parse_args()
     main(args)

tests/test_paste_cmd_line.py

@@ -0,0 +1,79 @@
+import pandas as pd
+from pandas.testing import assert_frame_equal
+from pathlib import Path
+import subprocess
+
+test_dir = Path(__file__).parent
+input_dir = test_dir / "data/input"
+output_dir = test_dir / "data/output"
+
+
+def test_cmd_line_center(tmp_path):
+    print(f"Running command in {tmp_path}")
+    result = subprocess.run(
+        [
+            "python",
+            f"{test_dir.parent}/src/paste/paste-cmd-line.py",
+            "-m",
+            "center",
+            "--seed",
+            "0",
+            "-f",
+            f"{input_dir}/slice1.csv",
+            f"{input_dir}/slice1_coor.csv",
+            f"{input_dir}/slice2.csv",
+            f"{input_dir}/slice2_coor.csv",
+            f"{input_dir}/slice3.csv",
+            f"{input_dir}/slice3_coor.csv",
+            "-d",
+            f"{tmp_path}",
+        ]
+    )
+    assert result.returncode == 0
+    assert_frame_equal(
+        pd.read_csv(tmp_path / "paste_output/W_center"),
+        pd.read_csv(output_dir / "W_center"),
+        check_names=False,
+        rtol=1e-05,
+        atol=1e-08,
+    )
+    assert_frame_equal(
+        pd.read_csv(tmp_path / "paste_output/H_center"),
+        pd.read_csv(output_dir / "H_center"),
+        rtol=1e-05,
+        atol=1e-08,
+    )
+
+    for i, pi in enumerate(range(3)):
+        assert_frame_equal(
+            pd.read_csv(
+                tmp_path / f"paste_output/slice_center_slice{i + 1}_pairwise.csv"
+            ),
+            pd.read_csv(output_dir / f"slice_center_slice{i + 1}_pairwise.csv"),
+        )
+
+
+def test_cmd_line_pairwise(tmp_path):
+    print(f"Running command in {tmp_path}")
+    result = subprocess.run(
+        [
+            "python",
+            f"{test_dir.parent}/src/paste/paste-cmd-line.py",
+            "-m",
+            "pairwise",
+            "-f",
+            f"{input_dir}/slice1.csv",
+            f"{input_dir}/slice1_coor.csv",
+            f"{input_dir}/slice2.csv",
+            f"{input_dir}/slice2_coor.csv",
+            f"{input_dir}/slice3.csv",
+            f"{input_dir}/slice3_coor.csv",
+            "-d",
+            f"{tmp_path}",
+        ]
+    )
+    assert result.returncode == 0
+    assert_frame_equal(
+        pd.read_csv(tmp_path / f"paste_output/slice1_slice2_pairwise.csv"),
+        pd.read_csv(output_dir / "slices_1_2_pairwise.csv"),
+    )