Bug fix exit code (#329)

* adjusted exit code and added full CLI test case

* corrected version

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 name = "arctic3d"
 license = "Apache-2.0"
-version = "0.1.0"
+version = "0.4.1"
 description = ""
 authors = [
   "Computational Structural Biology Group at Utrecht University <haddocking@gmail.com>",

src/arctic3d/cli.py

@@ -318,9 +318,11 @@ def main(
     )
 
     # check if there's at least one interface
-    if Path(run_dir_path, "clustered_interfaces.out").is_file() is False:
+    if Path("clustered_interfaces.out").is_file() is False:
         return 255
 
+    return 0
+
 
 if __name__ == "__main__":
     sys.exit(maincli())

tests/test_cli.py

@@ -35,3 +35,40 @@ def test_cli_empty():
     # remove folder
     if exp_dir.exists():
         shutil.rmtree(exp_dir)
+
+
+def test_cli_full():
+    target_uniprot = "W5JXD7"
+    start_cwd = os.getcwd()
+    exit_code = main(
+        input_arg=target_uniprot,
+        db=None,
+        interface_file=None,
+        out_partner=None,
+        out_pdb=None,
+        pdb_to_use="3wqb",
+        chain_to_use=None,
+        run_dir=None,
+        interface_data=None,
+        pdb_data=None,
+        full=None,
+        ligand="no",
+        linkage_strategy=None,
+        threshold=None,
+        min_clust_size=1,
+    )
+    assert exit_code == 0
+    os.chdir(start_cwd)
+    exp_dir = Path(f"arctic3d-{target_uniprot}")
+    assert exp_dir.exists() is True
+    # Check that the log file has been created
+    assert Path(exp_dir, "arctic3d.log").exists()
+    # check content of the clustered interfaces file
+    assert Path(exp_dir, "clustered_interfaces.out").exists()
+    # check content of the clustered interfaces file
+    obs_content = Path(exp_dir, "clustered_interfaces.out").read_text()
+    exp_content = f"Cluster 1 -> Q9L5A4-3wqb-A{os.linesep}"
+    assert exp_content == obs_content
+    # remove folder
+    if exp_dir.exists():
+        shutil.rmtree(exp_dir)