Directory might already exist when run in parallel

Author: w8jcik

.gitignore

@@ -19,6 +19,7 @@ ideas
 projects
 pkl
 tmp
+tmp*
 tox.ini
 
 build

src/moldrug/constraintconf.py

@@ -162,7 +162,7 @@ def generate_conformers(mol: Chem.rdchem.Mol,
     """
     # Creating the error directory if needed
     if not os.path.isdir('error'):
-        os.makedirs('error')
+        os.makedirs('error', exist_ok=True)
     # if SMILES to be fixed are not given, assume to the MCS
     if ref_smi:
         if not Chem.MolFromSmiles(ref_smi):

src/moldrug/fitness.py

@@ -311,7 +311,7 @@ def _vinadock(
 
     # Creating the error directory if needed
     if not os.path.isdir('error'):
-        os.makedirs('error')
+        os.makedirs('error', exist_ok=True)
     # Creating the working directory if needed
     if not os.path.exists(wd):
         os.makedirs(wd)

tests/test_moldrug.py

@@ -106,35 +106,35 @@ def test_single_receptor_command_line():
         }
     }
 
-    # if execution_mode == "multiprocessing":
-    #     pass
-    # elif execution_mode in ["smaug", "elwe"]:
-    #     assert dask_available
-
-    #     if execution_mode == "smaug":
-    #         Config['01_grow']['cluster'] = {
-    #             "SLURMCluster_kwargs": {
-    #                 "queue": "short",
-    #                 "cores": 12,
-    #                 "processes": 1,
-    #                 "memory": "8GB",
-    #                 "walltime": "00:15:00",
-    #                 "job_extra_directives": ["--gpus 1"]
-    #             }
-    #         }
-    #     elif execution_mode == "elwe":
-    #         Config['01_grow']['cluster'] = {
-    #             "SLURMCluster_kwargs": {
-    #                 "queue": "uds-hub",
-    #                 "cores": 10,
-    #                 "processes": 1,
-    #                 "memory": "8GB",
-    #                 "walltime": "00:15:00",
-    #                 "job_extra_directives": ["--gpus 1"]
-    #             }
-    #         }
-    # else:
-    #     raise ValueError(f"Unknown mode {execution_mode}")
+    if execution_mode == "multiprocessing":
+        pass
+    elif execution_mode in ["smaug", "elwe"]:
+        assert dask_available
+
+        if execution_mode == "smaug":
+            Config['01_grow']['cluster'] = {
+                "SLURMCluster_kwargs": {
+                    "queue": "short",
+                    "cores": 12,
+                    "processes": 1,
+                    "memory": "8GB",
+                    "walltime": "00:15:00",
+                    "job_extra_directives": ["--gpus 1"]
+                }
+            }
+        elif execution_mode == "elwe":
+            Config['01_grow']['cluster'] = {
+                "SLURMCluster_kwargs": {
+                    "queue": "uds-hub",
+                    "cores": 10,
+                    "processes": 1,
+                    "memory": "8GB",
+                    "walltime": "00:15:00",
+                    "job_extra_directives": ["--gpus 1"]
+                }
+            }
+    else:
+        raise ValueError(f"Unknown mode {execution_mode}")
 
     with open("test_single_receptor.yml", 'w') as c:
         yaml.dump(Config, c)