add check for output directory to tests

brainglobe_workflows/cellfinder/cellfinder_main.py

@@ -214,7 +214,7 @@ def setup_workflow(cellfinder_cache_dir=CELLFINDER_CACHE_DIR):
     timestamp = datetime.datetime.now()
     timestamp_formatted = timestamp.strftime("%Y%m%d_%H%M%S")
     output_path_timestamped = Path(
-        str(config.output_path) + timestamp_formatted
+        str(config.output_path_basename) + timestamp_formatted
     )
     output_path_timestamped.mkdir(parents=True, exist_ok=True)
     # add to config

tests/test_integration/test_cellfinder_workflow.py

@@ -75,6 +75,10 @@ def test_run_with_env_var_config(config_from_env_var, caplog, logger_str):
         "provided GIN repository" in caplog.messages
     )
 
+    # check output directory and output file exist
+    assert Path(cfg.output_path).exists()
+    assert (Path(cfg.output_path) / cfg.detected_cells_filename).is_file()
+
 
 def test_run_with_default_config(cellfinder_cache_dir, caplog, logger_str):
     # check environment var is not defined
@@ -92,6 +96,10 @@ def test_run_with_default_config(cellfinder_cache_dir, caplog, logger_str):
         "provided GIN repository" in caplog.messages
     )
 
+    # check output directory and output file exist
+    assert Path(cfg.output_path).exists()
+    assert (Path(cfg.output_path) / cfg.detected_cells_filename).is_file()
+
 
 # test running on local data?
 # def test_run_with_default_config_local(