add option for in memory sqlite db (for tests)

biomero/views.py

@@ -32,14 +32,25 @@ def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
         # Read database configuration from environment variables
-        database_url = URL.create(
-            drivername="postgresql+psycopg2",
-            username=os.getenv('POSTGRES_USER'),
-            password=os.getenv('POSTGRES_PASSWORD'),
-            host=os.getenv('POSTGRES_HOST', 'localhost'),
-            port=os.getenv('POSTGRES_PORT', 5432),
-            database=os.getenv('POSTGRES_DBNAME')
-        )
+        persistence_mod = os.getenv('PERSISTENCE_MODULE')
+        if 'postgres' in persistence_mod:
+            logger.info("Using postgres database")
+            database_url = URL.create(
+                drivername="postgresql+psycopg2",
+                username=os.getenv('POSTGRES_USER'),
+                password=os.getenv('POSTGRES_PASSWORD'),
+                host=os.getenv('POSTGRES_HOST', 'localhost'),
+                port=os.getenv('POSTGRES_PORT', 5432),
+                database=os.getenv('POSTGRES_DBNAME')
+            )
+        elif 'sqlite' in persistence_mod:
+            logger.info("Using sqlite in-mem database")
+            database_url = URL.create(
+                drivername="sqlite",
+                database=os.getenv('SQLITE_DBNAME')
+            )
+        else:
+            raise NotImplementedError(f"Can't handle {persistence_mod}")
 
         # Set up SQLAlchemy engine and session
         self.engine = create_engine(database_url)

tests/unit/test_slurm_client.py

@@ -3,6 +3,37 @@
 import mock
 from mock import patch, MagicMock
 from paramiko import SSHException
+import os
+
+# using actual env vars
+# @pytest.fixture(scope='session', autouse=True)
+# def set_env_vars():
+#     # Set environment variables
+#     os.environ["PERSISTENCE_MODULE"] = "eventsourcing.sqlite"
+#     os.environ["SQLITE_DBNAME"] = ":memory:"
+
+#     # Optional: Return a dictionary of the set variables if needed elsewhere
+#     yield {
+#         "PERSISTENCE_MODULE": "eventsourcing.sqlite",
+#         "SQLITE_DBNAME": ":memory:",
+#     }
+
+#     # Optionally, clean up the environment variables after tests are done
+#     del os.environ["PERSISTENCE_MODULE"]
+#     del os.environ["SQLITE_DBNAME"]
+
+
+@pytest.fixture(autouse=True)
+def mock_env_vars():
+    # Define mock environment variables
+    mock_env = {
+        "PERSISTENCE_MODULE": "eventsourcing.sqlite",
+        "SQLITE_DBNAME": ":memory:",
+    }
+
+    # Patch os.getenv to return values from the mock environment
+    with patch('os.getenv', lambda key, default=None: mock_env.get(key, default)):
+        yield
 
 
 @pytest.fixture