Fixes clustering and model update (#40)

Clustering and mode tracking is added with example code for both and a shared module for both.
Other small changes have been made.

---------
Co-authored-by: au650680 <au650680@uni.au.dk>

Author: au650680

config/test.json

@@ -1,6 +1,6 @@
 {
     "MQTT": {
-        "host": "mqtt.eclipseprojects.io",
+        "host": "public.mqttserver.eu",
         "port": 1883,
         "userId": "",
         "password": "",

pytest.ini

@@ -1,6 +1,6 @@
 [pytest]
 minversion = 8.3
-pythonpath = src src/data src/methods  tests
+pythonpath = src src/data src/methods tests models
 testpaths =
     tests
 addopts = --cov=src --ignore=src/examples --cov-report=term-missing --cov-report=html

src/pt_mock/publish_samples.py

@@ -196,8 +196,8 @@ def main(config_path: str = "config/R-PI.json",
          offset_path: str = "config/offset.json",
          run_once: bool = False) -> None:
     config = load_config(config_path)
-    mqtt_config = config["sysid"]
-    mqtt_client, _, _ = setup_mqtt_client(mqtt_config)
+    mqtt_config = config["MQTT"]
+    mqtt_client = setup_mqtt_client(mqtt_config,mqtt_config["TopicsToSubscribe"][0])
 
     mqtt_client.connect(mqtt_config["host"], mqtt_config["port"], 60)
     mqtt_client.loop_start()

tests/integration/data/accel/hbk/test_accelerometer.py

@@ -19,14 +19,16 @@ def mqtt_client():
     mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}"  
 
     topic_index = 0  
-    client, selected_topic = setup_mqtt_client(mqtt_config, topic_index)  
+    client = setup_mqtt_client(mqtt_config, topic_index)  
 
     client.connect(mqtt_config["host"], mqtt_config["port"], 60)
     client.loop_start()  
     connect_delay = float(os.environ.get("MQTT_CONNECT_DELAY"))
     time.sleep(connect_delay)  
 
-    yield client, selected_topic
+    topic = mqtt_config["TopicsToSubscribe"][0]
+
+    yield client, topic
     client.loop_stop()
     client.disconnect()
 

tests/integration/data/accel/hbk/test_aligner.py

@@ -19,7 +19,7 @@ def mqtt_client_and_config():
     mqtt_config = config["MQTT"].copy()
     mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}"
 
-    client, _ = setup_mqtt_client(mqtt_config, topic_index=0)
+    client = setup_mqtt_client(mqtt_config, mqtt_config["TopicsToSubscribe"][0])
     client.connect(mqtt_config["host"], mqtt_config["port"], 60)
     client.loop_start()
     time.sleep(connect_delay)
@@ -37,7 +37,7 @@ def mqtt_setup():
     mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}"
 
     # Setup MQTT client once
-    client, _ = setup_mqtt_client(mqtt_config, 0)
+    client = setup_mqtt_client(mqtt_config, mqtt_config["TopicsToSubscribe"][0])
     client.connect(mqtt_config["host"], mqtt_config["port"], 60)
     client.loop_start()
     time.sleep(connect_delay)

tests/integration/data/comm/test_mqtt.py

@@ -58,8 +58,8 @@ def test_setup_mqtt_client_invalid_index():
         "port": 1883
     }
 
-    with pytest.raises(ValueError):
-        setup_mqtt_client(dummy_config, topic_index=5)
+    with pytest.raises(IndexError):
+        setup_mqtt_client(dummy_config, dummy_config["TopicsToSubscribe"][5])
 
 
 def test_on_connect_callback_failure():
@@ -118,7 +118,7 @@ def test_setup_mqtt_client():
         "port": 1883
     }
     # Unpack the returned tuple
-    client, selected_topic = setup_mqtt_client(dummy_config)
+    client = setup_mqtt_client(dummy_config, dummy_config["TopicsToSubscribe"][0])
 
     # Check that the client has the correct client_id.
     client_id = client._client_id.decode() if isinstance(client._client_id, bytes) else client._client_id

tests/integration/methods/test_sys_id.py

@@ -39,7 +39,6 @@ def test_sysid():
     stored_cov_damping = stored_data['cov_damping']
     stored_mode_shapes = stored_data['mode_shapes']
 
-
     tolerance = 0.4
     assert np.allclose(frequencies, stored_frequencies, atol=tolerance, equal_nan=True), "Frequencies do not match!"
     assert np.allclose(cov_freq, stored_cov_freq, atol=tolerance, equal_nan=True), "Covariance frequencies do not match!"
@@ -90,11 +89,11 @@ def test_get_oma_results_integration(mocker):
 
     mock_aligner.extract.return_value = (mock_data, mock_timestamp)
 
-    sysid_output, timestamp = sysid.get_sysid_results(number_of_minutes, mock_aligner, fs)
+    sysid_output, timestamp = sysid.get_sysid_output(number_of_minutes, mock_aligner, fs)
 
     assert isinstance(sysid_output, dict)
     assert "Fn_poles" in sysid_output
-    assert timestamp == mock_timestamp
+    assert timestamp == mock_timestamp.isoformat()
 
 
 def test_oma_raises_on_empty_data():

tests/integration/mock_pt_test/test_publish_samples.py

@@ -19,17 +19,16 @@
 @pytest.fixture(scope="function")
 def mqtt_client():
     config = load_config("config/test.json")
-    mqtt_config = config["sysid"].copy()
+    mqtt_config = config["MQTT"].copy()
     mqtt_config["ClientID"] = f"test_{uuid.uuid4().hex[:6]}"
-    client = setup_mqtt_client(mqtt_config)
+    client = setup_mqtt_client(mqtt_config,mqtt_config["TopicsToSubscribe"][0])
     client.connect(mqtt_config["host"], mqtt_config["port"], 60)
     client.loop_start()
     time.sleep(1.0)
     yield client
     client.loop_stop()
     client.disconnect()
 
-
 def test_send_batch_actual_publish(mqtt_client):
     samples = [0.1 * i for i in range(SAMPLES_PER_MESSAGE)]
     batch = Batch(
@@ -81,7 +80,7 @@ def test_main_falls_back_when_offset_config_is_corrupt(mock_file):
             }
         }
         mock_sensor.return_value = MagicMock()
-        mock_mqtt.return_value = (MagicMock(), "topic")
+        mock_mqtt.return_value = (MagicMock())
         with patch("pt_mock.publish_samples.time.sleep", return_value=None):
             main(run_once=True)
         assert mock_send.call_count == 2

tests/unit/methods/test_sys_id_unit.py

@@ -118,7 +118,8 @@ def test_publish_oma_results_retries_and_publishes_once(mocker):
     aligner = MagicMock()
     aligner.client = MagicMock()
 
-    publish_sysid_output(0.1, aligner, mock_client, "test/topic", fs)
+    # publish_sysid_output(0.1, aligner, mock_client, "test/topic", fs)
+    publish_sysid_output(mock_client, ["test/topic"], 0.1, fs)
 
     assert mock_client.publish.called
     assert mock_client.publish.call_count == 1
@@ -129,15 +130,16 @@ def test_setup_client_with_multiple_topics(mocker):
     mqtt_config = {
         "host": "localhost",
         "port": 1883,
-        "topics": ["topic1", "topic2"]
+        "TopicsToSubscribe": ["topic1", "topic2"]
     }
 
     extract_mock = mocker.patch("methods.sysid.extract_fs_from_metadata", return_value=123.0)
 
     mock_mqtt_client = MagicMock()
-    mocker.patch("methods.sysid.setup_mqtt_client", return_value=(mock_mqtt_client, None))
+    mocker.patch("methods.sysid.setup_mqtt_client", return_value=(mock_mqtt_client))
 
     client, fs = setup_client(mqtt_config)
+    client.loop_stop()
 
     extract_mock.assert_called_once_with(mqtt_config)
     client.connect.assert_called_once_with("localhost", 1883, 60)

tests/unit/mock_pt_test/test_publish_samples.py

@@ -104,7 +104,7 @@ def test_main_executes_sensor_loop_once(self, _, mock_adxl,
         mock_load_config.return_value = {
             "MQTT": {
                 "ClientID": "test-client",
-                "host": "mqtt.eclipseprojects.io",
+                "host": "public.mqttserver.eu",
                 "port": 1883,
                 "userId": "",
                 "password": "",