changelog and test

Author: CamDavidsonPilon

CHANGELOG.md

@@ -2,8 +2,9 @@
 
 #### Enhancements
  - new _System logs_ under _Inventory_ to track logs happening outside of experiments in your cluster.
+  - Better organization of logs in the UI. System logs, like calibrations, worker additions, etc. won't show up on the Overview page.
  - Exported data zips have folders for each dataset requested.
- - Improvements to the Kalman filter. For users using the growth-rate model with dosing, you should see improvements to your growth-rate time series. We recommend the following configuration:
+ - Improvements to the Kalman filter. For users using the growth-rate model with media dosing, you should see improvements to your growth-rate time series. We recommend the following configuration:
  ```
 [growth_rate_kalman]
 # obs_std ↑ smooths growth rate, rate_std ↑ more responsive growth rate
@@ -14,13 +15,13 @@ rate_std=0.25
  - New image installs only:
    - updated base OS to the latest 25-05-06 Raspberry Pi OS. The big change is using Linux kernel 6.12.
  - Added the column `hours_since_experiment_created` to dataset exports that details hours since experiment was created.
- - Better organization of logs in the UI.
+ - Performance optimizations
 
 #### Bug fixes
  - fixed stirrer not spinning on Pioreactor page (UI) in some cases
  - alert user if their OD reading is constant before starting the growth-rate calculator, which would break things.
  - alert user if their software is installed in a non-standard location. If so, try `pio uninstall pioreactor -y`.
- - Added a warning if the OD calibration is invalid (constant)
+ - Added a warning if the OD calibration is invalid (ex: a constant line)
 
 
 

pioreactor/tests/test_mqtt_to_db_streaming.py

@@ -173,19 +173,6 @@ def test_kalman_filter_entries() -> None:
     with local_persistent_storage("od_normalization_variance") as cache:
         cache[exp] = json.dumps({"1": 1e-6, "2": 1e-4})
 
-    # turn on data collection
-    interval = 0.5
-    od = start_od_reading(
-        od_angle_channel1="135",
-        od_angle_channel2="90",
-        interval=interval,
-        fake_data=True,
-        unit=unit,
-        experiment=exp,
-    )
-
-    gr = GrowthRateCalculator(unit=unit, experiment=exp)
-
     # turn on our mqtt to db
     parsers = [
         m2db.TopicToParserToTable(
@@ -195,37 +182,46 @@ def test_kalman_filter_entries() -> None:
         )
     ]
 
-    m = m2db.MqttToDBStreamer(unit, exp, parsers)
-
-    # let data collect
-    sleep(10)
-
-    cursor.execute("SELECT * FROM kalman_filter_outputs WHERE experiment = ?", (exp,))
-    results = cursor.fetchall()
-    assert len(results) > 0
-
-    cursor.execute(
-        "SELECT state_0, state_1, state_2 FROM kalman_filter_outputs WHERE experiment = ? ORDER BY timestamp DESC LIMIT 1",
-        (exp,),
-    )
-    results = cursor.fetchone()
-    assert results[0] != 0.0
-    assert results[1] != 0.0
-    assert results[2] != 0.0
-
-    cursor.execute(
-        "SELECT cov_00, cov_11, cov_22 FROM kalman_filter_outputs WHERE experiment = ? ORDER BY timestamp DESC LIMIT 1",
-        (exp,),
-    )
-    results = cursor.fetchone()
+    # turn on data collection
+    interval = 0.5
 
-    assert results[0] != 0.0
-    assert results[1] != 0.0
-    assert results[2] != 0.0
+    with (
+        start_od_reading(
+            od_angle_channel1="135",
+            od_angle_channel2="90",
+            interval=interval,
+            fake_data=True,
+            unit=unit,
+            experiment=exp,
+        ),
+        GrowthRateCalculator(unit=unit, experiment=exp),
+        m2db.MqttToDBStreamer(unit, exp, parsers),
+    ):
+        # let data collect
+        sleep(10)
+
+        cursor.execute("SELECT * FROM kalman_filter_outputs WHERE experiment = ?", (exp,))
+        results = cursor.fetchall()
+        assert len(results) > 0
+
+        cursor.execute(
+            "SELECT state_0, state_1, state_2 FROM kalman_filter_outputs WHERE experiment = ? ORDER BY timestamp DESC LIMIT 1",
+            (exp,),
+        )
+        results = cursor.fetchone()
+        assert results[0] != 0.0
+        assert results[1] != 0.0
+        assert results[2] != 0.0
+
+        cursor.execute(
+            "SELECT cov_00, cov_11, cov_22 FROM kalman_filter_outputs WHERE experiment = ? ORDER BY timestamp DESC LIMIT 1",
+            (exp,),
+        )
+        results = cursor.fetchone()
 
-    od.clean_up()
-    gr.clean_up()
-    m.clean_up()
+        assert results[0] != 0.0
+        assert results[1] != 0.0
+        assert results[2] != 0.0
 
 
 def test_empty_payload_is_filtered_early() -> None:

pioreactor/utils/__init__.py

@@ -344,7 +344,7 @@ def __enter__(self):
         self.cursor.executescript(
             """
             PRAGMA busy_timeout = 5000;
-            PRAGMA temp_store = 2;  -- stop writing small files to disk, use mem
+            PRAGMA temp_store = 2;
             PRAGMA cache_size = -4000;
         """
         )