test fixes

CHANGELOG.md

@@ -1,7 +1,12 @@
 ### Upcoming
  - When installing plugins, any leader-only commands would not be run. This is fixed.
- - Base automations now subclass from `pioreactor.automations.BaseAutomationJob`. Nothing the user needs to worry about.
+ - Base automations now subclass from `pioreactor.automations.BaseAutomationJob`. You may need to change custom automation imports from, for example, `from pioreactor.automations import DosingAutomationJobContrib` to `from pioreactor.automations.dosing.base import DosingAutomationJobContrib`
  - Fixed bug that ignored `.yml` files in the UI.
+ - Improvements to experiment profiles, both in the UI and in the backend. Executing now verifies common mistakes in experiment profiles before it runs.
+ - Fixed a bug that could cause controllers to have a disconnected automation. #422
+ - SPI is on by default on all new image installs
+ - Plugin author information is presented on the `/plugins` page in the UI.
+
 
 ### 23.8.29
  - Pioreactor's IPv4 and hostname is now displayed under System in the UI.

pioreactor/actions/leader/experiment_profile.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 from __future__ import annotations
 
+from collections import defaultdict
 from pathlib import Path
 from threading import Timer
 from typing import Callable
@@ -112,7 +113,46 @@ def hours_to_seconds(hours: float) -> float:
 
 def load_and_verify_profile_file(profile_filename: str) -> struct.Profile:
     with open(profile_filename) as f:
-        return decode(f.read(), type=struct.Profile)
+        profile = decode(f.read(), type=struct.Profile)
+
+    actions_per_job = defaultdict(list)
+
+    for job in profile.common.keys():
+        for action in profile.common[job]["actions"]:
+            actions_per_job[job].append(action)
+
+    for unit in profile.pioreactors.values():
+        for job in unit["jobs"].keys():
+            for action in unit["jobs"][job]["actions"]:
+                actions_per_job[job].append(action)
+
+    # TODO: things to check for:
+    # 1. Don't "stop" any *_automations
+    # 2. Don't change generic settings on *_controllers, (Ex: changing target temp on temp_controller is wrong)
+
+    # 1.
+    def check_for_not_stopping_automations(act):
+        if act.type == "stop":
+            raise ValueError("Don't use 'stop' for automations. Use 'stop' for controllers.")
+        return True
+
+    for automation_type in ["temperature_automation", "dosing_automation", "led_automation"]:
+        assert all(
+            check_for_not_stopping_automations(act) for act in actions_per_job[automation_type]
+        )
+
+    # 2.
+    def check_for_settings_change_on_controllers(act):
+        if act.type == "update" and "automation-name" not in act.options:
+            raise ValueError("Update automations, not controllers, with settings.")
+        return True
+
+    for control_type in ["temperature_control", "dosing_control", "led_control"]:
+        assert all(
+            check_for_settings_change_on_controllers(act) for act in actions_per_job[control_type]
+        )
+
+    return profile
 
 
 def publish_labels_to_ui(labels_map: dict[str, str]) -> None:

pioreactor/tests/test_led_control.py

@@ -27,7 +27,9 @@ def pause(n=1) -> None:
 
 def test_silent() -> None:
     experiment = "test_silent"
-    with LEDController("silent", duration=60, unit=unit, experiment=experiment) as ld:
+    with LEDController(
+        automation_name="silent", duration=60, unit=unit, experiment=experiment
+    ) as ld:
         pause()
         pause()
         pause()
@@ -54,7 +56,7 @@ def test_changing_automation_over_mqtt() -> None:
     experiment = "test_changing_automation_over_mqtt"
     original_duration = 60
     with LEDController(
-        "silent", duration=original_duration, unit=unit, experiment=experiment
+        automation_name="silent", duration=original_duration, unit=unit, experiment=experiment
     ) as ld:
         assert ld.automation_name == "silent"
         assert ld.automation_job.duration == original_duration
@@ -110,7 +112,7 @@ def test_light_dark_cycle_starts_on() -> None:
     experiment = "test_light_dark_cycle_starts_on"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=60,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -130,7 +132,7 @@ def test_light_dark_cycle_turns_off_after_N_cycles() -> None:
     experiment = "test_light_dark_cycle_turns_off_after_N_cycles"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.01,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -155,7 +157,7 @@ def test_dark_duration_hour_to_zero() -> None:
     experiment = "test_dark_duration_hour_to_zero"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.005,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -185,7 +187,7 @@ def test_light_duration_hour_to_zero() -> None:
     experiment = "test_light_duration_hour_to_zero"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.01,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -205,7 +207,7 @@ def test_add_dark_duration_minutes() -> None:
     experiment = "test_add_dark_duration_minutes * 60"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.01,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -235,7 +237,7 @@ def test_remove_dark_duration_minutes() -> None:
     experiment = "test_remove_dark_duration_minutes * 60"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.005,
         light_intensity=50,
         light_duration_minutes=60 * 16,
@@ -269,7 +271,7 @@ def test_fractional_hours() -> None:
     experiment = "test_fractional_hours"
     unit = get_unit_name()
     with LEDController(
-        "light_dark_cycle",
+        automation_name="light_dark_cycle",
         duration=0.005,
         light_intensity=50,
         light_duration_minutes=60 * 0.9,

pioreactor/tests/test_temperature_approximation.py

@@ -34,7 +34,7 @@ def test_temperature_approximation_if_less_than_hardcoded_room_temp() -> None:
         ],
     }
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 19.0 <= t.approximate_temperature(features) <= 20.0
 
@@ -46,7 +46,7 @@ def test_temperature_approximation_if_constant() -> None:
     features = {"previous_heater_dc": 17, "time_series_of_temp": 30 * [32.0]}
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         for temp in range(20, 45):
             features = {
@@ -72,7 +72,7 @@ def test_temperature_approximation_even_if_very_tiny_heat_source() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert (32 * np.exp(-0.008 * 17)) < t.approximate_temperature(features) < 32
 
@@ -92,7 +92,7 @@ def test_temperature_approximation_even_if_very_large_heat_source() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert (24 * np.exp(-0.008 * 17)) < t.approximate_temperature(features) < 25
 
@@ -103,7 +103,7 @@ def test_temperature_approximation_if_dc_is_nil() -> None:
     unit = get_unit_name()
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert t.approximate_temperature(features) == 32.1875
 
@@ -150,7 +150,7 @@ def test_temperature_approximation1() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 33.389 <= t.approximate_temperature(features) <= 33.830
 
@@ -196,7 +196,7 @@ def test_temperature_approximation_heating_vial1() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 33.525 <= t.approximate_temperature(features) <= 34.00
 
@@ -242,7 +242,7 @@ def test_temperature_approximation_heating_vial2() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 33.695 <= t.approximate_temperature(features) <= 34.170
 
@@ -288,7 +288,7 @@ def test_temperature_approximation_heating_vial3() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 33.898 <= t.approximate_temperature(features) <= 34.339
 
@@ -334,7 +334,7 @@ def test_temperature_approximation_heating_vial4() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.068 <= t.approximate_temperature(features) <= 34.577
 
@@ -380,7 +380,7 @@ def test_temperature_approximation_heating_vial5() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.305 <= t.approximate_temperature(features) <= 34.814
 
@@ -426,7 +426,7 @@ def test_temperature_approximation6() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.475 <= t.approximate_temperature(features) <= 35.018
 
@@ -472,7 +472,7 @@ def test_temperature_approximation7() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.644 <= t.approximate_temperature(features) <= 35.153
 
@@ -518,7 +518,7 @@ def test_temperature_approximation8() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.746 <= t.approximate_temperature(features) <= 35.289
 
@@ -563,7 +563,7 @@ def test_temperature_approximation9() -> None:
         ],
     }
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.848 <= t.approximate_temperature(features) <= 35.391
 
@@ -609,7 +609,7 @@ def test_temperature_approximation10() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.950 <= t.approximate_temperature(features) <= 35.493
 
@@ -655,7 +655,7 @@ def test_temperature_approximation20() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 34.950 <= t.approximate_temperature(features) <= 35.493
 
@@ -702,7 +702,7 @@ def test_temperature_approximation_cooling1() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 32.169 <= t.approximate_temperature(features)
 
@@ -748,7 +748,7 @@ def test_temperature_approximation_cooling2() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 31.118 <= t.approximate_temperature(features)
 
@@ -794,7 +794,7 @@ def test_temperature_approximation11() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 29.628 <= t.approximate_temperature(features) <= 30.136
 
@@ -840,7 +840,7 @@ def test_temperature_approximation12() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 28.476 <= t.approximate_temperature(features) <= 28.747
 
@@ -886,7 +886,7 @@ def test_temperature_approximation13() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 28.374 <= t.approximate_temperature(features) <= 28.645
 
@@ -932,7 +932,7 @@ def test_temperature_approximation14() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 28.374 <= t.approximate_temperature(features) <= 28.578
 
@@ -977,7 +977,7 @@ def test_temperature_approximation15() -> None:
         ],
     }
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 28.815 <= t.approximate_temperature(features) <= 29.119
 
@@ -1024,7 +1024,7 @@ def test_temperature_approximation16() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 25.261 <= t.approximate_temperature(features) <= 25.430
 
@@ -1071,6 +1071,6 @@ def test_temperature_approximation17() -> None:
     }
 
     with temperature_control.TemperatureController(
-        "only_record_temperature", unit=unit, experiment=experiment
+        automation_name="only_record_temperature", unit=unit, experiment=experiment
     ) as t:
         assert 25.295 <= t.approximate_temperature(features) <= 25.430