introduce new temp config change, fix stirring not unpausing correctl…

…y when dodging'

config.dev.ini

@@ -36,6 +36,10 @@ target_rpm=500
 initial_duty_cycle=15
 pwm_hz=200
 use_rpm=True
+duration_between_updates_seconds=23
+post_delay_duration=0.25
+pre_delay_duration=2.0
+enable_dodging_od=True
 
 [stirring.pid]
 Kp=10.0

pioreactor/actions/od_blank.py

@@ -17,6 +17,7 @@
 from pioreactor import types as pt
 from pioreactor import whoami
 from pioreactor.config import config
+from pioreactor.config import temporary_config_change
 from pioreactor.logging import create_logger
 from pioreactor.pubsub import prune_retained_messages
 from pioreactor.utils import is_pio_job_running
@@ -26,10 +27,6 @@
 from pioreactor.utils.timing import current_utc_datetime
 
 
-# turn off dodging in the stirring, if set to true.
-config["stirring.config"]["enable_dodging_od"] = "False"
-
-
 def od_statistics(
     od_stream: Iterator,
     action_name: str,
@@ -257,13 +254,14 @@ def click_od_blank(ctx, od_angle_channel1, od_angle_channel2, n_samples: int) ->
     experiment = whoami.get_assigned_experiment_name(unit)
 
     if ctx.invoked_subcommand is None:
-        od_blank(
-            od_angle_channel1,
-            od_angle_channel2,
-            n_samples=n_samples,
-            unit=unit,
-            experiment=experiment,
-        )
+        with temporary_config_change(config, "stirring.config", "enable_dodging_od", "false"):
+            od_blank(
+                od_angle_channel1,
+                od_angle_channel2,
+                n_samples=n_samples,
+                unit=unit,
+                experiment=experiment,
+            )
 
 
 @click_od_blank.command(name="delete")

pioreactor/actions/self_test.py

@@ -32,6 +32,7 @@
 from pioreactor.background_jobs.od_reading import REF_keyword
 from pioreactor.background_jobs.od_reading import start_od_reading
 from pioreactor.config import config
+from pioreactor.config import temporary_config_change
 from pioreactor.hardware import is_HAT_present
 from pioreactor.hardware import is_heating_pcb_present
 from pioreactor.hardware import voltage_in_aux
@@ -57,10 +58,6 @@
 from pioreactor.whoami import is_testing_env
 
 
-# turn off dodging in the stirring, if set to true.
-config["stirring.config"]["enable_dodging_od"] = "False"
-
-
 def test_pioreactor_HAT_present(managed_state, logger: CustomLogger, unit: str, experiment: str) -> None:
     assert is_HAT_present(), "HAT is not connected"
 
@@ -518,7 +515,9 @@ def click_self_test(k: Optional[str], retry_failed: bool) -> int:
         test_positive_correlation_between_rpm_and_stirring,
     )
 
-    with managed_lifecycle(unit, experiment, "self_test") as managed_state:
+    with managed_lifecycle(unit, experiment, "self_test") as managed_state, temporary_config_change(
+        config, "stirring.config", "enable_dodging_od", "false"
+    ):
         if any(
             is_pio_job_running(
                 ["od_reading", "temperature_automation", "stirring", "dosing_automation", "led_automation"]

pioreactor/background_jobs/base.py

@@ -1024,7 +1024,6 @@ def action_to_do_after_od_reading(self):
 
     def __init__(self, *args, source="app", **kwargs) -> None:
         super().__init__(*args, source=source, **kwargs)  # type: ignore
-
         self.add_to_published_settings("enable_dodging_od", {"datatype": "boolean", "settable": True})
         self.set_enable_dodging_od(self.get_from_config("enable_dodging_od", cast=bool, fallback="True"))
 

pioreactor/background_jobs/stirring.py

@@ -284,7 +284,9 @@ def action_to_do_before_od_reading(self):
         self.on_ready_to_sleeping()
 
     def action_to_do_after_od_reading(self):
-        self.on_sleeping_to_ready()
+        self.duty_cycle = self._estimate_duty_cycle
+        self.rpm_check_repeated_thread.unpause()
+        self.start_stirring()
 
     def initialize_rpm_to_dc_lookup(self) -> Callable:
         if self.rpm_calculator is None:
@@ -314,6 +316,7 @@ def initialize_rpm_to_dc_lookup(self) -> Callable:
                 return lambda rpm: self._estimate_duty_cycle
 
     def on_disconnected(self) -> None:
+        super().on_disconnected()
         with suppress(AttributeError):
             self.rpm_check_repeated_thread.cancel()
         with suppress(AttributeError):
@@ -423,9 +426,12 @@ def on_ready_to_sleeping(self) -> None:
         self.set_duty_cycle(0.0)
 
     def on_sleeping_to_ready(self) -> None:
+        super().on_sleeping_to_ready()
         self.duty_cycle = self._estimate_duty_cycle
         self.rpm_check_repeated_thread.unpause()
-        self.start_stirring()
+        if not self.enable_dodging_od:
+            # if we aren't dodging OD readings, we can start stirring right away.
+            self.start_stirring()
 
     def set_duty_cycle(self, value: float) -> None:
         with self.duty_cycle_lock:

pioreactor/config.py

@@ -3,6 +3,7 @@
 
 import configparser
 import os
+from contextlib import contextmanager
 from functools import cache
 from pathlib import Path
 
@@ -126,7 +127,7 @@ def get_config() -> ConfigParserMod:
     from pioreactor.whoami import is_testing_env
 
     if is_testing_env():
-        global_config_path = os.environ.get("GLOBAL_CONFIG", "./config.dev.ini")
+        global_config_path = os.environ.get("GLOBAL_CONFIG", "./.pioreactor/config.dev.ini")
         local_config_path = os.environ.get("LOCAL_CONFIG", "")
     else:
         global_config_path = "/home/pioreactor/.pioreactor/config.ini"
@@ -136,7 +137,6 @@ def get_config() -> ConfigParserMod:
         raise FileNotFoundError(
             f"Configuration file at {global_config_path} is missing. Has it completed initializing? Does it need to connect to a leader? Alternatively, use the env variable GLOBAL_CONFIG to specify its location."
         )
-
     config_files = [global_config_path, local_config_path]
 
     try:
@@ -189,3 +189,34 @@ def get_leader_address() -> str:
 @cache
 def get_mqtt_address() -> str:
     return get_config().get("mqtt", "broker_address", fallback=get_leader_address())
+
+
+@contextmanager
+def temporary_config_change(config: ConfigParserMod, section: str, parameter: str, new_value: str):
+    """
+    A context manager to temporarily change a value in a ConfigParser object.
+
+    Args:
+        config (ConfigParser): The ConfigParser instance.
+        section (str): The section in the ConfigParser to modify.
+        parameter (str): The parameter in the section to modify.
+        new_value (str): The temporary value for the parameter.
+
+    Yields:
+        None: The context where the parameter is temporarily modified.
+    """
+    if not config.has_section(section):
+        raise ValueError(f"Section '{section}' does not exist in the configuration.")
+    if not config.has_option(section, parameter):
+        raise ValueError(f"Parameter '{parameter}' does not exist in section '{section}'.")
+
+    # Save the original value
+    original_value = config.get(section, parameter)
+
+    try:
+        # Apply the temporary change
+        config.set(section, parameter, new_value)
+        yield
+    finally:
+        # Restore the original value
+        config.set(section, parameter, original_value)

pioreactor/tests/test_od_reading.py

@@ -12,11 +12,13 @@
 from pioreactor import structs
 from pioreactor.background_jobs.od_reading import ADCReader
 from pioreactor.background_jobs.od_reading import CachedCalibrationTransformer
+from pioreactor.background_jobs.od_reading import closest_point_to_domain
 from pioreactor.background_jobs.od_reading import NullCalibrationTransformer
 from pioreactor.background_jobs.od_reading import ODReader
 from pioreactor.background_jobs.od_reading import PhotodiodeIrLedReferenceTrackerStaticInit
 from pioreactor.background_jobs.od_reading import start_od_reading
 from pioreactor.config import config
+from pioreactor.config import temporary_config_change
 from pioreactor.pubsub import collect_all_logs_of_level
 from pioreactor.utils import local_persistant_storage
 from pioreactor.utils.timing import current_utc_datetime
@@ -796,37 +798,34 @@ def test_calibration_multi_modal() -> None:
 def test_calibration_errors_when_ir_led_differs() -> None:
     experiment = "test_calibration_errors_when_ir_led_differs"
 
-    config["od_reading.config"]["ir_led_intensity"] = "90"
-
-    with local_persistant_storage("current_od_calibration") as c:
-        c["90"] = encode(
-            structs.OD90Calibration(
-                created_at=current_utc_datetime(),
-                curve_type="poly",
-                curve_data_=[1.0, 0, -0.1],
-                name="quad_test",
-                maximum_od600=2.0,
-                minimum_od600=0.0,
-                ir_led_intensity=50.0,
-                angle="90",
-                minimum_voltage=0.0,
-                maximum_voltage=1.0,
-                voltages=[],
-                od600s=[],
-                pd_channel="2",
-                pioreactor_unit=get_unit_name(),
+    with temporary_config_change(config, "od_reading.config", "ir_led_intensity", "90"):
+        with local_persistant_storage("current_od_calibration") as c:
+            c["90"] = encode(
+                structs.OD90Calibration(
+                    created_at=current_utc_datetime(),
+                    curve_type="poly",
+                    curve_data_=[1.0, 0, -0.1],
+                    name="quad_test",
+                    maximum_od600=2.0,
+                    minimum_od600=0.0,
+                    ir_led_intensity=50.0,
+                    angle="90",
+                    minimum_voltage=0.0,
+                    maximum_voltage=1.0,
+                    voltages=[],
+                    od600s=[],
+                    pd_channel="2",
+                    pioreactor_unit=get_unit_name(),
+                )
             )
-        )
 
-    with pytest.raises(exc.CalibrationError) as error:
-        with start_od_reading("REF", "90", interval=1, fake_data=True, experiment=experiment):
-            pass
-    assert "LED intensity" in str(error.value)
-
-    with local_persistant_storage("current_od_calibration") as c:
-        del c["90"]
+        with pytest.raises(exc.CalibrationError) as error:
+            with start_od_reading("REF", "90", interval=1, fake_data=True, experiment=experiment):
+                pass
+        assert "LED intensity" in str(error.value)
 
-    config["od_reading.config"]["ir_led_intensity"] = "auto"
+        with local_persistant_storage("current_od_calibration") as c:
+            del c["90"]
 
 
 def test_calibration_errors_when_pd_channel_differs() -> None:
@@ -1048,42 +1047,27 @@ def test_calibration_data_from_user2() -> None:
 
 
 def test_auto_ir_led_intensit_REF_and_90() -> None:
-    existing_intensity = config["od_reading.config"]["ir_led_intensity"]
+    with temporary_config_change(config, "od_reading.config", "ir_led_intensity", "auto"):
+        experiment = "test_auto_ir_led_intensity"
 
-    config["od_reading.config"]["ir_led_intensity"] = "auto"
-
-    experiment = "test_auto_ir_led_intensity"
-
-    with start_od_reading("REF", "90", interval=None, fake_data=True, experiment=experiment) as od:
-        assert abs(od.ir_led_intensity - 67.19794921875) < 0.01
-
-    config["od_reading.config"]["ir_led_intensity"] = existing_intensity
+        with start_od_reading("REF", "90", interval=None, fake_data=True, experiment=experiment) as od:
+            assert abs(od.ir_led_intensity - 67.19794921875) < 0.01
 
 
 def test_auto_ir_led_intensity_90_only() -> None:
-    existing_intensity = config["od_reading.config"]["ir_led_intensity"]
-
-    config["od_reading.config"]["ir_led_intensity"] = "auto"
-
-    experiment = "test_auto_ir_led_intensity"
+    with temporary_config_change(config, "od_reading.config", "ir_led_intensity", "auto"):
+        experiment = "test_auto_ir_led_intensity"
 
-    with start_od_reading(None, "90", interval=None, fake_data=True, experiment=experiment) as od:
-        assert od.ir_led_intensity == 70.0
-
-    config["od_reading.config"]["ir_led_intensity"] = existing_intensity
+        with start_od_reading(None, "90", interval=None, fake_data=True, experiment=experiment) as od:
+            assert od.ir_led_intensity == 70.0
 
 
 def test_auto_ir_led_intensity_90_and_90() -> None:
-    existing_intensity = config["od_reading.config"]["ir_led_intensity"]
-
-    config["od_reading.config"]["ir_led_intensity"] = "auto"
-
-    experiment = "test_auto_ir_led_intensity"
+    with temporary_config_change(config, "od_reading.config", "ir_led_intensity", "auto"):
+        experiment = "test_auto_ir_led_intensity"
 
-    with start_od_reading("90", "90", interval=None, fake_data=True, experiment=experiment) as od:
-        assert od.ir_led_intensity == 70.0
-
-    config["od_reading.config"]["ir_led_intensity"] = existing_intensity
+        with start_od_reading("90", "90", interval=None, fake_data=True, experiment=experiment) as od:
+            assert od.ir_led_intensity == 70.0
 
 
 def test_at_least_one_channel() -> None:
@@ -1214,3 +1198,31 @@ def test_CachedCalibrationTransformer_with_real_calibration() -> None:
     cal_transformer.hydate_models_from_disk({"2": "90"})
 
     assert abs(cal_transformer({"2": 0.096})["2"] - 0.06) < 0.01
+
+
+def test_closest_point_single_point_in_domain():
+    assert closest_point_to_domain([1.0], (0.5, 1.5)) == 1.0
+
+
+def test_closest_point_multiple_points_in_domain():
+    assert closest_point_to_domain([0.6, 0.8, 1.2], (0.5, 1.5)) == 0.6
+
+
+def test_closest_point_all_outside_domain():
+    assert closest_point_to_domain([2.0, 3.0], (0.5, 1.5)) == 2.0
+    assert closest_point_to_domain([-1.0, -2.0], (0.5, 1.5)) == -1.0
+
+
+def test_closest_point_empty_list():
+    with pytest.raises(AssertionError):
+        closest_point_to_domain([], (0.5, 1.5))
+
+
+def test_closest_point_on_boundaries():
+    assert closest_point_to_domain([0.5, 1.5], (0.5, 1.5)) == 0.5
+
+
+def test_missing_calibration_data():
+    cal_transformer = CachedCalibrationTransformer()
+    cal_transformer.models = {"1": lambda v: v * 2}
+    assert cal_transformer({"1": 1.0, "2": 2.0}) == {"1": 2.0, "2": 2.0}