updates

CHANGELOG.md

@@ -3,7 +3,7 @@
 #### Enhancements
  - UI chart legend's will support more than 8 Pioreactors.
  - UI chart colors are consistent across charts in the Overview.
- - reduce the number of pop-ups in the UI, so they'll be less distractions.
+ - reduce the severity of some messages, so there will be less pop-ups in the UI.
  - UI performance improvements.
    - Upgraded to React 18
    - Removed unused dependencies
@@ -13,14 +13,17 @@
    - faster `pio kill`
    - faster job start from UI
  - more humane error messages.
- - updated temperature inference model
+ - updated temperature inference model.
  - added exponentiation `**` to profile expressions. Ex: `${{ pio1:growth_rate_calculating:growth_rate.growth_rate ** 0.5 }}`
  - added `random()` to profile expressions. This returns a number between 0 and 1. Ex: `${{ 25 + 25 * random() }} `
 
 
-
 #### Bug fixes
- - fix `pio plugins` on workers
+ - fix `pio plugins` not working on workers.
+ - fix `enable_dodging_od=0` for background jobs that can dodge OD.
+ - fix jobs not cleaning up correctly if too many jobs try to end at the same time.
+ - fix `pio kill` not returning the correct count of jobs being killed.
+ - fix older Pioreactor HATs, with the ADS1115 chip, not have the method `from_voltage_to_raw_precise`.
 
 
 ### 24.5.1

config.dev.ini

@@ -53,7 +53,7 @@ samples_per_second=0.2
 
 pd_reference_ema=0.4
 
-ir_led_intensity=auto
+ir_led_intensity=50
 
 # use the most recent calibration file, if available
 use_calibration=1

pioreactor/actions/self_test.py

@@ -129,7 +129,7 @@ def test_all_positive_correlations_between_pds_and_leds(
     # the problem is that if an LED is directly across from a PD, a high intensity will quickly
     # saturate it and fail the test. So we try low intensities first, and if we exceed some threshold
     # we exit before moving to the high intensities.
-    INTENSITIES = [32, 35, 53, 44, 38, 47, 50, 41, 56, 59, 62, 65]
+    INTENSITIES = (32, 35, 53, 44, 38, 47, 50, 41, 56, 59, 62, 65)
 
     results: dict[tuple[LedChannel, PdChannel], float] = {}
 
@@ -458,20 +458,20 @@ def click_self_test(k: Optional[str]) -> int:
     experiment = get_assigned_experiment_name(unit)
     logger = create_logger("self_test", unit=unit, experiment=experiment)
 
-    A_TESTS = [
+    A_TESTS = (
         test_pioreactor_HAT_present,
         test_detect_heating_pcb,
         test_positive_correlation_between_temperature_and_heating,
         test_aux_power_is_not_too_high,
-    ]
-    B_TESTS = [
+    )
+    B_TESTS = (
         test_all_positive_correlations_between_pds_and_leds,
         test_ambient_light_interference,
         test_REF_is_lower_than_0_dot_256_volts,
         test_REF_is_in_correct_position,
         test_PD_is_near_0_volts_for_blank,
         test_positive_correlation_between_rpm_and_stirring,
-    ]
+    )
 
     with managed_lifecycle(unit, testing_experiment, "self_test") as state:
         client = state.mqtt_client

pioreactor/background_jobs/base.py

@@ -1079,8 +1079,10 @@ def _listen_for_od_reading(self) -> None:
     def set_enable_dodging_od(self, value: bool) -> None:
         self.enable_dodging_od = value
         if self.enable_dodging_od:
+            self.logger.info("Will attempt to stop during OD readings.")
             self._listen_for_od_reading()
         else:
+            self.logger.info("Running continuously through OD readings.")
             if hasattr(self, "sneak_in_timer"):
                 self.sneak_in_timer.cancel()
             try:

pioreactor/background_jobs/od_reading.py

@@ -697,17 +697,12 @@ def get_models_from_disk(
                         msg = f"The calibration `{name}` was calibrated with a different PD channel ({calibration_data.pd_channel} vs current: {channel})."
                         self.logger.error(msg)
                         raise exc.CalibrationError(msg)
-                    else:
-                        models[channel] = self._hydrate_model(calibration_data)
-                        self.logger.debug(
-                            f"Using calibration `{name}` for channel {channel}, {calibration_data.curve_type=}, {calibration_data.curve_data_=}"
-                        )
 
-                    # confirm that PD channel is the same as when calibration was performed
-                    if calibration_data.pd_channel != channel:
-                        msg = f"The calibration `{name}` was calibrated with a different PD channel ({calibration_data.pd_channel} vs current: {channel})."
-                        self.logger.error(msg)
-                        raise exc.CalibrationError(msg)
+                    models[channel] = self._hydrate_model(calibration_data)
+                    self.logger.info(f"Using OD calibration `{name}` for channel {channel}.")
+                    self.logger.debug(
+                        f"Using OD calibration `{name}` for channel {channel}, {calibration_data.curve_type=}, {calibration_data.curve_data_=}"
+                    )
 
                 else:
                     self.logger.debug(
@@ -839,7 +834,7 @@ class ODReader(BackgroundJob):
     if whoami.get_pioreactor_version() == (1, 0):
         TARGET_REF_VOLTAGE = 0.10
     elif whoami.get_pioreactor_version() >= (1, 1):
-        TARGET_REF_VOLTAGE = 0.04
+        TARGET_REF_VOLTAGE = 0.50
 
     def __init__(
         self,

pioreactor/background_jobs/temperature_control.py

@@ -36,6 +36,7 @@
 from pioreactor import hardware
 from pioreactor import whoami
 from pioreactor.background_jobs.base import BackgroundJob
+from pioreactor.config import config
 from pioreactor.structs import Temperature
 from pioreactor.structs import TemperatureAutomation
 from pioreactor.utils import clamp
@@ -45,6 +46,7 @@
 from pioreactor.utils.timing import current_utc_timestamp
 from pioreactor.utils.timing import RepeatedTimer
 from pioreactor.utils.timing import to_datetime
+from pioreactor.version import rpi_version_info
 
 
 class TemperatureController(BackgroundJob):
@@ -406,12 +408,23 @@ def infer_temperature(self) -> None:
             previous_heater_dc = self.heater_duty_cycle
 
             features: dict[str, Any] = {}
+
+            # add how much heat/energy we just applied
             features["previous_heater_dc"] = previous_heater_dc
 
             # figure out a better way to estimate this... luckily inference is not too sensitive to this parameter.
             # users can override this function with something more accurate later.
             features["room_temp"] = self._get_room_temperature()
 
+            # B models have a hotter ambient env. TODO: what about As?
+            features["is_rpi_zero"] = rpi_version_info.startswith("Raspberry Pi Zero")
+
+            # the amount of liquid in the vial is a factor!
+            features["volume"] = 0.5 * (
+                config.getfloat("bioreactor", "initial_volume_ml")
+                + config.getfloat("bioreactor", "max_volume_ml")
+            )
+
             # turn off active heating, and start recording decay
             self._update_heater(0)
             time_series_of_temp = []

pioreactor/cli/pio.py

@@ -31,17 +31,14 @@
 from pioreactor.utils.timing import current_utc_timestamp
 from pioreactor.whoami import am_I_leader
 
+lazy_subcommands = {
+    "run": "pioreactor.cli.run.run",
+    "plugins": "pioreactor.cli.plugins.plugins",
+}
+
 if am_I_leader():
-    lazy_subcommands = {
-        "workers": "pioreactor.cli.workers.workers",
-        "run": "pioreactor.cli.run.run",
-        "plugins": "pioreactor.cli.plugins.plugins",
-    }
-else:
-    lazy_subcommands = {
-        "run": "pioreactor.cli.run.run",
-        "plugins": "pioreactor.cli.plugins.plugins",
-    }
+    # add in ability to control workers
+    lazy_subcommands["workers"] = "pioreactor.cli.workers.workers"
 
 
 @click.group(
@@ -175,9 +172,8 @@ def kill(name: str | None, experiment: str | None, job_source: str | None, all_j
     if not (name or experiment or job_source or all_jobs):
         raise click.Abort("Provide an option to kill.")
     with JobManager() as jm:
-        count = jm.count_jobs(all_jobs=all_jobs, name=name, experiment=experiment, job_source=job_source)
-        jm.kill_jobs(all_jobs=all_jobs, name=name, experiment=experiment, job_source=job_source)
-    click.echo(f"Killed {count} job(s).")
+        count = jm.kill_jobs(all_jobs=all_jobs, name=name, experiment=experiment, job_source=job_source)
+    click.echo(f"Killed {count} job{'s' if count > 1 else ''}.")
 
 
 @pio.command(name="version", short_help="print the Pioreactor software version")

pioreactor/hardware.py

@@ -144,7 +144,7 @@ def voltage_in_aux(precision: float = 0.1) -> float:
 
     slope = 0.134  # from schematic
 
-    adc = ADC_class()
+    adc = ADC_class()  # type: ignore
     return round_to_precision(
         adc.from_raw_to_voltage(adc.read_from_channel(ADC_CHANNEL_FUNCS["aux"])) / slope,
         p=precision,

pioreactor/plugin_management/install_plugin.py

@@ -14,12 +14,12 @@
 def install_plugin(name_of_plugin: str, source: str | None = None) -> None:
     logger = create_logger("install_plugin", experiment=UNIVERSAL_EXPERIMENT)
     logger.debug(f"Installing plugin {name_of_plugin}.")
-    command = [
+    command = (
         "bash",
         "/usr/local/bin/install_pioreactor_plugin.sh",
         quote(name_of_plugin),
         source or "",
-    ]
+    )
     logger.debug(" ".join(command))
 
     result = subprocess.run(command, capture_output=True)

pioreactor/tests/test_monitor.py

@@ -85,22 +85,36 @@ def test_run_job_with_monitor() -> None:
 def test_job_options_and_args_to_shell_command() -> None:
     m = Monitor
     assert (
-        m._job_options_and_args_to_shell_command("stirring", [], {"target_rpm": 400})
-        == "JOB_SOURCE=user nohup pio run stirring --target-rpm 400 >/dev/null 2>&1 &"
+        m._job_options_and_args_to_shell_command("stirring", "Exp001", [], {"target_rpm": 400})
+        == "JOB_SOURCE=user EXPERIMENT=Exp001 nohup pio run stirring --target-rpm 400 >/dev/null 2>&1 &"
     )
     assert (
-        m._job_options_and_args_to_shell_command("stirring", [], {"ignore_rpm": None})
-        == "JOB_SOURCE=user nohup pio run stirring --ignore-rpm >/dev/null 2>&1 &"
+        m._job_options_and_args_to_shell_command("stirring", "Exp001", [], {"ignore_rpm": None})
+        == "JOB_SOURCE=user EXPERIMENT=Exp001 nohup pio run stirring --ignore-rpm >/dev/null 2>&1 &"
     )
     assert (
-        m._job_options_and_args_to_shell_command("stirring", [], {})
-        == "JOB_SOURCE=user nohup pio run stirring >/dev/null 2>&1 &"
+        m._job_options_and_args_to_shell_command("stirring", "Exp001", [], {})
+        == "JOB_SOURCE=user EXPERIMENT=Exp001 nohup pio run stirring >/dev/null 2>&1 &"
     )
     assert (
-        m._job_options_and_args_to_shell_command("od_calibration", ["list"], {})
-        == "JOB_SOURCE=user nohup pio run od_calibration list >/dev/null 2>&1 &"
+        m._job_options_and_args_to_shell_command("od_calibration", "Exp001", ["list"], {})
+        == "JOB_SOURCE=user EXPERIMENT=Exp001 nohup pio run od_calibration list >/dev/null 2>&1 &"
     )
     assert (
-        m._job_options_and_args_to_shell_command("stirring", [], {"job_source": "experiment_profile"})
+        m._job_options_and_args_to_shell_command(
+            "stirring", "Exp001", [], {"job_source": "experiment_profile"}
+        )
+        == "JOB_SOURCE=experiment_profile EXPERIMENT=Exp001 nohup pio run stirring >/dev/null 2>&1 &"
+    )
+
+    assert (
+        m._job_options_and_args_to_shell_command("stirring", None, [], {"job_source": "experiment_profile"})
         == "JOB_SOURCE=experiment_profile nohup pio run stirring >/dev/null 2>&1 &"
     )
+
+    assert (
+        m._job_options_and_args_to_shell_command(
+            "stirring", "white space", [], {"job_source": "experiment_profile"}
+        )
+        == "JOB_SOURCE=experiment_profile EXPERIMENT='white space' nohup pio run stirring >/dev/null 2>&1 &"
+    )

pioreactor/tests/test_od_reading.py

@@ -974,3 +974,116 @@ def test_auto_ir_led_intensity() -> None:
         assert od.ir_led_intensity == 20.0
 
     config["od_config"]["ir_led_intensity"] = existing_intensity
+
+
+def test_CachedCalibrationTransformer_with_real_calibration():
+    calibration = structs.OD90Calibration(
+        angle="90",
+        maximum_od600=1.0,
+        minimum_od600=0.0,
+        minimum_voltage=0.044709852782465254,
+        maximum_voltage=1.359234153183015,
+        curve_type="poly",
+        curve_data_=[
+            -0.9876751958847302,
+            1.2023377416112089,
+            0.2591472668916862,
+            0.8385902257553322,
+            0.0445071255201746,
+        ],
+        voltages=[
+            1.359234153183015,
+            1.1302469550069834,
+            0.9620188870414657,
+            0.8276740491499182,
+            0.7190293946984384,
+            0.7476589503369395,
+            0.566173065500996,
+            0.46932081671790027,
+            0.40529520650943107,
+            0.35571051870062176,
+            0.3671813602478582,
+            0.30365395611828694,
+            0.2546057746249075,
+            0.22793433386962852,
+            0.20673156637999296,
+            0.21349869357483414,
+            0.182990681059356,
+            0.15688343308939462,
+            0.1576635057554899,
+            0.12760694773293027,
+            0.1334217593444793,
+            0.12112005296098335,
+            0.10527636587260703,
+            0.10005326421654448,
+            0.08968165025432195,
+            0.0934433078631241,
+            0.08568480676160387,
+            0.07354768447704799,
+            0.07012049853534189,
+            0.06976807020449396,
+            0.0692776692431696,
+            0.06519934195388995,
+            0.05689993752281371,
+            0.06139548846791462,
+            0.05434995401134063,
+            0.058377357520436435,
+            0.05744855604656168,
+            0.051622250927144994,
+            0.04809794996045024,
+            0.044709852782465254,
+        ],
+        od600s=[
+            1.0,
+            0.8333333333333334,
+            0.7142857142857143,
+            0.625,
+            0.5555555555555556,
+            0.58,
+            0.48333333333333334,
+            0.41428571428571426,
+            0.3625,
+            0.3222222222222222,
+            0.3,
+            0.25,
+            0.21428571428571427,
+            0.1875,
+            0.16666666666666666,
+            0.18,
+            0.15,
+            0.12857142857142856,
+            0.11249999999999999,
+            0.09999999999999999,
+            0.1,
+            0.08333333333333333,
+            0.07142857142857142,
+            0.0625,
+            0.05555555555555555,
+            0.065,
+            0.05416666666666667,
+            0.04642857142857143,
+            0.040625,
+            0.036111111111111115,
+            0.04,
+            0.03333333333333333,
+            0.028571428571428574,
+            0.025,
+            0.022222222222222223,
+            0.03,
+            0.024999999999999998,
+            0.02142857142857143,
+            0.01875,
+            0.0,
+        ],
+        ir_led_intensity=50,
+        pd_channel="2",
+        created_at="2024-05-10T14:13:20.698706Z",
+        pioreactor_unit="pio1",
+        name="test",
+    )
+    with local_persistant_storage("current_od_calibration") as cc:
+        cc[calibration.angle] = encode(calibration)
+
+    cal_transformer = CachedCalibrationTransformer({"2": "90"})
+
+    assert abs(cal_transformer({"2": 0.096})["2"] - 0.06) < 0.01