fix tets

Author: CamDavidsonPilon

CHANGELOG.md

@@ -2,17 +2,41 @@
 
 Some big changes internally
 
+#### Highlights
+
+ - Users have been very creative in adapting the Pioreactor hardware and software to different bioreactors. We have a new tool you can use: adding custom bioreactors models to incorporate into the Pioreactor software! There is a new `.pioreactor/models/` directory where you can place custom bioreactors. For example:
+
+   ```
+   model_name: custom_100ml
+   model_version: "1.0"
+   display_name: "Custom 100 mL, v1.0"
+   reactor_capacity_ml: 100.0
+   reactor_max_fill_volume_ml: 95.0
+   reactor_diameter_mm: 50.0
+   max_temp_to_reduce_heating: 80.0
+   max_temp_to_disable_heating: 85.0
+   max_temp_to_shutdown: 90.0
+   ```
+
+   This data will be used throughout the software (including in the UI) to support other bioreactor shapes and sizes. Let us know what else you would like to see!
+
+ - adding mcp server
+
+#### Enhancements
  - time range filter in export data page
  - ability to change the pause between LEDs and OD snapshot
- - fix export data sorting
- - fix UI profile editing crashing
  - `pios X --experiments <experiment>` can be used to select workers on the leader command line.
- - ideally, if a published setting is settable: true, there should be a cli option to set it.
- - adding mcp server
+ - ideally, if a `published_setting` is `settable: True`, there should be a CLI option to set it. We've added a bunch of new CLI options to existing jobs.
+ - new `/unit_api/capabilities` and `/api/units/<name>/capabilities` to get lots of details about what a Pioreactor can run.
+
+#### Breaking changes
  - adding `/experiments/<exp>` to the end of endpoint `/api/workers/unit1/jobs/settings/job_name/stirring/`
  - removed `/api/workers/jobs/stop/experiments/<exp>`, use `/api/workers/$broadcast/jobs/stop/experiments/<exp>` instead.
  - removed `/api/experiments/<experiment>/jobs/settings/job_name/<job_name>`, use `/workers/$broadcast/jobs/settings/job_name/<job_name>/experiments/<experiment>`
- - New external models in .pioreactor/models
+
+#### Bug fixes
+ - fix export data sorting
+ - fix UI profile editing crashing
 
 ### 25.7.2
 

core/pioreactor/actions/od_blank.py

@@ -10,7 +10,6 @@
 
 import click
 from msgspec.json import encode
-
 from pioreactor import pubsub
 from pioreactor import structs
 from pioreactor import types as pt
@@ -90,7 +89,7 @@ def od_statistics(
                     f"OD reading for PD Channel {channel} is 0.0 - that shouldn't be. Is there a loose connection, or an extra channel in the configuration's [od_config.photodiode_channel] section?"
                 )
 
-        logger.debug(f"observed data: {od_reading_series}")
+        logger.debug(f"observed data: {readings}")
         logger.debug(f"measured mean: {means}")
         logger.debug(f"measured variances: {variances}")
 

core/pioreactor/background_jobs/dosing_automation.py

@@ -52,10 +52,6 @@ def pause_between_subdoses() -> float:
     return d
 
 
-def is_20ml() -> bool:
-    return whoami.get_pioreactor_model() == "pioreactor_20ml"
-
-
 """
 Calculators should ideally be state-less
 """
@@ -205,7 +201,7 @@ class DosingAutomationJob(AutomationJob):
 
     @classproperty
     def MAX_VIAL_VOLUME_TO_STOP(cls) -> float:
-        return 18.0 if is_20ml() else 38.0
+        return whoami.get_pioreactor_model().reactor_max_fill_volume_ml
 
     @classproperty
     def MAX_VIAL_VOLUME_TO_WARN(cls) -> float:
@@ -550,7 +546,7 @@ def _init_alt_media_fraction(self, alt_media_fraction: float | None) -> None:
         if alt_media_fraction is None:
             with local_persistent_storage("alt_media_fraction") as cache:
                 self.alt_media_fraction = cache.get(
-                    self.experiment, config.getfloat("bioreactor", "alt_media_fraction", fallback=0.0)
+                    self.experiment, config.getfloat("bioreactor", "initial_alt_media_fraction", fallback=0.0)
                 )
         else:
             self.alt_media_fraction = float(alt_media_fraction)
@@ -596,7 +592,7 @@ def _init_liquid_volume(
             # look in database first, fallback to config
             with local_persistent_storage("current_volume_ml") as cache:
                 self.current_volume_ml = cache.get(
-                    self.experiment, config.getfloat("bioreactor", "current_volume_ml", fallback=14)
+                    self.experiment, config.getfloat("bioreactor", "initial_volume_ml", fallback=14)
                 )
         else:
             self.current_volume_ml = float(current_volume_ml)

core/pioreactor/cluster_management/__init__.py

@@ -15,7 +15,6 @@
 from pioreactor.config import leader_hostname
 from pioreactor.exc import BashScriptError
 from pioreactor.logging import create_logger
-from pioreactor.models import registered_models
 from pioreactor.mureq import HTTPErrorStatus
 from pioreactor.mureq import HTTPException
 from pioreactor.pubsub import delete_from_leader
@@ -72,6 +71,8 @@ def add_worker(
     Add a new pioreactor worker to the cluster. The pioreactor should already have the worker image installed and is turned on.
     """
     # validate combo against registry
+    from pioreactor.models import registered_models
+
     if (model_name, model_version) not in registered_models:
         click.echo(
             f"Invalid model/version: {model_name} v{model_version}."

core/pioreactor/models.py

@@ -14,40 +14,47 @@
 
 
 ## Built-in Pioreactor models with hard-coded defaults
+
+PIOREACTOR_20ml__v1_0 = Model(
+    model_name="pioreactor_20ml",
+    model_version="1.0",
+    display_name="Pioreactor 20ml, v1.0",
+    reactor_capacity_ml=20.0,
+    reactor_max_fill_volume_ml=18.0,
+    reactor_diameter_mm=27.0,
+    max_temp_to_reduce_heating=63.0,
+    max_temp_to_disable_heating=65.0,
+    max_temp_to_shutdown=66.0,
+)
+
+PIOREACTOR_20ml__v1_1 = Model(
+    model_name="pioreactor_20ml",
+    model_version="1.1",
+    display_name="Pioreactor 20ml, v1.1",
+    reactor_capacity_ml=20.0,
+    reactor_max_fill_volume_ml=18.0,
+    reactor_diameter_mm=27.0,
+    max_temp_to_reduce_heating=78.0,
+    max_temp_to_disable_heating=80.0,
+    max_temp_to_shutdown=85.0,
+)
+
+PIOREACTOR_40ml__v1_0 = Model(
+    model_name="pioreactor_40ml",
+    model_version="1.0",
+    display_name="Pioreactor 40ml, v1.0",
+    reactor_capacity_ml=40.0,
+    reactor_max_fill_volume_ml=38.0,
+    reactor_diameter_mm=27.0,
+    max_temp_to_reduce_heating=78.0,
+    max_temp_to_disable_heating=80.0,
+    max_temp_to_shutdown=85.0,
+)
+
 CORE_MODELS = {
-    ("pioreactor_20ml", "1.0"): Model(
-        model_name="pioreactor_20ml",
-        model_version="1.0",
-        display_name="Pioreactor 20ml, v1.0",
-        reactor_capacity_ml=20.0,
-        reactor_max_fill_volume_ml=18.0,
-        reactor_diameter_mm=27.0,
-        max_temp_to_reduce_heating=63.0,
-        max_temp_to_disable_heating=65.0,
-        max_temp_to_shutdown=66.0,
-    ),
-    ("pioreactor_20ml", "1.1"): Model(
-        model_name="pioreactor_20ml",
-        model_version="1.1",
-        display_name="Pioreactor 20ml, v1.1",
-        reactor_capacity_ml=20.0,
-        reactor_max_fill_volume_ml=18.0,
-        reactor_diameter_mm=27.0,
-        max_temp_to_reduce_heating=78.0,
-        max_temp_to_disable_heating=80.0,
-        max_temp_to_shutdown=85.0,
-    ),
-    ("pioreactor_40ml", "1.0"): Model(
-        model_name="pioreactor_40ml",
-        model_version="1.0",
-        display_name="Pioreactor 40ml, v1.0",
-        reactor_capacity_ml=40.0,
-        reactor_max_fill_volume_ml=38.0,
-        reactor_diameter_mm=27.0,
-        max_temp_to_reduce_heating=78.0,
-        max_temp_to_disable_heating=80.0,
-        max_temp_to_shutdown=85.0,
-    ),
+    ("pioreactor_20ml", "1.0"): PIOREACTOR_20ml__v1_0,
+    ("pioreactor_20ml", "1.1"): PIOREACTOR_20ml__v1_1,
+    ("pioreactor_40ml", "1.0"): PIOREACTOR_40ml__v1_0,
 }
 
 

core/pioreactor/whoami.py

@@ -238,3 +238,5 @@ def check_firstboot_successful() -> bool:
     os.environ["BLINKA_FORCEBOARD"] = "RASPBERRY_PI_3A_PLUS"  # Raspberry Pi 3 Model A Plus Rev 1.0
     os.environ["FIRMWARE"] = "1.0"
     os.environ["HARDWARE"] = "1.2"
+    os.environ["MODEL_NAME"] = "pioreactor_40ml"
+    os.environ["MODEL_VERSION"] = "1.0"

core/tests/test_execute_experiment_profile.py

@@ -7,7 +7,6 @@
 import pytest
 from msgspec.json import encode
 from msgspec.yaml import decode
-
 from pioreactor.actions.leader.experiment_profile import _verify_experiment_profile
 from pioreactor.actions.leader.experiment_profile import execute_experiment_profile
 from pioreactor.actions.leader.experiment_profile import hours_to_seconds
@@ -30,8 +29,8 @@
 from pioreactor.pubsub import publish
 from pioreactor.pubsub import subscribe_and_callback
 from pioreactor.structs import RawODReading
-from tests.conftest import capture_requests
 from pioreactor.utils.timing import current_utc_datetime
+from tests.conftest import capture_requests
 
 
 def test_hours_to_seconds() -> None:
@@ -583,7 +582,11 @@ def test_execute_experiment_profile_when_action_simple(mock__load_experiment_pro
     # Simulate OD value
     publish(
         f"pioreactor/unit1/{experiment}/od_reading/od1",
-        encode(RawODReading(od=2.5, angle="90", timestamp=current_utc_datetime(), channel="1")),
+        encode(
+            RawODReading(
+                od=2.5, angle="90", timestamp=current_utc_datetime(), channel="1", ir_led_intensity=80
+            )
+        ),
         retain=True,
     )
 
@@ -625,7 +628,11 @@ def test_execute_experiment_profile_when_action_with_if(mock__load_experiment_pr
     # Simulate OD value
     publish(
         f"pioreactor/unit1/{experiment}/od_reading/od1",
-        encode(RawODReading(od=2.5, angle="90", timestamp=current_utc_datetime(), channel="1")),
+        encode(
+            RawODReading(
+                od=2.5, angle="90", timestamp=current_utc_datetime(), channel="1", ir_led_intensity=80
+            )
+        ),
         retain=True,
     )
 

core/tests/test_growth_rate_calculating.py

@@ -446,6 +446,7 @@ def __call__(self):
                                 "timestamp": "2021-06-06T15:08:12.081153Z",
                                 "channel": "1",
                                 "calibrated": 0,
+                                "ir_led_intensity": 80,
                             }
                         },
                         "timestamp": "2021-06-06T15:08:12.081153Z",
@@ -507,6 +508,7 @@ def __call__(self):
                                 "timestamp": "2021-06-06T15:08:12.081153Z",
                                 "channel": "1",
                                 "calibrated": 0,
+                                "ir_led_intensity": 80,
                             }
                         },
                         "timestamp": "2021-06-06T15:08:12.081153Z",

core/tests/test_od_reading.py

@@ -1354,7 +1354,7 @@ def float_to_od_readings_struct(ch: pt.PdChannel, v: float) -> structs.ODReading
             timestamp=current_utc_datetime(),
             ods={
                 ch: structs.RawODReading(
-                    ir_led_intensity=80, od=v, angle="90", channel=ch, timestamp=current_utc_datetime()
+                    ir_led_intensity=50, od=v, angle="90", channel=ch, timestamp=current_utc_datetime()
                 )
             },
         )

core/tests/test_parser.py

@@ -6,7 +6,6 @@
 
 import pytest
 from msgspec.json import encode
-
 from pioreactor import structs
 from pioreactor.experiment_profiles.parser import parse_profile_expression
 from pioreactor.experiment_profiles.parser import parse_profile_expression_to_bool
@@ -66,7 +65,11 @@ def test_mqtt_fetches() -> None:
 
     publish(
         f"pioreactor/{unit}/{experiment}/od_reading/od1",
-        encode(structs.RawODReading(timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2")),
+        encode(
+            structs.RawODReading(
+                timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2", ir_led_intensity=90
+            )
+        ),
         retain=True,
     )
 
@@ -107,7 +110,11 @@ def test_mqtt_fetches_with_env() -> None:
 
     publish(
         f"pioreactor/{unit}/{experiment}/od_reading/od1",
-        encode(structs.RawODReading(timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2")),
+        encode(
+            structs.RawODReading(
+                timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2", ir_led_intensity=80
+            )
+        ),
         retain=True,
     )
 
@@ -174,7 +181,11 @@ def test_mqtt_fetches_with_calculations() -> None:
     experiment = "_testing_experiment"
     publish(
         f"pioreactor/{unit}/{experiment}/od_reading/od1",
-        encode(structs.RawODReading(timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2")),
+        encode(
+            structs.RawODReading(
+                timestamp=datetime.utcnow(), angle="90", od=1.2, channel="2", ir_led_intensity=80
+            )
+        ),
         retain=True,
     )