more

Author: CamDavidsonPilon

Makefile

@@ -58,7 +58,7 @@ check-env:  ## Verify required environment variables are loaded
 
 # --- environment --------------------------------------------------------------
 $(VENV_DIR)/bin/activate:  ## Create virtual env + core tooling
-	@echo ">> Creating virtual env in $(VENV_DIR)"
+	@echo ">> Creating virtual env in $(VENV_DIR) with $(PYTHON)"
 	@$(PYTHON) -m venv $(VENV_DIR)
 	@$(ACTIVATE) && pip install -U pip wheel $(PIP_FLAGS)$(newline)
 	@touch $@
@@ -124,7 +124,7 @@ huey-dev: venv  ## Run the Huey consumer with sensible dev flags
 clean:  ## Delete bytecode, build artefacts, node deps
 	rm -rf $(VENV_DIR) dist/ build/ *.egg-info
 	find . -name '__pycache__' -exec rm -rf {} +
-	rm -rf $(NODE_DIR)/build node_modules .pytest_cache
+	rm -rf $(NODE_DIR)/build node_modules .pytest_cache .pioreactor/storage/local_intermittent_pioreactor_metadata.sqlite .pioreactor/storage/local_persistent_pioreactor_metadata.sqlite
 
 reinstall: clean install frontend-install  ## Freshen everything
 

core/pioreactor/background_jobs/od_reading.py

@@ -1180,7 +1180,7 @@ def record_from_adc(self) -> structs.ODReadings | None:
             self._log_relative_intensity_of_ir_led()
             self._unblock_internal_event()
 
-            return od_readings
+        return od_readings
 
     def start_ir_led(self) -> None:
         r = led_utils.led_intensity(

core/pytest.ini

@@ -341,6 +341,7 @@ def test_cant_change_target_in_turbidostat() -> None:
         assert algo.target_normalized_od is None
 
 
+@pytest.mark.slow
 def test_turbidostat_targeting_od() -> None:
     experiment = "test_turbidostat_targeting_od"
 
@@ -752,6 +753,7 @@ def test_execute_io_action() -> None:
         assert ca.current_volume_ml == 15.0
 
 
+@pytest.mark.slow
 def test_execute_io_action2() -> None:
     experiment = "test_execute_io_action2"
 
@@ -1147,6 +1149,7 @@ def test_strings_are_okay_for_chemostat(fast_dosing_timers) -> None:
         assert wait_for(lambda: close(chemostat.media_throughput, 0.7), timeout=5.0)
 
 
+@pytest.mark.slow
 def test_chemostat_from_cli() -> None:
     from pioreactor.cli.pio import pio
 
@@ -1231,6 +1234,7 @@ def test_chemostat_from_0_volume(fast_dosing_timers) -> None:
         assert wait_for(lambda: close(chemostat.current_volume_ml, 1.0), timeout=5.0)
 
 
+@pytest.mark.slow
 def test_execute_io_respects_dilutions_ratios(fast_dosing_timers) -> None:
     # https://forum.pioreactor.com/t/inconsistent-dosing-behavior-with-multiple-media/37/3
 

core/tests/test_dosing_automation.py

@@ -196,6 +196,7 @@ def test_execute_experiment_log_actions(mock__load_experiment_profile, active_wo
         ]
 
 
+@pytest.mark.slow
 @patch("pioreactor.actions.leader.experiment_profile._load_experiment_profile")
 def test_execute_experiment_start_and_stop_automations(mock__load_experiment_profile) -> None:
     experiment = "_testing_experiment"
@@ -213,6 +214,7 @@ def test_execute_experiment_start_and_stop_automations(mock__load_experiment_pro
     execute_experiment_profile("profile.yaml", experiment)
 
 
+@pytest.mark.slow
 @patch("pioreactor.actions.leader.experiment_profile._load_experiment_profile")
 def test_execute_experiment_update_automation(mock__load_experiment_profile) -> None:
     experiment = "_testing_experiment"
@@ -237,6 +239,7 @@ def test_execute_experiment_update_automation(mock__load_experiment_profile) ->
     execute_experiment_profile("profile.yaml", experiment)
 
 
+@pytest.mark.slow
 @patch("pioreactor.actions.leader.experiment_profile._load_experiment_profile")
 def test_execute_experiment_start_automation_succeeds(
     mock__load_experiment_profile,

core/tests/test_execute_experiment_profile.py

@@ -84,7 +84,7 @@ def test_light_dark_cycle_starts_on() -> None:
             assert c["C"] == 50
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 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()
@@ -109,7 +109,7 @@ def test_light_dark_cycle_turns_off_after_N_cycles() -> None:
             assert c["C"] == 0.0
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 def test_dark_duration_hour_to_zero() -> None:
     experiment = "test_dark_duration_hour_to_zero"
     unit = get_unit_name()
@@ -139,7 +139,7 @@ def test_dark_duration_hour_to_zero() -> None:
             assert c["C"] == 50.0
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 def test_light_duration_hour_to_zero() -> None:
     experiment = "test_light_duration_hour_to_zero"
     unit = get_unit_name()
@@ -159,7 +159,7 @@ def test_light_duration_hour_to_zero() -> None:
         assert not lc.light_active
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 def test_add_dark_duration_minutes() -> None:
     experiment = "test_add_dark_duration_minutes * 60"
     unit = get_unit_name()
@@ -189,7 +189,7 @@ def test_add_dark_duration_minutes() -> None:
             assert c["C"] == 0.0
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 def test_remove_dark_duration_minutes() -> None:
     experiment = "test_remove_dark_duration_minutes * 60"
     unit = get_unit_name()
@@ -223,7 +223,7 @@ def test_remove_dark_duration_minutes() -> None:
             assert c["C"] == 50.0
 
 
-@pytest.mark.skip(reason="flaky in CI")
+@pytest.mark.flakey
 def test_fractional_hours() -> None:
     experiment = "test_fractional_hours"
     unit = get_unit_name()

core/tests/test_led_automation.py

@@ -1,23 +1,17 @@
 # -*- coding: utf-8 -*-
 from __future__ import annotations
 
-import json
 import sqlite3
 from time import sleep
 
 import pioreactor.background_jobs.leader.mqtt_to_db_streaming as m2db
-import pytest
 from pioreactor import mureq
 from pioreactor import structs
 from pioreactor.automations import temperature  # noqa: F401
 from pioreactor.background_jobs.base import BackgroundJob
-from pioreactor.background_jobs.growth_rate_calculating import GrowthRateCalculator
-from pioreactor.background_jobs.od_reading import start_od_reading
 from pioreactor.config import config
-from pioreactor.config import temporary_config_changes
 from pioreactor.pubsub import collect_all_logs_of_level
 from pioreactor.pubsub import publish
-from pioreactor.utils import local_persistent_storage
 from pioreactor.utils.timing import current_utc_datetime
 from pioreactor.whoami import get_testing_experiment_name
 from pioreactor.whoami import get_unit_name
@@ -96,7 +90,6 @@ def test_updated_heater_dc() -> None:
     assert len(results) == 1
 
 
-@pytest.mark.xfail()
 def test_dosing_events_land_in_db() -> None:
     from pioreactor.actions.pump import add_media
 
@@ -153,88 +146,6 @@ def test_dosing_events_land_in_db() -> None:
     assert len(results) == 2
 
 
-@pytest.mark.xfail(reason="we stopped adding to kalman filter table in 25.1.x release")
-def test_kalman_filter_entries() -> None:
-    with temporary_config_changes(
-        config,
-        [
-            ("storage", "database", "test.sqlite"),
-            ("od_reading.config", "samples_per_second", "0.2"),
-            ("od_config.photodiode_channel", "1", "135"),
-            ("od_config.photodiode_channel", "2", "90"),
-        ],
-    ):
-        unit = "unit"
-        exp = "test_kalman_filter_entries"
-
-        # init the database
-        connection = sqlite3.connect(config["storage"]["database"])
-        cursor = connection.cursor()
-
-        cursor.executescript("DROP TABLE IF EXISTS kalman_filter_outputs;")
-        cursor.executescript(
-            mureq.get(
-                "https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/sql/create_tables.sql"
-            ).content.decode("utf-8")
-        )
-        connection.commit()
-
-        with local_persistent_storage("od_normalization_mean") as cache:
-            cache[exp] = json.dumps({"1": 0.5, "2": 0.5})
-
-        with local_persistent_storage("od_normalization_variance") as cache:
-            cache[exp] = json.dumps({"1": 1e-6, "2": 1e-4})
-
-        # turn on our mqtt to db
-        parsers = [
-            m2db.TopicToParserToTable(
-                "pioreactor/+/+/growth_rate_calculating/kalman_filter_outputs",
-                m2db.parse_kalman_filter_outputs,
-                "kalman_filter_outputs",
-            )
-        ]
-
-        # turn on data collection
-        interval = 0.5
-
-        with (
-            start_od_reading(
-                {"1": "135", "2": "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()
-
-        assert results[0] != 0.0
-        assert results[1] != 0.0
-        assert results[2] != 0.0
-
-
 def test_empty_payload_is_filtered_early() -> None:
     unit = "unit"
     exp = "test_empty_payload_is_filtered_early"

core/tests/test_mqtt_to_db_streaming.py

@@ -664,6 +664,7 @@ def cb(od_job):
     ODReader._pre_read.clear()
 
 
+@pytest.mark.slow
 def test_add_post_read_callback() -> None:
     def cb(self, batched_readings, *args):
         self.logger.critical(f"{batched_readings=}")
@@ -1146,6 +1147,7 @@ def capture_led_state_during_offset(batched_readings):
     assert led_states_seen[0] == {channel: pytest.approx(0.0) for channel in ALL_LED_CHANNELS}
 
 
+@pytest.mark.slow
 def test_ODReader_with_multiple_angles_and_a_ref() -> None:
     """
     Technically not possible, since there are only two PD channels.

core/tests/test_od_reading.py

@@ -392,6 +392,7 @@ def collect_pwm_updates(msg):
         assert update == r"{}"
 
 
+@pytest.mark.slow
 def test_published_mqtt_data_is_the_same_as_requested() -> None:
     exp = "test_manually_doesnt_trigger_pwm_dcs"
 

core/tests/test_pumps.py

@@ -100,6 +100,7 @@ def test_publish_target_rpm() -> None:
         assert float(message.payload) == 500
 
 
+@pytest.mark.slow
 def test_publish_measured_rpm() -> None:
     exp = "test_publish_measured_rpm"
 
@@ -239,6 +240,7 @@ def test_target_rpm_during_od_reading_defaults_to_zero() -> None:
             assert st.target_rpm_outside_od_reading == 500
 
 
+@pytest.mark.slow
 def test_block_until_rpm_is_close_to_target_will_timeout() -> None:
     exp = "test_block_until_rpm_is_close_to_target_will_timeout"
     rpm_calculator = RpmCalculator()