push back the adc change to later

CHANGELOG.md

@@ -3,7 +3,6 @@
 
 #### Enhancements
  - new OD calibration using standards (requires multiple vials). Try `pio calibrations run --device od`. This was inspired by the plugin by @odcambc.
- - new RP2040 firmware improvements (v0.4) => faster response over i2c.
  - Improved chart colors in the UI
  - The OD reading CLI has a new option, `--snapshot`, that will start the job, take a single reading, and exit. This is useful for scripting purposes.
  - A new CLI for pumps: `pio run pumps`. Add pumps as options:
@@ -18,7 +17,7 @@
  - Run multiple experiment profiles per experiment!
  - Specify which Pioreactor to update on the Updates page (option is only available with release archives.)
  - Choose the level of detail on the new Event Logs page.
- - Added index to stirring_rates table.
+ - Previously, when a worker's web server is down, it would halt an update from proceeding (since it can't send the command). Now, leader will try the webserver, and if it observes a 5xx error, will attempt an SSH communication.
 
 #### Web API changes
 

pioreactor/calibrations/od_calibration_using_standards.py

@@ -11,7 +11,6 @@
 """
 from __future__ import annotations
 
-from math import log2
 from time import sleep
 from typing import cast
 
@@ -56,12 +55,10 @@ def introduction() -> None:
 
     clear()
     echo(
-        """This routine will calibrate the current Pioreactor to (offline) OD600 readings. You'll need:
-    1. The Pioreactor you wish to calibrate (the one you are using)
-    2. At least 10mL of a culture with the highest density you'll ever observe, and its OD600 measurement
-    3. A micro-pipette, or accurate tool to dispense 1ml of liquid.
-    4. Accurate 10mL measurement tool (ex: graduated cylinder)
-    5. Sterile media, amount to be determined shortly.
+        """This routine will calibrate the current Pioreactor to (offline) OD600 readings using a set of standards. You'll need:
+    1. A Pioreactor
+    2. A set of OD600 standards in Pioreactor vials (at least 10 mL in each vial), each with a stirbar
+    3. One of the standards should be a blank (no cells, only media).
 """
     )
 
@@ -91,7 +88,7 @@ def get_name_from_user() -> str:
                 return name
 
 
-def get_metadata_from_user() -> tuple[pt.OD600, pt.OD600, pt.mL, pt.PdAngle, pt.PdChannel]:
+def get_metadata_from_user() -> tuple[pt.PdAngle, pt.PdChannel]:
     if config.get("od_reading.config", "ir_led_intensity") == "auto":
         echo(
             red(
@@ -100,49 +97,6 @@ def get_metadata_from_user() -> tuple[pt.OD600, pt.OD600, pt.mL, pt.PdAngle, pt.
         )
         raise click.Abort()
 
-    initial_od600 = prompt(
-        green("Provide the OD600 measurement of your initial, high density, culture"),
-        type=click.FloatRange(min=0.01, clamp=False),
-    )
-
-    minimum_od600 = prompt(
-        green("Provide the minimum OD600 measurement you wish to calibrate to"),
-        type=click.FloatRange(min=0, max=initial_od600, clamp=False),
-    )
-
-    while minimum_od600 >= initial_od600:
-        minimum_od600 = cast(
-            pt.OD600,
-            prompt(
-                "The minimum OD600 measurement must be less than the initial OD600 culture measurement",
-                type=click.FloatRange(min=0, max=initial_od600, clamp=False),
-            ),
-        )
-
-    if minimum_od600 == 0:
-        minimum_od600 = 0.01
-
-    dilution_amount = prompt(
-        green("Provide the volume to be added to your vial each iteration (default = 1 mL)"),
-        default=1,
-        type=click.FloatRange(min=0.01, max=10, clamp=False),
-    )
-
-    number_of_points = int(log2(initial_od600 / minimum_od600) * (10 / dilution_amount))
-
-    echo(f"This will require {number_of_points} data points.")
-    echo(f"You will need at least {number_of_points * dilution_amount + 10}mL of media available.")
-    confirm(green("Continue?"), abort=True, default=True)
-
-    if "REF" not in config["od_config.photodiode_channel_reverse"]:
-        echo(
-            red(
-                "REF required for OD calibration. Set an input to REF in [od_config.photodiode_channel] in your config."
-            )
-        )
-        raise click.Abort()
-        # technically it's not required? we just need a specific PD channel to calibrate from.
-
     ref_channel = config["od_config.photodiode_channel_reverse"]["REF"]
     pd_channel = cast(pt.PdChannel, "1" if ref_channel == "2" else "2")
 
@@ -154,7 +108,7 @@ def get_metadata_from_user() -> tuple[pt.OD600, pt.OD600, pt.mL, pt.PdAngle, pt.
         default=True,
     )
     angle = cast(pt.PdAngle, config["od_config.photodiode_channel"][pd_channel])
-    return initial_od600, minimum_od600, dilution_amount, angle, pd_channel
+    return angle, pd_channel
 
 
 def setup_HDC_instructions() -> None:
@@ -243,13 +197,14 @@ def get_voltage_from_adc() -> float:
             od_readings2 = od_reader.record_from_adc()
             return 0.5 * (od_readings1.ods[signal_channel].od + od_readings2.ods[signal_channel].od)
 
-        for _ in range(4):
+        for _ in range(3):
             # warm up
             od_reader.record_from_adc()
 
     while True:
-        click.echo("Recording next standard.")
-        standard_od = click.prompt("Enter OD600 measurement", type=float)
+        click.clear()
+        click.echo("Recording new standard.")
+        standard_od = click.prompt(green("Enter OD600 measurement of current vial"), type=float)
         for i in range(4):
             click.echo(".", nl=False)
             sleep(0.5)
@@ -276,16 +231,17 @@ def get_voltage_from_adc() -> float:
             )
             click.echo()
 
-        if not click.confirm("Record another OD600 standard?", default=True):
+        if not click.confirm(green("Record another OD600 standard?"), default=True):
             break
 
         click.echo()
-        click.echo(click.style("Stop❗", fg="red"))
-        click.echo("Carefully remove vial and replace with next standard.")
-        click.echo("Confirm vial outside is dry and clean.")
-        while not click.confirm("Continue?", default=True):
+        click.echo("Remove old vial.")
+        click.echo("Replace with new vial: confirm vial is dry and clean.")
+        click.echo()
+        while not click.confirm(green("Confirm vial is placed in Pioreactor?"), default=True):
             pass
         st.set_state("ready")
+        click.echo("Starting stirring.")
         st.block_until_rpm_is_close_to_target(abs_tolerance=120)
         sleep(1.0)
 
@@ -300,9 +256,9 @@ def get_voltage_from_adc() -> float:
         y_label="Voltage",
     )
     click.echo("Add media blank standard.")
-    od600_blank = click.prompt("What is the OD600 of your blank?", type=float)
-    click.echo("Confirm vial outside is dry and clean. Place into Pioreactor.")
-    while not click.confirm("Continue?", default=True):
+    od600_blank = click.prompt(green("What is the OD600 of your blank?"), type=float)
+    click.echo("Confirm blank vial outside is dry and clean. Place into Pioreactor.")
+    while not click.confirm(green("Continue?"), default=True):
         pass
 
     voltages.append(get_voltage_from_adc())
@@ -326,9 +282,6 @@ def run_od_calibration() -> structs.ODCalibration:
             raise click.Abort()
 
         (
-            initial_od600,
-            minimum_od600,
-            dilution_amount,
             angle,
             pd_channel,
         ) = get_metadata_from_user()

pioreactor/cli/calibrations.py

@@ -17,6 +17,10 @@
 from pioreactor.calibrations.utils import plot_data
 
 
+def green(string: str) -> str:
+    return click.style(string, fg="green")
+
+
 @click.group(short_help="calibration utils")
 def calibration() -> None:
     """
@@ -86,12 +90,14 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
             click.clear()
             click.echo()
             click.echo(f"Available protocols for {device}:")
+            click.echo()
             for protocol in calibration_protocols.get(device, {}).values():
                 click.echo(click.style(f"  • {protocol.protocol_name}", bold=True))
                 click.echo(f"        Description: {protocol.description}")
             click.echo()
             protocol_name = click.prompt(
-                "Choose a protocol", type=click.Choice(list(calibration_protocols.get(device, {}).keys()))
+                green("Choose a protocol"),
+                type=click.Choice(list(calibration_protocols.get(device, {}).keys())),
             )
 
     assistant = calibration_protocols.get(device, {}).get(protocol_name)
@@ -111,7 +117,8 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
 
     if not y:
         if click.confirm(
-            f"Do you want to set this calibration as the active calibration for {device}?", default=True
+            green(f"Do you want to set this calibration as the active calibration for {device}?"),
+            default=True,
         ):
             calibration_struct.set_as_active_calibration_for_device(device)
             click.echo(f"Set {calibration_struct.calibration_name} as the active calibration for {device}.")
@@ -122,6 +129,7 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
     else:
         calibration_struct.set_as_active_calibration_for_device(device)
 
+    click.echo()
     click.echo(
         f"Calibration '{calibration_struct.calibration_name}' of device '{device}' saved to {out_file} ✅"
     )
@@ -186,7 +194,7 @@ def set_active_calibration(device: str, calibration_name: str | None) -> None:
 @calibration.command(name="delete")
 @click.option("--device", required=True, help="Which calibration device to delete from.")
 @click.option("--name", "calibration_name", required=True, help="Which calibration name to delete.")
-@click.confirmation_option(prompt="Are you sure you want to delete this calibration?")
+@click.confirmation_option(prompt=green("Are you sure you want to delete this calibration?"))
 def delete_calibration(device: str, calibration_name: str) -> None:
     """
     Delete a calibration file from local storage.

pioreactor/cli/pios.py

@@ -286,11 +286,14 @@ def update(
 
             logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
             options: dict[str, str | None] = {}
+            args = ""
 
-            if source is not None:
-                options["source"] = source
-            elif branch is not None:
+            if branch is not None:
                 options["branch"] = branch
+                args = f"--branch {branch}"
+            elif source is not None:
+                options["source"] = source
+                args = f"--source {source}"
 
             def _thread_function(unit: str) -> tuple[bool, dict]:
                 try:
@@ -304,12 +307,6 @@ def _thread_function(unit: str) -> tuple[bool, dict]:
                         f"Unable to update on {unit} due to server error: {e}. Attempting SSH method..."
                     )
                     try:
-                        args: str
-                        if source is not None:
-                            args = f"--source {source}"
-                        elif branch is not None:
-                            args = f"--branch {branch}"
-
                         ssh(resolve_to_address(unit), f"pio update {args}")
                         return True, {"unit": unit}
                     except SSHError as e:
@@ -362,14 +359,18 @@ def update_app(
 
         logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         options: dict[str, str | None] = {}
+        args = ""
 
         # only one of these three is possible, mutually exclusive
         if version is not None:
             options["version"] = version
+            args = f"--version {version}"
         elif branch is not None:
             options["branch"] = branch
+            args = f"--branch {branch}"
         elif source is not None:
             options["source"] = source
+            args = f"--source {source}"
 
         if repo is not None:
             options["repo"] = repo
@@ -384,14 +385,6 @@ def _thread_function(unit: str) -> tuple[bool, dict]:
             except HTTPException as e:
                 logger.error(f"Unable to update on {unit} due to server error: {e}. Attempting SSH method...")
                 try:
-                    args: str
-                    if source is not None:
-                        args = f"--source {source}"
-                    elif branch is not None:
-                        args = f"--branch {branch}"
-                    elif version is not None:
-                        args = f"--version {version}"
-
                     ssh(resolve_to_address(unit), f"pio update app {args}")
                     return True, {"unit": unit}
                 except SSHError as e:
@@ -443,14 +436,18 @@ def update_ui(
 
         logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         options: dict[str, str | None] = {}
+        args = ""
 
         # only one of these three is possible, mutually exclusive
         if version is not None:
             options["version"] = version
+            args = f"--version {version}"
         elif branch is not None:
             options["branch"] = branch
+            args = f"--branch {branch}"
         elif source is not None:
             options["source"] = source
+            args = f"--source {source}"
 
         if repo is not None:
             options["repo"] = repo
@@ -465,14 +462,6 @@ def _thread_function(unit: str) -> tuple[bool, dict]:
             except HTTPException as e:
                 logger.error(f"Unable to update on {unit} due to server error: {e}. Attempting SSH method...")
                 try:
-                    args: str
-                    if source is not None:
-                        args = f"--source {source}"
-                    elif branch is not None:
-                        args = f"--branch {branch}"
-                    elif version is not None:
-                        args = f"--version {version}"
-
                     ssh(resolve_to_address(unit), f"pio update ui {args}")
                     return True, {"unit": unit}
                 except SSHError as e:

pioreactor/utils/adcs.py

@@ -94,7 +94,8 @@ class Pico_ADC(_ADC):
     def __init__(self) -> None:
         # set up i2c connection to hardware.ADC
         self.i2c = I2C(hardware.SCL, hardware.SDA)
-        assert self.get_firmware_version() == (0, 4), "Firmware version mismatch."
+        self.scale = 16
+        # assert self.get_firmware_version() == (0, 4), "Firmware version mismatch."
 
     def read_from_channel(self, channel: pt.AdcChannel) -> pt.AnalogValue:
         assert 0 <= channel <= 3
@@ -115,13 +116,13 @@ def get_firmware_version(self) -> tuple[int, int]:
         return (result[1], result[0])
 
     def from_voltage_to_raw(self, voltage: pt.Voltage) -> pt.AnalogValue:
-        return int((voltage / 3.3) * 4095 * 32)
+        return int((voltage / 3.3) * 4095 * self.scale)
 
     def from_voltage_to_raw_precise(self, voltage: pt.Voltage) -> float:
-        return (voltage / 3.3) * 4095 * 32
+        return (voltage / 3.3) * 4095 * self.scale
 
     def from_raw_to_voltage(self, raw: pt.AnalogValue) -> pt.Voltage:
-        return (raw / 4095 / 32) * 3.3
+        return (raw / 4095 / self.scale) * 3.3
 
     def check_on_gain(self, value: pt.Voltage, tol: float = 0.85) -> None:
         # pico has no gain.