updateS

pioreactor/background_jobs/stirring.py

@@ -309,10 +309,10 @@ def start_stirring(self) -> None:
     def kick_stirring(self) -> None:
         self.logger.debug("Kicking stirring")
         self.set_duty_cycle(100)
-        sleep(0.20)
+        sleep(0.10)
         self.set_duty_cycle(
             max(1.01 * self._previous_duty_cycle, 60)
-        )  # DC should never be above 60. We want to avoid the death spiral to 100%.
+        )  # DC should never need to be above 60 - simply not realistic. We want to avoid the death spiral to 100%.
 
     def kick_stirring_but_avoid_od_reading(self) -> None:
         """

pioreactor/cli/pio.py

@@ -499,9 +499,8 @@ def update_app(
             version_installed = source
             commands_and_priority.append((f"sudo pip3 install --force-reinstall --no-index {source}", 1))
         else:
-            raise click.Abort(
-                "Not a valid source file. Should be either a whl or release archive."
-            )  # TODO: this doesn't print any message on error...
+            click.echo("Not a valid source file. Should be either a whl or release archive.")
+            raise click.Abort()
 
     elif branch is not None:
         cleaned_branch = quote(branch)
@@ -526,6 +525,12 @@ def update_app(
         release_metadata = loads(response.body)
         version_installed = release_metadata["tag_name"]
         found_whl = False
+
+        # nuke all existing assets in /tmp
+        # TODO: just make a new tempdir, put all files there, and then nuke that temp dir......
+        # BETTER TODO: just download the release archive and run the script above.....
+        commands_and_priority.append(("rm -f /tmp/*update.sh /tmp/update.sql", -1))
+
         for asset in release_metadata["assets"]:
             # add the following files to the release. They should ideally be idempotent!
 
@@ -534,8 +539,6 @@ def update_app(
             # update.sh runs (if exists)
             # update.sql to update sqlite schema runs (if exists)
             # post_update.sh runs (if exists)
-
-            # TODO: potential supply chain attack is to add malicious assets to releases
             url = asset["browser_download_url"]
             asset_name = asset["name"]
 
@@ -600,7 +603,9 @@ def update_app(
 @click.option("-v", "--version", help="install a specific version, default is latest")
 def update_firmware(version: Optional[str]) -> None:
     """
-    Update the RP2040 firmware
+    Update the RP2040 firmware.
+
+    # TODO: this needs accept a --source arg
     """
     logger = create_logger("update-app", unit=whoami.get_unit_name(), experiment=whoami.UNIVERSAL_EXPERIMENT)
     commands_and_priority: list[tuple[str, int]] = []

pioreactor/tests/test_dosing_control.py

@@ -1591,7 +1591,7 @@ def test_warning_is_logged_if_under_remove_waste() -> None:
     experiment = "test_warning_is_logged_if_under_remove_waste"
 
     class BadWasteRemoval(DosingAutomationJob):
-        automation_name = "bad_waste_removal"
+        automation_name = "_test_bad_waste_removal"
 
         def remove_waste_from_bioreactor(self, unit, experiment, ml, source_of_event, mqtt_client):
             return ml / 2

pioreactor/version.py

@@ -20,7 +20,7 @@ def _get_hardware_version() -> tuple[int, int] | tuple[int, int, str]:
             text = f.read().rstrip("\x00")
             return (int(text[-2]), int(text[-1]))
     except FileNotFoundError:
-        # no eeprom? Probably dev board with no EEPROM, or testing env, or EEPROM not written.
+        # no eeprom? Probably dev board with no EEPROM, or testing env, or EEPROM not written, or cable exists between HAT and Pi -> signal degradation.
         return (0, 0)
 
 

update_scripts/23.12.11/update.sh

@@ -1,12 +1,19 @@
 #!/bin/bash
 
 set -x
-set -e
 
 export LC_ALL=C
 
 # Get the directory where the script is located
 SCRIPT_DIR=$(dirname "$0")
 
+# Attempt to download update_ui.sh
+if ! wget -O "${SCRIPT_DIR}/update_ui.sh" https://github.com/Pioreactor/pioreactor/releases/download/23.12.11/update_ui.sh; then
+    echo "Failed to download update_ui.sh"
+fi
+
+# Ensure the script is executable
+chmod +x "${SCRIPT_DIR}/update_ui.sh"
+
 # Copy update_ui.sh from the script's directory
 sudo cp "${SCRIPT_DIR}/update_ui.sh" /usr/local/bin/

update_scripts/README.md

@@ -8,7 +8,6 @@ Possible update scripts and their sequence:
 - `post_update.sh` runs (if exists). Useful for restarting jobs, or rebooting RPis.
 
 
-
 It's very important that update scripts are idempotent. Some tips:
 
  - Use ChatGPT to assist psuedo-check if a script is idempotent, or making suggestions.