fix stirring not cancelling correctly and race conditions

CHANGELOG.md

@@ -9,15 +9,14 @@
 
 #### Enhancements
  - improvements to Dodging background job code, including the ability to initialize the class based on dodging or not.
- - better error handling for failed OD blanks.
+ - better error handling for failed OD blank action.
  - better button state management in the UI.
- - job YAMLs' published_settings can have a new field, `editable` (bool), which controls whether it shows up on the Settings dialog or not. (False means it won't show up since it's not editable!). Default is true. This _should_ align with the `published_setting` in Python's job classes.
+ - a job YAMLs' published_settings can have a new field, `editable` (bool), which controls whether it shows up on the Settings dialog or not. (False means it won't show up since it's not editable!). Default is true. This _should_ align with the `published_setting` in Python's job classes.
  - you can add IPv4 addresses to the (new) `[cluster.addresses]` section to specify IPs for pioreactors. Example:
    ```
-
-  [cluster.addresses]
-  pio01_address=10.42.0.2
-  pio02_address=10.42.0.3
+   [cluster.addresses]
+   pio01=10.42.0.2
+   pio02=10.42.0.3
 
    ```
    Note that the leader's address is automatically added in our software.
@@ -28,7 +27,7 @@
  - Fixed "circulate X" actions in the Manage All dialog in the UI.
 
 #### Breaking changes
- - moved all the temporary caches, which previously where their own sqlite3 db in /tmp/ to /tmp/local_intermittent_pioreactor_metadata.sqlite. This shouldn't break anything unless you update _during_ an experiment - don't do that!
+ - moved all the temporary caches, which previously where their own sqlite3 dbs in `/tmp/` to `/tmp/local_intermittent_pioreactor_metadata.sqlite`. This shouldn't break anything unless you update _during_ an experiment - don't do that!
 
 ### 24.10.29
 

pioreactor/background_jobs/base.py

@@ -1053,8 +1053,12 @@ def __post__init__(self):
         self.set_enable_dodging_od(
             config.getboolean(f"{self.job_name}.config", "enable_dodging_od", fallback="False")
         )
-        self.start_passive_listeners()
-        super().__post__init__()
+        # now that `enable_dodging_od` is set, we can check for OD
+        self.subscribe_and_callback(
+            self._od_reading_changed_status,
+            f"pioreactor/{self.unit}/{self.experiment}/od_reading/interval",
+        )
+        super().__post__init__()  # set ready
 
     def set_currently_dodging_od(self, value: bool):
         self.currently_dodging_od = value
@@ -1094,13 +1098,6 @@ def initialize_dodging_operation(self) -> None:
     def initialize_continuous_operation(self) -> None:
         pass
 
-    def _start_general_passive_listeners(self) -> None:
-        super()._start_general_passive_listeners()
-        self.subscribe_and_callback(
-            self._od_reading_changed_status,
-            f"pioreactor/{self.unit}/{self.experiment}/od_reading/interval",
-        )
-
     def _od_reading_changed_status(self, msg):
         if self.enable_dodging_od:
             # only act if our internal state is discordant with the external state

pioreactor/background_jobs/stirring.py

@@ -281,18 +281,21 @@ def action_to_do_after_od_reading(self):
         self.poll_and_update_dc()
 
     def initialize_dodging_operation(self):
-        if config.getfloat("od_reading.config", "samples_per_second") > 0.121:
+        if config.getfloat("od_reading.config", "samples_per_second") > 0.12:
             self.logger.warning(
                 "Recommended to decrease `samples_per_second` to ensure there is time to start/stop stirring. Try 0.12 or less."
             )
 
+        with suppress(AttributeError):
+            self.rpm_check_repeated_thread.cancel()
+
         self.rpm_check_repeated_thread = RepeatedTimer(
             1_000,
             lambda *args: None,
             job_name=self.job_name,
             logger=self.logger,
         )
-        self.stop_stirring()  # we'll start it in action_to_do_after_od_reading
+        self.stop_stirring()  # we'll start it again in action_to_do_after_od_reading
 
     def initialize_continuous_operation(self):
         # set up thread to periodically check the rpm

pioreactor/cli/pio.py

@@ -531,7 +531,7 @@ def update_app(
             logger.error("Update failed. See logs.")
             # end early
             raise click.Abort()
-        else:
+        elif p.stdout:
             logger.debug(p.stdout)
 
     logger.notice(f"Updated Pioreactor app to version {version_installed}.")  # type: ignore

pioreactor/config.py

@@ -168,7 +168,7 @@ def get_config() -> ConfigParserMod:
 
     leader_hostname = config.get("cluster.topology", "leader_hostname")
     leader_address = config.get("cluster.topology", "leader_address")
-    config.set("cluster.addresses", f"{leader_hostname}_address", leader_address)
+    config.set("cluster.addresses", leader_hostname, leader_address)
 
     return config
 

pioreactor/utils/networking.py

@@ -147,7 +147,7 @@ def worker_hostnames(queue: Queue) -> None:
 def resolve_to_address(hostname: str) -> str:
     # TODO: make this more fleshed out: resolve to IP, etc.
     # add_local assumes a working mDNS.
-    address_in_config = config.get("cluster.addresses", f"{hostname}_address", fallback=None)
+    address_in_config = config.get("cluster.addresses", hostname, fallback=None)
     if address_in_config is not None:
         return address_in_config
     else:

pioreactor/utils/timing.py

@@ -179,7 +179,8 @@ def unpause(self) -> None:
         self.is_paused = False
 
     def cancel(self, timeout: t.Optional[float] = None) -> None:
-        self.event.set()
+        self.pause()  # this will exit from the _target early.
+        self.event.set()  # stop waiting in _target.
 
         with suppress(RuntimeError):
             # possible to happen if self.thread hasn't started yet,

update_scripts/upcoming/install_pioreactor_plugin.sh

@@ -81,7 +81,7 @@ fi
 if [ "$am_i_leader" = true ]; then
     # merge new config.ini
     if test -f "$install_folder/additional_config.ini"; then
-        crudini --merge /home/pioreactor/.pioreactor/config.ini < "$install_folder/additional_config.ini"
+        crudini  --ini-options=nospace --merge /home/pioreactor/.pioreactor/config.ini < "$install_folder/additional_config.ini"
     fi
 
     # add any new sql, restart mqtt_to_db job, too

update_scripts/upcoming/update.sh

@@ -12,7 +12,7 @@ HOSTNAME=$(hostname)
 
 # Get the leader hostname
 # Don't use `leader_address`, as users do change that.
-LEADER_HOSTNAME=$(crudini --get "$PIO_DIR"/config.ini cluster.topology leader_hostname)
+LEADER_HOSTNAME=$(crudini --get /home/pioreactor/.pioreactor/config.ini cluster.topology leader_hostname)
 
 if [ "$HOSTNAME" = "$LEADER_HOSTNAME" ]; then
     crudini  --set /home/pioreactor/.pioreactor/config.ini cluster_addresses \
@@ -37,5 +37,5 @@ if [ "$HOSTNAME" = "$LEADER_HOSTNAME" ]; then
 
 fi
 
-sudo -u pioreactor cp "$SCRIPT_DIR/install_pioreactor_plugin.sh" /usr/local/bin/install_pioreactor_plugin.sh
-sudo -u pioreactor cp "$SCRIPT_DIR/uninstall_pioreactor_plugin.sh" /usr/local/bin/uninstall_pioreactor_plugin.sh
+cp "$SCRIPT_DIR/install_pioreactor_plugin.sh" /usr/local/bin/install_pioreactor_plugin.sh
+cp "$SCRIPT_DIR/uninstall_pioreactor_plugin.sh" /usr/local/bin/uninstall_pioreactor_plugin.sh