prefer sys.exit over Abort

CHANGELOG.md

@@ -1,3 +1,8 @@
+### Upcoming
+ - API to set clock time
+ - deprecated `default` in background_jobs yaml fields.
+   - [ ] test self-test
+
 ### 24.12.10
  - Hotfix for UI settings bug
 

pioreactor/actions/leader/export_experiment_data.py

@@ -3,6 +3,7 @@
 # See create_tables.sql for all tables
 from __future__ import annotations
 
+import sys
 from base64 import b64decode
 from contextlib import closing
 from contextlib import ExitStack
@@ -137,11 +138,11 @@ def export_experiment_data(
 
     if not output.endswith(".zip"):
         click.echo("output should end with .zip")
-        raise click.Abort()
+        sys.exit(1)
 
     if len(dataset_names) == 0:
         click.echo("At least one dataset name must be provided.")
-        raise click.Abort()
+        sys.exit(1)
 
     logger = create_logger("export_experiment_data")
     logger.info(

pioreactor/background_jobs/od_reading.py

@@ -1214,11 +1214,11 @@ def create_channel_angle_map(
 def start_od_reading(
     od_angle_channel1: Optional[pt.PdAngleOrREF] = None,
     od_angle_channel2: Optional[pt.PdAngleOrREF] = None,
-    interval: Optional[float] = 1 / config.getfloat("od_reading.config", "samples_per_second"),
+    interval: Optional[float] = 1 / config.getfloat("od_reading.config", "samples_per_second", fallback=0.2),
     fake_data: bool = False,
     unit: Optional[str] = None,
     experiment: Optional[str] = None,
-    use_calibration: bool = config.getboolean("od_reading.config", "use_calibration"),
+    use_calibration: bool = config.getboolean("od_reading.config", "use_calibration", fallback="True"),
 ) -> ODReader:
     """
     This function prepares ODReader and other necessary transformation objects. It's a higher level API than using ODReader.

pioreactor/cli/pio.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import subprocess
+import sys
 from shlex import quote
 from typing import Optional
 
@@ -427,7 +428,7 @@ def update_app(
             commands_and_priority.append((f"sudo pip3 install --force-reinstall --no-index {source}", 1))
         else:
             click.echo("Not a valid source file. Should be either a whl or release archive.")
-            raise click.Abort()
+            sys.exit(1)
 
     elif branch is not None:
         cleaned_branch = quote(branch)
@@ -447,7 +448,7 @@ def update_app(
         response = get(f"https://api.github.com/repos/{repo}/releases/{tag}")
         if not response.ok:
             logger.error(f"Version {version} not found")
-            raise click.Abort()
+            sys.exit(1)
 
         release_metadata = loads(response.body)
         version_installed = release_metadata["tag_name"]
@@ -530,7 +531,7 @@ def update_app(
             logger.debug(p.stderr)
             logger.error("Update failed. See logs.")
             # end early
-            raise click.Abort()
+            sys.exit(1)
         elif p.stdout:
             logger.debug(p.stdout)
 
@@ -594,7 +595,7 @@ def update_firmware(version: Optional[str]) -> None:
             logger.debug(p.stderr)
             logger.error("Update failed. See logs.")
             # end early
-            raise click.Abort()
+            sys.exit(1)
 
     logger.info(f"Updated Pioreactor firmware to version {version_installed}.")  # type: ignore
 

pioreactor/cli/pios.py

@@ -4,6 +4,7 @@
 """
 from __future__ import annotations
 
+import sys
 from concurrent.futures import ThreadPoolExecutor
 
 import click
@@ -46,7 +47,7 @@ def pios(ctx) -> None:
     # this is run even if workers run `pios plugins etc.`
     if not am_I_leader():
         click.echo("workers cannot run `pios` commands. Try `pio` instead.", err=True)
-        raise click.Abort()
+        sys.exit(1)
 
 
 if am_I_leader() or is_testing_env():
@@ -189,7 +190,7 @@ def cp(
         if not y:
             confirm = input(f"Confirm copying {filepath} onto {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("cp", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
 
@@ -207,7 +208,7 @@ def _thread_function(unit: str) -> bool:
             results = executor.map(_thread_function, units)
 
         if not all(results):
-            raise click.Abort()
+            sys.exit(1)
 
     @pios.command("rm", short_help="rm a file across the cluster")
     @click.argument("filepath", type=click.Path(resolve_path=True))
@@ -223,7 +224,7 @@ def rm(
         if not y:
             confirm = input(f"Confirm deleting {filepath} on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("rm", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
 
@@ -244,7 +245,7 @@ def _thread_function(unit: str) -> bool:
             results = executor.map(_thread_function, units)
 
         if not all(results):
-            raise click.Abort()
+            sys.exit(1)
 
     @pios.group(invoke_without_command=True)
     @click.option("-s", "--source", help="use a release-***.zip already on the workers")
@@ -267,7 +268,7 @@ def update(
             if not y:
                 confirm = input(f"Confirm updating app and ui on {units}? Y/n: ").strip()
                 if confirm != "Y":
-                    raise click.Abort()
+                    sys.exit(1)
 
             logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
             options: dict[str, str | None] = {}
@@ -329,7 +330,7 @@ def update_app(
         if not y:
             confirm = input(f"Confirm updating app on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         options: dict[str, str | None] = {}
@@ -397,7 +398,7 @@ def update_ui(
         if not y:
             confirm = input(f"Confirm updating ui on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("update", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         options: dict[str, str | None] = {}
@@ -459,7 +460,7 @@ def install_plugin(plugin: str, source: str | None, units: tuple[str, ...], y: b
         if not y:
             confirm = input(f"Confirm installing {plugin} on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("install_plugin", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         commands = {"args": [plugin], "options": {}}
@@ -504,7 +505,7 @@ def uninstall_plugin(plugin: str, units: tuple[str, ...], y: bool, json: bool) -
         if not y:
             confirm = input(f"Confirm uninstalling {plugin} on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         logger = create_logger("uninstall_plugin", unit=get_unit_name(), experiment=UNIVERSAL_EXPERIMENT)
         commands = {"args": [plugin]}
@@ -587,7 +588,7 @@ def _thread_function(unit: str) -> bool:
             results = executor.map(_thread_function, units)
 
         if not all(results):
-            raise click.Abort()
+            sys.exit(1)
 
     @pios.command("kill", short_help="kill a job(s) on workers")
     @click.option("--job")
@@ -626,7 +627,7 @@ def kill(
         if not y:
             confirm = input(f"Confirm killing jobs on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         with ClusterJobManager() as cm:
             results = cm.kill_jobs(
@@ -672,15 +673,15 @@ def run(ctx, job: str, units: tuple[str, ...], y: bool, json: bool) -> None:
 
         if "unit" in extra_args:
             click.echo("Did you mean to use 'units' instead of 'unit'? Exiting.", err=True)
-            raise click.Abort()
+            sys.exit(1)
 
         units = universal_identifier_to_all_active_workers(units)
         assert len(units) > 0, "Empty units!"
 
         if not y:
             confirm = input(f"Confirm running {job} on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         data = parse_click_arguments(extra_args)
 
@@ -722,7 +723,7 @@ def shutdown(units: tuple[str, ...], y: bool) -> None:
         if not y:
             confirm = input(f"Confirm shutting down on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         def _thread_function(unit: str) -> bool:
             try:
@@ -755,7 +756,7 @@ def reboot(units: tuple[str, ...], y: bool) -> None:
         if not y:
             confirm = input(f"Confirm rebooting on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         def _thread_function(unit: str) -> bool:
             try:
@@ -800,7 +801,7 @@ def update_settings(ctx, job: str, units: tuple[str, ...], y: bool) -> None:
         if not y:
             confirm = input(f"Confirm updating {job}'s {extra_args} on {units}? Y/n: ").strip()
             if confirm != "Y":
-                raise click.Abort()
+                sys.exit(1)
 
         units = universal_identifier_to_all_active_workers(units)
 

pioreactor/cluster_management/__init__.py

@@ -81,7 +81,7 @@ def add_worker(hostname: str, password: str, version: str, model: str) -> None:
                     logger.error(
                         f"`{hostname}` not found on network after {round(elapsed())} seconds. Check that you provided the right i) the name is correct, ii) worker is powered on, iii) any WiFi credentials to the network are correct."
                     )
-                    sys.exit()
+                    sys.exit(1)
                 sleep(sleep_time)
 
         res = subprocess.run(