some small updates

Author: CamDavidsonPilon

core/pioreactor/background_jobs/monitor.py

@@ -295,7 +295,7 @@ def check_for_correct_permissions(self) -> None:
         for file in [
             storage_path / "pioreactor.sqlite",
         ]:
-            if file.exists() and (file.owner() != "pioreactor" or file.group() != "www-data"):
+            if file.is_file() and (file.owner() != "pioreactor" or file.group() != "www-data"):
                 self.logger.warning(
                     f"Pioreactor sqlite database file {file} has the wrong permissions or does not exist."
                 )

core/pioreactor/calibrations/__init__.py

@@ -54,7 +54,7 @@ def load_active_calibration(device: Device) -> structs.AnyCalibration | None:
 def load_calibration(device: Device, calibration_name: str) -> structs.AnyCalibration:
     target_file = CALIBRATION_PATH / device / f"{calibration_name}.yaml"
 
-    if not target_file.exists():
+    if not target_file.is_file():
         raise FileNotFoundError(
             f"Calibration {calibration_name} was not found in {CALIBRATION_PATH / device}"
         )
@@ -70,14 +70,14 @@ def load_calibration(device: Device, calibration_name: str) -> structs.AnyCalibr
 
 def list_of_calibrations_by_device(device: Device) -> list[str]:
     device_dir = CALIBRATION_PATH / device
-    if not device_dir.exists():
+    if not device_dir.is_dir():
         return []
     return [file.stem for file in device_dir.glob("*.yaml")]
 
 
 def list_devices() -> list[str]:
     calibration_dir = CALIBRATION_PATH
-    if not calibration_dir.exists():
+    if not calibration_dir.is_dir():
         return []
 
     return [f.name for f in calibration_dir.iterdir() if f.is_dir()]

core/pioreactor/calibrations/protocols/stirring_dc_based.py

@@ -214,7 +214,7 @@ class RunCalibration(SessionStep):
     def render(self, ctx: SessionContext) -> CalibrationStep:
         return steps.action(
             "Record calibration",
-            "Press Continue to run the stirring calibration. This will take a ~1 minute.",
+            "Press Continue to run the stirring calibration. This will take up to one minute.",
         )
 
     def advance(self, ctx: SessionContext) -> SessionStep | None:

core/pioreactor/cli/calibrations.py

@@ -53,7 +53,7 @@ def list_calibrations(device: str | None) -> None:
 
 def _display_calibrations_by_device(device: str) -> None:
     calibration_dir = CALIBRATION_PATH / device
-    if not calibration_dir.exists():
+    if not calibration_dir.is_dir():
         click.echo(
             f"No calibrations found for device '{device}'. Directory does not exist.",
             err=True,
@@ -263,7 +263,7 @@ def delete_calibration(device: str, calibration_name: str) -> None:
     """
     target_file = CALIBRATION_PATH / device / f"{calibration_name}.yaml"
 
-    if not target_file.exists():
+    if not target_file.is_file():
         click.echo(f"No such calibration file: {target_file}")
         raise click.Abort()
 
@@ -291,7 +291,7 @@ def analyze_calibration(device: str, calibration_name: str, fit: str) -> None:
     Analyze a calibration file from local storage.
     """
     target_file = CALIBRATION_PATH / device / f"{calibration_name}.yaml"
-    if not target_file.exists():
+    if not target_file.is_file():
         click.echo(f"No such calibration file: {target_file}")
         raise click.Abort()
 

core/pioreactor/cli/estimators.py

@@ -54,7 +54,7 @@ def list_estimators(device: str | None) -> None:
 
 def _display_estimators_by_device(device: str) -> None:
     estimator_dir = ESTIMATOR_PATH / device
-    if not estimator_dir.exists():
+    if not estimator_dir.is_dir():
         click.echo(
             f"No estimators found for device '{device}'. Directory does not exist.",
             err=True,
@@ -136,7 +136,7 @@ def delete_estimator(device: str, estimator_name: str) -> None:
     """
     target_file = ESTIMATOR_PATH / device / f"{estimator_name}.yaml"
 
-    if not target_file.exists():
+    if not target_file.is_file():
         click.echo(f"No such estimator file: {target_file}")
         raise click.Abort()
 
@@ -205,7 +205,7 @@ def analyze_estimator(device: str, estimator_name: str, fit: str) -> None:
     Analyze an estimator file from local storage.
     """
     target_file = ESTIMATOR_PATH / device / f"{estimator_name}.yaml"
-    if not target_file.exists():
+    if not target_file.is_file():
         click.echo(f"No such estimator file: {target_file}", err=True)
         raise click.Abort()
 

core/pioreactor/config.py

@@ -175,7 +175,7 @@ def get_config() -> ConfigParserMod:
         else:
             local_config_path = "/home/pioreactor/.pioreactor/unit_config.ini"
 
-    if not Path(global_config_path).exists():
+    if not Path(global_config_path).is_file():
         raise FileNotFoundError(
             f"Configuration file at {global_config_path} is missing. Has it completed initializing? Does it need to connect to a leader? Alternatively, use the env variable GLOBAL_CONFIG to specify its location."
         )

core/pioreactor/estimators/__init__.py

@@ -32,7 +32,7 @@ def load_active_estimator(device: Device) -> structs.ODFusionEstimator | None:
 
 def load_estimator(device: Device, estimator_name: str) -> structs.ODFusionEstimator:
     target_file = _estimator_path_for(device, estimator_name)
-    if not target_file.exists():
+    if not target_file.is_file():
         raise FileNotFoundError(f"Estimator {estimator_name} was not found in {ESTIMATOR_PATH / device}")
     if target_file.stat().st_size == 0:
         raise FileNotFoundError(f"Estimator {estimator_name} is empty")
@@ -45,12 +45,12 @@ def load_estimator(device: Device, estimator_name: str) -> structs.ODFusionEstim
 
 def list_of_estimators_by_device(device: Device) -> list[str]:
     device_dir = ESTIMATOR_PATH / device
-    if not device_dir.exists():
+    if not device_dir.is_dir():
         return []
     return [file.stem for file in device_dir.glob("*.yaml")]
 
 
 def list_estimator_devices() -> list[str]:
-    if not ESTIMATOR_PATH.exists():
+    if not ESTIMATOR_PATH.is_dir():
         return []
     return [path.name for path in ESTIMATOR_PATH.iterdir() if path.is_dir()]

core/pioreactor/hardware.py

@@ -62,7 +62,7 @@
 
 
 def _load_yaml_if_exists(path: Path) -> dict[str, Any]:
-    if path.exists():
+    if path.is_file():
         try:
             return yaml_decode(path.read_bytes()) or {}
         except Exception as e:

core/pioreactor/models.py

@@ -113,7 +113,7 @@ def load_contrib_model_definitions() -> list[Model]:
     MODEL_DEFINITIONS_PATH = Path(os.environ["DOT_PIOREACTOR"]) / "models"
 
     models: list[Model] = []
-    if not MODEL_DEFINITIONS_PATH.exists():
+    if not MODEL_DEFINITIONS_PATH.is_dir():
         return models
     for file in MODEL_DEFINITIONS_PATH.glob("*.y*ml"):
         try:

core/pioreactor/structs.py

@@ -261,7 +261,7 @@ def exists_on_disk_for_device(self, device: str) -> bool:
 
         target_file = CALIBRATION_PATH / device / f"{self.calibration_name}.yaml"
 
-        return target_file.exists()
+        return target_file.is_file()
 
     def x_to_y(self, x: X) -> Y:
         """
@@ -427,7 +427,7 @@ def exists_on_disk_for_device(self, device: str) -> bool:
 
         target_file = ESTIMATOR_PATH / device / f"{self.estimator_name}.yaml"
 
-        return target_file.exists()
+        return target_file.is_file()
 
     def is_active(self, device: str) -> bool:
         from pioreactor.utils import local_persistent_storage