shepherd-core 2025.6.1__tar.gz → 2025.6.2__tar.gz

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shepherd_core
-Version: 2025.6.1
+Version: 2025.6.2
 Summary: Programming- and CLI-Interface for the h5-dataformat of the Shepherd-Testbed
 Author-email: Ingmar Splitt <ingmar.splitt@tu-dresden.de>
 Maintainer-email: Ingmar Splitt <ingmar.splitt@tu-dresden.de>

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/examples/eenv_generator.py

@@ -8,7 +8,7 @@ from tqdm import trange
 
 from shepherd_core import Reader as ShpReader
 from shepherd_core import Writer as ShpWriter
-from shepherd_core import logger
+from shepherd_core.logger import log
 
 # Config
 voltages_V = [4.0, 2.0]
@@ -26,7 +26,7 @@ for _v, _c in product(voltages_V, currents_A):
     file_path = path_here / f"{name}.h5"
 
     if file_path.exists():
-        logger.info("File exists, will skip: %s", file_path.name)
+        log.info("File exists, will skip: %s", file_path.name)
     else:
         with ShpWriter(file_path) as file:
             file.store_hostname("artificial")

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/examples/uart_decode_waveform.py

@@ -3,8 +3,8 @@
 from pathlib import Path
 from timeit import timeit
 
-from shepherd_core import logger
 from shepherd_core.decoder_waveform import Uart
+from shepherd_core.logger import log
 
 # file captured with logic analyzer, 15.5k events (2700 symbols, 61 lines)
 trace = Path(__file__).parent / "uart_raw2.csv"
@@ -13,7 +13,7 @@ uwd = Uart(trace)
 sym = uwd.get_symbols()
 lne = uwd.get_lines()
 txt = uwd.get_text()
-logger.info(txt)
+log.info(txt)
 
 do_analysis = False
 if do_analysis:

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/__init__.py

@@ -17,7 +17,7 @@ from .data_models.task.emulation import Compression
 from .inventory import Inventory
 from .logger import get_verbose_level
 from .logger import increase_verbose_level
-from .logger import logger
+from .logger import log
 from .reader import Reader
 from .testbed_client.client_web import WebClient
 from .version import version
@@ -41,5 +41,5 @@ __all__ = [
     "increase_verbose_level",
     "local_now",
     "local_tz",
-    "logger",
+    "log",
 ]

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/__init__.py

@@ -3,7 +3,7 @@
 Public models are directly referenced here and are usable like:
 
 '''python
-from shepherd-core import data_models
+from shepherd_core import data_models
 
 cdata = data_models.CapeData(serial_number="A123")
 '''

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/base/shepherd.py

@@ -2,6 +2,7 @@
 
 import hashlib
 import pathlib
+import pickle
 from collections.abc import Generator
 from datetime import timedelta
 from ipaddress import IPv4Address
@@ -126,10 +127,12 @@ class ShpModel(BaseModel):
         comment: Optional[str] = None,
         *,
         minimal: bool = True,
+        use_pickle: bool = False,
     ) -> Path:
         """Store data to yaml in a wrapper.
 
         minimal: stores minimal set (filters out unset & default parameters)
+        pickle: uses pickle to serialize data, on BBB >100x faster for large files
         comment: documentation.
         """
         model_dict = self.model_dump(exclude_unset=minimal)
@@ -139,25 +142,39 @@ class ShpModel(BaseModel):
             created=local_now(),
             parameters=model_dict,
         )
-        model_yaml = yaml.safe_dump(
-            model_wrap.model_dump(exclude_unset=minimal, exclude_defaults=minimal),
-            default_flow_style=False,
-            sort_keys=False,
-        )
+        if use_pickle:
+            model_serial = pickle.dumps(model_dict, fix_imports=True)
+            model_path = Path(path).resolve().with_suffix(".pickle")
+        else:
+            # TODO: x64 windows supports CSafeLoader/dumper,
+            #       there are examples that replace load if avail
+            model_serial = yaml.safe_dump(
+                model_wrap.model_dump(exclude_unset=minimal, exclude_defaults=minimal),
+                default_flow_style=False,
+                sort_keys=False,
+            )
+            model_path = Path(path).resolve().with_suffix(".yaml")
         # TODO: handle directory
-        model_path = Path(path).resolve().with_suffix(".yaml")
+
         if not model_path.parent.exists():
             model_path.parent.mkdir(parents=True)
         with model_path.open("w") as f:
-            f.write(model_yaml)
+            f.write(model_serial)
         return model_path
 
     @classmethod
     def from_file(cls, path: Union[str, Path]) -> Self:
-        """Load from yaml."""
-        with Path(path).open() as shp_file:
-            shp_dict = yaml.safe_load(shp_file)
-        shp_wrap = Wrapper(**shp_dict)
+        """Load from YAML or pickle file."""
+        path: Path = Path(path)
+        if not Path(path).exists():
+            raise FileNotFoundError
+        if path.suffix.lower() == ".pickle":
+            with Path(path).open("rb") as shp_file:
+                shp_wrap = pickle.load(shp_file, fix_imports=True)  # noqa: S301
+        else:
+            with Path(path).open() as shp_file:
+                shp_dict = yaml.safe_load(shp_file)
+            shp_wrap = Wrapper(**shp_dict)
         if shp_wrap.datatype != cls.__name__:
             raise ValueError("Model in file does not match the requirement")
         return cls(**shp_wrap.parameters)

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/content/firmware.py

@@ -19,7 +19,7 @@ from typing_extensions import Unpack
 from shepherd_core import fw_tools
 from shepherd_core.data_models.base.content import ContentModel
 from shepherd_core.data_models.testbed.mcu import MCU
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 from shepherd_core.testbed_client import tb_client
 
 from .firmware_datatype import FirmwareDType
@@ -135,8 +135,8 @@ class Firmware(ContentModel, title="Firmware of Target"):
                 if ("nrf52" in arch or "arm" in arch) and not fw_tools.is_elf_nrf52(file):
                     raise ValueError("File is not a ELF for nRF52")
             except RuntimeError:
-                logger.warning("ObjCopy not found -> Arch of Firmware can't be verified")
-            logger.debug("ELF-File '%s' has arch: %s", file.name, arch)
+                log.warning("ObjCopy not found -> Arch of Firmware can't be verified")
+            log.debug("ELF-File '%s' has arch: %s", file.name, arch)
             if "mcu" not in kwargs:
                 kwargs["mcu"] = arch_to_mcu[arch]
 
@@ -159,7 +159,7 @@ class Firmware(ContentModel, title="Firmware of Target"):
             match = self.data_hash == hash_new
 
         if not match:
-            logger.warning("FW-Hash does not match with stored value!")
+            log.warning("FW-Hash does not match with stored value!")
             # TODO: it might be more appropriate to raise here
         return match
 

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/content/virtual_harvester.py

@@ -14,7 +14,7 @@ from shepherd_core.config import config
 from shepherd_core.data_models.base.calibration import CalibrationHarvester
 from shepherd_core.data_models.base.content import ContentModel
 from shepherd_core.data_models.base.shepherd import ShpModel
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 from shepherd_core.testbed_client import tb_client
 
 from .energy_environment import EnergyDType
@@ -310,7 +310,7 @@ class VirtualHarvesterConfig(ContentModel, title="Config for the Harvester"):
         if values["name"] == "neutral":
             # TODO: same test is later done in calc_algorithm_num() again
             raise ValueError("Resulting Harvester can't be neutral")
-        logger.debug("VHrv-Inheritances: %s", chain)
+        log.debug("VHrv-Inheritances: %s", chain)
 
         # post corrections -> should be in separate validator
         cal = CalibrationHarvester()  # TODO: as argument?
@@ -372,7 +372,7 @@ class VirtualHarvesterConfig(ContentModel, title="Config for the Harvester"):
         duration_ms = min(max(self.duration_ms, time_min_ms), interval_ms)
         _ratio = (duration_ms / interval_ms) / (self.duration_ms / self.interval_ms)
         if (_ratio - 1) > 0.1:
-            logger.debug(
+            log.debug(
                 "Ratio between interval & duration has changed "
                 "more than 10%% due to constraints (%.4f)",
                 _ratio,

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/content/virtual_source.py

@@ -10,7 +10,7 @@ from typing_extensions import Self
 from shepherd_core.config import config
 from shepherd_core.data_models.base.content import ContentModel
 from shepherd_core.data_models.base.shepherd import ShpModel
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 from shepherd_core.testbed_client import tb_client
 
 from .energy_environment import EnergyDType
@@ -128,7 +128,7 @@ class VirtualSourceConfig(ContentModel, title="Config for the virtual Source"):
     def query_database(cls, values: dict[str, Any]) -> dict[str, Any]:
         values, chain = tb_client.try_completing_model(cls.__name__, values)
         values = tb_client.fill_in_user_data(values)
-        logger.debug("VSrc-Inheritances: %s", chain)
+        log.debug("VSrc-Inheritances: %s", chain)
         return values
 
     @model_validator(mode="after")
@@ -187,7 +187,7 @@ class VirtualSourceConfig(ContentModel, title="Config for the virtual Source"):
         if not (isinstance(dV_output_en_thrs_mV, (int, float)) and (dV_output_en_thrs_mV >= 0)):
             dV_output_en_thrs_mV = 0
         if not (isinstance(dV_output_imed_low_mV, (int, float)) and (dV_output_imed_low_mV >= 0)):
-            logger.warning("VSrc: C_output shouldn't be larger than C_intermediate")
+            log.warning("VSrc: C_output shouldn't be larger than C_intermediate")
             dV_output_imed_low_mV = 0
 
         # decide which hysteresis-thresholds to use for buck-converter
@@ -224,7 +224,7 @@ class VirtualSourceConfig(ContentModel, title="Config for the virtual Source"):
         enable_storage = self.C_intermediate_uF > 0
         enable_boost = self.enable_boost and enable_storage
         if enable_boost != self.enable_boost:
-            logger.warning("VSrc - boost was disabled due to missing storage capacitor!")
+            log.warning("VSrc - boost was disabled due to missing storage capacitor!")
         enable_feedback = (
             self.enable_feedback_to_hrv
             and enable_storage
@@ -235,7 +235,7 @@ class VirtualSourceConfig(ContentModel, title="Config for the virtual Source"):
             reason = "enabled boost, " if enable_boost else ""
             reason += "" if dtype_in == EnergyDType.ivcurve else "input not ivcurve, "
             reason += "" if enable_storage else "no storage capacitor"
-            logger.warning("VSRC - feedback to harvester was disabled! Reasons: %s", reason)
+            log.warning("VSRC - feedback to harvester was disabled! Reasons: %s", reason)
         return (
             1 * int(enable_storage)
             + 2 * int(enable_boost)

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/experiment/observer_features.py

@@ -13,9 +13,9 @@ from pydantic import model_validator
 from typing_extensions import Self
 from typing_extensions import deprecated
 
-from shepherd_core import logger
 from shepherd_core.data_models.base.shepherd import ShpModel
 from shepherd_core.data_models.testbed.gpio import GPIO
+from shepherd_core.logger import log
 
 # defaults (pre-init complex types)
 zero_duration = timedelta(seconds=0)
@@ -190,7 +190,7 @@ class GpioTracing(ShpModel, title="Config for GPIO-Tracing"):
         if self.duration and self.duration.total_seconds() < 0:
             raise ValueError("Duration can't be negative.")
         if self.uart_decode:
-            logger.error(
+            log.error(
                 "Feature GpioTracing.uart_decode reserved for future use. "
                 "Use UartLogging or manually decode serial with the provided waveform decoder."
             )

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/__init__.py

@@ -3,6 +3,7 @@
 These models import externally from all other model-modules!
 """
 
+import pickle
 from pathlib import Path
 from typing import Optional
 from typing import Union
@@ -11,7 +12,7 @@ import yaml
 
 from shepherd_core.data_models.base.shepherd import ShpModel
 from shepherd_core.data_models.base.wrapper import Wrapper
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 
 from .emulation import Compression
 from .emulation import EmulationTask
@@ -44,7 +45,10 @@ def prepare_task(config: Union[ShpModel, Path, str], observer: Optional[str] = N
     if isinstance(config, str):
         config = Path(config)
 
-    if isinstance(config, Path):
+    if isinstance(config, Path) and config.exists() and config.suffix.lower() == ".pickle":
+        with config.resolve().open("rb") as shp_file:
+            shp_wrap = pickle.load(shp_file, fix_imports=True)  # noqa: S301
+    elif isinstance(config, Path) and config.exists() and config.suffix.lower() == ".yaml":
         with config.resolve().open() as shp_file:
             shp_dict = yaml.safe_load(shp_file)
         shp_wrap = Wrapper(**shp_dict)
@@ -59,12 +63,12 @@ def prepare_task(config: Union[ShpModel, Path, str], observer: Optional[str] = N
 
     if shp_wrap.datatype == TestbedTasks.__name__:
         if observer is None:
-            logger.debug(
+            log.debug(
                 "Task-Set contained TestbedTasks & no observer was provided -> will return TB-Tasks"
             )
             return shp_wrap
         tbt = TestbedTasks(**shp_wrap.parameters)
-        logger.debug("Loading Testbed-Tasks %s for %s", tbt.name, observer)
+        log.debug("Loading Testbed-Tasks %s for %s", tbt.name, observer)
         obt = tbt.get_observer_tasks(observer)
         if obt is None:
             msg = f"Observer '{observer}' is not in TestbedTask-Set"

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/emulation.py

@@ -1,10 +1,12 @@
 """Configuration for the Observer in Emulation-Mode."""
 
 import copy
+from collections.abc import Set as AbstractSet
 from datetime import datetime
 from datetime import timedelta
 from enum import Enum
 from pathlib import Path
+from pathlib import PurePosixPath
 from typing import Annotated
 from typing import Optional
 from typing import Union
@@ -28,7 +30,9 @@ from shepherd_core.data_models.experiment.observer_features import UartLogging
 from shepherd_core.data_models.experiment.target_config import vsrc_neutral
 from shepherd_core.data_models.testbed import Testbed
 from shepherd_core.data_models.testbed.cape import TargetPort
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
+
+from .helper_paths import path_posix
 
 
 class Compression(str, Enum):
@@ -149,9 +153,9 @@ class EmulationTask(ShpModel):
             _io is not None for _io in (self.gpio_actuation, self.gpio_tracing, self.uart_logging)
         )
         if self.enable_io and not io_requested:
-            logger.warning("Target IO enabled, but no feature requested IO")
+            log.warning("Target IO enabled, but no feature requested IO")
         if not self.enable_io and io_requested:
-            logger.warning("Target IO not enabled, but a feature requested IO")
+            log.warning("Target IO not enabled, but a feature requested IO")
         return self
 
     @classmethod
@@ -165,8 +169,8 @@ class EmulationTask(ShpModel):
         )
 
         return cls(
-            input_path=tgt_cfg.energy_env.data_path,
-            output_path=root_path / f"emu_{obs.name}.h5",
+            input_path=path_posix(tgt_cfg.energy_env.data_path),
+            output_path=path_posix(root_path / f"emu_{obs.name}.h5"),
             time_start=copy.copy(xp.time_start),
             duration=xp.duration,
             enable_io=io_requested,
@@ -180,6 +184,11 @@ class EmulationTask(ShpModel):
             sys_logging=xp.sys_logging,
         )
 
+    def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        all_ok = any(self.input_path.is_relative_to(path) for path in paths)
+        all_ok &= any(self.output_path.is_relative_to(path) for path in paths)
+        return all_ok
+
 
 # TODO: herdConfig
 #  - store if path is remote (read & write)

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/firmware_mod.py

@@ -1,7 +1,8 @@
 """Config for Task that adds the custom ID to the firmware & stores it into a file."""
 
-import copy
+from collections.abc import Set as AbstractSet
 from pathlib import Path
+from pathlib import PurePosixPath
 from typing import Annotated
 from typing import Optional
 from typing import TypedDict
@@ -22,7 +23,9 @@ from shepherd_core.data_models.experiment.experiment import Experiment
 from shepherd_core.data_models.testbed import Testbed
 from shepherd_core.data_models.testbed.target import IdInt16
 from shepherd_core.data_models.testbed.target import MCUPort
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
+
+from .helper_paths import path_posix
 
 
 class FirmwareModTask(ShpModel):
@@ -42,7 +45,7 @@ class FirmwareModTask(ShpModel):
             FirmwareDType.base64_hex,
             FirmwareDType.path_hex,
         }:
-            logger.warning("Firmware is scheduled to get custom-ID but is not in elf-format")
+            log.warning("Firmware is scheduled to get custom-ID but is not in elf-format")
         return self
 
     @classmethod
@@ -68,10 +71,10 @@ class FirmwareModTask(ShpModel):
             fw_id = obs.get_target(tgt_id).testbed_id
 
         return cls(
-            data=fw.data,
+            data=path_posix(fw.data) if isinstance(fw.data, Path) else fw.data,
             data_type=fw.data_type,
             custom_id=fw_id,
-            firmware_file=copy.copy(fw_path),
+            firmware_file=path_posix(fw_path),
         )
 
     @classmethod
@@ -90,3 +93,9 @@ class FirmwareModTask(ShpModel):
             path_new: Path = path / fw.name
             kwargs["firmware_file"] = path_new.with_suffix(".hex")
         return cls(**kwargs)
+
+    def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        all_ok = any(self.firmware_file.is_relative_to(path) for path in paths)
+        if isinstance(self.data, Path):
+            all_ok = any(self.data.is_relative_to(path) for path in paths)
+        return all_ok

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/harvest.py

@@ -1,8 +1,10 @@
 """Config for the Observer in Harvest-Mode to record IV data from a harvesting-source."""
 
+from collections.abc import Set as AbstractSet
 from datetime import datetime
 from datetime import timedelta
 from pathlib import Path
+from pathlib import PurePosixPath
 from typing import Annotated
 from typing import Optional
 
@@ -84,3 +86,6 @@ class HarvestTask(ShpModel):
         if self.duration and self.duration.total_seconds() < 0:
             raise ValueError("Task-Duration can't be negative.")
         return self
+
+    def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        return any(self.output_path.is_relative_to(path) for path in paths)

shepherd_core-2025.6.2/shepherd_core/data_models/task/helper_paths.py

@@ -0,0 +1,15 @@
+r"""Helper FN to avoid unwanted behavior.
+
+On windows Path("\xyz") gets transformed to "/xyz", but not on linux.
+When sending an experiment via fastapi, this bug gets triggered.
+"""
+
+from pathlib import Path
+
+
+def path_posix(path: Path) -> Path:
+    r"""Help Linux to get from "\xyz" to "/xyz".
+
+    This isn't a problem on windows and gets triggered when sending XP via fastapi.
+    """
+    return Path(path.as_posix().replace("\\", "/"))

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/observer_tasks.py

@@ -1,8 +1,9 @@
 """Collection of tasks for selected observer included in experiment."""
 
+from collections.abc import Set as AbstractSet
 from datetime import datetime
-from datetime import timedelta
 from pathlib import Path
+from pathlib import PurePosixPath
 from typing import Annotated
 from typing import Optional
 
@@ -18,6 +19,7 @@ from shepherd_core.data_models.testbed.testbed import Testbed
 
 from .emulation import EmulationTask
 from .firmware_mod import FirmwareModTask
+from .helper_paths import path_posix
 from .programming import ProgrammingTask
 
 
@@ -27,7 +29,7 @@ class ObserverTasks(ShpModel):
     observer: NameStr
 
     # PRE PROCESS
-    time_prep: datetime  # TODO: should be optional
+    time_prep: Optional[datetime] = None  # TODO: currently not used
     root_path: Path
 
     # fw mod, store as hex-file and program
@@ -55,24 +57,14 @@ class ObserverTasks(ShpModel):
         if not tb.shared_storage:
             raise ValueError("Implementation currently relies on shared storage!")
 
-        t_start = (
-            xp.time_start
-            if isinstance(xp.time_start, datetime)
-            else datetime.now().astimezone() + timedelta(minutes=3)
-        )  # TODO: this is messed up, just a hotfix
-
         obs = tb.get_observer(tgt_id)
-        xp_dir = "experiments/" + xp.name + "_" + t_start.strftime("%Y-%m-%d_%H-%M-%S")
-        root_path = tb.data_on_observer / xp_dir
-        # TODO: Paths should be "friendlier"
-        #    - replace whitespace with "_" and remove non-alphanum?
-
+        root_path = tb.data_on_observer / "experiments" / xp.folder_name()
         fw_paths = [root_path / f"fw{_i}_{obs.name}.hex" for _i in [1, 2]]
 
         return cls(
             observer=obs.name,
-            time_prep=t_start - tb.prep_duration,
-            root_path=root_path,
+            # time_prep=
+            root_path=path_posix(root_path),
             fw1_mod=FirmwareModTask.from_xp(xp, tb, tgt_id, 1, fw_paths[0]),
             fw2_mod=FirmwareModTask.from_xp(xp, tb, tgt_id, 2, fw_paths[1]),
             fw1_prog=ProgrammingTask.from_xp(xp, tb, tgt_id, 1, fw_paths[0]),
@@ -100,3 +92,12 @@ class ObserverTasks(ShpModel):
                 raise ValueError("Emu-Task should have a valid output-path")
             values[self.observer] = self.emulation.output_path
         return values
+
+    def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        all_ok = any(self.root_path.is_relative_to(path) for path in paths)
+        all_ok &= self.fw1_mod.is_contained(paths)
+        all_ok &= self.fw2_mod.is_contained(paths)
+        all_ok &= self.fw1_prog.is_contained(paths)
+        all_ok &= self.fw2_prog.is_contained(paths)
+        all_ok &= self.emulation.is_contained(paths)
+        return all_ok

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/programming.py

@@ -1,7 +1,8 @@
 """Config for a Task programming the selected target."""
 
-import copy
+from collections.abc import Set as AbstractSet
 from pathlib import Path
+from pathlib import PurePosixPath
 from typing import Annotated
 from typing import Optional
 
@@ -21,6 +22,8 @@ from shepherd_core.data_models.testbed.mcu import ProgrammerProtocol
 from shepherd_core.data_models.testbed.target import MCUPort
 from shepherd_core.data_models.testbed.testbed import Testbed
 
+from .helper_paths import path_posix
+
 
 class ProgrammingTask(ShpModel):
     """Config for a Task programming the selected target."""
@@ -66,7 +69,7 @@ class ProgrammingTask(ShpModel):
             return None
 
         return cls(
-            firmware_file=copy.copy(fw_path),
+            firmware_file=path_posix(fw_path),
             target_port=obs.get_target_port(tgt_id),
             mcu_port=mcu_port,
             mcu_type=fw.mcu.name,
@@ -74,3 +77,6 @@ class ProgrammingTask(ShpModel):
             datarate=fw.mcu.prog_datarate,
             protocol=fw.mcu.prog_protocol,
         )
+
+    def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        return any(self.firmware_file.is_relative_to(path) for path in paths)

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/data_models/task/testbed_tasks.py

@@ -1,6 +1,8 @@
 """Collection of tasks for all observers included in experiment."""
 
 from pathlib import Path
+from pathlib import PurePosixPath
+from typing import TYPE_CHECKING
 from typing import Annotated
 from typing import Optional
 
@@ -17,6 +19,9 @@ from shepherd_core.data_models.testbed.testbed import Testbed
 
 from .observer_tasks import ObserverTasks
 
+if TYPE_CHECKING:
+    from collections.abc import Set as AbstractSet
+
 
 class TestbedTasks(ShpModel):
     """Collection of tasks for all observers included in experiment."""
@@ -56,3 +61,10 @@ class TestbedTasks(ShpModel):
         for obt in self.observer_tasks:
             values = {**values, **obt.get_output_paths()}
         return values
+
+    def is_contained(self) -> bool:
+        paths_allowed: AbstractSet[PurePosixPath] = {
+            PurePosixPath("/var/shepherd/"),
+            PurePosixPath("/tmp/"),  # noqa: S108
+        }
+        return all(obt.is_contained(paths_allowed) for obt in self.observer_tasks)

{shepherd_core-2025.6.1 → shepherd_core-2025.6.2}/shepherd_core/decoder_waveform/uart.py

@@ -28,7 +28,7 @@ from typing import Union
 
 import numpy as np
 
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 
 
 class Parity(str, Enum):
@@ -109,10 +109,10 @@ class Uart:
             raise ValueError("Only bit-order LSB-first is supported ATM")
 
         if self.inversion:
-            logger.debug("inversion was detected / issued -> will invert signal")
+            log.debug("inversion was detected / issued -> will invert signal")
             self._convert_analog2digital(invert=True)
         if self.detect_inversion():
-            logger.error("Signal still inverted?!? Check parameters and input")
+            log.error("Signal still inverted?!? Check parameters and input")
 
         # results
         self.events_symbols: Optional[np.ndarray] = None
@@ -136,7 +136,7 @@ class Uart:
         self.events_sig = self.events_sig[data_f == 1]
 
         if len(data_0) > len(self.events_sig):
-            logger.debug(
+            log.debug(
                 "filtered out %d/%d events (redundant)",
                 len(data_0) - len(self.events_sig),
                 len(data_0),
@@ -145,7 +145,7 @@ class Uart:
     def _add_duration(self) -> None:
         """Calculate third column -> duration of state in [baud-ticks]."""
         if self.events_sig.shape[1] > 2:
-            logger.warning("Tried to add state-duration, but it seems already present")
+            log.warning("Tried to add state-duration, but it seems already present")
             return
         if not hasattr(self, "dur_tick"):
             raise ValueError("Make sure that baud-rate was calculated before running add_dur()")
@@ -223,7 +223,7 @@ class Uart:
                         symbol = 0
                     pos_df = None
                 else:
-                    logger.debug("Error - Long pause - but SigLow (@%d)", time)
+                    log.debug("Error - Long pause - but SigLow (@%d)", time)
                 continue
             if pos_df is None and value == 0:
                 # Start of frame (first low after pause / EOF)
@@ -245,7 +245,7 @@ class Uart:
                         symbol = 0
                     pos_df = None
                     if off_tick and value == 0:
-                        logger.debug("Error - Off-sized step - but SigLow (@%d)", time)
+                        log.debug("Error - Off-sized step - but SigLow (@%d)", time)
         self.events_symbols = np.concatenate(content).reshape((len(content), 2))
         # TODO: numpy is converting timestamp to string -> must be added as tuple (ts, symbol)
         # symbol_events[:, 0] = symbol_events[:, 0].astype(float)  # noqa: ERA001