shepherd-core 2023.8.7__tar.gz → 2023.8.8__tar.gz

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd_core
-Version: 2023.8.7
+Version: 2023.8.8
 Summary: Programming- and CLI-Interface for the h5-dataformat of the Shepherd-Testbed
 Home-page: https://pypi.org/project/shepherd-core/
 Author: Ingmar Splitt, Kai Geissdoerfer
@@ -77,6 +77,13 @@ The Library is available via PyPI and can be installed with
   pip install shepherd-data
 ```
 
+for bleeding-edge-features or dev-work it is possible to install directly from GitHub-Sources (here `dev`-branch):
+
+```Shell
+pip install git+https://github.com/orgua/shepherd-datalib.git@dev#subdirectory=shepherd_core -U
+```
+
+
 If you are working with ``.elf``-files (embedding into experiments) you make "objcopy" accessible to python. In Ubuntu, you can either install ``build-essential`` or ``binutils-$ARCH`` with arch being ``msp430`` or ``arm-none-eabi`` for the nRF52.
 
 ```shell

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/README.md

@@ -40,6 +40,13 @@ The Library is available via PyPI and can be installed with
   pip install shepherd-data
 ```
 
+for bleeding-edge-features or dev-work it is possible to install directly from GitHub-Sources (here `dev`-branch):
+
+```Shell
+pip install git+https://github.com/orgua/shepherd-datalib.git@dev#subdirectory=shepherd_core -U
+```
+
+
 If you are working with ``.elf``-files (embedding into experiments) you make "objcopy" accessible to python. In Ubuntu, you can either install ``build-essential`` or ``binutils-$ARCH`` with arch being ``msp430`` or ``arm-none-eabi`` for the nRF52.
 
 ```shell

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/__init__.py

@@ -21,7 +21,7 @@ from .testbed_client.client import TestbedClient
 from .testbed_client.client import tb_client
 from .writer import BaseWriter
 
-__version__ = "2023.8.7"
+__version__ = "2023.8.8"
 
 __all__ = [
     "BaseReader",

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/__init__.py

@@ -3,6 +3,7 @@ from .base.calibration import CalibrationEmulator
 from .base.calibration import CalibrationHarvester
 from .base.calibration import CalibrationPair
 from .base.calibration import CalibrationSeries
+from .base.calibration import CapeData
 from .base.content import ContentModel
 from .base.shepherd import ShpModel
 from .base.wrapper import Wrapper
@@ -23,6 +24,7 @@ from .experiment.target_config import TargetConfig
 
 __all__ = [
     # Core
+    "CapeData",
     "CalibrationCape",
     "CalibrationEmulator",
     "CalibrationHarvester",
@@ -46,4 +48,4 @@ __all__ = [
     "EnergyDType",
     "VirtualSourceConfig",
     "VirtualHarvesterConfig",
-]  # TODO: for pydantic 2 add @classmethod after @root_validator for cleaner type-checking
+]

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/base/cal_measurement.py

@@ -11,6 +11,7 @@ from .. import CalibrationCape
 from .. import CalibrationEmulator
 from .. import CalibrationHarvester
 from .. import CalibrationPair
+from .calibration import CapeData
 from .shepherd import ShpModel
 
 # TODO: move to shepherd_data to remove scipy-dependency from _core
@@ -75,12 +76,12 @@ class CalMeasurementEmulator(ShpModel):
 
 
 class CalMeasurementCape(ShpModel):
+    cape: Optional[CapeData] = None
+    host: Optional[str] = None
+
     harvester: Optional[CalMeasurementHarvester] = None
     emulator: Optional[CalMeasurementEmulator] = None
 
-    cape: Optional[str] = None
-    host: Optional[str] = None
-
     def to_cal(self) -> CalibrationCape:
         dv = self.model_dump()
         dcal = CalibrationCape().model_dump()

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/base/calibration.py

@@ -1,4 +1,5 @@
 import struct
+from datetime import date
 from typing import Callable
 from typing import Generator
 from typing import Optional
@@ -7,7 +8,10 @@ from typing import Union
 
 import numpy as np
 from numpy.typing import NDArray
+from pydantic import Field
 from pydantic import PositiveFloat
+from pydantic import conbytes
+from pydantic import constr
 from pydantic import validate_call
 
 from ...calibration_hw_def import adc_current_to_raw
@@ -146,6 +150,33 @@ class CalibrationEmulator(ShpModel):
         return cal_set
 
 
+class CapeData(ShpModel):
+    """Representation of Beaglebone Cape information
+        -> just provide serial-number on creation
+
+    According to BeagleBone specifications, each cape should host an EEPROM
+    that contains some standardized information about the type of cape,
+    manufacturer, version etc.
+
+    `See<https://github.com/beagleboard/beaglebone-black/wiki/System-Reference-Manual#824_EEPROM_Data_Format>`_
+    """
+
+    header: conbytes(max_length=4) = b"\xAA\x55\x33\xEE"
+    eeprom_revision: constr(max_length=2) = "A2"
+    board_name: constr(max_length=32) = "BeagleBone SHEPHERD2 Cape"
+    version: constr(max_length=4) = "24B0"
+    manufacturer: constr(max_length=16) = "NES TU DRESDEN"
+    part_number: constr(max_length=16) = "BB-SHPRD"
+
+    serial_number: constr(max_length=12)
+
+    cal_date: constr(max_length=12) = Field(default_factory=date.today().isoformat)
+
+    def __repr__(self) -> str:
+        """string-representation allows print(model)"""
+        return str(self.model_dump())
+
+
 class CalibrationCape(ShpModel):
     """Represents calibration data of shepherd cape.
     Defines the format of calibration data and provides convenient functions
@@ -154,19 +185,20 @@ class CalibrationCape(ShpModel):
     YAML: .to_file() and .from_file() already in ShpModel
     """
 
+    cape: Optional[CapeData] = None
+    host: Optional[str] = None
+
     harvester: CalibrationHarvester = CalibrationHarvester()
     emulator: CalibrationEmulator = CalibrationEmulator()
 
-    cape: Optional[str] = None
-    host: Optional[str] = None
-
     @classmethod
-    def from_bytestr(cls, data: bytes):
+    def from_bytestr(cls, data: bytes, cape: Optional[CapeData] = None):
         """Instantiates calibration data based on byte string.
         This is mainly used to deserialize data read from an EEPROM memory.
 
         Args:
             data: Byte string containing calibration data.
+            cape: data can be supplied
         Returns:
             CalibrationCape object with extracted calibration data.
         """
@@ -177,6 +209,7 @@ class CalibrationCape(ShpModel):
         for _i, walk in enumerate(lw):
             # hardcoded fixed depth ... bad but easy
             dv[walk[0]][walk[1]][walk[2]] = float(values[_i])
+        dv["cape"] = cape
         return cls(**dv)
 
     def to_bytestr(self) -> bytes:

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/base/shepherd.py

@@ -67,6 +67,15 @@ class ShpModel(BaseModel):
         """allows dict access -> model["key"], in addition to model.key"""
         return self.__getattribute__(key)
 
+    def keys(self):
+        """Fn of dict"""
+        return self.model_dump().keys()
+
+    def items(self):
+        """Fn of dict"""
+        for key in self.keys():
+            yield key, self[key]
+
     @classmethod
     def schema_to_file(cls, path: Union[str, Path]) -> None:
         """store schema to yaml (for frontend-generators)"""

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/experiment/experiment.py

@@ -28,6 +28,7 @@ class Experiment(ShpModel, title="Config of an Experiment"):
         description="Unique ID",
         default_factory=id_default,
     )
+    # ⤷ TODO: automatic ID is problematic for identification by hash
     name: NameStr
     description: Annotated[
         Optional[SafeStr], Field(description="Required for public instances")

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/experiment/observer_features.py

@@ -61,7 +61,7 @@ class GpioTracing(ShpModel, title="Config for GPIO-Tracing"):
     gpios: Optional[
         Annotated[List[GPIO], Field(min_length=1, max_length=10)]
     ] = None  # = all
-    # ⤷ TODO: list of GPIO to build mask, one of both should be internal
+    # ⤷ TODO: list of GPIO to build mask, one of both should be internal / computed field
 
     # time
     delay: timedelta = 0  # seconds

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/experiment/target_config.py

@@ -33,6 +33,7 @@ class TargetConfig(ShpModel, title="Target Config"):
         Annotated[List[Annotated[int, Field(ge=0)]], Field(min_length=1, max_length=64)]
     ] = None
     # ⤷ individual starting times -> allows to use the same environment
+    # TODO: delays not used ATM
 
     firmware1: Firmware
     firmware2: Optional[Firmware] = None

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/task/__init__.py

@@ -50,16 +50,18 @@ def prepare_task(
     elif isinstance(config, ShpModel):
         shp_wrap = Wrapper(
             datatype=type(config).__name__,
-            parameters=config.dict(),
+            parameters=config.model_dump(),
         )
     else:
         raise ValueError("had unknown input: %s", type(config))
 
     if shp_wrap.datatype == TestbedTasks:
         if observer is None:
-            raise ValueError(
-                "Task-Set contained TestbedTasks -> FN needs a observer-name"
+            logger.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)
         obt = tbt.get_observer_tasks(observer)
@@ -67,12 +69,12 @@ def prepare_task(
             raise ValueError("Observer '%s' is not in TestbedTask-Set", observer)
         shp_wrap = Wrapper(
             datatype=type(obt).__name__,
-            parameters=obt.dict(),
+            parameters=obt.model_dump(),
         )
     return shp_wrap
 
 
-def extract_tasks(shp_wrap: Wrapper) -> List[ShpModel]:
+def extract_tasks(shp_wrap: Wrapper, no_task_sets: bool = True) -> List[ShpModel]:
     """ """
     if shp_wrap.datatype == ObserverTasks:
         obt = ObserverTasks(**shp_wrap.parameters)
@@ -85,6 +87,12 @@ def extract_tasks(shp_wrap: Wrapper) -> List[ShpModel]:
         content = [FirmwareModTask(**shp_wrap.parameters)]
     elif shp_wrap.datatype == ProgrammingTask.__name__:
         content = [ProgrammingTask(**shp_wrap.parameters)]
+    elif shp_wrap.datatype == TestbedTasks.__name__:
+        if no_task_sets:
+            raise ValueError(
+                "Model in Wrapper was TestbedTasks -> Task-Sets not allowed!"
+            )
+        content = [TestbedTasks(**shp_wrap.parameters)]
     else:
         raise ValueError("Extractor had unknown task: %s", shp_wrap.datatype)
 

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/task/emulation.py

@@ -46,7 +46,7 @@ class EmulationTask(ShpModel):
     #   - providing a directory -> file is named emu_timestamp.h5
     #   - for a complete path the filename is not changed except it exists and
     #     overwrite is disabled -> emu#num.h5
-    # TODO: should the path be mandatory?
+    # TODO: should the output-path be mandatory?
     force_overwrite: bool = False
     # ⤷ Overwrite existing file
     output_compression: Optional[Compression] = Compression.default
@@ -92,8 +92,10 @@ class EmulationTask(ShpModel):
     @model_validator(mode="before")
     @classmethod
     def pre_correction(cls, values: dict) -> dict:
-        # add local timezone-data
+        # convert & add local timezone-data
         has_time = values.get("time_start") is not None
+        if has_time and isinstance(values["time_start"], (int, float)):
+            values["time_start"] = datetime.fromtimestamp(values["time_start"])
         if has_time and isinstance(values["time_start"], str):
             values["time_start"] = datetime.fromisoformat(values["time_start"])
         if has_time and values["time_start"].tzinfo is None:
@@ -104,8 +106,12 @@ class EmulationTask(ShpModel):
     def post_validation(self):
         # TODO: limit paths
         has_time = self.time_start is not None
-        if has_time and self.time_start < datetime.now().astimezone():
-            raise ValueError("Start-Time for Emulation can't be in the past.")
+        time_now = datetime.now().astimezone()
+        if has_time and self.time_start < time_now:
+            raise ValueError(
+                "Start-Time for Emulation can't be in the past "
+                f"('{self.time_start}' vs '{time_now}'."
+            )
         if self.duration and self.duration.total_seconds() < 0:
             raise ValueError("Task-Duration can't be negative.")
         if isinstance(self.voltage_aux, str) and self.voltage_aux not in [

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/task/harvest.py

@@ -55,8 +55,10 @@ class HarvestTask(ShpModel):
     @model_validator(mode="before")
     @classmethod
     def pre_correction(cls, values: dict) -> dict:
-        # add local timezone-data
+        # convert & add local timezone-data, TODO: used twice, refactor
         has_time = values.get("time_start") is not None
+        if has_time and isinstance(values["time_start"], (int, float)):
+            values["time_start"] = datetime.fromtimestamp(values["time_start"])
         if has_time and isinstance(values["time_start"], str):
             values["time_start"] = datetime.fromisoformat(values["time_start"])
         if has_time and values["time_start"].tzinfo is None:
@@ -67,8 +69,12 @@ class HarvestTask(ShpModel):
     def post_validation(self):
         # TODO: limit paths
         has_time = self.time_start is not None
-        if has_time and self.time_start < datetime.now().astimezone():
-            raise ValueError("Start-Time for Harvest can't be in the past.")
+        time_now = datetime.now().astimezone()
+        if has_time and self.time_start < time_now:
+            raise ValueError(
+                "Start-Time for Emulation can't be in the past "
+                f"('{self.time_start}' vs '{time_now}'."
+            )
         if self.duration and self.duration.total_seconds() < 0:
             raise ValueError("Task-Duration can't be negative.")
         return self

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/task/observer_tasks.py

@@ -3,6 +3,7 @@ from pathlib import Path
 from typing import List
 from typing import Optional
 
+from pydantic import computed_field
 from pydantic import validate_call
 
 from ..base.content import IdInt
@@ -78,3 +79,12 @@ class ObserverTasks(ShpModel):
                 continue
             tasks.append(task)
         return tasks
+
+    @computed_field
+    def output_paths(self) -> dict:
+        values = {}
+        if isinstance(self.emulation, EmulationTask):
+            if self.emulation.output_path is None:
+                raise ValueError("Emu-Task should have a valid output-path")
+            values[self.observer] = self.emulation.output_path
+        return values

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/data_models/task/testbed_tasks.py

@@ -3,6 +3,7 @@ from typing import Optional
 
 from pydantic import EmailStr
 from pydantic import Field
+from pydantic import computed_field
 from pydantic import validate_call
 from typing_extensions import Annotated
 
@@ -34,6 +35,13 @@ class TestbedTasks(ShpModel):
 
     def get_observer_tasks(self, observer) -> Optional[ObserverTasks]:
         for tasks in self.observer_tasks:
-            if observer in tasks.observer:
+            if observer == tasks.observer:
                 return tasks
         return None
+
+    @computed_field
+    def output_paths(self) -> dict:
+        values = {}
+        for obt in self.observer_tasks:
+            values = {**values, **obt.output_paths}
+        return values

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/inventory/__init__.py

@@ -43,7 +43,7 @@ class Inventory(PythonInventory, SystemInventory, TargetInventory):
 
 
 class InventoryList(ShpModel):
-    items: Annotated[List[Inventory], Field(min_length=1)]
+    elements: Annotated[List[Inventory], Field(min_length=1)]
 
     def to_csv(self, path: Path) -> None:
         """TODO: pretty messed up (raw lists and dicts for sub-elements)
@@ -53,8 +53,8 @@ class InventoryList(ShpModel):
         if path.is_dir():
             path = path / "inventory.yaml"
         with open(path.as_posix(), "w") as fd:
-            fd.write(", ".join(self.items[0].model_dump().keys()) + "\r\n")
-            for item in self.items:
+            fd.write(", ".join(self.elements[0].model_dump().keys()) + "\r\n")
+            for item in self.elements:
                 content = list(item.model_dump().values())
                 content = ["" if value is None else str(value) for value in content]
                 fd.write(", ".join(content) + "\r\n")

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/testbed_client/client.py

@@ -65,10 +65,12 @@ class TestbedClient:
     def insert(self, data: ShpModel) -> bool:
         wrap = Wrapper(
             datatype=type(data).__name__,
-            parameters=data.dict(),
+            parameters=data.model_dump(),
         )
         if self._connected:
-            r = self._req.post(self._server + "/add", data=wrap.json(), timeout=2)
+            r = self._req.post(
+                self._server + "/add", data=wrap.model_dump_json(), timeout=2
+            )
             r.raise_for_status()
         else:
             self._fixtures.insert_model(wrap)

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core/testbed_client/user_model.py

@@ -49,11 +49,12 @@ class User(ShpModel):
     email: EmailStr
 
     pw_hash: Optional[SecretBytes] = None
-    # ⤷ = hash_password("this_will_become_a_salted_slow_hash") -> slowed BBB down
+    # ⤷ was hash_password("this_will_become_a_salted_slow_hash") -> slowed BBB down
     # ⤷ TODO (min_length=128, max_length=512)
 
     token: SecretStr
     # ⤷ TODO (min_length=128), request with: token.get_secret_value()
+    active: bool = False
 
     @model_validator(mode="before")
     @classmethod

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/shepherd_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd-core
-Version: 2023.8.7
+Version: 2023.8.8
 Summary: Programming- and CLI-Interface for the h5-dataformat of the Shepherd-Testbed
 Home-page: https://pypi.org/project/shepherd-core/
 Author: Ingmar Splitt, Kai Geissdoerfer
@@ -77,6 +77,13 @@ The Library is available via PyPI and can be installed with
   pip install shepherd-data
 ```
 
+for bleeding-edge-features or dev-work it is possible to install directly from GitHub-Sources (here `dev`-branch):
+
+```Shell
+pip install git+https://github.com/orgua/shepherd-datalib.git@dev#subdirectory=shepherd_core -U
+```
+
+
 If you are working with ``.elf``-files (embedding into experiments) you make "objcopy" accessible to python. In Ubuntu, you can either install ``build-essential`` or ``binutils-$ARCH`` with arch being ``msp430`` or ``arm-none-eabi`` for the nRF52.
 
 ```shell

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/tests/data_models/example_cal_data.yaml

@@ -1,7 +1,8 @@
 datatype: CalibrationCape
 parameters:
   host: sheep0
-  cape: xyz1
+  cape:
+    serial_number: A123
   emulator:
     adc_C_A:
       gain: 2.2306053900482405e-07

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/tests/data_models/example_cal_meas.yaml

@@ -2,7 +2,8 @@
 datatype: CalMeasurementCape
 parameters:
   host: sheep0
-  cape: xyz1
+  cape:
+    serial_number: A123
   emulator:
     adc_C_A:
     - reference_si: 1.0e-05

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/tests/data_models/test_base_models.py

@@ -11,9 +11,19 @@ from shepherd_core.data_models.base.calibration import CalibrationEmulator
 from shepherd_core.data_models.base.calibration import CalibrationHarvester
 from shepherd_core.data_models.base.calibration import CalibrationPair
 from shepherd_core.data_models.base.calibration import CalibrationSeries
+from shepherd_core.data_models.base.calibration import CapeData
 from shepherd_core.data_models.base.content import ContentModel
 
 
+def test_base_model_cape_data() -> None:
+    CapeData(serial_number="xyz1")
+
+
+def test_base_model_cape_data_fail() -> None:
+    with pytest.raises(ValueError):
+        CapeData()
+
+
 def test_base_model_cal_pair_conv() -> None:
     cal = CalibrationPair(gain=4.9)
     val_raw = 500
@@ -61,6 +71,13 @@ def test_base_model_cal_cape_bytestr() -> None:
     assert cal1.get_hash() == cal2.get_hash()
 
 
+def test_base_model_cal_cape_bytestr_with_cape_data() -> None:
+    cal1 = CalibrationCape(cape=CapeData(serial_number="123"))
+    cb = cal1.to_bytestr()
+    cal2 = CalibrationCape.from_bytestr(cb, cal1.cape)
+    assert cal1.get_hash() == cal2.get_hash()
+
+
 def test_base_model_cal_cape_example(tmp_path: Path) -> None:
     cal0 = CalMeasurementCape()
     path1 = Path(__file__).resolve().with_name("example_cal_data.yaml")

{shepherd_core-2023.8.7 → shepherd_core-2023.8.8}/tests/inventory/test_inventory.py

@@ -19,5 +19,5 @@ def test_collect_data(inv: Callable) -> None:
 
 def test_inventorize(tmp_path: Path) -> None:
     inv = Inventory.collect()
-    inl = InventoryList(items=[inv])
+    inl = InventoryList(elements=[inv])
     inl.to_csv(tmp_path / "some.csv")