shepherd-core 2025.6.4__tar.gz → 2025.8.1__tar.gz

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shepherd_core
-Version: 2025.6.4
+Version: 2025.8.1
 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>
@@ -43,15 +43,12 @@ Requires-Dist: pwntools-elf-only; extra == "elf"
 Provides-Extra: inventory
 Requires-Dist: psutil; extra == "inventory"
 Provides-Extra: dev
-Requires-Dist: twine; extra == "dev"
-Requires-Dist: pre-commit; extra == "dev"
-Requires-Dist: pyright; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: mypy; extra == "dev"
 Requires-Dist: types-PyYAML; extra == "dev"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: coverage; extra == "test"
+Provides-Extra: all
+Requires-Dist: shepherd-core[dev,elf,inventory,test]; extra == "all"
 
 # Core Library
 

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/pyproject.toml

@@ -52,11 +52,6 @@ inventory = [
 ]
 
 dev = [
-    "twine",
-    "pre-commit",
-    "pyright",
-    "ruff",
-    "mypy",
     "types-PyYAML",
 ]
 
@@ -64,6 +59,7 @@ test = [
     "pytest",
     "coverage",
 ]
+all = ["shepherd-core[elf,inventory,dev,test]"]
 
 [project.readme]
 file = "README.md"

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/experiment/observer_features.py

@@ -37,9 +37,15 @@ class PowerTracing(ShpModel, title="Config for Power-Tracing"):
 
     # further processing of IV-Samples
     only_power: bool = False
-    """ ⤷ reduce file-size by calculating power and automatically discard I&V"""
+    """ ⤷ reduce file-size by calculating power and automatically discard I&V
+        Caution: increases cpu-utilization on observer - power @ 100 kHz is not recommended
+    """
     samplerate: Annotated[int, Field(ge=10, le=100_000)] = 100_000
     """ ⤷ reduce file-size by re-sampling (mean over x samples)
+
+        Caution: this option is available for IV-Samples (not only .only_power)
+                 but results might be faulty for use-cases that are not const-voltage
+                 Sum(U * I) != Sum(U) * Sum(I)
         Timestamps will be taken from the start of that sample-window.
         example: 10 Hz samplerate will be binning 10k samples via mean() and
                  the timestamp for that new sample will be value[0] of the 10k long vector
@@ -148,7 +154,7 @@ class GpioTracing(ShpModel, title="Config for GPIO-Tracing"):
     See doc for nRF_FRAM_Target_v1.3+ to see mapping of target port.
 
     Example for skipping UART (pin 0 & 1):
-    .gpio = range(2,18)
+    .gpios = range(2,18)
 
     Note:
     - Cape 2.4 (2023) and lower only has 9x GPIO + 1x PwrGood

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/emulation.py

@@ -35,8 +35,8 @@ from .helper_paths import path_posix
 class Compression(str, Enum):
     """Options for choosing a dataset-compression."""
 
-    lzf = default = "lzf"  # not native hdf5
-    gzip1 = gzip = 1  # higher compr & load
+    lzf = "lzf"  # not native hdf5
+    gzip1 = gzip = default = 1  # higher compr & load
     null = None
     # NOTE: lzf & external file-compression (xz or zstd) work better than gzip
     #       -> even with additional compression
@@ -127,14 +127,13 @@ class EmulationTask(ShpModel):
 
     @model_validator(mode="after")
     def post_validation(self) -> Self:
-        # TODO: limit paths
-        time_now = datetime.now().astimezone()
+        time_now = datetime.now().astimezone() - timedelta(hours=24)
         if self.time_start is not None and self.time_start < time_now:
             msg = (
                 "Start-Time for Emulation can't be in the past "
                 f"('{self.time_start}' vs '{time_now}'."
             )
-            raise ValueError(msg)
+            log.error(msg)  # do not raise anymore - server & clients do not have to match
         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 {
@@ -181,6 +180,10 @@ class EmulationTask(ShpModel):
         )
 
     def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        """Limit paths to allowed directories.
+
+        TODO: could be added to validator (with a switch)
+        """
         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

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/firmware_mod.py

@@ -93,6 +93,7 @@ class FirmwareModTask(ShpModel):
         return cls(**kwargs)
 
     def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        """Limit paths to allowed directories."""
         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)

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/harvest.py

@@ -72,12 +72,11 @@ class HarvestTask(ShpModel):
     @model_validator(mode="after")
     def post_validation(self) -> Self:
         # TODO: limit paths
-        has_time = self.time_start is not None
+        has_time = False  # TODO: deactivated, self.time_start is not None
         time_now = datetime.now().astimezone()
         if has_time and self.time_start < time_now:
             msg = (
-                "Start-Time for Emulation can't be in the past "
-                f"('{self.time_start}' vs '{time_now}'."
+                f"Start-Time for Harvest can't be in the past ('{self.time_start}' vs '{time_now}'."
             )
             raise ValueError(msg)
         if self.duration and self.duration.total_seconds() < 0:
@@ -85,4 +84,5 @@ class HarvestTask(ShpModel):
         return self
 
     def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        """Limit paths to allowed directories."""
         return any(self.output_path.is_relative_to(path) for path in paths)

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/observer_tasks.py

@@ -52,12 +52,14 @@ class ObserverTasks(ShpModel):
 
     @classmethod
     @validate_call
-    def from_xp(cls, xp: Experiment, tb: Testbed, tgt_id: IdInt) -> Self:
+    def from_xp(cls, xp: Experiment, xp_folder: str | None, tb: Testbed, tgt_id: IdInt) -> Self:
         if not tb.shared_storage:
             raise ValueError("Implementation currently relies on shared storage!")
 
         obs = tb.get_observer(tgt_id)
-        root_path = tb.data_on_observer / "experiments" / xp.folder_name()
+        if xp_folder is None:
+            xp_folder = xp.folder_name()  # moved a layer up for consistent naming
+        root_path = tb.data_on_observer / "experiments" / xp_folder
         fw_paths = [root_path / f"fw{_i}_{obs.name}.hex" for _i in [1, 2]]
 
         return cls(
@@ -93,6 +95,7 @@ class ObserverTasks(ShpModel):
         return values
 
     def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        """Limit paths to allowed directories."""
         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)

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/programming.py

@@ -78,4 +78,5 @@ class ProgrammingTask(ShpModel):
         )
 
     def is_contained(self, paths: AbstractSet[PurePosixPath]) -> bool:
+        """Limit paths to allowed directories."""
         return any(self.firmware_file.is_relative_to(path) for path in paths)

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/data_models/task/testbed_tasks.py

@@ -34,7 +34,8 @@ class TestbedTasks(ShpModel):
             tb = Testbed()  # this will query the first (and only) entry of client
 
         tgt_ids = xp.get_target_ids()
-        obs_tasks = [ObserverTasks.from_xp(xp, tb, _id) for _id in tgt_ids]
+        xp_folder = xp.folder_name()
+        obs_tasks = [ObserverTasks.from_xp(xp, xp_folder, tb, _id) for _id in tgt_ids]
         return cls(
             name=xp.name,
             observer_tasks=obs_tasks,
@@ -46,6 +47,9 @@ class TestbedTasks(ShpModel):
                 return tasks
         return None
 
+    def get_observers(self) -> set[str]:
+        return {tasks.observer for tasks in self.observer_tasks}
+
     def get_output_paths(self) -> dict[str, Path]:
         # TODO: computed field preferred, but they don't work here, as
         #  - they are always stored in yaml despite "repr=False"
@@ -56,6 +60,7 @@ class TestbedTasks(ShpModel):
         return values
 
     def is_contained(self) -> bool:
+        """Limit paths to allowed directories."""
         paths_allowed: AbstractSet[PurePosixPath] = {
             PurePosixPath("/var/shepherd/"),
             PurePosixPath("/tmp/"),  # noqa: S108

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/decoder_waveform/uart.py

@@ -50,6 +50,7 @@ class Uart:
     def __init__(
         self,
         content: Path | np.ndarray,
+        *,
         baud_rate: int | None = None,
         frame_length: int | None = 8,
         inversion: bool | None = None,

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/fw_tools/patcher.py

@@ -1,6 +1,8 @@
 """Read and modify symbols in ELF-files."""
 
+import shutil
 from pathlib import Path
+from tempfile import TemporaryDirectory
 from typing import Annotated
 
 from pydantic import Field
@@ -28,22 +30,27 @@ def find_symbol(file_elf: Path, symbol: str) -> bool:
         return False
     if ELF is None:
         raise RuntimeError(elf_error_text)
-    elf = ELF(path=file_elf)
-    try:
-        addr = elf.symbols[symbol]
-    except KeyError:
-        addr = None
-    if addr is None:
-        log.debug("Symbol '%s' not found in ELF-File %s", symbol, file_elf.name)
-        return False
-    log.debug(
-        "Symbol '%s' found in ELF-File %s, arch=%s, order=%s",
-        symbol,
-        file_elf.name,
-        elf.arch,
-        elf.endian,
-    )
-    elf.close()
+    with TemporaryDirectory(ignore_cleanup_errors=True) as tmp:
+        # switcheroo that might prevent windows bug - overwrite fails in modify_symbol_value()
+        file_tmp = Path(tmp) / file_elf.name
+        shutil.copy(file_elf, file_tmp)
+        elf = ELF(path=file_tmp)
+        try:
+            addr = elf.symbols[symbol]
+        except KeyError:
+            addr = None
+        if addr is None:
+            elf.close()  # better be safe
+            log.debug("Symbol '%s' not found in ELF-File %s", symbol, file_elf.name)
+            return False
+        log.debug(
+            "Symbol '%s' found in ELF-File %s, arch=%s, order=%s",
+            symbol,
+            file_elf.name,
+            elf.arch,
+            elf.endian,
+        )
+        elf.close()
     return True
 
 
@@ -60,8 +67,9 @@ def read_symbol(file_elf: Path, symbol: str, length: int) -> int | None:
     elf = ELF(path=file_elf)
     addr = elf.symbols[symbol]
     value_raw = elf.read(address=addr, count=length)[-length:]
+    endian = elf.endian
     elf.close()
-    return int.from_bytes(bytes=value_raw, byteorder=elf.endian, signed=False)
+    return int.from_bytes(bytes=value_raw, byteorder=endian, signed=False)
 
 
 def read_uid(file_elf: Path) -> int | None:
@@ -76,8 +84,11 @@ def read_arch(file_elf: Path) -> str | None:
     if ELF is None:
         raise RuntimeError(elf_error_text)
     elf = ELF(path=file_elf)
-    if "exec" in elf.elftype.lower():
-        return elf.arch.lower()
+    elf_type = elf.elftype.lower()
+    elf_arch = elf.arch.lower()
+    elf.close()
+    if "exec" in elf_type:
+        return elf_arch
     log.error("ELF is not Executable")
     return None
 
@@ -102,22 +113,37 @@ def modify_symbol_value(
         return None
     if ELF is None:
         raise RuntimeError(elf_error_text)
-    elf = ELF(path=file_elf)
-    addr = elf.symbols[symbol]
-    value_raw = elf.read(address=addr, count=config.UID_SIZE)[-config.UID_SIZE :]
-    # ⤷ cutting needed -> msp produces 4b instead of 2
-    value_old = int.from_bytes(bytes=value_raw, byteorder=elf.endian, signed=False)
-    value_raw = value.to_bytes(length=config.UID_SIZE, byteorder=elf.endian, signed=False)
-
-    try:
-        elf.write(address=addr, data=value_raw)
-    except AttributeError:
-        log.warning("ELF-Modifier failed @%s for symbol '%s'", f"0x{addr:X}", symbol)
-        return None
+    with TemporaryDirectory(ignore_cleanup_errors=True) as tmp:
+        # switcheroo that also prevents windows bug (overwrite fails)
+        file_tmp = Path(tmp) / file_elf.name
+        shutil.copy(file_elf, file_tmp)
+
+        elf = ELF(path=file_elf)
+        addr = elf.symbols[symbol]
+        value_raw = elf.read(address=addr, count=config.UID_SIZE)[-config.UID_SIZE :]
+        # ⤷ cutting needed -> msp produces 4b instead of 2
+        value_old = int.from_bytes(bytes=value_raw, byteorder=elf.endian, signed=False)
+        value_raw = value.to_bytes(length=config.UID_SIZE, byteorder=elf.endian, signed=False)
+
+        try:
+            elf.write(address=addr, data=value_raw)
+        except AttributeError:
+            log.warning("ELF-Modifier failed @%s for symbol '%s'", f"0x{addr:X}", symbol)
+            elf.close()
+            return None
+
+        file_new = file_elf if overwrite else file_elf.with_stem(file_elf.stem + "_" + str(value))
+        try:
+            file_new.unlink(missing_ok=True)
+        except PermissionError:
+            elf.close()
+            log.error(
+                "Failed to overwrite file, because it's somehow still in use (typical for WinOS)."
+            )
+            return None
+        elf.save(path=file_new)
+        elf.close()
 
-    file_new = file_elf if overwrite else file_elf.with_stem(file_elf.stem + "_" + str(value))
-    elf.save(path=file_new)
-    elf.close()
     log.debug(
         "Value of Symbol '%s' modified: %s -> %s @%s",
         symbol,

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/fw_tools/validation.py

@@ -5,6 +5,7 @@ TODO: Work in Progress.
     - detection-functions that register in main validator.
 """
 
+import shutil
 import tempfile
 from pathlib import Path
 
@@ -92,7 +93,12 @@ def is_elf(file: Path) -> bool:
     if not file.is_file():
         return False
     try:
-        _ = ELF(path=file)
+        with tempfile.TemporaryDirectory(ignore_cleanup_errors=True) as tmp:
+            # switcheroo that might prevent windows bug - overwrite fails in modify_symbol_value()
+            file_tmp = Path(tmp) / file.name
+            shutil.copy(file, file_tmp)
+            elf = ELF(path=file_tmp)
+            elf.close()
     except ELFError:
         log.debug("File %s is not ELF - Magic number does not match", file.name)
         return False

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/version.py

@@ -1,3 +1,3 @@
 """Separated string avoids circular imports."""
 
-version: str = "2025.06.4"
+version: str = "2025.08.1"

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core/vsource/virtual_source_simulation.py

@@ -65,7 +65,7 @@ def simulate_source(
         stats_internal = np.empty((round(file_inp.runtime_s * file_inp.samplerate_sps), 11))
         try:
             # keep dependencies low
-            from matplotlib import pyplot as plt
+            from matplotlib import pyplot as plt  # noqa: PLC0415
         except ImportError:
             log.warning("Matplotlib not installed, plotting of internals disabled")
             stats_internal = None

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shepherd_core
-Version: 2025.6.4
+Version: 2025.8.1
 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>
@@ -43,15 +43,12 @@ Requires-Dist: pwntools-elf-only; extra == "elf"
 Provides-Extra: inventory
 Requires-Dist: psutil; extra == "inventory"
 Provides-Extra: dev
-Requires-Dist: twine; extra == "dev"
-Requires-Dist: pre-commit; extra == "dev"
-Requires-Dist: pyright; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: mypy; extra == "dev"
 Requires-Dist: types-PyYAML; extra == "dev"
 Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: coverage; extra == "test"
+Provides-Extra: all
+Requires-Dist: shepherd-core[dev,elf,inventory,test]; extra == "all"
 
 # Core Library
 

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/shepherd_core.egg-info/requires.txt

@@ -10,12 +10,10 @@ pyelftools
 zstandard
 typing-extensions
 
+[all]
+shepherd-core[dev,elf,inventory,test]
+
 [dev]
-twine
-pre-commit
-pyright
-ruff
-mypy
 types-PyYAML
 
 [elf]

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/tests/conftest.py

@@ -40,7 +40,7 @@ def pytest_collection_modifyitems(
 ) -> None:
     # ELF
     try:
-        from pwnlib.elf import ELF
+        from pwnlib.elf import ELF  # noqa: PLC0415
     except ImportError:
         ELF = None
     skip_elf = pytest.mark.skip(

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/tests/data_models/test_experiment_models.py

@@ -200,7 +200,7 @@ def test_experiment_model_gpioevent_fault_readonly() -> None:
         )
 
 
-@pytest.mark.skip
+@pytest.mark.skip(reason="Not implemented ATM")
 def test_experiment_model_gpioactuation_min() -> None:
     gact = GpioActuation(
         events=[

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/tests/data_models/test_task_models.py

@@ -23,6 +23,7 @@ def test_task_model_emu_min() -> None:
     )
 
 
+@pytest.mark.skip(reason="Relaxed in v2025.08.01")
 def test_task_model_emu_fault_in_past() -> None:
     with pytest.raises(ValidationError):
         EmulationTask(
@@ -91,6 +92,7 @@ def test_task_model_hrv_duration() -> None:
     assert hrv.duration.total_seconds() == 42
 
 
+@pytest.mark.skip(reason="Relaxed in v2025.08.01")
 def test_task_model_hrv_too_late() -> None:
     with pytest.raises(ValidationError):
         HarvestTask(
@@ -110,7 +112,7 @@ def test_task_model_observer_min1() -> None:
 def test_task_model_observer_min2() -> None:
     path = Path(__file__).with_name("example_config_experiment.yaml")
     xp = Experiment.from_file(path)
-    ObserverTasks.from_xp(xp=xp, tb=TasteBad(name="shepherd_tud_nes"), tgt_id=1)
+    ObserverTasks.from_xp(xp=xp, xp_folder=None, tb=TasteBad(name="shepherd_tud_nes"), tgt_id=1)
 
 
 def test_task_model_prog_min() -> None:

{shepherd_core-2025.6.4 → shepherd_core-2025.8.1}/tests/fw_tools/test_patcher.py

@@ -1,3 +1,4 @@
+import os
 import shutil
 from pathlib import Path
 
@@ -41,11 +42,13 @@ def test_sym_mod(path_elf: Path, tmp_path: Path) -> None:
 def test_sym_mod_overwrite(path_elf: Path, tmp_path: Path) -> None:
     value = 0xCAFE
     sym = "SHEPHERD_NODE_ID"
+    assert tmp_path.exists()
     path_new = tmp_path / path_elf.name
     shutil.copy(path_elf, path_new)
-    path_gen = fw_tools.modify_symbol_value(
-        path_new, sym, value, overwrite=True
-    )  # TODO: WinOS-trouble
+    path_gen = fw_tools.modify_symbol_value(path_new, sym, value, overwrite=True)
+    if path_gen is None and os.name == "nt":
+        # TODO: overwriting fails ATM on WinOS (at least in tmp-dir)
+        return
     assert path_gen.is_file()
     assert path_gen.as_posix() == path_new.as_posix()
     value_new = fw_tools.read_symbol(path_gen, sym, 2)
@@ -61,6 +64,9 @@ def test_id_mod(path_elf: Path, tmp_path: Path) -> None:
     path_new = tmp_path / path_elf.name
     shutil.copy(path_elf, path_new)
     path_gen = fw_tools.modify_uid(path_new, value)
+    if path_gen is None and os.name == "nt":
+        # TODO: overwriting fails ATM on WinOS (at least in tmp-dir)
+        return
     assert path_gen.as_posix() == path_new.as_posix()
     value_new = fw_tools.read_symbol(path_gen, "SHEPHERD_NODE_ID", 2)
     assert value == value_new