shepherd-core 2024.4.2__tar.gz → 2024.7.1__tar.gz

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd_core
-Version: 2024.4.2
+Version: 2024.7.1
 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>
@@ -33,7 +33,6 @@ Requires-Dist: numpy
 Requires-Dist: pyYAML
 Requires-Dist: chromalog
 Requires-Dist: pydantic[email]>2.0.0
-Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: intelhex
 Requires-Dist: requests

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/pyproject.toml

@@ -6,7 +6,6 @@ keywords = ["testbed", "beaglebone", "pru", "batteryless", "energyharvesting", "
 authors = [{name = "Ingmar Splitt", email = "ingmar.splitt@tu-dresden.de"},]
 maintainers = [{name = "Ingmar Splitt", email = "ingmar.splitt@tu-dresden.de"},]
 
-readme = {file = "README.md", content-type = "text/markdown"}
 license = {file = "LICENSE"}
 dynamic = ["version"]
 
@@ -32,7 +31,6 @@ dependencies = [
     "pyYAML",
     "chromalog",
     "pydantic[email]>2.0.0",
-    "scipy",
     "tqdm",
     "intelhex",
     "requests",
@@ -54,7 +52,6 @@ inventory = [
     "psutil",
 ]
 
-
 dev = [
     "twine",
     "pre-commit",
@@ -69,13 +66,17 @@ test = [
     "coverage",
 ]
 
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
 [project.urls]
 Documentation = "https://github.com/orgua/shepherd-datalib/blob/main/README.md"
 Issues = "https://github.com/orgua/shepherd-datalib/issues"
 Source = "https://pypi.org/project/shepherd-core/"
 
 [build-system]
-requires = ["setuptools", "setuptools-scm"]
+requires = ["setuptools>=61.2", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools]
@@ -98,7 +99,7 @@ version = {attr = "shepherd_core.__version__"}
 [tool.pytest.ini_options]
 markers = [
     "converter: automatically added when no objcopy is found (on ubuntu install build-essential)",
-    "elf: automatically added when no elf-support is found (on windows or missing shepherd-core[elf])"
+    "elf: automatically added when no elf-support is found (on windows or missing shepherd-core[elf])",
 ]
 
 addopts = "-vvv --stepwise" # opts: verbose result for each tests

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/__init__.py

@@ -23,7 +23,7 @@ from .testbed_client.client import TestbedClient
 from .testbed_client.client import tb_client
 from .writer import Writer
 
-__version__ = "2024.4.2"
+__version__ = "2024.7.1"
 
 __all__ = [
     "Reader",

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/data_models/base/cal_measurement.py

@@ -16,8 +16,6 @@ from .calibration import CalibrationPair
 from .calibration import CapeData
 from .shepherd import ShpModel
 
-# TODO: move to shepherd_data to remove scipy-dependency from _core
-
 
 class CalMeasurementPair(ShpModel):
     """Value-container for a calibration-measurement."""
@@ -32,17 +30,23 @@ CalMeasPairs = Annotated[List[CalMeasurementPair], Field(min_length=2)]
 @validate_call
 def meas_to_cal(data: CalMeasPairs, component: str) -> CalibrationPair:
     """Convert values from calibration-measurement to the calibration itself."""
-    from scipy import stats  # placed here due to massive delay
-
     x = np.empty(len(data))
     y = np.empty(len(data))
     for i, pair in enumerate(data):
         x[i] = pair.shepherd_raw
         y[i] = pair.reference_si
-    result = stats.linregress(x, y)
-    offset = float(result.intercept)
-    gain = float(result.slope)
-    rval = result.rvalue  # test quality of regression
+
+    model = np.polyfit(x, y, 1)
+    offset = model[1]
+    gain = model[0]
+
+    # r-squared, Pearson correlation coefficient
+    p = np.poly1d(model)
+    yhat = p(x)
+    ybar = np.sum(y) / len(y)
+    ssreg = np.sum((yhat - ybar) ** 2)
+    sstot = np.sum((y - ybar) ** 2)
+    rval = ssreg / sstot
 
     if rval < 0.999:
         msg = (

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/data_models/base/calibration.py

@@ -71,6 +71,7 @@ class CalibrationPair(ShpModel):
         if isinstance(values_raw, np.ndarray):
             values_raw[values_raw < 0.0] = 0.0
             values_raw = np.around(values_raw)
+            # TODO: overflow should also be prevented (add bit-width) -> fail or warn at both?
         else:
             values_raw = round(max(values_raw, 0.0))
         return values_raw

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/data_models/task/emulation.py

@@ -60,7 +60,7 @@ class EmulationTask(ShpModel):
     # timestamp or unix epoch time, None = ASAP
     duration: Optional[timedelta] = None
     # ⤷ Duration of recording in seconds, None = till EOF
-    abort_on_error: bool = False
+    abort_on_error: bool = False  # TODO: remove, should not exist
 
     # emulation-specific
     use_cal_default: bool = False

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/data_models/task/programming.py

@@ -43,7 +43,7 @@ class ProgrammingTask(ShpModel):
     def post_validation(self) -> Self:
         d_type = suffix_to_DType.get(self.firmware_file.suffix.lower())
         if d_type != FirmwareDType.base64_hex:
-            ValueError(f"Firmware is not intel-.hex ('{self.firmware_file}')")
+            raise ValueError("Firmware is not intel-.hex ('%s')", self.firmware_file.as_posix())
         return self
 
     @classmethod

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/data_models/testbed/observer.py

@@ -70,11 +70,13 @@ class Observer(ShpModel, title="Shepherd-Sheep"):
         return self
 
     def has_target(self, target_id: int) -> bool:
-        if self.target_a is not None and target_id == self.target_a.id and self.target_a.active:
-            return True
-        if self.target_b is not None and target_id == self.target_b.id and self.target_b.active:
-            return True
-        return False
+        case_a = (
+            self.target_a is not None and target_id == self.target_a.id and self.target_a.active
+        )
+        case_b = (
+            self.target_b is not None and target_id == self.target_b.id and self.target_b.active
+        )
+        return case_a or case_b
 
     def get_target_port(self, target_id: int) -> TargetPort:
         if self.has_target(target_id):

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/fw_tools/patcher.py

@@ -17,7 +17,7 @@ try:
 except ImportError as e:
     ELF = None
     elf_error_text = (
-        "Please install functionality with 'pip install shepherd_core[elf] -U' first, "
+        "Please install functionality with 'pip install shepherd-core[elf] -U' first, "
         f"underlying exception: {e.msg}"
     )
 

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/fw_tools/validation.py

@@ -23,7 +23,7 @@ except ImportError as e:
     ELF = None
     ELFError = None
     elf_error_text = (
-        "Please install functionality with 'pip install shepherd_core[elf] -U' first, "
+        "Please install functionality with 'pip install shepherd-core[elf] -U' first, "
         f"underlying exception: {e.msg}"
     )
 
@@ -56,10 +56,9 @@ def is_hex_msp430(file: Path) -> bool:
         value = int.from_bytes(ih.gets(0xFFFE, 2), byteorder="little", signed=False)
         if 0x4000 > value >= 0xFF80:
             return False
-        if ih.get_memory_size() >= 270_000:
-            # conservative test for now - should be well below 128 kB + 8kB for msp430fr5962
-            return False
-        return True
+
+        # conservative test for now - should be well below 128 kB + 8kB for msp430fr5962
+        return ih.get_memory_size() <= 270_000
     return False
 
 
@@ -74,10 +73,9 @@ def is_hex_nrf52(file: Path) -> bool:
         ih = IntelHex(file.as_posix())
         if ih.minaddr() != 0x0000:
             return False
-        if ih.get_memory_size() >= 1310720:
-            # conservative test for now - should be well below 1 MB + 256 kB
-            return False
-        return True
+
+        # conservative test for now - should be well below 1 MB + 256 kB
+        return ih.get_memory_size() < 1310720
     return False
 
 

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/inventory/system.py

@@ -3,8 +3,8 @@
 import platform
 import subprocess
 import time
-from contextlib import suppress
 from datetime import datetime
+from pathlib import Path
 from typing import Optional
 
 from typing_extensions import Self
@@ -48,6 +48,9 @@ class SystemInventory(ShpModel):
     #   ip IPvAnyAddress
     #   mac MACStr
 
+    fs_root: Optional[str] = None
+    beagle: Optional[str] = None
+
     model_config = ConfigDict(str_min_length=0)
 
     @classmethod
@@ -67,6 +70,31 @@ class SystemInventory(ShpModel):
             ifs2 = {name: (_if[1].address, _if[0].address) for name, _if in ifs1 if len(_if) > 1}
             uptime = time.time() - psutil.boot_time()
 
+        fs_cmd = ["/usr/bin/df", "-h", "/"]
+        fs_out = None
+        if Path(fs_cmd[0]).is_file():
+            reply = subprocess.run(  # noqa: S603
+                fs_cmd, timeout=30, capture_output=True, check=False
+            )
+            fs_out = str(reply.stdout)
+
+        beagle_cmd = ["/usr/bin/beagle-version"]
+        beagle_out = None
+        if Path(beagle_cmd[0]).is_file():
+            reply = subprocess.run(  # noqa: S603
+                beagle_cmd, timeout=30, capture_output=True, check=False
+            )
+            beagle_out = str(reply.stdout)
+
+        ptp_cmd = ["/usr/sbin/ptp4l", "-v"]
+        ptp_out = None
+        if Path(ptp_cmd[0]).is_file():
+            reply = subprocess.run(  # noqa: S603
+                ptp_cmd, timeout=30, capture_output=True, check=False
+            )
+            ptp_out = f"{ reply.stdout }, { reply.stderr }"
+            # alternative: check_output - seems to be lighter
+
         model_dict = {
             "uptime": round(uptime),
             "timestamp": ts,
@@ -77,12 +105,9 @@ class SystemInventory(ShpModel):
             "processor": platform.processor(),
             "hostname": platform.node(),
             "interfaces": ifs2,
-            # TODO: add free space on /
+            "fs_root": fs_out,
+            "beagle": beagle_out,
+            "ptp": ptp_out,
         }
 
-        with suppress(FileNotFoundError):
-            ret = subprocess.run(["/usr/sbin/ptp4l", "-v"], check=False)  # noqa: S603
-            model_dict["ptp"] = ret.stdout
-            # alternative: check_output - seems to be lighter
-
         return cls(**model_dict)

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/reader.py

@@ -124,7 +124,10 @@ class Reader:
         if not hasattr(self, "_cal"):
             cal_dict = CalibrationSeries().model_dump()
             for ds, param in product(["current", "voltage", "time"], ["gain", "offset"]):
-                cal_dict[ds][param] = self.h5file["data"][ds].attrs[param]
+                try:
+                    cal_dict[ds][param] = self.h5file["data"][ds].attrs[param]
+                except KeyError:  # noqa: PERF203
+                    self._logger.debug("Cal-Param '%s' for dataset '%s' not found!", param, ds)
             self._cal = CalibrationSeries(**cal_dict)
 
         self._refresh_file_stats()
@@ -257,6 +260,8 @@ class Reader:
                 return EnergyDType[self.h5file["data"].attrs["datatype"]]
         except KeyError:
             return None
+        except ValueError:
+            return None
         else:
             return None
 
@@ -631,7 +636,7 @@ class Reader:
         Algo: create an offset-by-one vector and compare against original.
         """
         if len(data.shape) > 1:
-            ValueError("Array must be 1D")
+            raise ValueError("Array must be 1D")
         data_1 = np.concatenate(([not data[0]], data[:-1]))
         return data != data_1
 

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/testbed_client/fixtures.py

@@ -168,9 +168,7 @@ def file_older_than(file: Path, delta: timedelta) -> bool:
     """Decide if file is older than a specific duration of time."""
     cutoff = local_now() - delta
     mtime = datetime.fromtimestamp(file.stat().st_mtime, tz=local_tz())
-    if mtime < cutoff:
-        return True
-    return False
+    return mtime < cutoff
 
 
 class Fixtures:

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core/writer.py

@@ -229,7 +229,7 @@ class Writer(Reader):
         """Initialize the structure of the HDF5 file.
 
         HDF5 is hierarchically structured and before writing data, we have to
-        setup this structure, i.e. creating the right groups with corresponding
+        set up this structure, i.e. creating the right groups with corresponding
         data types. We will store 3 types of data in a database: The
         actual IV samples recorded either from the harvester (during recording)
         or the target (during emulation). Any log messages, that can be used to
@@ -367,7 +367,7 @@ class Writer(Reader):
         TODO: use data-model?
         :param data: from virtual harvester or converter / source.
         """
-        self.h5file["data"].attrs["config"] = yaml.safe_dump(
+        self.h5file.attrs["config"] = yaml.safe_dump(
             data, default_flow_style=False, sort_keys=False
         )
 

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd_core
-Version: 2024.4.2
+Version: 2024.7.1
 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>
@@ -33,7 +33,6 @@ Requires-Dist: numpy
 Requires-Dist: pyYAML
 Requires-Dist: chromalog
 Requires-Dist: pydantic[email]>2.0.0
-Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: intelhex
 Requires-Dist: requests

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/shepherd_core.egg-info/requires.txt

@@ -3,7 +3,6 @@ numpy
 pyYAML
 chromalog
 pydantic[email]>2.0.0
-scipy
 tqdm
 intelhex
 requests

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/tests/data_models/test_task_models.py

@@ -125,8 +125,9 @@ def test_task_model_prog_min() -> None:
 
 
 def test_task_model_prog_fault_elf() -> None:
-    ProgrammingTask(
-        firmware_file=Path("fw_to_load.elf"),
-        protocol=ProgrammerProtocol.SWD,
-        mcu_type="nrf52",
-    )
+    with pytest.raises(ValidationError):
+        ProgrammingTask(
+            firmware_file=Path("fw_to_load.elf"),
+            protocol=ProgrammerProtocol.SWD,
+            mcu_type="nrf52",
+        )

{shepherd_core-2024.4.2 → shepherd_core-2024.7.1}/tests/test_reader.py

@@ -179,20 +179,6 @@ def test_reader_fault_no_voltage(data_h5: Path) -> None:
         Reader(data_h5, verbose=True)
 
 
-def test_reader_fault_no_gain(data_h5: Path) -> None:
-    with Writer(data_h5, modify_existing=True) as sfw:
-        del sfw.h5file["data"]["time"].attrs["gain"]
-    with pytest.raises(KeyError):
-        Reader(data_h5, verbose=True)
-
-
-def test_reader_fault_no_offset(data_h5: Path) -> None:
-    with Writer(data_h5, modify_existing=True) as sfw:
-        del sfw.h5file["data"]["time"].attrs["offset"]
-    with pytest.raises(KeyError):
-        Reader(data_h5, verbose=True)
-
-
 def test_reader_fault_non_eq_time(data_h5: Path) -> None:
     with Writer(data_h5, modify_existing=True) as sfw:
         sfw.h5file["data"]["time"].resize((0,))