shepherd-data 2024.4.1__tar.gz → 2024.5.1__tar.gz

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd_data
-Version: 2024.4.1
+Version: 2024.5.1
 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>
@@ -35,7 +35,7 @@ Requires-Dist: numpy
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyYAML
 Requires-Dist: scipy
-Requires-Dist: shepherd-core[inventory]>=2024.04.1
+Requires-Dist: shepherd-core[inventory]>=2024.5.1
 Requires-Dist: tqdm
 Provides-Extra: elf
 Requires-Dist: shepherd-core[elf]; extra == "elf"

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/pyproject.toml

@@ -38,7 +38,7 @@ dependencies = [
     "pandas>=2.0.0",  # full-version, v2 is OK
     "pyYAML",
     "scipy",   # full-version
-    "shepherd-core[inventory]>=2024.04.1",
+    "shepherd-core[inventory]>=2024.5.1",
     "tqdm",    # full-version
 ]
 

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data/__init__.py

@@ -1,15 +1,17 @@
-"""shepherd.datalib
-~~~~~
-Provides classes for storing and retrieving sampled IV data to/from
-HDF5 files.
+"""Provides higher functionality compared to core, with additional lib-requirements.
 
+Provides classes for storing and retrieving sampled IV data to/from
+HDF5 files, with
+- resampling
+- plotting
+- extracting metadata
 """
 
 from shepherd_core import Writer
 
 from .reader import Reader
 
-__version__ = "2024.04.1"
+__version__ = "2024.5.1"
 
 __all__ = [
     "Reader",

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data/cli.py

@@ -1,4 +1,4 @@
-"""Command definitions for CLI"""
+"""Command definitions for CLI."""
 
 import logging
 import os
@@ -16,15 +16,17 @@ from shepherd_core import increase_verbose_level
 from shepherd_core import local_tz
 from shepherd_core.commons import samplerate_sps_default
 
-from . import Reader
 from . import Writer
 from . import __version__
+from .reader import Reader
 
 logger = logging.getLogger("SHPData.cli")
 
 
 def path_to_flist(data_path: Path) -> List[Path]:
-    """Every path gets transformed to a list of paths
+    """Every path gets transformed to a list of paths.
+
+    Transformations:
     - if directory: list of files inside
     - if existing file: list with 1 element
     - or else: empty list
@@ -57,7 +59,7 @@ def path_to_flist(data_path: Path) -> List[Path]:
 )
 @click.pass_context  # TODO: is the ctx-type correct?
 def cli(ctx: click.Context, verbose: bool, version: bool) -> None:  # noqa: FBT001
-    """Shepherd: Synchronized Energy Harvesting Emulator and Recorder"""
+    """Shepherd: Synchronized Energy Harvesting Emulator and Recorder."""
     if verbose:
         increase_verbose_level(3)
     if version:
@@ -71,7 +73,7 @@ def cli(ctx: click.Context, verbose: bool, version: bool) -> None:  # noqa: FBT0
 @cli.command(short_help="Validates a file or directory containing shepherd-recordings")
 @click.argument("in_data", type=click.Path(exists=True, resolve_path=True))
 def validate(in_data: Path) -> None:
-    """Validates a file or directory containing shepherd-recordings"""
+    """Validate a file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()  # TODO: should be stored and passed in ctx
     valid_dir = True
@@ -85,8 +87,8 @@ def validate(in_data: Path) -> None:
                 valid_dir &= valid_file
                 if not valid_file:
                     logger.error(" -> File '%s' was NOT valid", file.name)
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
     sys.exit(int(not valid_dir))
 
 
@@ -107,7 +109,7 @@ def validate(in_data: Path) -> None:
     help="Set an individual csv-separator",
 )
 def extract(in_data: Path, ds_factor: float, separator: str) -> None:
-    """Extracts recorded IVSamples and stores it to csv"""
+    """Extract recorded IVSamples and store them to csv."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()
     if not isinstance(ds_factor, (float, int)) or ds_factor < 1:
@@ -143,8 +145,8 @@ def extract(in_data: Path, ds_factor: float, separator: str) -> None:
 
                 with Reader(ds_file, verbose=verbose_level > 2) as shpd:
                     shpd.save_csv(shpd["data"], separator)
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(
@@ -159,18 +161,19 @@ def extract(in_data: Path, ds_factor: float, separator: str) -> None:
     help="Set an individual csv-separator",
 )
 def extract_meta(in_data: Path, separator: str) -> None:
-    """Extracts metadata and logs from file or directory containing shepherd-recordings"""
+    """Extract metadata and logs from file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()
     for file in files:
         logger.info("Extracting metadata & logs from '%s' ...", file.name)
         # TODO: add default exports (user-centric) and allow specifying --all or specific ones
         # TODO: could also be combined with other extractors (just have one)
-        # TODO remove deprecated: timesync; "shepherd-log", "dmesg", "exceptions"
         try:
             with Reader(file, verbose=verbose_level > 2) as shpr:
                 shpr.save_metadata()
-                for element in ["ptp", "sysutil", "timesync"]:
+                csvs_depr = ["sysutil", "timesync"]
+                csvs = ["ptp", "sys_util", "pru_util"]
+                for element in csvs + csvs_depr:
                     if element in shpr.h5file:
                         shpr.save_csv(shpr[element], separator)
                 logs_depr = ["shepherd-log", "dmesg", "exceptions"]
@@ -181,8 +184,8 @@ def extract_meta(in_data: Path, separator: str) -> None:
                         # TODO: allow omitting timestamp,
                         #       also test if segmented uart is correctly written
                         shpr.warn_logs(element, show=True)
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(
@@ -190,7 +193,7 @@ def extract_meta(in_data: Path, separator: str) -> None:
 )
 @click.argument("in_data", type=click.Path(exists=True, resolve_path=True))
 def extract_uart(in_data: Path) -> None:
-    """Extracts uart from gpio-trace in file or directory containing shepherd-recordings"""
+    """Extract UART from GPIO-trace in file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()
     for file in files:
@@ -213,8 +216,8 @@ def extract_uart(in_data: Path) -> None:
                             # TODO: allow to skip Timestamp and export raw text
                             log_file.write(f"\t{str.encode(line[1])}")
                             log_file.write("\n")
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(short_help="Extracts gpio-trace from file or directory containing shepherd-recordings")
@@ -227,7 +230,7 @@ def extract_uart(in_data: Path) -> None:
     help="Set an individual csv-separator",
 )
 def extract_gpio(in_data: Path, separator: str) -> None:
-    """Extracts uart from gpio-trace in file or directory containing shepherd-recordings"""
+    """Extract UART from gpio-trace in file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()
     for file in files:
@@ -237,8 +240,8 @@ def extract_gpio(in_data: Path, separator: str) -> None:
                 wfs = shpr.gpio_to_waveforms()
                 for name, wf in wfs.items():
                     shpr.waveform_to_csv(name, wf, separator)
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(
@@ -261,9 +264,7 @@ def extract_gpio(in_data: Path, separator: str) -> None:
     help="Alternative Input to determine a downsample-factor (Choose One)",
 )
 def downsample(in_data: Path, ds_factor: Optional[float], sample_rate: Optional[int]) -> None:
-    """Creates an array of downsampling-files from file
-    or directory containing shepherd-recordings
-    """
+    """Create an array of down-sampled files from file or dir containing shepherd-recordings."""
     if ds_factor is None and sample_rate is not None and sample_rate >= 1:
         ds_factor = int(samplerate_sps_default / sample_rate)
         # TODO: shouldn't current sps be based on file rather than default?
@@ -303,8 +304,8 @@ def downsample(in_data: Path, ds_factor: Optional[float], sample_rate: Optional[
                         shpr.downsample(shpr.ds_time, shpw.ds_time, ds_factor=_factor, is_time=True)
                         shpr.downsample(shpr.ds_voltage, shpw.ds_voltage, ds_factor=_factor)
                         shpr.downsample(shpr.ds_current, shpw.ds_current, ds_factor=_factor)
-        except TypeError as _xpc:
-            logger.error("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(short_help="Plots IV-trace from file or directory containing shepherd-recordings")
@@ -351,7 +352,7 @@ def plot(
     height: int,
     multiplot: bool,  # noqa: FBT001
 ) -> None:
-    """Plots IV-trace from file or directory containing shepherd-recordings"""
+    """Plot IV-trace from file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data)
     verbose_level = get_verbose_level()
     multiplot = multiplot and len(files) > 1
@@ -364,8 +365,8 @@ def plot(
                     data.append(shpr.generate_plot_data(start, end, relative_timestamp=True))
                 else:
                     shpr.plot_to_file(start, end, width, height)
-        except TypeError as _xpc:
-            logger.exception("ERROR: will skip file, caught exception: %s", _xpc)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
     if multiplot:
         logger.info("Got %d datasets to plot", len(data))
         mpl_path = Reader.multiplot_to_file(data, in_data, width, height)

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data/ivonne.py

@@ -1,7 +1,4 @@
-"""prototype of a file-reader with various converters
-to generate valid shepherd-data for emulation
-
-"""
+"""file-reader with various converters to generate valid shepherd-data for emulation."""
 
 import errno
 import logging

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: shepherd_data
-Version: 2024.4.1
+Version: 2024.5.1
 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>
@@ -35,7 +35,7 @@ Requires-Dist: numpy
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyYAML
 Requires-Dist: scipy
-Requires-Dist: shepherd-core[inventory]>=2024.04.1
+Requires-Dist: shepherd-core[inventory]>=2024.5.1
 Requires-Dist: tqdm
 Provides-Extra: elf
 Requires-Dist: shepherd-core[elf]; extra == "elf"

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data.egg-info/SOURCES.txt

@@ -2,7 +2,6 @@ README.md
 pyproject.toml
 shepherd_data/__init__.py
 shepherd_data/cli.py
-shepherd_data/debug_resampler.py
 shepherd_data/ivonne.py
 shepherd_data/mppt.py
 shepherd_data/reader.py

{shepherd_data-2024.4.1 → shepherd_data-2024.5.1}/shepherd_data.egg-info/requires.txt

@@ -5,7 +5,7 @@ numpy
 pandas>=2.0.0
 pyYAML
 scipy
-shepherd-core[inventory]>=2024.04.1
+shepherd-core[inventory]>=2024.5.1
 tqdm
 
 [dev]

shepherd_data-2024.4.1/shepherd_data/debug_resampler.py

@@ -1,30 +0,0 @@
-import logging
-from pathlib import Path
-
-import shepherd_data as shpd
-
-file = Path("./hrv_sawtooth_1h.h5")
-samplerate_sps = 1000
-
-logger = logging.getLogger("SHPData.debug")
-logger.setLevel(logging.DEBUG)
-
-with shpd.Reader(file) as shpr:
-    out_file = file.with_suffix(f".fs_{samplerate_sps}.h5")
-    logger.info(
-        "Resampling '%s' from %d Hz to %d Hz ...",
-        file.name,
-        shpr.samplerate_sps,
-        samplerate_sps,
-    )
-    with shpd.Writer(
-        out_file,
-        mode=shpr.get_mode(),
-        datatype=shpr.get_datatype(),
-        window_samples=shpr.get_window_samples(),
-        cal_data=shpr.get_calibration_data(),
-    ) as shpw:
-        shpr.resample(shpr.ds_time, shpw.ds_time, samplerate_dst=samplerate_sps, is_time=True)
-        shpr.resample(shpr.ds_voltage, shpw.ds_voltage, samplerate_dst=samplerate_sps)
-        shpr.resample(shpr.ds_current, shpw.ds_current, samplerate_dst=samplerate_sps)
-        shpw.save_metadata()