shepherd-data 2025.5.3__tar.gz → 2025.6.2__tar.gz

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: shepherd_data
-Version: 2025.5.3
+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>
-Project-URL: Documentation, https://github.com/orgua/shepherd-datalib/blob/main/README.md
+Project-URL: Documentation, https://github.com/nes-lab/shepherd-tools/blob/main/README.md
 Project-URL: Issues, https://pypi.org/project/shepherd-data/issues
 Project-URL: Source, https://pypi.org/project/shepherd-data/
 Keywords: testbed,beaglebone,pru,batteryless,energyharvesting,solar
@@ -35,7 +35,7 @@ Requires-Dist: numpy
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyYAML
 Requires-Dist: scipy
-Requires-Dist: shepherd-core[inventory]>=2025.05.3
+Requires-Dist: shepherd-core[inventory]>=2025.06.2
 Requires-Dist: tqdm
 Provides-Extra: elf
 Requires-Dist: shepherd-core[elf]; extra == "elf"
@@ -50,20 +50,20 @@ Requires-Dist: coverage; extra == "test"
 
 # Shepherd-Data-Tool
 
-[![PyPiVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
+[![PyPIVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
 [![image](https://img.shields.io/pypi/pyversions/shepherd_data.svg)](https://pypi.python.org/pypi/shepherd-data)
-[![Pytest](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml/badge.svg)](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml)
+[![QA-Tests](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml/badge.svg)](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml)
 [![CodeStyle](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-**Main Documentation**: <https://orgua.github.io/shepherd>
+**Main Documentation**: <https://nes-lab.github.io/shepherd>
 
-**Source Code**: <https://github.com/orgua/shepherd-datalib>
+**Source Code**: <https://github.com/nes-lab/shepherd-tools>
 
-**Main Project**: <https://github.com/orgua/shepherd>
+**Main Project**: <https://github.com/nes-lab/shepherd>
 
 ---
 
-`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/orgua/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
+`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/nes-lab/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
 
 ## Installation
 
@@ -76,12 +76,12 @@ pip3 install shepherd-data -U
 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_data -U
+pip install git+https://github.com/nes-lab/shepherd-tools.git@dev#subdirectory=shepherd_data -U
 ```
 
 ## More
 
-Please consult the [official documentation](https://orgua.github.io/shepherd) for more, it covers:
+Please consult the [official documentation](https://nes-lab.github.io/shepherd) for more, it covers:
 
 - general context
 - command-line interface

shepherd_data-2025.6.2/README.md

@@ -0,0 +1,38 @@
+# Shepherd-Data-Tool
+
+[![PyPIVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
+[![image](https://img.shields.io/pypi/pyversions/shepherd_data.svg)](https://pypi.python.org/pypi/shepherd-data)
+[![QA-Tests](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml/badge.svg)](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml)
+[![CodeStyle](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+
+**Main Documentation**: <https://nes-lab.github.io/shepherd>
+
+**Source Code**: <https://github.com/nes-lab/shepherd-tools>
+
+**Main Project**: <https://github.com/nes-lab/shepherd>
+
+---
+
+`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/nes-lab/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
+
+## Installation
+
+### PIP - Online
+
+```shell
+pip3 install shepherd-data -U
+```
+
+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/nes-lab/shepherd-tools.git@dev#subdirectory=shepherd_data -U
+```
+
+## More
+
+Please consult the [official documentation](https://nes-lab.github.io/shepherd) for more, it covers:
+
+- general context
+- command-line interface
+- programming interface

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
     "pandas>=2.0.0",  # full-version, v2 is OK
     "pyYAML",
     "scipy",   # full-version
-    "shepherd-core[inventory]>=2025.05.3",  # libs are strongly coupled
+    "shepherd-core[inventory]>=2025.06.2",  # libs are strongly coupled
     "tqdm",    # full-version
 ]
 
@@ -59,7 +59,7 @@ test = [
 ]
 
 [project.urls]
-Documentation = "https://github.com/orgua/shepherd-datalib/blob/main/README.md"
+Documentation = "https://github.com/nes-lab/shepherd-tools/blob/main/README.md"
 Issues = "https://pypi.org/project/shepherd-data/issues"
 Source = "https://pypi.org/project/shepherd-data/"
 

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/shepherd_data/__init__.py

@@ -11,7 +11,7 @@ from shepherd_core import Writer
 
 from .reader import Reader
 
-__version__ = "2025.05.3"
+__version__ = "2025.06.2"
 
 __all__ = [
     "Reader",

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/shepherd_data/cli.py

@@ -177,7 +177,15 @@ def extract(
     is_flag=True,
     help="Also consider files in sub-folders",
 )
-def extract_meta(in_data: Path, separator: str, *, recurse: bool = False) -> None:
+@click.option(
+    "--debug",
+    "-d",
+    is_flag=True,
+    help="Also extract system logs like kernel, ",
+)
+def extract_meta(
+    in_data: Path, separator: str, *, recurse: bool = False, debug: bool = False
+) -> None:
     """Extract metadata and logs from file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data, recurse=recurse)
     verbose_level = get_verbose_level()
@@ -188,25 +196,54 @@ def extract_meta(in_data: Path, separator: str, *, recurse: bool = False) -> Non
         try:
             with Reader(file, verbose=verbose_level > 2) as shpr:
                 shpr.save_metadata()
-                csvs_depr = ["sysutil", "timesync"]
-                csvs = ["ptp", "phc2sys", "sys_util", "pru_util"]
-                for element in csvs + csvs_depr:
-                    if element in shpr.h5file:
-                        shpr.save_csv(shpr[element], separator)
+                if "uart" in shpr.h5file:
+                    shpr.save_log(shpr["uart"])
+
                 logs_depr = ["shepherd-log", "dmesg", "exceptions"]
-                logs = ["sheep", "kernel", "ntp", "uart"]
-                for element in logs + logs_depr:
+                logs_meta = ["sheep", "kernel", "ntp"]
+                for element in logs_meta + logs_depr:
                     if element in shpr.h5file:
-                        shpr.save_log(shpr[element])
+                        if debug:
+                            shpr.save_log(shpr[element])
                         # TODO: allow omitting timestamp,
                         #       also test if segmented uart is correctly written
                         shpr.warn_logs(element, show=True)
+                if not debug:
+                    continue
+                csv_depr = ["sysutil", "timesync"]
+                csv_meta = ["ptp", "phc2sys", "sys_util", "pru_util"]
+                for element in csv_meta + csv_depr:
+                    if element in shpr.h5file:
+                        shpr.save_csv(shpr[element], separator)
+        except TypeError:
+            logger.exception("ERROR: Will skip file. It caused an exception.")
+
+
+@cli.command()
+@click.argument("in_data", type=click.Path(exists=True, resolve_path=True))
+@click.option(
+    "--recurse",
+    "-a",
+    is_flag=True,
+    help="Also consider files in sub-folders",
+)
+def extract_uart(in_data: Path, *, recurse: bool = False) -> None:
+    """Log from file or directory containing shepherd-recordings."""
+    files = path_to_flist(in_data, recurse=recurse)
+    verbose_level = get_verbose_level()
+    for file in files:
+        logger.info("Extracting UART-log from '%s' ...", file.name)
+        try:
+            with Reader(file, verbose=verbose_level > 2) as shpr:
+                shpr.save_metadata()
+                if "uart" in shpr.h5file:
+                    shpr.save_log(shpr["uart"])
         except TypeError:
             logger.exception("ERROR: Will skip file. It caused an exception.")
 
 
 @cli.command(
-    short_help="Extracts uart from gpio-trace in file or directory containing shepherd-recordings"
+    short_help="Decode uart from gpio-trace in file or directory containing shepherd-recordings"
 )
 @click.argument("in_data", type=click.Path(exists=True, resolve_path=True))
 @click.option(
@@ -215,8 +252,8 @@ def extract_meta(in_data: Path, separator: str, *, recurse: bool = False) -> Non
     is_flag=True,
     help="Also consider files in sub-folders",
 )
-def extract_uart(in_data: Path, *, recurse: bool = False) -> None:
-    """Extract UART from GPIO-trace in file or directory containing shepherd-recordings."""
+def decode_uart(in_data: Path, *, recurse: bool = False) -> None:
+    """Decode UART from GPIO-trace in file or directory containing shepherd-recordings."""
     files = path_to_flist(in_data, recurse=recurse)
     verbose_level = get_verbose_level()
     for file in files:

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/shepherd_data/reader.py

@@ -18,7 +18,7 @@ from shepherd_core import Writer as CoreWriter
 from shepherd_core import local_tz
 from shepherd_core.data_models import EnergyDType
 from shepherd_core.logger import get_verbose_level
-from shepherd_core.logger import logger
+from shepherd_core.logger import log
 
 # import samplerate  # noqa: ERA001, TODO: just a test-fn for now
 
@@ -308,12 +308,12 @@ class Reader(CoreReader):
 
         dst_file = self.file_path.resolve().with_suffix(cut_str + ds_str + ".h5")
         if dst_file.exists():
-            logger.warning(
+            self._logger.warning(
                 "Cut & Downsample skipped because output-file %s already exists.", dst_file.name
             )
             return dst_file
 
-        logger.debug(
+        self._logger.debug(
             "Cut & Downsample '%s' from %.3f s to %.3f s with factor = %.1f ...",
             self.file_path.name,
             start_s,
@@ -635,7 +635,7 @@ class Reader(CoreReader):
             Path(plot_path).resolve().with_suffix(f".multiplot_{start_str}_to_{end_str}.png")
         )
         if plot_path.exists():
-            logger.warning("Plot exists, will skip & not overwrite!")
+            log.warning("Plot exists, will skip & not overwrite!")
             return None
         fig = Reader.assemble_plot(data, width, height, only_pwr=only_pwr)
         plt.savefig(plot_path)

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/shepherd_data.egg-info/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.4
 Name: shepherd_data
-Version: 2025.5.3
+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>
-Project-URL: Documentation, https://github.com/orgua/shepherd-datalib/blob/main/README.md
+Project-URL: Documentation, https://github.com/nes-lab/shepherd-tools/blob/main/README.md
 Project-URL: Issues, https://pypi.org/project/shepherd-data/issues
 Project-URL: Source, https://pypi.org/project/shepherd-data/
 Keywords: testbed,beaglebone,pru,batteryless,energyharvesting,solar
@@ -35,7 +35,7 @@ Requires-Dist: numpy
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyYAML
 Requires-Dist: scipy
-Requires-Dist: shepherd-core[inventory]>=2025.05.3
+Requires-Dist: shepherd-core[inventory]>=2025.06.2
 Requires-Dist: tqdm
 Provides-Extra: elf
 Requires-Dist: shepherd-core[elf]; extra == "elf"
@@ -50,20 +50,20 @@ Requires-Dist: coverage; extra == "test"
 
 # Shepherd-Data-Tool
 
-[![PyPiVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
+[![PyPIVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
 [![image](https://img.shields.io/pypi/pyversions/shepherd_data.svg)](https://pypi.python.org/pypi/shepherd-data)
-[![Pytest](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml/badge.svg)](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml)
+[![QA-Tests](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml/badge.svg)](https://github.com/nes-lab/shepherd-tools/actions/workflows/quality_assurance.yaml)
 [![CodeStyle](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
-**Main Documentation**: <https://orgua.github.io/shepherd>
+**Main Documentation**: <https://nes-lab.github.io/shepherd>
 
-**Source Code**: <https://github.com/orgua/shepherd-datalib>
+**Source Code**: <https://github.com/nes-lab/shepherd-tools>
 
-**Main Project**: <https://github.com/orgua/shepherd>
+**Main Project**: <https://github.com/nes-lab/shepherd>
 
 ---
 
-`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/orgua/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
+`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/nes-lab/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
 
 ## Installation
 
@@ -76,12 +76,12 @@ pip3 install shepherd-data -U
 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_data -U
+pip install git+https://github.com/nes-lab/shepherd-tools.git@dev#subdirectory=shepherd_data -U
 ```
 
 ## More
 
-Please consult the [official documentation](https://orgua.github.io/shepherd) for more, it covers:
+Please consult the [official documentation](https://nes-lab.github.io/shepherd) for more, it covers:
 
 - general context
 - command-line interface

{shepherd_data-2025.5.3 → shepherd_data-2025.6.2}/shepherd_data.egg-info/requires.txt

@@ -5,7 +5,7 @@ numpy
 pandas>=2.0.0
 pyYAML
 scipy
-shepherd-core[inventory]>=2025.05.3
+shepherd-core[inventory]>=2025.06.2
 tqdm
 
 [dev]

shepherd_data-2025.5.3/README.md

@@ -1,38 +0,0 @@
-# Shepherd-Data-Tool
-
-[![PyPiVersion](https://img.shields.io/pypi/v/shepherd_data.svg)](https://pypi.org/project/shepherd_data)
-[![image](https://img.shields.io/pypi/pyversions/shepherd_data.svg)](https://pypi.python.org/pypi/shepherd-data)
-[![Pytest](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml/badge.svg)](https://github.com/orgua/shepherd-datalib/actions/workflows/py_unittest.yml)
-[![CodeStyle](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
-
-**Main Documentation**: <https://orgua.github.io/shepherd>
-
-**Source Code**: <https://github.com/orgua/shepherd-datalib>
-
-**Main Project**: <https://github.com/orgua/shepherd>
-
----
-
-`shepherd-data` eases the handling of hdf5-recordings used by the [shepherd](https://github.com/orgua/shepherd)-testbed. Users can read, validate and create files and also extract, down-sample and plot information.
-
-## Installation
-
-### PIP - Online
-
-```shell
-pip3 install shepherd-data -U
-```
-
-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_data -U
-```
-
-## More
-
-Please consult the [official documentation](https://orgua.github.io/shepherd) for more, it covers:
-
-- general context
-- command-line interface
-- programming interface