shepherd-data 2025.5.3__py3-none-any.whl → 2025.6.2__py3-none-any.whl

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/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/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.dist-info → shepherd_data-2025.6.2.dist-info}/METADATA

@@ -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.dist-info/RECORD

@@ -0,0 +1,11 @@
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+shepherd_data/cli.py,sha256=8CShRsqJ5w6_nirNKInFEwYGv0gG5caXVLzExSeRGL4,15902
+shepherd_data/ivonne.py,sha256=sH7c2aj9i5ygkpw6xQbjRwrbl9wtU_Toj_ZFyJVywG8,11930
+shepherd_data/mppt.py,sha256=y9gVIhMs-ZG3ScL9UQTc5n8T146B13Q5dA5sfqqfjg0,3999
+shepherd_data/reader.py,sha256=NEIwXC5f5fkSiBEsyY85gIcgjhYHFS1tavNnA6ViE3k,25741
+shepherd_data-2025.6.2.dist-info/METADATA,sha256=D8yzzlUl9GeZjRycigoNOWRF3NdyLLLI9Mcj85s4jVU,3404
+shepherd_data-2025.6.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+shepherd_data-2025.6.2.dist-info/entry_points.txt,sha256=6PBfY36A1xNOdzLiz-Qoukya_UzFZAwOapwmRNnPeZ8,56
+shepherd_data-2025.6.2.dist-info/top_level.txt,sha256=7-SCTY-TG1mLY72OVKCaqte1hy-X8woxknIUAD3OIxs,14
+shepherd_data-2025.6.2.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+shepherd_data-2025.6.2.dist-info/RECORD,,

{shepherd_data-2025.5.3.dist-info → shepherd_data-2025.6.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

shepherd_data-2025.5.3.dist-info/RECORD

@@ -1,11 +0,0 @@
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-shepherd_data/cli.py,sha256=wunO1ZQktJ_-uTGVIfq-E-sD9nGJPYSAfw7Gw6dgXco,14740
-shepherd_data/ivonne.py,sha256=sH7c2aj9i5ygkpw6xQbjRwrbl9wtU_Toj_ZFyJVywG8,11930
-shepherd_data/mppt.py,sha256=y9gVIhMs-ZG3ScL9UQTc5n8T146B13Q5dA5sfqqfjg0,3999
-shepherd_data/reader.py,sha256=LMHaLM8SKu8g8_CZOjZlQsOcOXkweP4cLPRf0dnJlhY,25735
-shepherd_data-2025.5.3.dist-info/METADATA,sha256=FAabfAxowIM36FReB9DjfJ3o2H3EKgwoyel5kMKIwUw,3380
-shepherd_data-2025.5.3.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-shepherd_data-2025.5.3.dist-info/entry_points.txt,sha256=6PBfY36A1xNOdzLiz-Qoukya_UzFZAwOapwmRNnPeZ8,56
-shepherd_data-2025.5.3.dist-info/top_level.txt,sha256=7-SCTY-TG1mLY72OVKCaqte1hy-X8woxknIUAD3OIxs,14
-shepherd_data-2025.5.3.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-shepherd_data-2025.5.3.dist-info/RECORD,,