shepherd-data 2023.12.1__py3-none-any.whl → 2024.4.2__py3-none-any.whl

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()

shepherd_data-2023.12.1.dist-info/METADATA

@@ -1,274 +0,0 @@
-Metadata-Version: 2.1
-Name: shepherd-data
-Version: 2023.12.1
-Summary: Programming- and CLI-Interface for the h5-dataformat of the Shepherd-Testbed
-Home-page: https://pypi.org/project/shepherd-data/
-Author: Ingmar Splitt, Kai Geissdoerfer
-Author-email: ingmar.splitt@tu-dresden.de
-Maintainer-email: ingmar.splitt@tu-dresden.de
-License: MIT
-Project-URL: Tracker, https://github.com/orgua/shepherd-datalib/issues
-Project-URL: Source, https://github.com/orgua/shepherd-datalib
-Keywords: testbed,beaglebone,pru,batteryless,energyharvesting,solar
-Platform: unix
-Platform: linux
-Platform: osx
-Platform: cygwin
-Platform: win32
-Platform: win64
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Information Technology
-Classifier: Intended Audience :: Science/Research
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Natural Language :: English
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-Requires-Dist: h5py
-Requires-Dist: numpy
-Requires-Dist: pyYAML
-Requires-Dist: shepherd-core[inventory] >=2023.12.1
-Requires-Dist: click
-Requires-Dist: matplotlib
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: tqdm
-Provides-Extra: dev
-Requires-Dist: shepherd-core[dev] ; extra == 'dev'
-Requires-Dist: pandas-stubs ; extra == 'dev'
-Provides-Extra: elf
-Requires-Dist: shepherd-core[elf] ; extra == 'elf'
-Provides-Extra: test
-Requires-Dist: shepherd-core[test] ; extra == 'test'
-Requires-Dist: pytest-click ; extra == 'test'
-
-# Data Module
-
-[![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)
-
-**Documentation**: <https://orgua.github.io/shepherd/external/shepherd_data.html>
-
-**Source Code**: <https://github.com/orgua/shepherd-datalib>
-
-**Main Project**: <https://github.com/orgua/shepherd>
-
----
-
-This Python Module 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
-```
-
-## Programming Interface
-
-### Basic Usage (recommendation)
-
-```python
-import shepherd_data as sd
-
-with sd.Reader("./hrv_sawtooth_1h.h5") as db:
-    print(f"Mode: {db.get_mode()}")
-    print(f"Window: {db.get_window_samples()}")
-    print(f"Config: {db.get_config()}")
-```
-
-### Available Functionality
-
-- `Reader()`
-  - file can be checked for plausibility and validity (`is_valid()`)
-  - internal structure of h5file (`get_metadata()` or `save_metadata()` ... to yaml) with lots of additional data
-  - access data and various converters, calculators
-    - `read_buffers()` -> generator that provides one buffer per call, can be configured on first call
-    - `get_calibration_data()`
-    - `get_windows_samples()`
-    - `get_mode()`
-    - `get_config()`
-    - direct access to root h5-structure via `reader['element']`
-    - converters for raw / physical units: `si_to_raw()` & `raw_to_si()`
-    - `energy()` sums up recorded power over time
-  - `downsample()` (if needed) visualize recording (`plot_to_file()`)
-- `Writer()`
-  - inherits all functionality from Reader
-  - `append_iv_data_raw()`
-  - `append_iv_data_si()`
-  - `set_config()`
-  - `set_windows_samples()`
-- IVonne Reader
-  - `convert_2_ivcurves()` converts ivonne-recording into a shepherd ivcurve
-  - `upsample_2_isc_voc()` TODO: for now a upsampled but unusable version of samples of short-circuit-current and open-circuit-voltage
-  - `convert_2_ivsamples()` already applies a simple harvesting-algo and creates ivsamples
-- `./examples/`
-  - `example_convert_ivonne.py` converts IVonne recording (`jogging_10m.iv`) to shepherd ivcurves, NOTE: slow implementation
-  - `example_extract_logs.py` is analyzing all files in directory, saves logging-data and calculates cpu-load and data-rate
-  - `example_generate_sawtooth.py` is using Writer to generate a 60s ramp with 1h repetition and uses Reader to dump metadata of that file
-  - `example_plot_traces.py` demos some mpl-plots with various zoom levels
-  - `example_repair_recordings.py` makes old recordings from shepherd 1.x fit for v2
-  - `jogging_10m.iv`
-      - 50 Hz measurement with Short-Circuit-Current and two other parameters
-      - recorded with "IVonne"
-
-### Functionality Update (WIP)
-
-- Core.`Reader`
-  - `__repr__()`
-  - `read_buffers`
-  - `get_calibration_data`
-  - `get_window_samples`
-  - `get_mode`
-  - `get_config`
-  - `get_hostname`
-  - `get_datatype`
-  - `get_hrv_config`
-  - `is_valid`
-  - `energy()`
-  - `check_timediffs()`
-  - `get_metadata()`
-  - `save_metadata()`
-
-- `Writer(Reader)` (core, data are the same)
-  - `append_iv_data_raw`
-  - `append_iv_data_si`
-  - `store_config`
-  - `store_hostname`
-
-- data.`Reader(CoreReader)`
-  - `save_csv()`
-  - `save_log()`
-  - `downsample()`
-  - `resample()`
-  - `generate_plot_data()`
-  - `assemble_plot()`
-  - `plot_to_file()`
-  - `multiplot_to_file()`
-
-## CLI-Interface
-
-After installing the module the datalib offers some often needed functionality on the command line:
-
-**Validate Recordings**
-
-- takes a file or directory as an argument
-
-```shell
-shepherd-data validate dir_or_file
-
-# examples:
-shepherd-data validate ./
-shepherd-data validate hrv_saw_1h.h5
-```
-
-**Extract IV-Samples to csv**
-
-- takes a file or directory as an argument
-- can take down-sample-factor as an argument
-
-```shell
-shepherd-data extract [-f ds-factor] [-s separator_symbol] dir_or_file
-
-# examples:
-shepherd-data extract ./
-shepherd-data extract -f 1000 -s ; hrv_saw_1h.h5
-```
-
-**Extract meta-data and sys-logs**
-
-- takes a file or directory as an argument
-
-```shell
-shepherd-data extract-meta dir_or_file
-
-# examples:
-shepherd-data extract-meta ./
-shepherd-data extract-meta hrv_saw_1h.h5
-```
-
-**Plot IVSamples**
-
-- takes a file or directory as an argument
-- can take start- and end-time as an argument
-- can take image-width and -height as an argument
-
-```shell
-shepherd-data plot [-s start_time] [-e end_time] [-w plot_width] [-h plot_height] [--multiplot] dir_or_file
-
-# examples:
-shepherd-data plot --multiplot ./
-shepherd-data plot -s10 -e20 hrv_saw_1h.h5
-```
-
-**Downsample IVSamples (for later GUI-usage, TODO)**
-
-- generates a set of downsamplings (20 kHz to 0.1 Hz in x4 to x5 Steps)
-- takes a file or directory as an argument
-- can take down-sample-factor as an argument
-
-```shell
-shepherd-data downsample [-f ds-factor] [-r sample-rate] dir_or_file
-
-# examples:
-shepherd-data downsample ./
-shepherd-data downsample -f 1000 hrv_saw_1h.h5
-shepherd-data downsample -r 100 hrv_saw_1h.h5
-```
-
-## Data-Layout and Design choices
-
-Details about the file-structure can be found in the [main-project](https://github.com/orgua/shepherd/blob/main/docs/user/data_format.rst).
-
-TODO:
-- update design of file
-- data dtype, mode, ...
-
-### Modes and Datatypes
-
-- Mode `harvester` recorded a harvesting-source like solar with one of various algorithms
-  - Datatype `ivsample` is directly usable by shepherd, input for virtual source / converter
-  - Datatype `ivcurve` is directly usable by shepherd, input for a virtual harvester (output are ivsamples)
-  - Datatype `isc_voc` is specially for solar-cells and needs to be (at least) transformed into ivcurves later
-- Mode `emulator` replayed a harvester-recording through a virtual converter and supplied a target while recording the power-consumption
-  - Datatype `ivsample` is the only output of this mode
-
-### Compression & Beaglebone
-
-- supported are uncompressed, lzf and gzip with level 1 (order of recommendation)
-  - lzf seems better-suited due to lower load, or if space isn't a constraint: uncompressed (None as argument)
-  - note: lzf seems to cause trouble with some third party hdf5-tools
-  - compression is a heavy load for the beaglebone, but it got more performant with recent python-versions
-- size-experiment A: 24 h of ramping / sawtooth (data is repetitive with 1 minute ramp)
-  - gzip-1: 49'646 MiB -> 588 KiB/s
-  - lzf: 106'445 MiB -> 1262 KiB/s
-  - uncompressed: 131'928 MiB -> 1564 KiB/s
-- cpu-load-experiments (input is 24h sawtooth, python 3.10 with most recent libs as of 2022-04)
-  - warning: gpio-traffic and other logging-data can cause lots of load
-
-```
-  emu_120s_gz1_to_gz1.h5 	-> emulator, cpu_util [%] = 65.59, data-rate =  352.0 KiB/s
-  emu_120s_gz1_to_lzf.h5 	-> emulator, cpu_util [%] = 57.37, data-rate =  686.0 KiB/s
-  emu_120s_gz1_to_unc.h5 	-> emulator, cpu_util [%] = 53.63, data-rate = 1564.0 KiB/s
-  emu_120s_lzf_to_gz1.h5 	-> emulator, cpu_util [%] = 63.18, data-rate =  352.0 KiB/s
-  emu_120s_lzf_to_lzf.h5 	-> emulator, cpu_util [%] = 58.60, data-rate =  686.0 KiB/s
-  emu_120s_lzf_to_unc.h5 	-> emulator, cpu_util [%] = 55.75, data-rate = 1564.0 KiB/s
-  emu_120s_unc_to_gz1.h5 	-> emulator, cpu_util [%] = 63.84, data-rate =  351.0 KiB/s
-  emu_120s_unc_to_lzf.h5 	-> emulator, cpu_util [%] = 57.28, data-rate =  686.0 KiB/s
-  emu_120s_unc_to_unc.h5 	-> emulator, cpu_util [%] = 51.69, data-rate = 1564.0 KiB/s
-```

shepherd_data-2023.12.1.dist-info/RECORD

@@ -1,22 +0,0 @@
-shepherd_data/__init__.py,sha256=ysHj9J6TMflWnfscRnZ0Z4I622XD0mmyeVQ_NimE95E,242
-shepherd_data/cli.py,sha256=XnW-SGEUZpFS0IkrhC0wAB_t3eafB7MD2Z1-iJHJW6Y,15013
-shepherd_data/debug_resampler.py,sha256=0VNGuUqOeKii6fvkRJUpv-27uv9p1VFsvShU3tvxwYQ,961
-shepherd_data/ivonne.py,sha256=wkEciyxXuNMFtA6HEm9zR9CIrukwR0CDiuJMtt6_wEA,11601
-shepherd_data/mppt.py,sha256=Ifvx7NdsBoyBJGbc5PEEpHFja20SuouXmRpaCHoODWs,3583
-shepherd_data/reader.py,sha256=hAxvMUt86c3EJif_Q4oYb4zhhCr3nS6Rjk-fWmMrDSY,18035
-tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/conftest.py,sha256=BCtm2TbfVf85_AsGOUZLXd6TquicWRMgBq2-q5UA2UM,985
-tests/test_cli.py,sha256=PPbRwgOQbWjNcgR7mIXTnGdboCQ4QDC4Kh74kSaEFhc,181
-tests/test_cli_downsample.py,sha256=i8AKw-doGlw5xtg9YG3kFGShV9we6zv7F48D-t-l8us,1775
-tests/test_cli_extract.py,sha256=-8HdLL1sDF-ygAGpbUeA46fKu1mAP8aZN5xde9tMP3M,2504
-tests/test_cli_plot.py,sha256=jDDoDtvyChQyS4CX2cPq1jDLJNfzDjtJXOftBxL-meM,3242
-tests/test_cli_validate.py,sha256=DOfaRq6r05eu8x4SnZOPrPfbbMNu0PTus7lSV8Gkzwo,405
-tests/test_examples.py,sha256=e_uc5h_I4wwJnIWuh-PjpSSTICkYemI831iqhxIy_R0,576
-tests/test_ivonne.py,sha256=cIMtpx7tjRFxL9hpr5OPPgroGLzRZxGC4x9Y7vWgze8,1367
-tests/test_reader.py,sha256=Xt__Khgldv8klZJ3OQcMZevC6_3gPH2_TpOorq2ytNI,90
-shepherd_data-2023.12.1.dist-info/METADATA,sha256=GnWaKvPEEr5JbBXZIeUiCCeSEIVA845WhBOb1dwLLN4,9999
-shepherd_data-2023.12.1.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-shepherd_data-2023.12.1.dist-info/entry_points.txt,sha256=6PBfY36A1xNOdzLiz-Qoukya_UzFZAwOapwmRNnPeZ8,56
-shepherd_data-2023.12.1.dist-info/top_level.txt,sha256=Bk61YO7iYS43TSWtwdSKb2moGBvJqJIYfGaZsQsv09M,20
-shepherd_data-2023.12.1.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-shepherd_data-2023.12.1.dist-info/RECORD,,

tests/conftest.py

@@ -1,33 +0,0 @@
-from pathlib import Path
-
-import numpy as np
-import pytest
-
-from shepherd_core import Compression
-from shepherd_data import Writer
-
-
-def generate_h5_file(file_path: Path, file_name: str = "harvest_example.h5") -> Path:
-    store_path = file_path / file_name
-
-    with Writer(store_path, compression=Compression.gzip1) as file:
-        file.store_hostname("artificial")
-
-        duration_s = 2
-        repetitions = 5
-        timestamp_vector = np.arange(0.0, duration_s, file.sample_interval_ns / 1e9)
-
-        # values in SI units
-        voltages = np.linspace(3.60, 1.90, int(file.samplerate_sps * duration_s))
-        currents = np.linspace(100e-6, 2000e-6, int(file.samplerate_sps * duration_s))
-
-        for idx in range(repetitions):
-            timestamps = idx * duration_s + timestamp_vector
-            file.append_iv_data_si(timestamps, voltages, currents)
-
-    return store_path
-
-
-@pytest.fixture
-def data_h5(tmp_path: Path) -> Path:
-    return generate_h5_file(tmp_path)

tests/test_cli.py

@@ -1,8 +0,0 @@
-from click.testing import CliRunner
-
-from shepherd_data.cli import cli
-
-
-def test_cli_invoke_help() -> None:
-    res = CliRunner().invoke(cli, ["-h"])
-    assert res.exit_code == 0

tests/test_cli_downsample.py

@@ -1,47 +0,0 @@
-from pathlib import Path
-
-from click.testing import CliRunner
-
-from shepherd_data.cli import cli
-
-
-def test_cli_downsample_file_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["--verbose", "downsample", "--ds-factor", "10", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x10.h5").exists()
-
-
-def test_cli_downsample_file_short(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "downsample", "-f", "20", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x20.h5").exists()
-
-
-def test_cli_downsample_file_min(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["--verbose", "downsample", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x5.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x25.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x100.h5").exists()
-
-
-def test_cli_downsample_dir_full(data_h5: Path) -> None:
-    print(data_h5.parent)
-    print(data_h5.parent.is_dir())
-    res = CliRunner().invoke(
-        cli, ["--verbose", "downsample", "--ds-factor", "40", str(data_h5.parent)]
-    )
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x40.h5").exists()
-
-
-def test_cli_downsample_rate_file_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["--verbose", "downsample", "--sample-rate", "100", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x1000.h5").exists()
-
-
-def test_cli_downsample_rate_file_short(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "downsample", "-r", "200", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x500.h5").exists()

tests/test_cli_extract.py

@@ -1,80 +0,0 @@
-from pathlib import Path
-
-from click.testing import CliRunner
-
-from shepherd_data.cli import cli
-
-
-def test_cli_extract_file_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(
-        cli,
-        [
-            "--verbose",
-            "extract",
-            "--ds-factor",
-            "100",
-            "--separator",
-            ",",
-            str(data_h5),
-        ],
-    )
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x100.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x100.data.csv").exists()
-
-
-def test_cli_extract_file_short(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "extract", "-f", "200", "-s", ";", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x200.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x200.data.csv").exists()
-
-
-def test_cli_extract_file_min(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "extract", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x1000.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x1000.data.csv").exists()
-
-
-def test_cli_extract_dir_full(data_h5: Path) -> None:
-    print(data_h5.parent)
-    print(data_h5.parent.is_dir())
-    res = CliRunner().invoke(
-        cli,
-        [
-            "--verbose",
-            "extract",
-            "--ds-factor",
-            "2000",
-            "--separator",
-            ";",
-            str(data_h5.parent),
-        ],
-    )
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".downsampled_x2000.h5").exists()
-    assert data_h5.with_suffix(".downsampled_x2000.data.csv").exists()
-
-
-def test_cli_extract_meta_file_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["--verbose", "extract-meta", "--separator", ";", str(data_h5)])
-    assert res.exit_code == 0
-    # TODO: nothing to grab here, add in base-file, same for tests below
-
-
-def test_cli_extract_meta_file_short(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "extract-meta", "-s", "-", str(data_h5)])
-    assert res.exit_code == 0
-
-
-def test_cli_extract_meta_file_min(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "extract-meta", "-s", "-", str(data_h5)])
-    assert res.exit_code == 0
-
-
-def test_cli_extract_meta_dir_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(
-        cli, ["--verbose", "extract-meta", "--separator", ";", str(data_h5.parent)]
-    )
-    assert res.exit_code == 0

tests/test_cli_plot.py

@@ -1,120 +0,0 @@
-from pathlib import Path
-
-from click.testing import CliRunner
-
-from shepherd_data.cli import cli
-
-from .conftest import generate_h5_file
-
-
-def test_cli_plot_file_full(data_h5: Path) -> None:
-    res = CliRunner().invoke(
-        cli,
-        [
-            "--verbose",
-            "plot",
-            "--start",
-            "0",
-            "--end",
-            "8",
-            "--width",
-            "50",
-            "--height",
-            "10",
-            str(data_h5),
-        ],
-    )
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".plot_0s000_to_8s000.png").exists()
-
-
-def test_cli_plot_file_short(data_h5: Path) -> None:
-    res = CliRunner().invoke(
-        cli,
-        [
-            "-v",
-            "plot",
-            "-s",
-            "2.345",
-            "-e",
-            "8.765",
-            "-w",
-            "30",
-            "-h",
-            "20",
-            str(data_h5),
-        ],
-    )
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".plot_2s345_to_8s765.png").exists()
-
-
-def test_cli_plot_file_min(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "plot", str(data_h5)])
-    assert res.exit_code == 0
-    assert data_h5.with_suffix(".plot_0s000_to_10s000.png").exists()  # full duration of file
-
-
-def test_cli_plot_dir_min(tmp_path: Path) -> None:
-    file1_path = generate_h5_file(tmp_path, "hrv_file1.h5")
-    file2_path = generate_h5_file(tmp_path, "hrv_file2.h5")
-    res = CliRunner().invoke(cli, ["-v", "plot", str(tmp_path.resolve())])
-    assert res.exit_code == 0
-    assert file1_path.with_suffix(".plot_0s000_to_10s000.png").exists()  # full duration of file
-    assert file2_path.with_suffix(".plot_0s000_to_10s000.png").exists()  # full duration of file
-
-
-def test_cli_multiplot_dir_full(tmp_path: Path) -> None:
-    generate_h5_file(tmp_path, "hrv_file1.h5")
-    generate_h5_file(tmp_path, "hrv_file2.h5")
-    res = CliRunner().invoke(
-        cli,
-        [
-            "--verbose",
-            "plot",
-            "--start",
-            "1",
-            "--end",
-            "7",
-            "--width",
-            "40",
-            "--height",
-            "10",
-            "--multiplot",
-            str(tmp_path),
-        ],
-    )
-    assert res.exit_code == 0
-    assert tmp_path.with_suffix(".multiplot_1s000_to_7s000.png").exists()
-
-
-def test_cli_multiplot_dir_short(tmp_path: Path) -> None:
-    generate_h5_file(tmp_path, "hrv_file1.h5")
-    generate_h5_file(tmp_path, "hrv_file2.h5")
-    res = CliRunner().invoke(
-        cli,
-        [
-            "-v",
-            "plot",
-            "-s",
-            "2.345",
-            "-e",
-            "8.765",
-            "-w",
-            "30",
-            "-h",
-            "20",
-            "-m",
-            str(tmp_path),
-        ],
-    )
-    assert res.exit_code == 0
-    assert tmp_path.with_suffix(".multiplot_2s345_to_8s765.png").exists()
-
-
-def test_cli_multiplot_dir_min(tmp_path: Path) -> None:
-    generate_h5_file(tmp_path, "hrv_file1.h5")
-    generate_h5_file(tmp_path, "hrv_file2.h5")
-    res = CliRunner().invoke(cli, ["-v", "plot", "-m", str(tmp_path)])
-    assert res.exit_code == 0
-    assert tmp_path.with_suffix(".multiplot_0s000_to_10s000.png").exists()  # full duration of file

tests/test_cli_validate.py

@@ -1,15 +0,0 @@
-from pathlib import Path
-
-from click.testing import CliRunner
-
-from shepherd_data.cli import cli
-
-
-def test_cli_validate_file(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "validate", str(data_h5)])
-    assert res.exit_code == 0
-
-
-def test_cli_validate_dir(data_h5: Path) -> None:
-    res = CliRunner().invoke(cli, ["-v", "validate", str(data_h5.parent)])
-    assert res.exit_code == 0

tests/test_examples.py

@@ -1,26 +0,0 @@
-import os
-import subprocess
-from pathlib import Path
-
-import pytest
-
-
-@pytest.fixture
-def example_path() -> Path:
-    path = Path(__file__).resolve().parent.parent / "examples"
-    os.chdir(path)
-    return path
-
-
-examples = [
-    "example_convert_ivonne.py",
-    "example_extract_logs.py",
-    "example_generate_sawtooth.py",
-    "example_plot_traces.py",
-    "example_repair_recordings.py",
-]
-
-
-@pytest.mark.parametrize("file", examples)
-def test_example_scripts(example_path: Path, file: str) -> None:
-    subprocess.check_call(f"python {example_path / file}", shell=True)