shepherd-data 2023.11.1__py3-none-any.whl → 2024.4.1__py3-none-any.whl

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

@@ -1,51 +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

@@ -1,84 +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

@@ -1,128 +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)

tests/test_ivonne.py

@@ -1,42 +0,0 @@
-from pathlib import Path
-
-import pytest
-
-from shepherd_data import Reader
-from shepherd_data import ivonne
-from shepherd_data import mppt
-
-
-@pytest.fixture
-def example_path() -> Path:
-    here = Path(__file__).resolve().parent
-    return here.parent / "examples"
-
-
-def test_convert_ivonne(tmp_path: Path, example_path: Path) -> None:
-    input_file = "jogging_10m"
-    inp_path = example_path / (input_file + ".iv")
-    isc_path = tmp_path / (input_file + "_isc.h5")
-    ivc_path = tmp_path / (input_file + "_ivc.h5")
-    voc_path = tmp_path / (input_file + "_voc.h5")
-    opt_path = tmp_path / (input_file + "_opt.h5")
-
-    with ivonne.Reader(inp_path) as ifr:
-        ifr.upsample_2_isc_voc(isc_path, duration_s=20)
-        ifr.convert_2_ivcurves(ivc_path, duration_s=20)
-
-        tr_voc = mppt.OpenCircuitTracker(ratio=0.76)
-        tr_opt = mppt.OptimalTracker()
-
-        ifr.convert_2_ivsamples(voc_path, tracker=tr_voc, duration_s=20)
-        ifr.convert_2_ivsamples(opt_path, tracker=tr_opt, duration_s=20)
-
-    energies = {}
-    for file_path in [isc_path, ivc_path, voc_path, opt_path]:
-        with Reader(file_path) as sfr:
-            assert sfr.runtime_s == 20
-            energies[file_path.stem[-3:]] = sfr.energy()
-
-    assert energies["isc"] > energies["opt"]
-    assert energies["opt"] > energies["voc"]
-    assert energies["voc"] > energies["ivc"]

tests/test_reader.py

@@ -1,3 +0,0 @@
-# TODO:
-#  - confirm energy stays same after resampling
-#  - length should also stay same