autogaita 1.5.2__py3-none-any.whl → 1.5.4__py3-none-any.whl

tests/test_group_unit.py

@@ -1,393 +0,0 @@
-from autogaita.group.group_main import (
-    group,
-    import_data,
-    avg_and_std,
-    PCA_main,
-    create_stats_df,
-    cluster_extent_test,
-    anova_design_sanity_check,
-    tukeys_only_info_message,
-    ANOVA_main,
-    plot_results,
-    print_finish,
-)
-from autogaita.group.group_1_preparation import some_prep
-from autogaita.group.group_2_data_processing import (
-    load_previous_runs_dataframes,
-    check_PCA_and_stats_variables,
-)
-from autogaita.group.group_3_PCA import run_PCA, convert_PCA_bins_to_list
-from autogaita.group.group_4_stats import run_ANOVA, multcompare_SC_Percentages
-from autogaita.resources.utils import bin_num_to_percentages
-import os
-import math
-import pytest
-from sklearn import datasets
-import pandas as pd
-import pandas.testing as pdt
-import numpy as np
-
-
-# %%................................  fixtures  ........................................
-@pytest.fixture
-def extract_folderinfo(tmp_path):
-    return {
-        "group_names": ["group1", "group2"],
-        "group_dirs": ["/path/to/group1", "/path/to/group2"],
-        "results_dir": tmp_path,
-        "load_dir": "",
-    }
-
-
-@pytest.fixture
-def extract_cfg():
-    return {
-        "do_permtest": True,
-        "do_anova": True,
-        "permutation_number": 100,
-        "PCA_n_components": 3,
-        "PCA_custom_scatter_PCs": "",
-        "PCA_save_3D_video": False,  # True
-        "PCA_bins": "",
-        "stats_threshold": 0.05,
-        "plot_SE": False,
-        "color_palette": "viridis",
-        "dont_show_plots": True,
-        "legend_outside": True,
-        "which_leg": "left",
-        "anova_design": "Mixed ANOVA",
-        "PCA_variables": [],
-        "stats_variables": [],
-    }
-
-
-# %%..............................  1. preparation  ....................................
-def test_some_preps_cfg_files(extract_folderinfo, extract_cfg):
-    """Check for equivalence of the cfg file using load dir and the cfg dict generated by some_prep"""
-    # 1. Ensure that the cfg is equal to that used in group approval (with repo data)
-    extract_folderinfo["group_names"] = ["5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["group_dirs"] = [
-        "example data/5mm/Results/",
-        "example data/12mm/Results/",
-        "example data/25mm/Results/",
-    ]
-    extract_cfg["do_permtest"] = False
-    extract_cfg["anova_design"] = "RM ANOVA"
-    extract_cfg["PCA_variables"] = [
-        "Knee y",
-        "Ankle y",
-        "Hind paw tao y",
-        "Ankle Angle",
-        "Knee Angle",
-        "Hip Angle",
-    ]
-    extract_cfg["stats_variables"] = extract_cfg["PCA_variables"]
-    # 2. Run some_prep twice with and without load dir & test cfg match
-    extract_folderinfo, generated_cfg = some_prep(extract_folderinfo, extract_cfg)
-    extract_folderinfo["load_dir"] = "example data/group"
-    extract_folderinfo, loaded_cfg = some_prep(extract_folderinfo, extract_cfg)
-    # 3. Check that cfgs are result of different processes (being loaded or not) and
-    #    not exact copies (e.g. references to the same object) for some Python-reason
-    assert "loaded" in loaded_cfg.keys()
-    assert "loaded" not in generated_cfg.keys()
-    # 4. Check that the cfgs are equivalent
-    loaded_cfg.pop("loaded")  # except this key of course - get rid of it
-    generated_cfg == loaded_cfg
-    # 5. Finally change some cfg key and assert that it has not been overwritten by
-    # loading a previous run's cfg
-    # => might seem unnecessary but the way this was implemented initially did
-    #    overwrite cfgs due to how it was loading stuff
-    extract_cfg["do_permtest"] = True
-    extract_cfg["anova_design"] = "Mixed ANOVA"
-    extract_cfg["PCA_variables"] = ["Ankle Angle", "Knee Angle", "Hip Angle"]
-    extract_folderinfo, loaded_cfg_2 = some_prep(extract_folderinfo, extract_cfg)
-    differing_keys = ["do_permtest", "anova_design", "PCA_variables"]
-    for key in differing_keys:
-        assert loaded_cfg_2[key] != loaded_cfg[key]
-
-
-# %%............................  2. data processing  ..................................
-def test_check_PCA_and_stats_variables(extract_folderinfo, extract_cfg):
-    """Test this sanity check does not have the necessary columns"""
-    group_names = ["5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["group_names"] = group_names
-    extract_folderinfo["load_dir"] = "example data/group"
-    # changing PCA/stats vars like this already performs a first test because the load
-    # function only runs successfully, if the test_PCA_.. function does
-    # => i.e. the features are present in the all 3 kinds of dfs
-    extract_cfg["PCA_variables"] = ["Ankle Angle", "Knee Angle"]
-    extract_cfg["stats_variables"] = ["Ankle Angle", "Knee Angle"]
-    avg_dfs, _, _, extract_cfg = load_repos_group_data(extract_folderinfo, extract_cfg)
-    # test correct failure
-    # => code means: test that after removing the column our check correctly raises a
-    #    ValueError
-    avg_dfs[0].drop(columns=["Ankle Angle"], inplace=True)
-    with pytest.raises(ValueError):
-        check_PCA_and_stats_variables(
-            avg_dfs[0], "5 mm", "Average", extract_folderinfo, extract_cfg
-        )
-
-
-def test_smoke_load_dir(extract_folderinfo, extract_cfg):
-    """Test that load dir runs through without errors and produces Results"""
-    extract_folderinfo["group_names"] = ["5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["load_dir"] = "example data/group"
-    group(extract_folderinfo, extract_cfg)
-    # I checked and hardcoded the 39 here, shouldn't change.
-    # If it does I want to know and this should fail
-    assert len(os.listdir(extract_folderinfo["results_dir"])) == 39
-
-
-def test_load_previous_runs_dataframes(extract_folderinfo, extract_cfg):
-    """Testing if errors are raised correctly and if the loaded dfs are eqiuvalent to the ones import_data generates"""
-    # NOTE
-    # ----
-    # => last tests fail on git actions but not locally
-    # => quite sure it's because of how git actions' os lists the files when loading
-    # => we have a similar issue in test_group_approval see os.getenv("CI") there
-    # 1: fails as wanted if group name wrong (df not found in load dir)
-    extract_folderinfo["group_names"] = ["not 5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["load_dir"] = "example data/group"
-    with pytest.raises(FileNotFoundError):
-        avg_dfs, _, _, extract_cfg = load_repos_group_data(
-            extract_folderinfo, extract_cfg
-        )
-    # 2: avg_dfs equivalent to import_data's avg_dfs
-    extract_folderinfo["group_names"] = ["5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["group_dirs"] = [  # for "import_data" later
-        "example data/5mm/Results/",
-        "example data/12mm/Results/",
-        "example data/25mm/Results/",
-    ]
-    avg_dfs, _, _, extract_cfg = load_repos_group_data(extract_folderinfo, extract_cfg)
-    # some prep required for import data & avg_and_std
-    extract_cfg["sampling_rate"] = 100
-    extract_cfg["bin_num"] = 25
-    extract_cfg["save_to_xls"] = [True, True, True]
-    extract_cfg["tracking_software"] = "DLC"
-    extract_cfg["analyse_average_x"] = True
-    i_dfs, _, extract_cfg = import_data(extract_folderinfo, extract_cfg)
-    i_avg_dfs, _ = avg_and_std(i_dfs, extract_folderinfo, extract_cfg)
-    if not os.getenv("CI"):
-        for g in range(len(extract_folderinfo["group_names"])):
-            pdt.assert_frame_equal(
-                avg_dfs[g], i_avg_dfs[g], check_dtype=False, check_exact=False
-            )
-    # 3: check that it also works for Universal 3D
-    # => only do it locally, I don't want to upload the MoVi Data to git
-    if not os.getenv("CI"):
-        extract_folderinfo["group_names"] = ["crawling", "jogging"]
-        extract_folderinfo["group_dirs"] = [
-            "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/Final/crawling/Results/",
-            "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/Final/jogging/Results/",
-        ]
-        extract_folderinfo["load_dir"] = (
-            "/Users/mahan/sciebo/Research/AutoGaitA/Showcase 3/MOVI/Unit Test of load_prev_groupruns_dfs/"
-        )
-        avg_dfs, _, _, extract_cfg = load_repos_group_data(
-            extract_folderinfo, extract_cfg
-        )
-        extract_cfg["tracking_software"] = "Universal 3D"
-        extract_cfg["which_leg"] = "right"
-        extract_cfg["analyse_average_y"] = True
-        i_dfs, _, extract_cfg = import_data(extract_folderinfo, extract_cfg)
-        i_avg_dfs, _ = avg_and_std(i_dfs, extract_folderinfo, extract_cfg)
-        if not os.getenv("CI"):
-            for g in range(len(extract_folderinfo["group_names"])):
-                pdt.assert_frame_equal(
-                    avg_dfs[g], i_avg_dfs[g], check_dtype=False, check_exact=False
-                )
-
-
-# %%..............................  4. statistics  .....................................
-
-
-def test_load_dfs_stats_df_perm_test_smoke(extract_folderinfo, extract_cfg):
-    """Smoke test three functions:
-    1. load_previous_runs-dataframes
-    2. create_stats_df
-    3. cluster_extent_test
-    => Check if it all runs without errors on our repo's example data
-    """
-    # first, prepare approrpiately & overwrite the fixtures of this script as needed
-    # 1) for load_previous_runs_dataframes (called by load repos group data)
-    extract_folderinfo["group_names"] = ["5 mm", "12 mm", "25 mm"]
-    extract_folderinfo["load_dir"] = "example data/group"
-    avg_dfs, g_avg_dfs, g_std_dfs, extract_cfg = load_repos_group_data(
-        extract_folderinfo, extract_cfg
-    )
-    # 2) for stats_df & the permutation test functions
-    extract_cfg["sampling_rate"] = 100
-    extract_cfg["do_permtest"] = True
-    extract_cfg["dont_show_plots"] = True
-    extract_cfg["tracking_software"] = "DLC"
-    extract_cfg["group_color_dict"] = {"5 mm": "red", "12 mm": "blue", "25 mm": "green"}
-    extract_folderinfo["contrasts"] = ["5 mm & 12 mm", "5 mm & 25 mm", "12 mm & 25 mm"]
-    stats_df = create_stats_df(avg_dfs, extract_folderinfo, extract_cfg)
-    plot_panel_instance = None
-    cluster_extent_test(
-        stats_df,
-        g_avg_dfs,
-        g_std_dfs,
-        "Ankle Angle",
-        extract_folderinfo,
-        extract_cfg,
-        plot_panel_instance,
-    )
-
-
-def test_Mixed_ANOVA(extract_cfg):
-    # Adopted example data from https://real-statistics.com/
-    # See the Mixed ANOVA xlsx file for complete link
-    extract_cfg["do_anova"] = True
-    extract_cfg["anova_design"] = "Mixed ANOVA"
-    stats_df = pd.read_excel("tests/test_data/group_data/Mixed ANOVA Example Data.xlsx")
-    stats_var = "Value"
-    result = run_ANOVA(stats_df, stats_var, extract_cfg)
-    # no GG p vals here
-    assert math.isclose(result["p-unc"][0], stats_df["p(A)"][0], abs_tol=1e-05)
-    assert math.isclose(result["p-unc"][1], stats_df["p(B)"][0], abs_tol=1e-05)
-    assert math.isclose(result["p-unc"][2], stats_df["p(AxB)"][0], abs_tol=1e-05)
-
-
-def test_multcomp_df_with_scipy_example(extract_folderinfo, extract_cfg):
-    # Adopted example from https://docs.scipy.org/doc/scipy-1.15.0/reference/generated/
-    # scipy.stats.tukey_hsd.html
-    extract_folderinfo["group_names"] = ["group0", "group1", "group2"]
-    extract_folderinfo["contrasts"] = [
-        "group0 & group1",
-        "group0 & group2",
-        "group1 & group2",
-    ]
-    # fmt: off
-    scipy_example = [24.5, 23.5, 26.4, 27.1, 29.9, 28.4, 34.2, 29.5, 32.2, 30.1, 26.1, 28.3, 24.3, 26.2, 27.8]  # fmt: on
-    # prep data
-    data = []
-    bin_num = 25
-    for i in scipy_example:
-        data.append([i] * bin_num)
-    data = np.ravel(data)
-    # prep group_col
-    subject_num = 5
-    group_col = []
-    for group in extract_folderinfo["group_names"]:
-        for _ in range(subject_num):
-            group_col.append([group] * bin_num)
-    group_col = np.ravel(group_col)
-    # prep ID_col
-    total_subject_num = 15
-    IDs = np.arange(1, total_subject_num + 1)
-    ID_col = np.repeat(IDs, bin_num)
-    # prep SC percentage col
-    extract_cfg["bin_num"] = 25
-    SC_percentages = bin_num_to_percentages(extract_cfg["bin_num"])
-    SC_percentage_col = [SC_percentages] * total_subject_num
-    SC_percentage_col = np.ravel(SC_percentage_col)
-    # pytest.set_trace()
-    # manually create dummy stats df
-    stats_df = pd.DataFrame(data=data, columns=["Variable"])
-    stats_df["Group"] = group_col
-    stats_df["ID"] = ID_col
-    stats_df["SC Percentage"] = SC_percentage_col
-    # run the func and perform hard-coded check with vals of doc's example
-    # => multcomp_df's rows are all equal because our SC percentages were all equal here
-    # => correct results correspond to doc-example's rows 1, 4 and 2 first listing all
-    #    stats-values, then p then CI low & CI high since that corresponds to the order
-    #    of multcomp df's columns
-    # => i.e., col1= SC %, then 3 cols for each contrast's q, then p, then CI low, then
-    #    CI high in the order of groups0 & 1, 0 & 2, and 1 & 2
-    multcomp_df = multcompare_SC_Percentages(
-        stats_df, "Variable", extract_folderinfo, extract_cfg
-    )
-    # fmt: off
-    correct_results = [-4.6, -0.260, 4.34, 0.014, 0.980, 0.02, -8.249, -3.909, 0.691, -0.951, 3.389, 7.989]  
-    for r, result in enumerate(correct_results):
-        assert math.isclose(result, multcomp_df.iloc[0, r+1], abs_tol=0.001)
-
-
-# %%..................................  PCA  ...........................................
-def test_run_PCA(extract_folderinfo, extract_cfg):
-    # Replicate the example found in https://www.kdnuggets.com/2023/05/
-    # principal-component-analysis-pca-scikitlearn.html using our PCA df and PCA_info
-    # structure
-    # fmt: off
-    true_results_PCA_eigenvectors = [[0.1443294, -0.24518758, -0.00205106, -0.23932041,  0.14199204,  0.39466085, 0.4229343, -0.2985331, 0.31342949, -0.0886167,0.29671456,  0.37616741, 0.28675223],
-    [-0.48365155, -0.22493093, -0.31606881,  0.0105905,  -0.299634,   -0.06503951
-    , 0.00335981, -0.02877949, -0.03930172, -0.52999567,  0.27923515,  0.16449619,
-    -0.36490283],
-    [-0.20738262,  0.08901289,  0.6262239,   0.61208035,  0.13075693,  0.14617896,
-    0.1506819,   0.17036816,  0.14945431, -0.13730621,  0.08522192,  0.16600459,
-    -0.12674592]]
-    true_results_PCA_explained_var = [0.36198848, 0.1920749 , 0.11123631]
-    # fmt: on
-    wine_data = datasets.load_wine(as_frame=True)
-    wine_df = wine_data.data
-    features = wine_df.columns
-    PCA_df, PCA_info = run_PCA(wine_df, features, extract_folderinfo, extract_cfg)
-    for i in range(3):
-        # absolute values are compared because the signs can be different w. eigenvecs
-        assert np.allclose(
-            np.absolute(PCA_info["eigenvectors"][i]),
-            np.absolute(true_results_PCA_eigenvectors[i]),
-            atol=1e-05,
-        )
-    assert np.allclose(
-        PCA_info["explained_vars"], true_results_PCA_explained_var, atol=1e-05
-    )
-
-
-cases = (
-    (
-        "1-30,50,70-100",
-        100,
-        np.arange(1, 31).tolist() + [50] + np.arange(70, 101).tolist(),
-    ),
-    ("1-70", 25, [4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60, 64, 68]),
-    ("2, 10, 22, 44, 50, 79", 50, [2, 10, 22, 44, 50]),
-    ("1-50,70-80", 10, [10, 20, 30, 40, 50, 70, 80]),
-)  # fmt: skip
-@pytest.mark.parametrize("PCA_bins, bin_num, expected_bins_list", cases)
-def test_convert_PCA_bins_to_list(
-    PCA_bins, bin_num, expected_bins_list, extract_folderinfo, extract_cfg
-):
-    extract_cfg["PCA_bins"] = PCA_bins
-    extract_cfg["bin_num"] = bin_num
-    updated_cfg = convert_PCA_bins_to_list(extract_folderinfo, extract_cfg)
-    assert np.array_equal(updated_cfg["PCA_bins"], np.array(expected_bins_list))
-
-
-def load_repos_group_data(extract_folderinfo, extract_cfg):
-    """Use load_previous_runs_dataframes to load example data from the repo"""
-    extract_cfg["sampling_rate"] = 100
-    extract_cfg["group_color_dict"] = {"5 mm": "red", "12 mm": "blue", "25 mm": "green"}
-    extract_folderinfo["contrasts"] = ["5 mm & 12 mm", "5 mm & 25 mm", "12 mm & 25 mm"]
-    avg_dfs, g_avg_dfs, g_std_dfs, extract_cfg = load_previous_runs_dataframes(
-        extract_folderinfo, extract_cfg
-    )
-    return avg_dfs, g_avg_dfs, g_std_dfs, extract_cfg
-
-
-# NOTE !!!
-# => This test is outdated and wrong because it is for two within subject factors (for
-#    example 3 separate behavioural tests and pre/post medication treatment or so -
-#    done by each subject)
-# => I will not delete this since I might want to re-use it if I should support such
-#    designs
-#
-# def test_twoway_RM_ANOVA(extract_cfg):
-#     # Adopted example data from https://real-statistics.com/
-#     # See the RM ANOVA xlsx file for complete link
-#     extract_cfg["do_anova"] = True
-#     extract_cfg["anova_design"] = "RM ANOVA"
-#     stats_df = pd.read_excel("tests/test_data/group_data/RM ANOVA Example Data.xlsx")
-#     stats_var = "Value"
-#     result = run_ANOVA(stats_df, stats_var, extract_cfg)
-#     # Note that the last 2 assert statements have a different tolerance because those
-#     # p-values differed a bit. Not sure why but it's a tiny amount and tolerable IMO
-#     pytest.set_trace()
-#     assert math.isclose(result["p-unc"][0], stats_df["p(A)"][0], abs_tol=1e-05)
-#     assert math.isclose(result["p-unc"][1], stats_df["p(B)"][0], abs_tol=1e-05)
-#     assert math.isclose(result["p-unc"][2], stats_df["p(AxB)"][0], abs_tol=1e-05)
-#     assert math.isclose(result["p-GG-corr"][0], stats_df["GG-p(A)"][0], abs_tol=1e-05)
-#     assert math.isclose(result["p-GG-corr"][1], stats_df["GG-p(B)"][0], abs_tol=1e-04)
-#     assert math.isclose(result["p-GG-corr"][2], stats_df["GG-p(AxB)"][0], abs_tol=1e-02)

tests/test_universal3D_approval.py

@@ -1,89 +0,0 @@
-from autogaita.resources.utils import try_to_run_gaita
-import pandas as pd
-import pandas.testing as pdt
-import os
-import shutil
-import pdb
-import pytest
-
-
-# ............................  SIMI APPROVAL TESTS STRUCTURE  .........................
-# 1. Run autogaita.simi for Subject (with the cfg used there)
-# 2. Load the "Average Stepcycles".xlsx file from the repo and compare for
-#    equivalence to average_data
-# 3. Do the same for "Standard Devs. Stepcycle.xlsx" and std_data
-# 4. Pass the test if the two df-pairs are equal
-
-
-# ...............................  PREPARE - FOUR FIXTURES   ...........................
-
-
-@pytest.fixture
-def extract_true_dir():
-    return "tests/test_data/universal3D_data/true_data/"
-
-
-@pytest.fixture
-def extract_info(tmp_path):
-    info = {}
-    info["name"] = "TestSubject"
-    info["results_dir"] = os.path.join(tmp_path, info["name"])
-    return info
-
-
-@pytest.fixture
-def extract_folderinfo():
-    folderinfo = {}
-    folderinfo["root_dir"] = "tests/test_data/universal3D_data/test_data/"
-    folderinfo["sctable_filename"] = "SC Latency Table"
-    folderinfo["postname_string"] = ""
-    return folderinfo
-
-
-@pytest.fixture
-def extract_cfg():
-    cfg = {}
-    cfg["sampling_rate"] = 100
-    cfg["dont_show_plots"] = True
-    cfg["y_acceleration"] = True
-    cfg["angular_acceleration"] = True
-    cfg["bin_num"] = 25
-    cfg["plot_SE"] = True
-    cfg["standardise_z_at_SC_level"] = True
-    cfg["standardise_z_to_a_joint"] = False
-    cfg["z_standardisation_joint"] = ["Midfoot, left"]
-    cfg["plot_joint_number"] = 7
-    cfg["legend_outside"] = True
-    cfg["flip_gait_direction"] = True
-    cfg["color_palette"] = "viridis"
-    cfg["analyse_average_y"] = False
-    cfg["standardise_y_coordinates"] = True
-    cfg["y_standardisation_joint"] = ["Midfoot, left"]
-    cfg["coordinate_standardisation_xls"] = ""
-    cfg["joints"] = ["Midfoot", "Ankle", "Knee", "Hip", "Pelvis "]
-    cfg["angles"] = {
-        "name": ["Ankle", "Knee", "Hip"],
-        "lower_joint": ["Midfoot", "Ankle", "Knee"],
-        "upper_joint": ["Knee", "Hip", "Pelvis "],
-    }
-    return cfg
-
-
-# ...............................  RUN - ONE APPROVAL TEST  ............................
-
-
-@pytest.mark.slow  # https://docs.pytest.org/en/7.1.x/example/markers.html
-def test_universal3D_approval(
-    extract_true_dir, extract_info, extract_folderinfo, extract_cfg
-):
-    # run
-    try_to_run_gaita(
-        "Universal 3D", extract_info, extract_folderinfo, extract_cfg, False
-    )
-    for true_df_file in os.listdir(extract_true_dir):
-        if true_df_file.endswith(".xlsx"):
-            true_df = pd.read_excel(os.path.join(extract_true_dir, true_df_file))
-            test_df = pd.read_excel(
-                os.path.join(extract_info["results_dir"], true_df_file)
-            )
-            pdt.assert_frame_equal(test_df, true_df)

tests/test_universal3D_unit_1_preparation.py

@@ -1,69 +0,0 @@
-from autogaita.universal3D.universal3D_datafile_preparation import (
-    clean_a_file,
-    rename_a_column,
-)
-from hypothesis import given, strategies as st
-import pandas as pd
-
-
-# %%..............................  preparation  .......................................
-
-
-# property test for removing a string from column names via clean a file
-column_names = st.lists(st.text(min_size=1), min_size=1, max_size=10, unique=True)
-strings_to_remove = st.text(min_size=1)
-
-
-@given(df_columns=column_names, string_to_remove=strings_to_remove)
-def test_clean_a_file(df_columns, string_to_remove):
-    df = pd.DataFrame(columns=df_columns)
-    cleaned_df = clean_a_file(df, string_to_remove)
-    for col in df_columns:
-        if string_to_remove in col:
-            assert col.replace(string_to_remove, "") in cleaned_df.columns
-        else:
-            assert col in cleaned_df.columns
-
-
-# Property test for renaming a given column according to 3 possible cases
-candidate_side_ids = st.sampled_from(
-    ["l", "L", "left", "LEFT", "Left", "r", "R", "right", "RIGHT", "Right"]
-)
-candidate_coord_ids = st.sampled_from(["x", "y", "z", "X", "Y", "Z"])
-candidate_joint_ids = st.text(min_size=2)
-separators = st.sampled_from(["_", "-", ":", "."])
-
-
-@given(
-    candidate_side_id=candidate_side_ids,
-    candidate_coord_id=candidate_coord_ids,
-    candidate_joint_id=candidate_joint_ids,
-    separator=separators,
-)
-def test_rename_a_column(
-    candidate_side_id, candidate_coord_id, candidate_joint_id, separator
-):
-    # only run main test below if separator is not the joint id anywhere
-    # => we require separators to be unique in column strings
-    if separator in candidate_joint_id:
-        return
-    # preparation - what output we are expecting
-    expected_side = "left" if candidate_side_id.lower() in ["l", "left"] else "right"
-    expected_coord = candidate_coord_id.capitalize()
-    # test 1 - column is side-specific
-    col_string = separator.join(
-        [candidate_side_id, candidate_coord_id, candidate_joint_id]
-    )
-    result = rename_a_column(col_string, separator)
-    assert isinstance(result, str)
-    assert (
-        result == f"{candidate_joint_id}, {expected_side} {expected_coord.capitalize()}"
-    )
-    # test 2 - column is central
-    col_string = separator.join([candidate_coord_id, candidate_joint_id])
-    result = rename_a_column(col_string, separator)
-    assert result == f"{candidate_joint_id} {expected_coord.capitalize()}"
-    # test 3 - column is not a coordinate column
-    col_string = separator.join([candidate_joint_id])
-    result = rename_a_column(col_string, separator)
-    assert result == col_string

tests/test_universal3D_unit_2_sc_extraction.py

@@ -1,108 +0,0 @@
-from autogaita.universal3D.universal3D_1_preparation import some_prep
-from autogaita.universal3D.universal3D_2_sc_extraction import (
-    check_different_angle_joint_coords,
-)
-import os
-import numpy as np
-import pytest
-
-
-# %%................................  fixtures  ........................................
-@pytest.fixture
-def extract_info(tmp_path):
-    info = {}
-    info["name"] = "TestSubject"
-    info["results_dir"] = os.path.join(tmp_path, info["name"])
-    return info
-
-
-@pytest.fixture
-def extract_folderinfo():
-    folderinfo = {}
-    folderinfo["root_dir"] = "tests/test_data/universal3D_data/test_data"
-    folderinfo["sctable_filename"] = "SC Latency Table.xlsx"
-    folderinfo["postname_string"] = ""
-    return folderinfo
-
-
-@pytest.fixture
-def extract_cfg():
-    # note space in end of "Midfoot, left " must be here bc. we don't run our fix and
-    # check cfg function of 1_prep_
-    cfg = {}
-    cfg["sampling_rate"] = 100  # base cfg
-    cfg["dont_show_plots"] = True
-    cfg["y_acceleration"] = True
-    cfg["angular_acceleration"] = True
-    cfg["bin_num"] = 25
-    cfg["plot_SE"] = True
-    cfg["standardise_z_at_SC_level"] = True
-    cfg["standardise_z_to_a_joint"] = True
-    cfg["z_standardisation_joint"] = ["Midfoot, left "]
-    cfg["plot_joint_number"] = 5
-    cfg["color_palette"] = "Set2"
-    cfg["legend_outside"] = True
-    cfg["flip_gait_direction"] = True
-    cfg["analyse_average_y"] = True
-    cfg["standardise_y_coordinates"] = True
-    cfg["y_standardisation_joint"] = ["Midfoot, left "]
-    cfg["coordinate_standardisation_xls"] = ""
-    cfg["joints"] = [
-        "Midfoot",
-        "Ankle",
-        "Knee",
-        "Hip",
-    ]
-    cfg["angles"] = {
-        "name": ["Ankle", "Knee"],
-        "lower_joint": ["Midfoot", "Ankle"],
-        "upper_joint": ["Knee", "Hip"],
-    }
-    cfg["direction_joint"] = "Midfoot, left Y"
-    return cfg
-
-
-# ..................................  tests  .........................................
-
-
-def test_clean_cycles_different_angle_joint_coords(
-    extract_info, extract_folderinfo, extract_cfg
-):
-    # start conditions
-    data, _ = some_prep(extract_info, extract_folderinfo, extract_cfg)
-    all_cycles = [[[111, 222], [333, 444]], [[555, 666], [777, 888]]]
-    # test one: leads to both lists still being non-empty, one SC removed
-    data.loc[123, "Ankle, left Y"] = 5.5
-    data.loc[123, "Ankle, left Z"] = 2.1
-    data.loc[123, "Midfoot, left Y"] = 5.5
-    data.loc[123, "Midfoot, left Z"] = 2.1
-    all_cycles = check_different_angle_joint_coords(
-        all_cycles, data, extract_info, extract_cfg
-    )
-    assert all_cycles == [[[333, 444]], [[555, 666], [777, 888]]]
-    with open(os.path.join(extract_info["results_dir"], "Issues.txt")) as f:
-        content = f.read()
-    assert "Run #1 - SC #1" in content
-    assert "equal LEFT" in content
-    assert "Lower joint: Midfoot" in content
-    # test two: leads to one empty list
-    data.loc[345, "Hip, right Y"] = 10.1
-    data.loc[345, "Hip, right Z"] = 0.333
-    data.loc[345, "Ankle, right Y"] = 10.1
-    data.loc[345, "Ankle, right Z"] = 0.333
-    all_cycles = check_different_angle_joint_coords(
-        all_cycles, data, extract_info, extract_cfg
-    )
-    assert all_cycles == [[], [[555, 666], [777, 888]]]
-    with open(os.path.join(extract_info["results_dir"], "Issues.txt")) as f:
-        content = f.read()
-    assert "RIGHT" in content
-    # test three: leads to all_cycles being None
-    data.loc[[567, 789], "Hip, right Y"] = 22.2
-    data.loc[[567, 789], "Hip, right Z"] = 0.11
-    data.loc[[567, 789], "Knee, right Y"] = 22.2
-    data.loc[[567, 789], "Knee, right Z"] = 0.11
-    assert (
-        check_different_angle_joint_coords(all_cycles, data, extract_info, extract_cfg)
-        is None
-    )