Skip the copilot tests.

cubids/tests/test_cli.py

@@ -19,7 +19,7 @@
 from cubids.cli import _path_exists, _is_file, _get_parser, _main
 
 
-def test_path_exists():
+def _test_path_exists():
     """Test whether a given path exists or not.
 
     This function tests the `_path_exists` function by providing a path that exists
@@ -33,7 +33,7 @@ def test_path_exists():
         _path_exists("/path/to/nonexistent/file", None)
 
 
-def test_is_file():
+def _test_is_file():
     """Test whether a given path is a file or a directory.
 
     This function tests the `_is_file` function by providing a path that is a file
@@ -47,7 +47,7 @@ def test_is_file():
         _is_file("/path/to/directory", None)
 
 
-def test_get_parser():
+def _test_get_parser():
     """Test the creation and configuration of the argument parser.
 
     This function tests the `_get_parser` function by asserting that the returned object is an
@@ -62,7 +62,7 @@ def test_get_parser():
     # Add more assertions for the parser configuration
 
 
-def test_main():
+def _test_main():
     """Test the main function of the CLI.
 
     This function tests the `_main` function by providing different sets of arguments.

cubids/tests/test_cubids.py

@@ -0,0 +1,258 @@
+"""This file contains unit tests for the CuBIDS class in the CuBIDS package."""
+
+import pandas as pd
+import pytest
+
+from cubids.cubids import CuBIDS
+
+
+@pytest.fixture
+def cubids_instance():
+    data_root = "/path/to/bids/dataset"
+    return CuBIDS(data_root)
+
+
+def _test_init_cubids(cubids_instance):
+    assert cubids_instance.path == "/path/to/bids/dataset"
+    assert cubids_instance.use_datalad is False
+    assert cubids_instance.acq_group_level == "subject"
+    assert cubids_instance.grouping_config is None
+    assert cubids_instance.force_unlock is False
+
+
+def _test_reset_bids_layout(cubids_instance):
+    cubids_instance.reset_bids_layout()
+    assert cubids_instance.layout is not None
+
+
+def _test_create_cubids_code_dir(cubids_instance):
+    cubids_instance.create_cubids_code_dir()
+    assert cubids_instance.cubids_code_dir is True
+
+
+def _test_init_datalad(cubids_instance):
+    cubids_instance.init_datalad()
+    assert cubids_instance.datalad_ready is True
+    assert cubids_instance.datalad_handle is not None
+
+
+def _test_add_nifti_info(cubids_instance):
+    cubids_instance.add_nifti_info()
+    # Add assertions here
+
+
+def _test_datalad_save(cubids_instance):
+    cubids_instance.datalad_save()
+    # Add assertions here
+
+
+def _test_is_datalad_clean(cubids_instance):
+    assert cubids_instance.is_datalad_clean() is True
+
+
+def _test_datalad_undo_last_commit(cubids_instance):
+    cubids_instance.datalad_undo_last_commit()
+    # Add assertions here
+
+
+def _test_apply_tsv_changes(cubids_instance):
+    summary_tsv = "/path/to/summary.tsv"
+    files_tsv = "/path/to/files.tsv"
+    new_prefix = "new_prefix"
+    cubids_instance.apply_tsv_changes(summary_tsv, files_tsv, new_prefix)
+    # Add assertions here
+
+
+def _test_change_filename(cubids_instance):
+    filepath = "/path/to/file.nii.gz"
+    entities = {"subject": "sub-01", "session": "ses-01"}
+    cubids_instance.change_filename(filepath, entities)
+    # Add assertions here
+
+
+def _test_copy_exemplars(cubids_instance):
+    exemplars_dir = "/path/to/exemplars"
+    exemplars_tsv = "/path/to/exemplars.tsv"
+    min_group_size = 2
+    cubids_instance.copy_exemplars(exemplars_dir, exemplars_tsv, min_group_size)
+    # Add assertions here
+
+
+def _test_purge(cubids_instance):
+    scans_txt = "/path/to/scans.txt"
+    cubids_instance.purge(scans_txt)
+    # Add assertions here
+
+
+def _test__purge_associations(cubids_instance):
+    scans = ["scan-01", "scan-02"]
+    cubids_instance._purge_associations(scans)
+    # Add assertions here
+
+
+def _test_get_nifti_associations(cubids_instance):
+    nifti = "/path/to/file.nii.gz"
+    associations = cubids_instance.get_nifti_associations(nifti)
+    # Add assertions here
+
+
+def _test__cache_fieldmaps(cubids_instance):
+    cubids_instance._cache_fieldmaps()
+    # Add assertions here
+
+
+def _test_get_param_groups_from_key_group(cubids_instance):
+    key_group = "group-01"
+    param_groups = cubids_instance.get_param_groups_from_key_group(key_group)
+    # Add assertions here
+
+
+def _test_create_data_dictionary(cubids_instance):
+    cubids_instance.create_data_dictionary()
+    # Add assertions here
+
+
+def _test_get_data_dictionary(cubids_instance):
+    df = pd.DataFrame({"subject": ["sub-01", "sub-02"], "age": [25, 30]})
+    data_dict = cubids_instance.get_data_dictionary(df)
+    # Add assertions here
+
+
+def _test_get_param_groups_dataframes(cubids_instance):
+    param_groups_dataframes = cubids_instance.get_param_groups_dataframes()
+    # Add assertions here
+
+
+def _test_get_tsvs(cubids_instance):
+    path_prefix = "/path/to/tsvs"
+    tsvs = cubids_instance.get_tsvs(path_prefix)
+    # Add assertions here
+
+
+def _test_get_key_groups(cubids_instance):
+    key_groups = cubids_instance.get_key_groups()
+    # Add assertions here
+
+
+def _test_change_metadata(cubids_instance):
+    filters = {"subject": "sub-01"}
+    metadata = {"age": 25}
+    cubids_instance.change_metadata(filters, metadata)
+    # Add assertions here
+
+
+def _test_get_all_metadata_fields(cubids_instance):
+    metadata_fields = cubids_instance.get_all_metadata_fields()
+    # Add assertions here
+
+
+def _test_remove_metadata_fields(cubids_instance):
+    fields_to_remove = ["age", "sex"]
+    cubids_instance.remove_metadata_fields(fields_to_remove)
+    # Add assertions here
+
+
+def _test_get_filenames(cubids_instance):
+    filenames = cubids_instance.get_filenames()
+    # Add assertions here
+
+
+def _test_get_fieldmap_lookup(cubids_instance):
+    fieldmap_lookup = cubids_instance.get_fieldmap_lookup()
+    # Add assertions here
+
+
+def _test_get_layout(cubids_instance):
+    layout = cubids_instance.get_layout()
+    # Add assertions here
+
+
+def _test__validate_json(cubids_instance):
+    cubids_instance._validate_json()
+    # Add assertions here
+
+
+def _test__update_json(cubids_instance):
+    json_file = "/path/to/file.json"
+    metadata = {"age": 25}
+    cubids_instance._update_json(json_file, metadata)
+    # Add assertions here
+
+
+def _test__key_group_to_entities(cubids_instance):
+    key_group = "group-01"
+    entities = cubids_instance._key_group_to_entities(key_group)
+    # Add assertions here
+
+
+def _test__entities_to_key_group(cubids_instance):
+    entities = {"subject": "sub-01", "session": "ses-01"}
+    key_group = cubids_instance._entities_to_key_group(entities)
+    # Add assertions here
+
+
+def _test__file_to_key_group(cubids_instance):
+    filename = "sub-01_ses-01_task-rest_bold.nii.gz"
+    key_group = cubids_instance._file_to_key_group(filename)
+    # Add assertions here
+
+
+def _test__get_intended_for_reference(cubids_instance):
+    scan = "sub-01_ses-01_task-rest_bold.nii.gz"
+    reference = cubids_instance._get_intended_for_reference(scan)
+    # Add assertions here
+
+
+def _test__get_param_groups(cubids_instance):
+    files = ["sub-01_ses-01_task-rest_bold.nii.gz", "sub-02_ses-01_task-rest_bold.nii.gz"]
+    fieldmap_lookup = {"sub-01_ses-01_task-rest_bold.nii.gz": "fieldmap.nii.gz"}
+    key_group_name = "group-01"
+    grouping_config = {"group-01": {"modality": "bold"}}
+    modality = "bold"
+    keys_files = {"group-01": ["sub-01_ses-01_task-rest_bold.nii.gz"]}
+    param_groups = cubids_instance._get_param_groups(
+        files, fieldmap_lookup, key_group_name, grouping_config, modality, keys_files
+    )
+    # Add assertions here
+
+
+def _test_round_params(cubids_instance):
+    param_group_df = pd.DataFrame({"param": [0.123456789]})
+    config = {"param": {"round": 3}}
+    modality = "bold"
+    rounded_params = cubids_instance.round_params(param_group_df, config, modality)
+    # Add assertions here
+
+
+def _test_get_sidecar_metadata(cubids_instance):
+    json_file = "/path/to/file.json"
+    metadata = cubids_instance.get_sidecar_metadata(json_file)
+    # Add assertions here
+
+
+def _test_format_params(cubids_instance):
+    param_group_df = pd.DataFrame({"param": [0.123456789]})
+    config = {"param": {"format": "{:.2f}"}}
+    modality = "bold"
+    formatted_params = cubids_instance.format_params(param_group_df, config, modality)
+    # Add assertions here
+
+
+def _test__order_columns(cubids_instance):
+    df = pd.DataFrame({"b": [2], "a": [1]})
+    ordered_df = cubids_instance._order_columns(df)
+    # Add assertions here
+
+
+def _test_img_to_new_ext(cubids_instance):
+    img_path = "/path/to/image.nii.gz"
+    new_ext = ".nii"
+    new_img_path = cubids_instance.img_to_new_ext(img_path, new_ext)
+    # Add assertions here
+
+
+def _test_get_key_name(cubids_instance):
+    path = "/path/to/file.nii.gz"
+    key = "subject"
+    key_name = cubids_instance.get_key_name(path, key)
+    # Add assertions here