[MAINT] nilearn.interface: make private functions used outside of their module public

doc/changes/latest.rst

@@ -46,4 +46,5 @@ Changes
 - :bdg-dark:`Code` Private utility context manager ``write_tmp_imgs`` is refactored into function ``write_imgs_to_path`` (:gh:`4094` by `Yasmin Mzayek`_).
 - :bdg-danger:`Deprecation` :func:`~plotting.plot_surf_roi` will raise a warning if ``roi_map`` contains negative or non-integer values; in version 0.13 this will be a ``ValueError`` (:gh:`4131` by `Michelle Wang`_).
 - :bdg-dark:`Code` Remove leading underscore from non private functions to align with PEP8 (:gh:`4086` by `Rémi Gau`_).
-- :bdg-dark:`Code` Make ``decoding/proximal_operator`` explicitly private to align with PEP8 (:gh:`4153` by `Rémi Gau`_).
+- :bdg-dark:`Code` Make ``decoding/proximal_operator`` explicitly private to align with PEP8 (:gh:`4153` by `Rémi Gau`_).
+- :bdg-dark:`Code` Make private functions public when used outside of their module ``nilearn.interface`` to align with PEP8 (:gh:`4168` by `Rémi Gau`_).

nilearn/_utils/data_gen.py

@@ -15,8 +15,13 @@
 
 from nilearn import datasets, image, maskers, masking
 from nilearn._utils import as_ndarray, logger
-from nilearn._utils.bids import create_bids_filename
-from nilearn.interfaces.bids._utils import _bids_entities, _check_bids_label
+from nilearn.interfaces.bids.utils import (
+    bids_entities,
+    check_bids_label,
+    create_bids_filename,
+)
+
+# TODO get legal_confounds out of private testing module
 from nilearn.interfaces.fmriprep.tests._testing import get_legal_confound
 
 
@@ -926,7 +931,7 @@ def create_fake_bids_dataset(
     bids_path = Path(base_dir) / bids_dataset_dir
 
     for task_ in tasks:
-        _check_bids_label(task_)
+        check_bids_label(task_)
 
     if not isinstance(n_runs, list) or not all(
         isinstance(x, int) for x in n_runs
@@ -991,15 +996,15 @@ def _check_entities_and_labels(entities):
         raise ValueError("Only a single extra entity is supported for now.")
 
     for key in entities:
-        if key not in [*_bids_entities()["raw"],
-                       *_bids_entities()["derivatives"]]:
-            allowed_entities = [*_bids_entities()['raw'],
-                                *_bids_entities()['derivatives']]
+        if key not in [*bids_entities()["raw"],
+                       *bids_entities()["derivatives"]]:
+            allowed_entities = [*bids_entities()['raw'],
+                                *bids_entities()['derivatives']]
             raise ValueError(
                 f"Invalid entity: {key}. Allowed entities are: "
                 f"{allowed_entities}"
             )
-        [_check_bids_label(label_) for label_ in entities[key]]
+        [check_bids_label(label_) for label_ in entities[key]]
 
 
 def _mock_bids_dataset(
@@ -1073,7 +1078,7 @@ def _mock_bids_dataset(
                                 task=task,
                                 run=run,
                             )
-                            if key in _bids_entities()["raw"]:
+                            if key in bids_entities()["raw"]:
                                 fields["entities"][key] = label
                             _write_bids_raw_func(
                                 func_path=func_path,
@@ -1362,7 +1367,7 @@ def _write_bids_derivative_func(
         fields["suffix"] = confounds_tag
         fields["extension"] = "tsv"
         confounds_path = func_path / create_bids_filename(
-            fields=fields, entities_to_include=_bids_entities()["raw"]
+            fields=fields, entities_to_include=bids_entities()["raw"]
         )
         confounds, metadata = get_legal_confound()
         confounds.to_csv(
@@ -1377,8 +1382,8 @@ def _write_bids_derivative_func(
     shape = [n_voxels, n_voxels, n_voxels, n_time_points]
 
     entities_to_include = [
-        *_bids_entities()["raw"],
-        *_bids_entities()["derivatives"]
+        *bids_entities()["raw"],
+        *bids_entities()["derivatives"]
     ]
 
     for space in ("MNI", "T1w"):

nilearn/_utils/tests/test_common.py

@@ -34,7 +34,7 @@ def test_number_public_functions():
     If this is intentional, then the number should be updated in the test.
     Otherwise it means that the public API of nilearn has changed by mistake.
     """
-    assert len({_[0] for _ in all_functions()}) == 211
+    assert len({_[0] for _ in all_functions()}) == 228
 
 
 def test_number_public_classes():

nilearn/glm/first_level/first_level.py

@@ -43,11 +43,11 @@
 )
 from nilearn.image import get_data
 from nilearn.interfaces.bids import get_bids_files, parse_bids_filename
-from nilearn.interfaces.bids._utils import _bids_entities, _check_bids_label
 from nilearn.interfaces.bids.query import (
-    _infer_repetition_time_from_dataset,
-    _infer_slice_timing_start_time_from_dataset,
+    infer_repetition_time_from_dataset,
+    infer_slice_timing_start_time_from_dataset,
 )
+from nilearn.interfaces.bids.utils import bids_entities, check_bids_label
 from nilearn.interfaces.fmriprep.load_confounds import load_confounds
 
 
@@ -1165,23 +1165,23 @@ def first_level_from_bids(
         task_label=task_label,
         space_label=space_label,
         supported_filters=[
-            *_bids_entities()["raw"],
-            *_bids_entities()["derivatives"],
+            *bids_entities()["raw"],
+            *bids_entities()["derivatives"],
         ],
         extra_filter=img_filters,
         verbose=verbose,
     )
-    inferred_t_r = _infer_repetition_time_from_dataset(
+    inferred_t_r = infer_repetition_time_from_dataset(
         bids_path=derivatives_path, filters=filters, verbose=verbose
     )
     if inferred_t_r is None:
         filters = _make_bids_files_filter(
             task_label=task_label,
-            supported_filters=[*_bids_entities()["raw"]],
+            supported_filters=[*bids_entities()["raw"]],
             extra_filter=img_filters,
             verbose=verbose,
         )
-        inferred_t_r = _infer_repetition_time_from_dataset(
+        inferred_t_r = infer_repetition_time_from_dataset(
             bids_path=dataset_path, filters=filters, verbose=verbose
         )
 
@@ -1211,13 +1211,13 @@ def first_level_from_bids(
         task_label=task_label,
         space_label=space_label,
         supported_filters=[
-            *_bids_entities()["raw"],
-            *_bids_entities()["derivatives"],
+            *bids_entities()["raw"],
+            *bids_entities()["derivatives"],
         ],
         extra_filter=img_filters,
         verbose=verbose,
     )
-    StartTime = _infer_slice_timing_start_time_from_dataset(
+    StartTime = infer_slice_timing_start_time_from_dataset(
         bids_path=derivatives_path, filters=filters, verbose=verbose
     )
     if StartTime is not None and t_r is not None:
@@ -1426,8 +1426,8 @@ def _get_processed_imgs(
     filters = _make_bids_files_filter(
         task_label=task_label,
         space_label=space_label,
-        supported_filters=_bids_entities()["raw"]
-        + _bids_entities()["derivatives"],
+        supported_filters=bids_entities()["raw"]
+        + bids_entities()["derivatives"],
         extra_filter=img_filters,
         verbose=verbose,
     )
@@ -1491,7 +1491,7 @@ def _get_events_files(
     """
     events_filters = _make_bids_files_filter(
         task_label=task_label,
-        supported_filters=_bids_entities()["raw"],
+        supported_filters=bids_entities()["raw"],
         extra_filter=img_filters,
         verbose=verbose,
     )
@@ -1564,7 +1564,7 @@ def _get_confounds(
     """
     filters = _make_bids_files_filter(
         task_label=task_label,
-        supported_filters=_bids_entities()["raw"],
+        supported_filters=bids_entities()["raw"],
         extra_filter=img_filters,
         verbose=verbose,
     )
@@ -1684,26 +1684,26 @@ def _check_args_first_level_from_bids(
             f"{derivatives_folder}"
         )
 
-    _check_bids_label(task_label)
+    check_bids_label(task_label)
 
     if space_label is not None:
-        _check_bids_label(space_label)
+        check_bids_label(space_label)
 
     if not isinstance(sub_labels, list):
         raise TypeError(
             f"sub_labels must be a list, instead {type(sub_labels)} was given"
         )
     for sub_label_ in sub_labels:
-        _check_bids_label(sub_label_)
+        check_bids_label(sub_label_)
 
     if not isinstance(img_filters, list):
         raise TypeError(
             f"'img_filters' must be a list. "
             f"Got {type(img_filters)} instead."
         )
     supported_filters = [
-        *_bids_entities()["raw"],
-        *_bids_entities()["derivatives"],
+        *bids_entities()["raw"],
+        *bids_entities()["derivatives"],
     ]
     for filter_ in img_filters:
         if len(filter_) != 2 or not all(isinstance(x, str) for x in filter_):
@@ -1716,7 +1716,7 @@ def _check_args_first_level_from_bids(
                 f"Entity {filter_[0]} for {filter_} is not a possible filter. "
                 f"Only {supported_filters} are allowed."
             )
-        _check_bids_label(filter_[1])
+        check_bids_label(filter_[1])
 
 
 def _check_kwargs_load_confounds(**kwargs):
@@ -1932,7 +1932,7 @@ def _check_bids_events_list(
         "sub",
         "ses",
         "task",
-        *_bids_entities()["raw"],
+        *bids_entities()["raw"],
     ]
     for this_img in imgs:
         parsed_filename = parse_bids_filename(this_img)