diff --git a/.gitignore b/.gitignore
index 95f82a10..336385a0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -136,4 +136,5 @@ data/*
 .DS_Store
 notebooks/testdata
 .vscode/settings.json
-notebooks/test1
\ No newline at end of file
+notebooks/test1
+docs/generated
\ No newline at end of file
diff --git a/cubids/cli.py b/cubids/cli.py
index a6bcce32..846b401f 100644
--- a/cubids/cli.py
+++ b/cubids/cli.py
@@ -118,6 +118,7 @@ def _parse_validate():
     parser = argparse.ArgumentParser(
         description="cubids validate: Wrapper around the official BIDS Validator",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -245,6 +246,7 @@ def _parse_bids_version():
     parser = argparse.ArgumentParser(
         description="cubids bids-version: Get BIDS Validator and Schema version",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -328,6 +330,7 @@ def _parse_bids_sidecar_merge():
     parser = argparse.ArgumentParser(
         description=("bids-sidecar-merge: merge critical keys from one sidecar to another"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     IsFile = partial(_is_file, parser=parser)
 
@@ -412,6 +415,7 @@ def _parse_group():
     parser = argparse.ArgumentParser(
         description="cubids group: find key and parameter groups in BIDS",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -534,6 +538,7 @@ def _parse_apply():
     parser = argparse.ArgumentParser(
         description=("cubids apply: apply the changes specified in a tsv to a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
@@ -549,7 +554,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "edited_summary_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _summary.tsv that has been edited "
@@ -561,7 +566,7 @@ def _parse_apply():
     )
     parser.add_argument(
         "files_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the _files.tsv that has been edited "
@@ -669,6 +674,7 @@ def _parse_datalad_save():
     parser = argparse.ArgumentParser(
         description=("cubids datalad-save: perform a DataLad save on a BIDS directory"),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -756,6 +762,7 @@ def _parse_undo():
     parser = argparse.ArgumentParser(
         description="cubids undo: revert most recent commit",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -852,9 +859,10 @@ def _parse_copy_exemplars():
             "one subject from each Acquisition Group in the BIDS dataset"
         ),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
-    IsFile = partial(_is_file, parser=parser)
+    # IsFile = partial(_is_file, parser=parser)
 
     parser.add_argument(
         "bids_dir",
@@ -868,7 +876,7 @@ def _parse_copy_exemplars():
     )
     parser.add_argument(
         "exemplars_dir",
-        type=PathExists,
+        type=Path,
         action="store",
         help=(
             "name of the directory to create where to store exemplar dataset. "
@@ -879,7 +887,7 @@ def _parse_copy_exemplars():
     )
     parser.add_argument(
         "exemplars_tsv",
-        type=IsFile,
+        type=Path,
         action="store",
         help=(
             "path to the .tsv that lists one "
@@ -987,6 +995,7 @@ def _parse_add_nifti_info():
             "files to the sidecars of each dataset"
         ),
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1081,6 +1090,7 @@ def _parse_purge():
     parser = argparse.ArgumentParser(
         description="cubids purge: purge associations from the dataset",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
@@ -1182,6 +1192,7 @@ def _parse_remove_metadata_fields():
     parser = argparse.ArgumentParser(
         description="cubids remove-metadata-fields: delete fields from metadata",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1274,6 +1285,7 @@ def _parse_print_metadata_fields():
     parser = argparse.ArgumentParser(
         description="cubids print-metadata-fields: print all unique metadata fields",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        allow_abbrev=False,
     )
     PathExists = partial(_path_exists, parser=parser)
 
@@ -1359,7 +1371,7 @@ def _get_parser():
     """
     from cubids import __version__
 
-    parser = argparse.ArgumentParser(prog="cubids")
+    parser = argparse.ArgumentParser(prog="cubids", allow_abbrev=False)
     parser.add_argument("-v", "--version", action="version", version=__version__)
     subparsers = parser.add_subparsers(help="CuBIDS commands")
 
@@ -1371,6 +1383,7 @@ def _get_parser():
             parents=[subparser],
             help=subparser.description,
             add_help=False,
+            allow_abbrev=False,
         )
 
     return parser
diff --git a/cubids/cubids.py b/cubids/cubids.py
index fde4012b..4ae210c4 100644
--- a/cubids/cubids.py
+++ b/cubids/cubids.py
@@ -87,6 +87,8 @@ class CuBIDS(object):
         A data dictionary for TSV outputs.
     use_datalad : :obj:`bool`
         If True, use datalad to track changes to the BIDS dataset.
+    is_longitudinal : :obj:`bool`
+        If True, adds "ses" in filepath.
     """
 
     def __init__(
@@ -115,12 +117,17 @@ def __init__(
         self.data_dict = {}  # data dictionary for TSV outputs
         self.use_datalad = use_datalad  # True if flag set, False if flag unset
         self.schema = load_schema(schema_json)
+        self.is_longitudinal = self._infer_longitudinal()  # inferred from dataset structure
 
         if self.use_datalad:
             self.init_datalad()
 
-        if self.acq_group_level == "session":
+        if self.is_longitudinal and self.acq_group_level == "session":
             NON_KEY_ENTITIES.remove("session")
+        elif not self.is_longitudinal and self.acq_group_level == "session":
+            raise ValueError(
+                'Data is not longitudinal, so "session" is not a valid grouping level.'
+            )
 
     @property
     def layout(self):
@@ -134,6 +141,10 @@ def layout(self):
             # print("LAYOUT OBJECT SET")
         return self._layout
 
+    def _infer_longitudinal(self):
+        """Infer if the dataset is longitudinal based on its structure."""
+        return any("ses-" in str(f) for f in Path(self.path).rglob("*"))
+
     def reset_bids_layout(self, validate=False):
         """Reset the BIDS layout.
 
@@ -480,6 +491,7 @@ def change_filename(self, filepath, entities):
             out_entities=entities,
             out_dir=str(self.path),
             schema=self.schema,
+            is_longitudinal=self.is_longitudinal,
         )
 
         exts = Path(filepath).suffixes
@@ -488,7 +500,8 @@ def change_filename(self, filepath, entities):
         suffix = entities["suffix"]
 
         sub = get_entity_value(filepath, "sub")
-        ses = get_entity_value(filepath, "ses")
+        if self.is_longitudinal:
+            ses = get_entity_value(filepath, "ses")
 
         # Add the scan path + new path to the lists of old, new filenames
         self.old_filenames.append(filepath)
@@ -584,7 +597,10 @@ def change_filename(self, filepath, entities):
                 self.new_filenames.append(new_labeling)
 
         # RENAME INTENDED FORS!
-        ses_path = self.path + "/" + sub + "/" + ses
+        if self.is_longitudinal:
+            ses_path = self.path + "/" + sub + "/" + ses
+        elif not self.is_longitudinal:
+            ses_path = self.path + "/" + sub
         files_with_if = []
         files_with_if += Path(ses_path).rglob("fmap/*.json")
         files_with_if += Path(ses_path).rglob("perf/*_m0scan.json")
@@ -607,6 +623,7 @@ def change_filename(self, filepath, entities):
                         data["IntendedFor"].remove(item)
                         # add new filename
                         data["IntendedFor"].append(_get_participant_relative_path(new_path))
+
                     if item == _get_bidsuri(filepath, self.path):
                         # remove old filename
                         data["IntendedFor"].remove(item)
@@ -1370,6 +1387,7 @@ def get_layout(self):
         return self.layout
 
 
+# XXX: Remove _validate_json?
 def _validate_json():
     """Validate a JSON file's contents.
 
@@ -1409,8 +1427,29 @@ def _get_participant_relative_path(scan):
 
     This is what will appear in the IntendedFor field of any association.
 
+    Examples:
+    >>> _get_participant_relative_path(
+    ...    "/path/to/dset/sub-01/ses-01/func/sub-01_ses-01_bold.nii.gz",
+    ... )
+    'ses-01/func/sub-01_ses-01_bold.nii.gz'
+
+    >>> _get_participant_relative_path(
+    ...    "/path/to/dset/sub-01/func/sub-01_bold.nii.gz",
+    ... )
+    'func/sub-01_bold.nii.gz'
+
+    >>> _get_participant_relative_path(
+    ...    "/path/to/dset/ses-01/func/ses-01_bold.nii.gz",
+    ... )
+    Traceback (most recent call last):
+    ValueError: Could not find subject in ...
     """
-    return "/".join(Path(scan).parts[-3:])
+    parts = Path(scan).parts
+    # Find the first part that starts with "sub-"
+    for i, part in enumerate(parts):
+        if part.startswith("sub-"):
+            return "/".join(parts[i + 1 :])
+    raise ValueError(f"Could not find subject in {scan}")
 
 
 def _get_bidsuri(filename, dataset_root):
@@ -1741,7 +1780,7 @@ def get_entity_value(path, key):
             return part
 
 
-def build_path(filepath, out_entities, out_dir, schema):
+def build_path(filepath, out_entities, out_dir, schema, is_longitudinal):
     """Build a new path for a file based on its BIDS entities.
 
     This function could ultimately be replaced with bids.BIDSLayout.build_path(),
@@ -1765,6 +1804,8 @@ def build_path(filepath, out_entities, out_dir, schema):
             (e.g., acquisition) to their corresponding keys (e.g., acq).
         -   schema["objects"]["datatypes"]: a dictionary defining the valid datatypes.
             This function only uses the keys of this dictionary.
+    is_longitudinal : bool
+        If True, add "ses" to file path.
 
     Returns
     -------
@@ -1783,6 +1824,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"acquisition": "VAR", "suffix": "T2w"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/anat/sub-01_ses-01_acq-VAR_T2w.nii.gz'
 
@@ -1793,6 +1835,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "run": "2", "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
 
@@ -1804,6 +1847,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "run": 2, "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-00002_bold.nii.gz'
 
@@ -1815,6 +1859,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "run": 2, "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
 
@@ -1825,6 +1870,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "run": "2", "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_run-2_bold.nii.gz'
 
@@ -1836,6 +1882,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_bold.nii.gz'
 
@@ -1846,6 +1893,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"subject": "02", "task": "rest", "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_bold.nii.gz'
 
@@ -1856,6 +1904,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"task": "rest", "acquisition": "VAR", "echo": 1, "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     '/output/sub-01/ses-01/func/sub-01_ses-01_task-rest_acq-VAR_echo-1_bold.nii.gz'
 
@@ -1866,6 +1915,7 @@ def build_path(filepath, out_entities, out_dir, schema):
     ...    {"datatype": "perf", "acquisition": "VAR", "suffix": "asl"},
     ...    "/output",
     ...    schema,
+    ...    True,
     ... )
     WARNING: DATATYPE CHANGE DETECTED
     '/output/sub-01/ses-01/perf/sub-01_ses-01_acq-VAR_asl.nii.gz'
@@ -1884,14 +1934,15 @@ def build_path(filepath, out_entities, out_dir, schema):
     It expects a longitudinal structure, so providing a cross-sectional filename won't work.
     XXX: This is a bug.
 
+    It also works for cross-sectional filename.
     >>> build_path(
     ...    "/input/sub-01/func/sub-01_task-rest_run-01_bold.nii.gz",
-    ...    {"task": "rest", "acquisition": "VAR", "echo": 1, "suffix": "bold"},
+    ...    {"task": "rest", "acquisition": "VAR", "suffix": "bold"},
     ...    "/output",
     ...    schema,
+    ...    False,
     ... )
-    Traceback (most recent call last):
-    ValueError: Could not extract subject or session from ...
+    '/output/sub-01/func/sub-01_task-rest_acq-VAR_bold.nii.gz'
     """
     exts = Path(filepath).suffixes
     old_ext = "".join(exts)
@@ -1912,9 +1963,13 @@ def build_path(filepath, out_entities, out_dir, schema):
     file_entities = {entity_names_to_keys[k]: v for k, v in file_entities.items()}
 
     sub = get_entity_value(filepath, "sub")
-    ses = get_entity_value(filepath, "ses")
-    if sub is None or ses is None:
-        raise ValueError(f"Could not extract subject or session from {filepath}")
+    if sub is None:
+        raise ValueError(f"Could not extract subject from {filepath}")
+
+    if is_longitudinal:
+        ses = get_entity_value(filepath, "ses")
+        if ses is None:
+            raise ValueError(f"Could not extract session from {filepath}")
 
     # Add leading zeros to run entity if it's an integer.
     # If it's a string, respect the value provided.
@@ -1928,7 +1983,10 @@ def build_path(filepath, out_entities, out_dir, schema):
 
     filename = "_".join([f"{key}-{value}" for key, value in file_entities.items()])
     if len(filename) > 0:
-        filename = f"{sub}_{ses}_{filename}_{suffix}{old_ext}"
+        if is_longitudinal:
+            filename = f"{sub}_{ses}_{filename}_{suffix}{old_ext}"
+        elif not is_longitudinal:
+            filename = f"{sub}_{filename}_{suffix}{old_ext}"
     else:
         raise ValueError(f"Could not construct new filename for {filepath}")
 
@@ -1946,5 +2004,9 @@ def build_path(filepath, out_entities, out_dir, schema):
         print("WARNING: DATATYPE CHANGE DETECTED")
 
     # Construct the new filename
-    new_path = str(Path(out_dir) / sub / ses / dtype_new / filename)
+    if is_longitudinal:
+        new_path = str(Path(out_dir) / sub / ses / dtype_new / filename)
+    elif not is_longitudinal:
+        new_path = str(Path(out_dir) / sub / dtype_new / filename)
+
     return new_path
diff --git a/cubids/metadata_merge.py b/cubids/metadata_merge.py
index 6562f35b..f3decd19 100644
--- a/cubids/metadata_merge.py
+++ b/cubids/metadata_merge.py
@@ -1,4 +1,8 @@
-"""Tools for merging metadata."""
+"""Metadata merging utilities for CuBIDS.
+
+This module provides utilities for merging metadata in CuBIDS, including functions
+for checking merging operations, grouping acquisitions, and handling metadata fields.
+"""
 
 import json
 from collections import defaultdict
@@ -179,7 +183,18 @@ def merge_without_overwrite(source_meta, dest_meta_orig, raise_on_error=False):
 
 
 def is_nan(val):
-    """Return True if val is NaN."""
+    """Check if the given value is NaN (Not a Number).
+
+    Parameters
+    ----------
+    val : any
+        The value to check.
+
+    Returns
+    -------
+    bool
+        True if the value is NaN, False otherwise.
+    """
     if not isinstance(val, float):
         return False
 
@@ -187,7 +202,25 @@ def is_nan(val):
 
 
 def print_merges(merge_list):
-    """Print formatted text of merges."""
+    """Print formatted text of merges.
+
+    Parameters
+    ----------
+    merge_list : list of tuple
+        A list of tuples where each tuple contains two elements:
+
+        - src_id : tuple
+            The source identifier, where the last element is the source ID and
+            the first element is the source name.
+        - dest_id : tuple
+            The destination identifier, where the last element is the destination
+            ID and the first element is the destination name.
+
+    Returns
+    -------
+    str
+        A formatted string representing the merges, with each merge on a new line.
+    """
     merge_strings = []
     for src_id, dest_id in merge_list:
         src_id_str = f"{src_id[-1]}:{src_id[0]}"
@@ -243,13 +276,13 @@ def merge_json_into_json(from_file, to_file, raise_on_error=False):
     return 0
 
 
-def get_acq_dictionary():
+def get_acq_dictionary(is_longitudinal=False):
     """Create a BIDS data dictionary from dataframe columns.
 
     Parameters
     ----------
-    df : :obj:`pandas.DataFrame`
-        Pre export TSV that will be converted to a json dictionary.
+    is_longitudinal : :obj:`bool`, optional
+       If True, add "session" to acq_dict. Default is False.
 
     Returns
     -------
@@ -258,7 +291,8 @@ def get_acq_dictionary():
     """
     acq_dict = {}
     acq_dict["subject"] = {"Description": "Participant ID"}
-    acq_dict["session"] = {"Description": "Session ID"}
+    if is_longitudinal:
+        acq_dict["session"] = {"Description": "Session ID"}
     docs = " https://cubids.readthedocs.io/en/latest/about.html#definitions"
     desc = "Acquisition Group. See Read the Docs for more information"
     acq_dict["AcqGroup"] = {"Description": desc + docs}
@@ -266,7 +300,7 @@ def get_acq_dictionary():
     return acq_dict
 
 
-def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
+def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level, is_longitudinal=False):
     """Find unique sets of Key/Param groups across subjects.
 
     This writes out the following files:
@@ -284,6 +318,8 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
         Prefix for output files.
     acq_group_level : {"subject", "session"}
         Level at which to group acquisitions.
+    is_longitudinal : :obj:`bool`, optional
+       If True, add "session" to acq_dict. Default is False.
     """
     from bids import config
     from bids.layout import parse_file_entities
@@ -298,9 +334,12 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
         file_entities = parse_file_entities(row.FilePath)
 
         if acq_group_level == "subject":
-            acq_id = (file_entities.get("subject"), file_entities.get("session"))
+            if is_longitudinal:
+                acq_id = (file_entities.get("subject"), file_entities.get("session"))
+            elif not is_longitudinal:
+                acq_id = file_entities.get("subject")
             acq_groups[acq_id].append((row.EntitySet, row.ParamGroup))
-        else:
+        elif is_longitudinal and acq_group_level == "session":
             acq_id = (file_entities.get("subject"), None)
             acq_groups[acq_id].append(
                 (row.EntitySet, row.ParamGroup, file_entities.get("session"))
@@ -326,17 +365,21 @@ def group_by_acquisition_sets(files_tsv, output_prefix, acq_group_level):
     for groupnum, content_id_row in enumerate(descending_order, start=1):
         content_id = content_ids[content_id_row]
         acq_group_info.append((groupnum, content_id_counts[content_id_row]) + content_id)
-        for subject, session in contents_to_subjects[content_id]:
-            grouped_sub_sess.append(
-                {"subject": "sub-" + subject, "session": session, "AcqGroup": groupnum}
-            )
+        if is_longitudinal:
+            for subject, session in contents_to_subjects[content_id]:
+                grouped_sub_sess.append(
+                    {"subject": "sub-" + subject, "session": session, "AcqGroup": groupnum}
+                )
+        elif not is_longitudinal:
+            for subject in contents_to_subjects[content_id]:
+                grouped_sub_sess.append({"subject": "sub-" + subject, "AcqGroup": groupnum})
 
     # Write the mapping of subject/session to
     acq_group_df = pd.DataFrame(grouped_sub_sess)
     acq_group_df.to_csv(output_prefix + "_AcqGrouping.tsv", sep="\t", index=False)
 
     # Create data dictionary for acq group tsv
-    acq_dict = get_acq_dictionary()
+    acq_dict = get_acq_dictionary(is_longitudinal)
     with open(output_prefix + "_AcqGrouping.json", "w") as outfile:
         json.dump(acq_dict, outfile, indent=4)
 
diff --git a/cubids/tests/test_apply.py b/cubids/tests/test_apply.py
index ba92b603..51afa64f 100644
--- a/cubids/tests/test_apply.py
+++ b/cubids/tests/test_apply.py
@@ -237,33 +237,35 @@ def summary_data():
 
 
 @pytest.mark.parametrize(
-    ("name", "skeleton", "intended_for", "expected"),
+    ("name", "skeleton", "intended_for", "is_longitudinal", "expected"),
     [
         (
             "relpath_long",
             relpath_intendedfor_long,
             "ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
+            True,
             "pass",
         ),
         (
             "bidsuri_long",
             bidsuri_intendedfor_long,
             "bids::sub-01/ses-01/dwi/sub-01_ses-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
+            True,
             "pass",
         ),
         (
             "relpath_cs",
             relpath_intendedfor_cs,
-            # XXX: CuBIDS enforces longitudinal dataset, so this fails.
             "dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
-            ValueError,
+            False,
+            "pass",
         ),
         (
             "bidsuri_cs",
             bidsuri_intendedfor_cs,
-            # XXX: CuBIDS enforces longitudinal dataset, so this fails.
             "bids::sub-01/dwi/sub-01_acq-VAR_dir-AP_run-01_dwi.nii.gz",
-            ValueError,
+            False,
+            "pass",
         ),
     ],
 )
@@ -274,6 +276,7 @@ def test_cubids_apply_intendedfor(
     name,
     skeleton,
     intended_for,
+    is_longitudinal,
     expected,
 ):
     """Test cubids apply with different IntendedFor types.
@@ -292,6 +295,8 @@ def test_cubids_apply_intendedfor(
         BIDS skeleton structure.
     intended_for : str
         IntendedFor field value.
+    is_longitudinal : bool
+        Indicate whether the data structure is longitudinal or cross-sectional.
     expected : str or Exception
         Expected result or exception.
 
@@ -308,7 +313,7 @@ def test_cubids_apply_intendedfor(
     bids_dir = tmpdir / name
     generate_bids_skeleton(str(bids_dir), skeleton)
 
-    if "long" in name:
+    if is_longitudinal:
         fdata = files_data["longitudinal"]
         fmap_json = bids_dir / "sub-01/ses-01/fmap/sub-01_ses-01_dir-AP_epi.json"
     else:
diff --git a/cubids/tests/test_bond.py b/cubids/tests/test_bond.py
index a4da48a2..9f7f5b39 100644
--- a/cubids/tests/test_bond.py
+++ b/cubids/tests/test_bond.py
@@ -946,7 +946,11 @@ def test_session_apply(tmp_path):
 
     data_root = get_data(tmp_path)
 
-    ses_cubids = CuBIDS(data_root / "inconsistent", acq_group_level="session", use_datalad=True)
+    ses_cubids = CuBIDS(
+        data_root / "inconsistent",
+        acq_group_level="session",
+        use_datalad=True,
+    )
 
     ses_cubids.get_tsvs(str(tmp_path / "originals"))
 
@@ -1193,32 +1197,6 @@ def test_bids_version(tmp_path):
     ), f"Schema version {schema_version} is less than minimum {min_schema_version}"
 
 
-def test_docker():
-    """Verify that docker is installed and the user has permission to run docker images.
-
-    Returns
-    -------
-    int
-        -1 if Docker can't be found.
-         0 if Docker is found, but the user can't connect to the daemon.
-         1 if the test run is OK.
-    """
-    try:
-        return_status = 1
-        ret = subprocess.run(["docker", "version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    except OSError as e:
-        from errno import ENOENT
-
-        if e.errno == ENOENT:
-            print("Cannot find Docker engine!")
-            return_status = 0
-        raise e
-    if ret.stderr.startswith(b"Cannot connect to the Docker daemon."):
-        print("Cannot connect to Docker daemon!")
-        return_status = 0
-    assert return_status
-
-
 # def test_image(image='pennlinc/bond:latest'):
 #     """Check whether image is present on local system."""
 #     ret = subprocess.run(['docker', 'images', '-q', image],
diff --git a/cubids/validator.py b/cubids/validator.py
index 2ee09c25..5c7d97cc 100644
--- a/cubids/validator.py
+++ b/cubids/validator.py
@@ -1,4 +1,8 @@
-"""Methods for validating BIDS datasets."""
+"""Methods for validating BIDS datasets.
+
+This module provides functions for validating BIDS datasets, including building
+subprocess commands for the BIDS validator and handling validation results.
+"""
 
 import glob
 import json
@@ -60,7 +64,24 @@ def get_bids_validator_version():
 
 
 def build_subject_paths(bids_dir):
-    """Build a list of BIDS dirs with 1 subject each."""
+    """Build a dictionary of BIDS directories with one subject each.
+
+    Parameters
+    ----------
+    bids_dir : str
+        The root directory of the BIDS dataset.
+
+    Returns
+    -------
+    dict
+        A dictionary where the keys are subject labels and the values are
+        lists of file paths associated with each subject.
+
+    Raises
+    ------
+    ValueError
+        If no subjects are found in the specified directory.
+    """
     bids_dir = str(bids_dir)
     if not bids_dir.endswith("/"):
         bids_dir += "/"
@@ -88,7 +109,21 @@ def build_subject_paths(bids_dir):
 
 
 def build_first_subject_path(bids_dir, subject):
-    """Build a list of BIDS dirs with 1 subject each."""
+    """Build a dictionary containing BIDS directory paths for a single subject.
+
+    Parameters
+    ----------
+    bids_dir : str
+        The root directory of the BIDS dataset.
+    subject : str
+        The path to the subject directory.
+
+    Returns
+    -------
+    dict
+        A dictionary where the key is the subject label and the value is a list of file paths
+        within the subject directory and the root BIDS directory.
+    """
     bids_dir = str(bids_dir)
     if not bids_dir.endswith("/"):
         bids_dir += "/"
@@ -224,7 +259,7 @@ def extract_summary_info(output):
 
 
 def update_dataset_description(path, new_info):
-    """Update or append information to dataset_description.json.
+    """Update or append information to dataset_description.json with new information.
 
     Parameters
     ----------
diff --git a/cubids/workflows.py b/cubids/workflows.py
index c09366d1..5f419edf 100644
--- a/cubids/workflows.py
+++ b/cubids/workflows.py
@@ -952,15 +952,36 @@ def remove_metadata_fields(bids_dir, container, fields):
 
 
 def print_metadata_fields(bids_dir, container):
-    """Print unique metadata fields.
+    """Print unique metadata fields from a BIDS dataset.
+
+    This function identifies and prints all unique metadata fields from
+    the `dataset_description.json` file in a BIDS directory. It can run
+    either directly in Python or within a specified container (Docker or
+    Singularity).
 
     Parameters
     ----------
     bids_dir : :obj:`pathlib.Path`
-        Path to the BIDS directory.
+        Path to the BIDS directory containing the `dataset_description.json` file.
     container : :obj:`str`
-        Container in which to run the workflow.
+        Name of the container (e.g., Docker, Singularity) to use for running the
+        `cubids print-metadata-fields` command. If `None`, the operation is performed
+        directly in Python without a container.
+
+    Raises
+    ------
+    SystemExit
+        Raised in the following cases:
+        - The `dataset_description.json` file is not found in the BIDS directory.
+        - The subprocess returns a non-zero exit code when executed in a container.
+
     """
+    # Check if dataset_description.json exists
+    dataset_description = bids_dir / "dataset_description.json"
+    if not dataset_description.exists():
+        logger.error("dataset_description.json not found in the BIDS directory.")
+        sys.exit(1)
+
     # Run directly from python
     if container is None:
         bod = CuBIDS(data_root=str(bids_dir), use_datalad=False)
diff --git a/docs/conf.py b/docs/conf.py
index ae90cf8c..9da1b27f 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -56,6 +56,7 @@
     "sphinx_gallery.load_style",
     "sphinxarg.ext",  # argparse extension
     "sphinxcontrib.bibtex",  # bibtex-based bibliographies
+    "sphinx_design",  # for adding in-line badges etc
 ]
 
 # Mock modules in autodoc:
@@ -259,3 +260,12 @@
     "term",
     "footcite",
 ]
+
+# -----------------------------------------------------------------------------
+# sphinx_copybutton
+# -----------------------------------------------------------------------------
+# Configuration for sphinx_copybutton to remove shell prompts, i.e. $
+copybutton_prompt_text = "$ "
+copybutton_only_copy_prompt_lines = (
+    False  # ensures all lines are copied, even those without a prompt
+)
diff --git a/docs/example.rst b/docs/example.rst
index c10d5110..b6370f4b 100644
--- a/docs/example.rst
+++ b/docs/example.rst
@@ -174,9 +174,6 @@ Since we ran ``cubids add-nifti-info`` with the ``--use-datalad`` flag set,
 BIDS validation
 ---------------
 
-The next step in the ``CuBIDS`` workflow is to run BIDS validation
-to detect potential curation errors using ``cubids validate``.
-
 .. code-block:: console
 
     $ cubids validate BIDS_Dataset_DataLad v0 --sequential
@@ -187,6 +184,16 @@ to detect potential curation errors using ``cubids validate``.
     This can be helpful for identifying heterogeneous elements,
     but can be slowed down by extremely large datasets.
 
+.. warning::
+    For internetless use cases, please see dedicated section of the `Installation page 
+    <https://cubids.readthedocs.io/en/latest/installation.html>`_ on how to download a local version 
+    of the validator.
+
+    After that, you will need to add ``--local-validator`` option to the command string above.
+
+The next step in the ``CuBIDS`` workflow is to run BIDS validation
+to detect potential curation errors using ``cubids validate``.
+
 This command produces the following tsv:
 
 .. csv-table:: v0_validation.tsv
diff --git a/docs/installation.rst b/docs/installation.rst
index b6ebda3b..b8c323e7 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -54,6 +54,26 @@ We can accomplish this using the following command:
 The new schema-based ``bids-validator`` doesn't need to be installed 
 and will be implemented automatically when `cubids validate` is called
 
+.. dropdown:: If there is no Internet connection on compute nodes
+
+    If your HPC doesn't allow internet access on its compute nodes, it won't be able to run the online 
+    version of the BIDS validator. In that scenario, you need to install the BIDS validator on your HPC 
+    and then point to the installed version in your cubids validate calls. 
+    To do that, you should run one of these commands below, after installing deno, that downloads the latest version 
+    of the bids-validator in your virtual environment either by installing a lightscript version 
+    (into ``$HOME/.deno/bin``) or by compiling, respectively:
+
+    ..  code-block:: console
+
+        $ deno install -ERN -g -n bids-validator jsr:@bids/validator
+    
+    or:
+
+    ..  code-block:: console
+
+        $ deno compile -ERN -o bids-validator jsr:@bids/validator
+
+    For more information, you can read: https://bids-validator.readthedocs.io/en/latest/user_guide/command-line.html
 
 We also recommend using ``CuBIDS`` with the optional ``DataLad`` version control capabilities.
 We use ``DataLad`` throughout our walkthrough of the CuBIDS Workflow on
diff --git a/pyproject.toml b/pyproject.toml
index b90d2032..1337663e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ license = {file = "LICENSE"}
 requires-python = ">=3.9"
 dependencies = [
     "datalad>=0.13.5,!=0.17.3,!=0.17.0,!=0.16.1",
-    "numpy<=2.2.1",
+    "numpy<=2.2.2",
     "pandas<=2.2.3",
     "pybids<=0.18.1",
     "pyyaml",
@@ -51,6 +51,7 @@ doc = [
     "sphinx_markdown_tables",
     "sphinx_rtd_theme",
     "sphinxcontrib-bibtex",
+    "sphinx_design",
 ]
 tests = [
     "codespell",