Merge pull request #4 from PennLINC/reduce-dependencies

Reduce dependencies

Author: tsalo

pyproject.toml

@@ -19,14 +19,8 @@ classifiers = [
 ]
 dependencies = [
   "acres",
-  "fmriprep @ git+https://github.com/nipreps/fmriprep.git@master",
-  "nipype >= 1.8.5",
-  "nireports @ git+https://github.com/nipreps/nireports.git@main",
-  "nitransforms >= 24.0.2",
-  "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+  "nipype",
   "pybids >= 0.15.6",
-  "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-  "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
   "typer",
 ]
 dynamic = ["version"]

src/simbids/cli/parser.py

@@ -115,8 +115,7 @@ def _bids_filter(value, parser):
 
     parser = ArgumentParser(
         description=(
-            'SimBIDS: fMRI POSTprocessing template workflow '
-            f'v{config.environment.version}'
+            f'SimBIDS: fMRI POSTprocessing template workflow v{config.environment.version}'
         ),
         formatter_class=ArgumentDefaultsHelpFormatter,
         **kwargs,
@@ -185,11 +184,11 @@ def _bids_filter(value, parser):
         type=BIDSFilter,
         metavar='FILE',
         help=(
-            "A JSON file describing custom BIDS input filters using PyBIDS. "
-            "For further details, please check out "
-            "https://fmriprep.readthedocs.io/en/"
-            f"{currentv.base_version if is_release else 'latest'}/faq.html#"
-            "how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep"
+            'A JSON file describing custom BIDS input filters using PyBIDS. '
+            'For further details, please check out '
+            'https://fmriprep.readthedocs.io/en/'
+            f'{currentv.base_version if is_release else "latest"}/faq.html#'
+            'how-do-I-select-only-certain-files-to-be-input-to-fMRIPrep'
         ),
     )
     g_bids.add_argument(
@@ -546,8 +545,7 @@ def parse_args(args=None, namespace=None):
         from simbids.utils.bids import validate_input_dir
 
         build_log.info(
-            'Making sure the input data is BIDS compliant '
-            '(warnings can be ignored in most cases).'
+            'Making sure the input data is BIDS compliant (warnings can be ignored in most cases).'
         )
         validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
@@ -567,8 +565,8 @@ def parse_args(args=None, namespace=None):
     missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
         parser.error(
-            "One or more participant labels were not found in the BIDS directory: "
-            f"{', '.join(missing_subjects)}."
+            'One or more participant labels were not found in the BIDS directory: '
+            f'{", ".join(missing_subjects)}.'
         )
 
     config.execution.participant_label = sorted(participant_label)

src/simbids/cli/run.py

@@ -141,9 +141,7 @@ def main():
 
     config.loggers.workflow.log(
         15,
-        '\n'.join(
-            ['SimBIDS config:'] + [f'\t\t{s}' for s in config.dumps().splitlines()]
-        ),
+        '\n'.join(['SimBIDS config:'] + [f'\t\t{s}' for s in config.dumps().splitlines()]),
     )
     config.loggers.workflow.log(25, 'SimBIDS started!')
     errno = 1  # Default is error exit unless otherwise set

src/simbids/cli/version.py

@@ -66,9 +66,7 @@ def check_latest():
     if latest is None or outdated is True:
         response = None
         with suppress(Exception):
-            response = requests.get(
-                url='https://pypi.org/pypi/simbids/json', timeout=1.0
-            )
+            response = requests.get(url='https://pypi.org/pypi/simbids/json', timeout=1.0)
 
         if response and response.status_code == 200:
             versions = [Version(rel) for rel in response.json()['releases'].keys()]

src/simbids/cli/workflow.py

@@ -58,11 +58,11 @@ def build_workflow(config_file, retval):
     notice_path = Path(pkgrf('simbids', 'data/NOTICE'))
     if notice_path.exists():
         banner[0] += '\n'
-        banner += [f"License NOTICE {'#' * 50}"]
+        banner += [f'License NOTICE {"#" * 50}']
         banner += [f'SimBIDS {version}']
         banner += notice_path.read_text().splitlines(keepends=False)[1:]
         banner += ['#' * len(banner[1])]
-    build_log.log(25, f"\n{' ' * 9}".join(banner))
+    build_log.log(25, f'\n{" " * 9}'.join(banner))
 
     # warn if older results exist: check for dataset_description.json in output folder
     msg = check_pipeline_version(
@@ -110,7 +110,7 @@ def build_workflow(config_file, retval):
     if config.execution.derivatives:
         init_msg += [f'Searching for derivatives: {config.execution.derivatives}.']
 
-    build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
+    build_log.log(25, f'\n{" " * 11}* '.join(init_msg))
 
     retval['workflow'] = init_simbids_wf()
 

src/simbids/config.py

@@ -430,7 +430,7 @@ class execution(_Config):
     the command line) as spatial references for outputs."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
-    run_uuid = f"{strftime('%Y%m%d-%H%M%S')}_{uuid4()}"
+    run_uuid = f'{strftime("%Y%m%d-%H%M%S")}_{uuid4()}'
     """Unique identifier of this particular run."""
     participant_label = None
     """List of participant identifiers that are to be preprocessed."""

src/simbids/tests/run_local_tests.py

@@ -83,7 +83,7 @@ def run_command(command, env=None):
 
     if process.returncode != 0:
         raise RuntimeError(
-            f'Non zero return code: {process.returncode}\n' f'{command}\n\n{process.stdout.read()}'
+            f'Non zero return code: {process.returncode}\n{command}\n\n{process.stdout.read()}'
         )
 
 

src/simbids/tests/utils.py

@@ -131,7 +131,7 @@ def run_command(command, env=None):
 
     if process.returncode != 0:
         raise Exception(
-            f'Non zero return code: {process.returncode}\n' f'{command}\n\n{process.stdout.read()}'
+            f'Non zero return code: {process.returncode}\n{command}\n\n{process.stdout.read()}'
         )
 
 

src/simbids/utils/bids.py

@@ -26,8 +26,10 @@
 
 import json
 from collections import defaultdict
+from copy import deepcopy
 from pathlib import Path
 
+import yaml
 from bids.layout import BIDSLayout
 from bids.utils import listify
 from niworkflows.utils.spaces import SpatialReferences
@@ -477,3 +479,97 @@ def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
             subprocess.check_call(['bids-validator', str(bids_dir), '-c', temp.name])  # noqa: S607
         except FileNotFoundError:
             print('bids-validator does not appear to be installed', file=sys.stderr)
+
+
+def generate_bids_skeleton(target_path, bids_config):
+    """
+    Converts a BIDS directory in dictionary form to a file structure.
+
+    The BIDS configuration can either be a YAML or JSON file, or :obj:dict: object.
+
+    Parameters
+    ----------
+    target_path : str
+        Path to generate BIDS directory at (must not exist)
+    bids_config : dict or str
+        Configuration on how to create the BIDS directory.
+    """
+
+    if isinstance(bids_config, dict):
+        # ensure dictionary remains unaltered
+        bids_dict = deepcopy(bids_config)
+    elif isinstance(bids_config, str):
+        bids_config = Path(bids_config).read_text()
+        try:
+            bids_dict = json.loads(bids_config)
+        except json.JSONDecodeError:
+            bids_dict = yaml.safe_load(bids_config)
+
+    _bids_dict = deepcopy(bids_dict)
+    root = Path(target_path).absolute()
+    root.mkdir(parents=True)
+
+    desc = bids_dict.pop('dataset_description', None)
+    if desc is None:
+        # default description
+        desc = {'Name': 'Default', 'BIDSVersion': '1.6.0'}
+    to_json(root / 'dataset_description.json', desc)
+
+    cached_subject_data = None
+    for subject, sessions in bids_dict.items():
+        bids_subject = subject if subject.startswith('sub-') else f'sub-{subject}'
+        subj_path = root / bids_subject
+        subj_path.mkdir(exist_ok=True)
+
+        if sessions == '*':  # special case to copy previous subject data
+            sessions = cached_subject_data.copy()
+
+        if isinstance(sessions, dict):  # single session
+            sessions.update({'session': None})
+            sessions = [sessions]
+
+        cached_subject_data = deepcopy(sessions)
+        for session in sessions:
+            ses_name = session.pop('session', None)
+            if ses_name is not None:
+                bids_session = ses_name if ses_name.startswith('ses-') else f'ses-{ses_name}'
+                bids_prefix = f'{bids_subject}_{bids_session}'
+                curr_path = subj_path / bids_session
+                curr_path.mkdir(exist_ok=True)
+            else:
+                bids_prefix = bids_subject
+                curr_path = subj_path
+
+            # create modalities
+            for modality, files in session.items():
+                modality_path = curr_path / modality
+                modality_path.mkdir(exist_ok=True)
+
+                if isinstance(files, dict):  # single file / metadata combo
+                    files = [files]
+
+                for bids_file in files:
+                    metadata = bids_file.pop('metadata', None)
+                    extension = bids_file.pop('extension', '.nii.gz')
+                    suffix = bids_file.pop('suffix')
+                    entities = combine_entities(**bids_file)
+                    data_file = modality_path / f'{bids_prefix}{entities}_{suffix}{extension}'
+                    data_file.touch()
+
+                    if metadata is not None:
+                        out_metadata = data_file.parent / data_file.name.replace(
+                            extension, '.json'
+                        )
+                        to_json(out_metadata, metadata)
+
+    return _bids_dict
+
+
+def to_json(filename, data):
+    filename = Path(filename)
+    filename.write_text(json.dumps(data))
+    return filename
+
+
+def combine_entities(**entities):
+    return f'_{"_".join([f"{lab}-{val}" for lab, val in entities.items()])}' if entities else ''

src/simbids/utils/utils.py

@@ -43,7 +43,7 @@ def _get_wf_name(bold_fname, prefix):
 
     fname = split_filename(bold_fname)[1]
     fname_nosub = '_'.join(fname.split('_')[1:-1])
-    return f"{prefix}_{fname_nosub.replace('-', '_')}_wf"
+    return f'{prefix}_{fname_nosub.replace("-", "_")}_wf'
 
 
 def update_dict(orig_dict, new_dict):