Merge pull request #448 from mgxd/rf/load

RF: Load package data with acres

docs/requirements.txt

@@ -11,3 +11,4 @@ sphinx_rtd_theme
 sphinxcontrib-apidoc ~= 0.3.0
 templateflow
 networkx != 2.8.1
+acres

pyproject.toml

@@ -19,6 +19,7 @@ classifiers = [
 license = {file = "LICENSE"}
 requires-python = ">=3.10"
 dependencies = [
+    "acres",
     "indexed_gzip >= 0.8.8",
     "lockfile",
     "looseversion",

smriprep/__init__.py

@@ -9,6 +9,8 @@
 
 """
 
+from smriprep.data import load as load_data
+
 from .__about__ import (
     __copyright__,
     __credits__,
@@ -19,4 +21,5 @@
     '__copyright__',
     '__credits__',
     '__version__',
+    'load_data',
 ]

smriprep/cli/run.py

@@ -51,7 +51,7 @@ def get_parser():
         SpatialReferences,
     )
 
-    from ..__about__ import __version__
+    import smriprep
 
     parser = ArgumentParser(
         description='sMRIPrep: Structural MRI PREProcessing workflows',
@@ -82,7 +82,11 @@ def get_parser():
     )
 
     # optional arguments
-    parser.add_argument('--version', action='version', version=f'smriprep v{__version__}')
+    parser.add_argument(
+        '--version',
+        action='version',
+        version=f'smriprep v{smriprep.__version__}',
+    )
 
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument(
@@ -470,9 +474,8 @@ def build_workflow(opts, retval):
     from nipype import logging
     from niworkflows.utils.bids import collect_participants
 
-    from ..__about__ import __version__
-    from ..data import load_resource
-    from ..workflows.base import init_smriprep_wf
+    import smriprep
+    from smriprep.workflows.base import init_smriprep_wf
 
     logger = logging.getLogger('nipype.workflow')
 
@@ -596,7 +599,7 @@ def build_workflow(opts, retval):
     logger.log(
         25,
         INIT_MSG(
-            version=__version__,
+            version=smriprep.__version__,
             bids_dir=bids_dir,
             subject_list=subject_list,
             uuid=run_uuid,
@@ -651,7 +654,7 @@ def build_workflow(opts, retval):
         boilerplate,
     )
 
-    boilerplate_bib = load_resource('boilerplate.bib')
+    boilerplate_bib = smriprep.load_data('boilerplate.bib')
 
     # Generate HTML file resolving citations
     cmd = [

smriprep/conftest.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pytest
 
-from smriprep.data import load_resource
+from smriprep.data import load
 
 os.environ['NO_ET'] = '1'
 
@@ -12,5 +12,5 @@
 def _populate_namespace(doctest_namespace, tmp_path):
     doctest_namespace['os'] = os
     doctest_namespace['np'] = np
-    doctest_namespace['load'] = load_resource
+    doctest_namespace['load'] = load
     doctest_namespace['testdir'] = tmp_path

smriprep/data/__init__.py

@@ -1,25 +1,14 @@
-import atexit
-from contextlib import ExitStack
-from pathlib import Path
+"""sMRIPRep data files
 
-try:
-    from functools import cache
-except ImportError:  # PY38
-    from functools import lru_cache as cache
+.. autofunction:: load
 
-try:  # Prefer backport to leave consistency to dependency spec
-    from importlib_resources import as_file, files
-except ImportError:
-    from importlib.resources import as_file, files
+.. automethod:: load.readable
 
-__all__ = ['load_resource']
+.. automethod:: load.as_path
 
-exit_stack = ExitStack()
-atexit.register(exit_stack.close)
+.. automethod:: load.cached
+"""
 
-path = files(__package__)
+from acres import Loader
 
-
-@cache
-def load_resource(fname: str) -> Path:
-    return exit_stack.enter_context(as_file(path.joinpath(fname)))
+load = Loader(__package__)

smriprep/interfaces/tests/data/__init__.py

@@ -0,0 +1,3 @@
+from acres import Loader
+
+load = Loader(__package__)

smriprep/interfaces/tests/test_surf.py

@@ -2,19 +2,15 @@
 import numpy as np
 from nipype.pipeline import engine as pe
 
-from ...data import load_resource
+from smriprep.interfaces.tests.data import load as load_test_data
+
 from ..surf import MakeRibbon
 
 
 def test_MakeRibbon(tmp_path):
-    res_template = '{path}/sub-fsaverage_res-4_hemi-{hemi}_desc-cropped_{surf}dist.nii.gz'
+    res_template = 'sub-fsaverage_res-4_hemi-{hemi}_desc-cropped_{surf}dist.nii.gz'
     white, pial = (
-        [
-            load_resource(
-                res_template.format(path='../interfaces/tests/data', hemi=hemi, surf=surf)
-            )
-            for hemi in 'LR'
-        ]
+        [load_test_data(res_template.format(hemi=hemi, surf=surf)) for hemi in 'LR']
         for surf in ('wm', 'pial')
     )
 
@@ -27,9 +23,7 @@ def test_MakeRibbon(tmp_path):
     result = make_ribbon.run()
 
     ribbon = nb.load(result.outputs.ribbon)
-    expected = nb.load(
-        load_resource('../interfaces/tests/data/sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz')
-    )
+    expected = nb.load(load_test_data('sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz'))
 
     assert ribbon.shape == expected.shape
     assert np.allclose(ribbon.affine, expected.affine)

smriprep/utils/bids.py

@@ -28,13 +28,13 @@
 from bids.layout import BIDSLayout
 from niworkflows.data import load as nwf_load
 
-from ..data import load_resource
+import smriprep
 
 
 def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patterns=None):
     """Gather existing derivatives and compose a cache."""
     if spec is None or patterns is None:
-        _spec, _patterns = tuple(loads(load_resource('io_spec.json').read_text()).values())
+        _spec, _patterns = tuple(loads(smriprep.load_data('io_spec.json').read_text()).values())
 
         if spec is None:
             spec = _spec
@@ -96,11 +96,11 @@ def write_derivative_description(bids_dir, deriv_dir):
 
     .. testsetup::
 
-    >>> from smriprep.data import load_resource
+    >>> from smriprep.data import load
     >>> from pathlib import Path
     >>> from tempfile import TemporaryDirectory
     >>> tmpdir = TemporaryDirectory()
-    >>> bids_dir = load_resource('tests')
+    >>> bids_dir = load('tests')
     >>> deriv_desc = Path(tmpdir.name) / 'dataset_description.json'
 
     .. doctest::

smriprep/utils/tests/__init__.py

@@ -1,4 +1,4 @@
-from niworkflows.data import Loader
+from acres import Loader
 
 load_data = Loader(__package__)
 

smriprep/workflows/anatomical.py

@@ -54,7 +54,8 @@
 from niworkflows.utils.misc import add_suffix
 from niworkflows.utils.spaces import Reference, SpatialReferences
 
-from ..data import load_resource
+import smriprep
+
 from ..interfaces import DerivativesDataSink
 from ..utils.misc import apply_lut as _apply_bids_lut
 from ..utils.misc import fs_isRunning as _fs_isRunning
@@ -1461,7 +1462,7 @@ def init_anat_template_wf(
 
     if num_files == 1:
         get1st = pe.Node(niu.Select(index=[0]), name='get1st')
-        outputnode.inputs.anat_realign_xfm = [str(load_resource('itkIdentityTransform.txt'))]
+        outputnode.inputs.anat_realign_xfm = [str(smriprep.load_data('itkIdentityTransform.txt'))]
 
         # fmt:off
         workflow.connect([

smriprep/workflows/surfaces.py

@@ -53,10 +53,10 @@
     MetricResample,
 )
 
+import smriprep
 from smriprep.interfaces.surf import MakeRibbon
 from smriprep.interfaces.workbench import SurfaceResample
 
-from ..data import load_resource
 from ..interfaces.freesurfer import MakeMidthickness, ReconAll
 from ..interfaces.gifti import MetricMath
 from ..interfaces.workbench import CreateSignedDistanceVolume
@@ -723,7 +723,7 @@ def init_fsLR_reg_wf(*, name='fsLR_reg_wf'):
         iterfield=['sphere_in', 'sphere_project_to', 'sphere_unproject_from'],
         name='project_unproject',
     )
-    atlases = load_resource('atlases')
+    atlases = smriprep.load_data('atlases')
     project_unproject.inputs.sphere_project_to = [
         atlases / 'fs_L' / 'fsaverage.L.sphere.164k_fs_L.surf.gii',
         atlases / 'fs_R' / 'fsaverage.R.sphere.164k_fs_R.surf.gii',
@@ -804,8 +804,8 @@ def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
     # --indata=sub-${SUB}_ses-${SES}_hemi-${HEMI)_sulc.shape.gii \
     # --refdata=tpl-fsaverage_hemi-${HEMI}_den-164k_sulc.shape.gii \
     # --out=${HEMI}. --verbose
-    atlases = load_resource('atlases')
-    msm_conf = load_resource(f'msm/MSMSulcStrain{"Sloppy" if sloppy else "Final"}conf')
+    atlases = smriprep.load_data('atlases')
+    msm_conf = smriprep.load_data(f'msm/MSMSulcStrain{"Sloppy" if sloppy else "Final"}conf')
     msmsulc = pe.MapNode(
         MSM(verbose=True, config_file=msm_conf),
         iterfield=['in_mesh', 'reference_mesh', 'in_data', 'reference_data', 'out_base'],
@@ -1512,7 +1512,7 @@ def init_morph_grayords_wf(
         name='outputnode',
     )
 
-    atlases = load_resource('atlases')
+    atlases = smriprep.load_data('atlases')
     select_surfaces = pe.Node(
         KeySelect(
             fields=[

smriprep/workflows/tests/test_surfaces.py

@@ -7,7 +7,8 @@
 import pytest
 from nipype.pipeline import engine as pe
 
-from ...data import load_resource
+from smriprep.interfaces.tests.data import load as load_test_data
+
 from ..surfaces import init_anat_ribbon_wf, init_gifti_surfaces_wf
 
 
@@ -23,9 +24,7 @@ def test_ribbon_workflow(tmp_path: Path):
 
     # Low-res file that includes the fsaverage surfaces in its bounding box
     # We will use it both as a template and a comparison.
-    test_ribbon = load_resource(
-        '../interfaces/tests/data/sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz'
-    )
+    test_ribbon = load_test_data('sub-fsaverage_res-4_desc-cropped_ribbon.nii.gz')
 
     gifti_surfaces_wf = init_gifti_surfaces_wf(surfaces=['white', 'pial'])
     anat_ribbon_wf = init_anat_ribbon_wf()