PY312: Drop implicit setuptools dependency

Author: effigies

smriprep/cli/run.py

@@ -445,13 +445,13 @@ def build_workflow(opts, retval):
     import warnings
     from time import strftime
     from subprocess import check_call, CalledProcessError, TimeoutExpired
-    from pkg_resources import resource_filename as pkgrf
 
     import json
     from bids import BIDSLayout
     from nipype import logging, config as ncfg
     from niworkflows.utils.bids import collect_participants
     from ..__about__ import __version__
+    from ..data import load_resource
     from ..workflows.base import init_smriprep_wf
 
     logger = logging.getLogger("nipype.workflow")
@@ -628,12 +628,14 @@ def build_workflow(opts, retval):
         boilerplate,
     )
 
+    boilerplate_bib = load_resource("boilerplate.bib")
+
     # Generate HTML file resolving citations
     cmd = [
         "pandoc",
         "-s",
         "--bibliography",
-        pkgrf("smriprep", "data/boilerplate.bib"),
+        str(boilerplate_bib),
         "--citeproc",
         "--metadata",
         'pagetitle="sMRIPrep citation boilerplate"',
@@ -651,7 +653,7 @@ def build_workflow(opts, retval):
         "pandoc",
         "-s",
         "--bibliography",
-        pkgrf("smriprep", "data/boilerplate.bib"),
+        str(boilerplate_bib),
         "--natbib",
         str(log_dir / "CITATION.md"),
         "-o",
@@ -662,7 +664,7 @@ def build_workflow(opts, retval):
     except (FileNotFoundError, CalledProcessError, TimeoutExpired):
         logger.warning("Could not generate CITATION.tex file:\n%s", " ".join(cmd))
     else:
-        copyfile(pkgrf("smriprep", "data/boilerplate.bib"), str(log_dir / "CITATION.bib"))
+        copyfile(str(boilerplate_bib), str(log_dir / "CITATION.bib"))
     return retval
 
 

smriprep/utils/bids.py

@@ -23,16 +23,15 @@
 """Utilities to handle BIDS inputs."""
 from pathlib import Path
 from json import loads
-from pkg_resources import resource_filename as pkgrf
 from bids.layout import BIDSLayout
 
+from ..data import load_resource
+
 
 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(Path(pkgrf("smriprep", "data/io_spec.json")).read_text()).values()
-        )
+        _spec, _patterns = tuple(loads(load_resource("io_spec.json").read_text()).values())
 
         if spec is None:
             spec = _spec
@@ -92,11 +91,11 @@ def write_derivative_description(bids_dir, deriv_dir):
 
     .. testsetup::
 
-    >>> from pkg_resources import resource_filename
+    >>> from smriprep.data import load_resource
     >>> from pathlib import Path
     >>> from tempfile import TemporaryDirectory
     >>> tmpdir = TemporaryDirectory()
-    >>> bids_dir = resource_filename('smriprep', 'data/tests')
+    >>> bids_dir = load_resource('tests')
     >>> deriv_desc = Path(tmpdir.name) / 'dataset_description.json'
 
     .. doctest::

smriprep/workflows/anatomical.py

@@ -23,8 +23,6 @@
 """Anatomical reference preprocessing workflows."""
 import typing as ty
 
-from pkg_resources import resource_filename as pkgr
-
 from nipype import logging
 from nipype.pipeline import engine as pe
 from nipype.interfaces import (
@@ -50,6 +48,7 @@
 from niworkflows.utils.spaces import SpatialReferences, Reference
 from niworkflows.utils.misc import add_suffix
 from niworkflows.anat.ants import init_brain_extraction_wf, init_n4_only_wf
+from ..data import load_resource
 from ..interfaces import DerivativesDataSink
 from ..utils.misc import apply_lut as _apply_bids_lut, fs_isRunning as _fs_isRunning
 from .fit.registration import init_register_template_wf
@@ -1454,7 +1453,7 @@ def init_anat_template_wf(
 
     if num_files == 1:
         get1st = pe.Node(niu.Select(index=[0]), name="get1st")
-        outputnode.inputs.anat_realign_xfm = [pkgr("smriprep", "data/itkIdentityTransform.txt")]
+        outputnode.inputs.anat_realign_xfm = [str(load_resource("itkIdentityTransform.txt"))]
 
         # fmt:off
         workflow.connect([