RF: Drop pkg_resources, use loaders where feasible

niworkflows/anat/ants.py

@@ -25,7 +25,6 @@
 # general purpose
 from collections import OrderedDict
 from multiprocessing import cpu_count
-from pkg_resources import resource_filename as pkgr_fn
 from warnings import warn
 
 # nipype
@@ -40,6 +39,7 @@
     ThresholdImage,
 )
 
+from ..data import load as load_data
 from ..utils.misc import get_template_specs
 from ..utils.connections import pop_file as _pop
 
@@ -302,9 +302,7 @@ def init_brain_extraction_wf(
         else "antsBrainExtractionNoLaplacian_%s.json"
     )
     norm = pe.Node(
-        Registration(
-            from_file=pkgr_fn("niworkflows.data", settings_file % normalization_quality)
-        ),
+        Registration(from_file=load_data(settings_file % normalization_quality)),
         name="norm",
         n_procs=omp_nthreads,
         mem_gb=mem_gb,

niworkflows/conftest.py

@@ -30,6 +30,8 @@
 import pytest
 import tempfile
 
+from . import load_resource
+
 try:
     import importlib_resources
 except ImportError:
@@ -40,7 +42,7 @@
 
 
 def find_resource_or_skip(resource):
-    pathlike = importlib_resources.files("niworkflows") / resource
+    pathlike = load_resource(resource)
     if not pathlike.exists():
         pytest.skip(f"Missing resource {resource}; run this test from a source repository")
     return pathlike
@@ -63,7 +65,7 @@ def add_np(doctest_namespace):
     doctest_namespace["datadir"] = data_dir
     doctest_namespace["data_dir_canary"] = data_dir_canary
     doctest_namespace["bids_collect_data"] = collect_data
-    doctest_namespace["test_data"] = importlib_resources.files("niworkflows") / "tests" / "data"
+    doctest_namespace["test_data"] = load_resource('tests/data')
 
     tmpdir = tempfile.TemporaryDirectory()
 

niworkflows/func/util.py

@@ -22,13 +22,13 @@
 #
 """Utility workflows."""
 from packaging.version import parse as parseversion, Version
-from pkg_resources import resource_filename as pkgr_fn
 
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, fsl, afni
 
 from templateflow.api import get as get_template
 
+from .. import data
 from ..engine.workflows import LiterateWorkflow as Workflow
 from ..interfaces.fixes import (
     FixHeaderRegistration as Registration,
@@ -452,9 +452,7 @@ def init_enhance_and_skullstrip_bold_wf(
 
         # Set up spatial normalization
         norm = pe.Node(
-            Registration(
-                from_file=pkgr_fn("niworkflows.data", "epi_atlasbased_brainmask.json")
-            ),
+            Registration(from_file=data.load("epi_atlasbased_brainmask.json")),
             name="norm",
             n_procs=omp_nthreads,
         )

niworkflows/interfaces/bids.py

@@ -27,7 +27,6 @@
 from pathlib import Path
 import shutil
 import os
-from pkg_resources import resource_filename as _pkgres
 import re
 
 import nibabel as nb
@@ -50,12 +49,13 @@
 )
 from nipype.interfaces.io import add_traits
 import templateflow as tf
+from .. import data
 from ..utils.bids import _init_layout, relative_to_root
 from ..utils.images import set_consumables, unsafe_write_nifti_header_and_data
 from ..utils.misc import _copy_any, unlink
 
 regz = re.compile(r"\.gz$")
-_pybids_spec = loads(Path(_pkgres("niworkflows", "data/nipreps.json")).read_text())
+_pybids_spec = loads(data.load.readable("nipreps.json").read_text())
 BIDS_DERIV_ENTITIES = _pybids_spec["entities"]
 BIDS_DERIV_PATTERNS = tuple(_pybids_spec["default_path_patterns"])
 

niworkflows/interfaces/norm.py

@@ -24,7 +24,6 @@
 from os import path as op
 
 from multiprocessing import cpu_count
-import pkg_resources as pkgr
 from packaging.version import Version
 import numpy as np
 
@@ -40,6 +39,7 @@
 
 from templateflow.api import get as get_template
 from .. import NIWORKFLOWS_LOG, __version__
+from ..data import load as load_data
 from .fixes import FixHeaderRegistration as Registration
 
 
@@ -166,16 +166,13 @@ def _get_settings(self):
             self.inputs.moving.lower(), self.inputs.flavor
         )
 
+        data_dir = load_data()
         # Get a list of settings files that match the flavor.
         filenames = [
-            i
-            for i in pkgr.resource_listdir("niworkflows", "data")
-            if i.startswith(filestart) and i.endswith(".json")
+            i for i in data_dir.iterdir() if i.startswith(filestart) and i.endswith(".json")
         ]
         # Return the settings files.
-        return [
-            pkgr.resource_filename("niworkflows.data", f) for f in sorted(filenames)
-        ]
+        return [str(data_dir / f) for f in sorted(filenames)]
 
     def _run_interface(self, runtime):
         # Get a list of settings files.

niworkflows/interfaces/tests/test_itk.py

@@ -22,6 +22,7 @@
 #
 import pytest
 from ..itk import _applytfms
+from ... import data
 from nipype.interfaces.ants.base import Info
 
 
@@ -32,14 +33,13 @@
 def test_applytfms(tmpdir, ext, copy_dtype, in_dtype):
     import numpy as np
     import nibabel as nb
-    from pkg_resources import resource_filename as pkgr_fn
 
     in_file = str(tmpdir / ("src" + ext))
     nii = nb.Nifti1Image(np.zeros((5, 5, 5), dtype=np.float32), np.eye(4))
     nii.set_data_dtype(in_dtype)
     nii.to_filename(in_file)
 
-    in_xform = pkgr_fn("niworkflows", "data/itkIdentityTransform.txt")
+    in_xform = data.load("itkIdentityTransform.txt")
 
     ifargs = {"copy_dtype": copy_dtype, "reference_image": in_file}
     args = (in_file, in_xform, ifargs, 0, str(tmpdir))

niworkflows/interfaces/tests/test_plotting.py

@@ -26,18 +26,17 @@
 from niworkflows import viz
 from niworkflows.utils.timeseries import _cifti_timeseries, _nifti_timeseries
 from niworkflows.interfaces.plotting import _get_tr
-from niworkflows.tests.conftest import datadir
+from niworkflows.tests.data import load_test_data
 
 
 def test_cifti_carpetplot():
     """Exercise extraction of timeseries from CIFTI2."""
     save_artifacts = os.getenv("SAVE_CIRCLE_ARTIFACTS", False)
 
-    cifti_file = os.path.join(
-        datadir,
-        "sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii",
+    cifti_file = load_test_data(
+        "sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii"
     )
-    data, segments = _cifti_timeseries(cifti_file)
+    data, segments = _cifti_timeseries(str(cifti_file))
     viz.plot_carpet(
         data,
         segments,
@@ -56,15 +55,13 @@ def test_nifti_carpetplot():
     """Exercise extraction of timeseries from CIFTI2."""
     save_artifacts = os.getenv("SAVE_CIRCLE_ARTIFACTS", False)
 
-    nifti_file = os.path.join(
-        datadir,
-        "sub-ds205s03_task-functionallocalizer_run-01_bold_volreg.nii.gz",
+    nifti_file = load_test_data(
+        "sub-ds205s03_task-functionallocalizer_run-01_bold_volreg.nii.gz"
     )
-    seg_file = os.path.join(
-        datadir,
-        "sub-ds205s03_task-functionallocalizer_run-01_bold_parc.nii.gz",
+    seg_file = load_test_data(
+        "sub-ds205s03_task-functionallocalizer_run-01_bold_parc.nii.gz"
     )
-    data, segments = _nifti_timeseries(nifti_file, seg_file)
+    data, segments = _nifti_timeseries(str(nifti_file), str(seg_file))
     viz.plot_carpet(
         data,
         segments,

niworkflows/reports/core.py

@@ -30,14 +30,15 @@
 import re
 from itertools import compress
 from collections import defaultdict
-from pkg_resources import resource_filename as pkgrf
 from bids.layout import BIDSLayout, add_config_paths
 import jinja2
 from nipype.utils.filemanip import copyfile
 
+from .. import data, load_resource
+
 # Add a new figures spec
 try:
-    add_config_paths(figures=pkgrf("niworkflows", "data/nipreps.json"))
+    add_config_paths(figures=data.load('nipreps.json'))
 except ValueError as e:
     if "Configuration 'figures' already exists" != str(e):
         raise
@@ -100,17 +101,13 @@ class Reportlet(Element):
 
     .. testsetup::
 
-        >>> cwd = os.getcwd()
-        >>> os.chdir(tmpdir)
-
         >>> from shutil import copytree
         >>> from bids.layout import BIDSLayout
-        >>> test_data_path = find_resource_or_skip('data/tests/work')
+        >>> source = find_resource_or_skip('data/tests/work')
         >>> testdir = Path(tmpdir)
-        >>> with importlib_resources.as_file(test_data_path) as source:
-        ...     data_dir = copytree(source, str(testdir / 'work'))
+        >>> _ = copytree(source, testdir / 'work')
         >>> out_figs = testdir / 'out' / 'fmriprep'
-        >>> bl = BIDSLayout(str(testdir / 'work' / 'reportlets'),
+        >>> bl = BIDSLayout(testdir / 'work' / 'reportlets',
         ...                 config='figures', validate=False)
 
     >>> bl.get(subject='01', desc='reconall') # doctest: +ELLIPSIS
@@ -165,10 +162,6 @@ class Reportlet(Element):
     >>> r.is_empty()
     True
 
-    .. testcleanup::
-
-        >>> os.chdir(cwd)
-
     """
 
     def __init__(self, layout, out_dir, config=None):
@@ -249,15 +242,11 @@ class Report:
 
     .. testsetup::
 
-        >>> cwd = os.getcwd()
-        >>> os.chdir(tmpdir)
-
         >>> from shutil import copytree
         >>> from bids.layout import BIDSLayout
-        >>> test_data_path = find_resource_or_skip('data/tests/work')
+        >>> source = find_resource_or_skip('data/tests/work')
         >>> testdir = Path(tmpdir)
-        >>> with importlib_resources.as_file(test_data_path) as source:
-        ...     data_dir = copytree(source, str(testdir / 'work'))
+        >>> _ = copytree(source, str(testdir / 'work'))
         >>> out_figs = testdir / 'out' / 'fmriprep'
 
     >>> robj = Report(testdir / 'out', 'madeoutuuid', subject_id='01', packagename='fmriprep',
@@ -270,10 +259,6 @@ class Report:
     >>> len((testdir / 'out' / 'fmriprep' / 'sub-01.html').read_text())
     36713
 
-    .. testcleanup::
-
-        >>> os.chdir(cwd)
-
     """
 
     def __init__(
@@ -303,8 +288,8 @@ def __init__(
             self.out_filename = f"sub-{self.subject_id}.html"
 
         # Default template from niworkflows
-        self.template_path = Path(pkgrf("niworkflows", "reports/report.tpl"))
-        self._load_config(Path(config or pkgrf("niworkflows", "reports/default.yml")))
+        self.template_path = load_resource('reports') / 'report.tpl'
+        self._load_config(Path(config or load_resource('reports') / 'default.yml'))
         assert self.template_path.exists()
 
     def _load_config(self, config):
@@ -424,14 +409,12 @@ def generate_report(self):
                 .findall((logs_path / "CITATION.tex").read_text())[0]
                 .strip()
             )
+            bib = data.Loader(self.packagename).readable("data/boilerplate.bib")
             boilerplate.append(
                 (
                     boiler_idx,
                     "LaTeX",
-                    f"""<pre>{text}</pre>
-<h3>Bibliography</h3>
-<pre>{Path(pkgrf(self.packagename, 'data/boilerplate.bib')).read_text()}</pre>
-""",
+                    f"<pre>{text}</pre>\n<h3>Bibliography</h3>\n<pre>{bib.read_text()}</pre>\n",
                 )
             )
             boiler_idx += 1
@@ -519,24 +502,16 @@ def run_reports(
 
     .. testsetup::
 
-        >>> cwd = os.getcwd()
-        >>> os.chdir(tmpdir)
-
         >>> from shutil import copytree
-        >>> test_data_path = find_resource_or_skip('data/tests/work')
+        >>> source = find_resource_or_skip('data/tests/work')
         >>> testdir = Path(tmpdir)
-        >>> with importlib_resources.as_file(test_data_path) as source:
-        ...     data_dir = copytree(source, str(testdir / 'work'))
+        >>> _ = copytree(source, testdir / 'work')
         >>> (testdir / 'fmriprep').mkdir(parents=True, exist_ok=True)
 
     >>> run_reports(testdir / 'out', '01', 'madeoutuuid', packagename='fmriprep',
     ...             reportlets_dir=testdir / 'work' / 'reportlets')
     0
 
-    .. testcleanup::
-
-        >>> os.chdir(cwd)
-
     """
     return Report(
         out_dir,