Merge pull request nipreps#1199 from nipreps/fix/move-to-loader

FIX: Move from ``pkg_resources`` to ``niworkflows.data.Loader``

mriqc/data/config.py

@@ -23,7 +23,7 @@
 """Utilities: Jinja2 templates."""
 from pathlib import Path
 
-from pkg_resources import resource_filename as pkgrf
+from niworkflows.data import Loader
 
 
 class GroupTemplate:
@@ -37,7 +37,7 @@ class GroupTemplate:
  def __init__(self):
  import jinja2
 
- self.template_str = pkgrf("mriqc", "data/reports/group.html")
+ self.template_str = Loader(__package__)("data/reports/group.html")
  self.env = jinja2.Environment(
  loader=jinja2.FileSystemLoader(searchpath="/"),
  trim_blocks=True,

mriqc/interfaces/common/ensure_size.py

@@ -37,12 +37,13 @@
  isdefined,
  traits,
 )
-from pkg_resources import resource_filename as pkgrf
+from niworkflows.data import Loader
 
 OUT_FILE_NAME = "{prefix}_resampled{ext}"
 OUT_MASK_NAME = "{prefix}_resmask{ext}"
 REF_FILE_NAME = "resample_ref.nii.gz"
 REF_MASK_NAME = "mask_ref.nii.gz"
+load_data = Loader(__package__)
 
 
 class EnsureSizeInputSpec(BaseInterfaceInputSpec):
@@ -146,7 +147,7 @@ def _run_interface(self, runtime):
  input_image=self.inputs.in_file,
  reference_image=REF_FILE_NAME,
  interpolation="LanczosWindowedSinc",
- transforms=[pkgrf("mriqc", "data/itk_identity.tfm")],
+ transforms=[load_data("data/itk_identity.tfm")],
  output_image=out_file,
  ).run()
 
@@ -167,7 +168,7 @@ def _run_interface(self, runtime):
  input_image=self.inputs.in_mask,
  reference_image=REF_MASK_NAME,
  interpolation="NearestNeighbor",
- transforms=[pkgrf("mriqc", "data/itk_identity.tfm")],
+ transforms=[load_data("data/itk_identity.tfm")],
  output_image=out_mask,
  ).run()
 

mriqc/reports/group.py

@@ -33,7 +33,7 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
  import datetime
  import os.path as op
 
- from pkg_resources import resource_filename as pkgrf
+ from niworkflows.data import Loader
 
  from .. import __version__ as ver
  from mriqc.data.config import GroupTemplate
@@ -43,6 +43,8 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
  else:
  from io import BytesIO as TextIO
 
+ load_data = Loader(__package__)
+
  QCGROUPS = {
  "T1w": [
  (["cjv"], None),
@@ -266,21 +268,13 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None):
  "csv_groups": csv_groups,
  "failed": failed,
  "boxplots_js": open(
- pkgrf(
- "mriqc",
- op.join("data", "reports", "embed_resources", "boxplots.js"),
- )
+ load_data("data/reports/embed_resources/boxplots.js"),
  ).read(),
  "d3_js": open(
- pkgrf(
- "mriqc", op.join("data", "reports", "embed_resources", "d3.min.js")
- )
+ load_data("data/reports/embed_resources/d3.min.js"),
  ).read(),
  "boxplots_css": open(
- pkgrf(
- "mriqc",
- op.join("data", "reports", "embed_resources", "boxplots.css"),
- )
+ load_data("data/reports/embed_resources/boxplots.css"),
  ).read(),
  },
  out_file,

mriqc/reports/individual.py

@@ -23,8 +23,10 @@
 """Encapsulates report generation functions."""
 from pathlib import Path
 from json import loads
-from pkg_resources import resource_filename as pkgrf
 from nireports.assembler.report import Report
+from niworkflows.data import Loader
+
+_load_data = Loader(__package__)
 
 
 def generate_reports():
@@ -86,7 +88,7 @@ def _single_report(in_file):
  config.execution.output_dir,
  config.execution.run_uuid,
  reportlets_dir=config.execution.work_dir / "reportlets",
- bootstrap_file=pkgrf("mriqc", f"data/bootstrap-{report_type}.yml"),
+ bootstrap_file=_load_data(f"data/bootstrap-{report_type}.yml"),
  metadata={
  "dataset": config.execution.dsname,
  "about-metadata": {

mriqc/testing.py

@@ -24,17 +24,19 @@
 from contextlib import contextmanager
 from pathlib import Path
 from tempfile import mkdtemp
-
-from pkg_resources import resource_filename as pkgrf
 from toml import loads
 
+from niworkflows.data import Loader
+
+_load_data = Loader(__package__)
+
 
 @contextmanager
 def mock_config():
  """Create a mock config for documentation and testing purposes."""
  from . import config
 
- filename = Path(pkgrf("mriqc", "data/config-example.toml"))
+ filename = Path(_load_data("data/config-example.toml"))
  settings = loads(filename.read_text())
  for sectionname, configs in settings.items():
  if sectionname != "environment":
@@ -44,7 +46,7 @@ def mock_config():
  config.loggers.init()
 
  config.execution.work_dir = Path(mkdtemp())
- config.execution.bids_dir = Path(pkgrf("mriqc", "data/tests/ds000005")).absolute()
+ config.execution.bids_dir = Path(_load_data("data/tests/ds000005")).absolute()
  config.execution.init()
 
  yield