MNT: Fully drop pkg_resources

Author: effigies

fmriprep/cli/run.py

@@ -202,7 +202,7 @@ def main():
             _copy_any(dseg_tsv, str(config.execution.fmriprep_dir / "desc-aparcaseg_dseg.tsv"))
         errno = 0
     finally:
-        from pkg_resources import resource_filename as pkgrf
+        from .. import data
 
         # Code Carbon
         if config.execution.track_carbon:
@@ -218,7 +218,7 @@ def main():
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            config=pkgrf("fmriprep", "data/reports-spec.yml"),
+            config=data.load("reports-spec.yml"),
             packagename="fmriprep",
         )
         write_derivative_description(config.execution.bids_dir, config.execution.fmriprep_dir)

fmriprep/cli/workflow.py

@@ -38,12 +38,11 @@ def build_workflow(config_file, retval):
 
     from niworkflows.utils.bids import collect_participants
     from niworkflows.utils.misc import check_valid_fs_license
-    from pkg_resources import resource_filename as pkgrf
 
     from fmriprep.reports.core import generate_reports
     from fmriprep.utils.bids import check_pipeline_version
 
-    from .. import config
+    from .. import config, data
     from ..utils.misc import check_deps
     from ..workflows.base import init_fmriprep_wf
 
@@ -57,7 +56,7 @@ def build_workflow(config_file, retval):
     retval["workflow"] = None
 
     banner = [f"Running fMRIPrep version {version}"]
-    notice_path = Path(pkgrf("fmriprep", "data/NOTICE"))
+    notice_path = data.load.readable("NOTICE")
     if notice_path.exists():
         banner[0] += "\n"
         banner += [f"License NOTICE {'#' * 50}"]
@@ -91,7 +90,7 @@ def build_workflow(config_file, retval):
             config.execution.participant_label,
             config.execution.fmriprep_dir,
             config.execution.run_uuid,
-            config=pkgrf("fmriprep", "data/reports-spec.yml"),
+            config=data.load("reports-spec.yml"),
             packagename="fmriprep",
         )
         return retval
@@ -183,9 +182,9 @@ def build_boilerplate(config_file, workflow):
         from pathlib import Path
         from subprocess import CalledProcessError, TimeoutExpired, check_call
 
-        from pkg_resources import resource_filename as pkgrf
+        from .. import data
 
-        bib_text = Path(pkgrf("fmriprep", "data/boilerplate.bib")).read_text()
+        bib_text = data.load.readable("boilerplate.bib").read_text()
         citation_files["bib"].write_text(
             bib_text.replace("fMRIPrep <version>", f"fMRIPrep {config.environment.version}")
         )

fmriprep/tests/test_config.py

@@ -27,10 +27,9 @@
 
 import pytest
 from niworkflows.utils.spaces import format_reference
-from pkg_resources import resource_filename as pkgrf
 from toml import loads
 
-from .. import config
+from .. import config, data
 
 
 def _reset_config():
@@ -59,8 +58,7 @@ def test_reset_config():
 
 def test_config_spaces():
     """Check that all necessary spaces are recorded in the config."""
-    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
-    settings = loads(filename.read_text())
+    settings = loads(data.load.readable("tests/config.toml").read_text())
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)

fmriprep/workflows/bold/registration.py

@@ -33,12 +33,11 @@
 import os.path as op
 import typing as ty
 
-import pkg_resources as pkgr
 from nipype.interfaces import c3, fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 
-from ... import config
+from ... import config, data
 from ...interfaces import DerivativesDataSink
 
 DEFAULT_MEMORY_MIN_GB = config.DEFAULT_MEMORY_MIN_GB
@@ -588,7 +587,7 @@ def init_fsl_bbr_wf(
     else:
         # Should mostly be hit while building docs
         LOGGER.warning("FSLDIR unset - using packaged BBR schedule")
-        flt_bbr.inputs.schedule = pkgr.resource_filename('fmriprep', 'data/flirtsch/bbr.sch')
+        flt_bbr.inputs.schedule = data.load('flirtsch/bbr.sch')
     # fmt:off
     workflow.connect([
         (inputnode, wm_mask, [('t1w_dseg', 'in_seg')]),

fmriprep/workflows/tests/__init__.py

@@ -27,9 +27,10 @@
 from pathlib import Path
 from tempfile import mkdtemp
 
-from pkg_resources import resource_filename as pkgrf
 from toml import loads
 
+from ... import data
+
 
 @contextmanager
 def mock_config():
@@ -40,8 +41,7 @@ def mock_config():
     if not _old_fs:
         os.environ['FREESURFER_HOME'] = mkdtemp()
 
-    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
-    settings = loads(filename.read_text())
+    settings = loads(data.load.readable('tests/config.toml').read_text())
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
@@ -52,7 +52,7 @@ def mock_config():
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
-    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
+    config.execution.bids_dir = data.load('tests/ds000005').absolute()
     config.execution.fmriprep_dir = Path(mkdtemp())
     config.execution.init()