refactor: update references from fmriprep to petprep

Author: mnoergaard

petprep/cli/parser.py

@@ -630,7 +630,7 @@ def _reference_frame(value, parser):
         default=False,
         help='Opt-out of sending tracking information of this run to '
         'the PETPREP developers. This information helps to '
-        'improve FMRIPREP and provides an indicator of real '
+        'improve PETPrep and provides an indicator of real '
         'world usage crucial for obtaining funding.',
     )
     g_other.add_argument(

petprep/cli/run.py

@@ -54,7 +54,7 @@ def main():
         tracker.start()
 
     if 'pdb' in config.execution.debug:
-        from fmriprep.utils.debug import setup_exceptionhook
+        from petprep.utils.debug import setup_exceptionhook
 
         setup_exceptionhook()
         config.nipype.plugin = 'Linear'
@@ -205,7 +205,7 @@ def main():
             config.loggers.workflow.log(25, f'Saving logs at: {config.execution.log_dir}')
             config.loggers.workflow.log(25, f'Carbon emissions: {emissions} kg')
 
-        from fmriprep.reports.core import generate_reports
+        from petprep.reports.core import generate_reports
 
         # Generate reports phase
         session_list = (

petprep/cli/tests/test_parser.py

@@ -117,7 +117,7 @@ def _mock_check_latest(*args, **kwargs):
     msg = f"""\
 You are using fMRIPrep-{current}, and a newer version of fMRIPrep is available: {latest}.
 Please check out our documentation about how and when to upgrade:
-https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading"""
+https://petprep.readthedocs.io/en/latest/faq.html#upgrading"""
 
     assert (msg in captured) is expectation
 

petprep/cli/workflow.py

@@ -38,8 +38,8 @@ def build_workflow(config_file, retval):
     from niworkflows.utils.bids import collect_participants
     from niworkflows.utils.misc import check_valid_fs_license
 
-    from fmriprep.reports.core import generate_reports
-    from fmriprep.utils.bids import check_pipeline_version
+    from petprep.reports.core import generate_reports
+    from petprep.utils.bids import check_pipeline_version
 
     from .. import config, data
     from ..utils.misc import check_deps

petprep/config.py

@@ -37,7 +37,7 @@
    :caption: **Example file representation of PETPrep settings**.
 
 This config file is used to pass the settings across processes,
-using the :py:func:`~fmriprep.config.load` function.
+using the :py:func:`~petprep.config.load` function.
 
 Configuration sections
 ----------------------

petprep/interfaces/reports.py

@@ -211,8 +211,8 @@ def _generate_segment(self):
 
 
 class AboutSummaryInputSpec(BaseInterfaceInputSpec):
-    version = Str(desc='FMRIPREP version')
-    command = Str(desc='FMRIPREP command')
+    version = Str(desc='PETPrep version')
+    command = Str(desc='PETPrep command')
     # Date not included - update timestamp only if version or command changes
 
 

petprep/interfaces/tests/test_bids.py

@@ -1,9 +1,9 @@
-"""Tests for fmriprep.interfaces.bids."""
+"""Tests for petprep.interfaces.bids."""
 
 
 def test_BIDSURI():
     """Test the BIDSURI interface."""
-    from fmriprep.interfaces.bids import BIDSURI
+    from petprep.interfaces.bids import BIDSURI
 
     dataset_links = {
         'raw': '/data',

petprep/interfaces/tests/test_confounds.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from nipype.pipeline import engine as pe
 
-from fmriprep.interfaces import confounds
+from petprep.interfaces import confounds
 
 
 def test_RenameACompCor(tmp_path, data_dir):

petprep/interfaces/tests/test_maths.py

@@ -2,7 +2,7 @@
 import numpy as np
 from nipype.pipeline import engine as pe
 
-from fmriprep.interfaces.maths import Clip
+from petprep.interfaces.maths import Clip
 
 
 def test_Clip(tmp_path):

petprep/interfaces/workbench.py

@@ -569,7 +569,7 @@ class VolumeToSurfaceMapping(WBCommand, OpenMPCommandMixin):
         intended to be larger than where the cylinder cutoff should have been.
 
     Examples:
-    >>> from fmriprep.interfaces.workbench import VolumeToSurfaceMapping
+    >>> from petprep.interfaces.workbench import VolumeToSurfaceMapping
     >>> vol2surf = VolumeToSurfaceMapping()
     >>> vol2surf.inputs.volume_file = 'bold.nii.gz'
     >>> vol2surf.inputs.surface_file = 'lh.midthickness.surf.gii'
@@ -659,7 +659,7 @@ class MetricMask(WBCommand):
 
     Examples
 
-    >>> from fmriprep.interfaces.workbench import MetricMask
+    >>> from petprep.interfaces.workbench import MetricMask
     >>> metric_mask = MetricMask()
     >>> metric_mask.inputs.in_file = 'lh.bold.func.gii'
     >>> metric_mask.inputs.mask = 'lh.roi.shape.gii'
@@ -725,7 +725,7 @@ class MetricFillHoles(WBCommand):
 
     Examples
 
-    >>> from fmriprep.interfaces.workbench import MetricFillHoles
+    >>> from petprep.interfaces.workbench import MetricFillHoles
     >>> fill_holes = MetricFillHoles()
     >>> fill_holes.inputs.surface_file = 'lh.midthickness.surf.gii'
     >>> fill_holes.inputs.metric_file = 'lh.roi.shape.gii'
@@ -792,7 +792,7 @@ class MetricRemoveIslands(WBCommand):
 
     Examples
 
-    >>> from fmriprep.interfaces.workbench import MetricRemoveIslands
+    >>> from petprep.interfaces.workbench import MetricRemoveIslands
     >>> remove_islands = MetricRemoveIslands()
     >>> remove_islands.inputs.surface_file = 'lh.midthickness.surf.gii'
     >>> remove_islands.inputs.metric_file = 'lh.roi.shape.gii'