Apply suggestions from code review [skip ci]

Co-Authored-By: Ariel Rokem <[email protected]>

Author: oesteban

dmriprep/cli/parser.py

@@ -131,7 +131,7 @@ def _bids_filter(value):
 colon-separated parameters. \
 Non-standard spaces imply specific orientations and sampling grids. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization. To generate no BOLD outputs, use this option without specifying \
+the spatial normalization. To generate no DWI outputs, use this option without specifying \
 any spatial references. For further details, please check out \
 https://www.nipreps.org/dmriprep/%s/spaces.html""" % (currentv.base_version
                                                       if is_release else 'latest'))
@@ -205,8 +205,8 @@ def _bids_filter(value):
                               ' was specified.')
     g_other.add_argument('--notrack', action='store_true', default=False,
                          help='Opt-out of sending tracking information of this run to '
-                              'the FMRIPREP developers. This information helps to '
-                              'improve FMRIPREP and provides an indicator of real '
+                              'the dMRIPREP developers. This information helps to '
+                              'improve dMRIPREP and provides an indicator of real '
                               'world usage crucial for obtaining funding.')
     g_other.add_argument('--sloppy', dest='debug', action='store_true', default=False,
                          help='Use low-quality tools for speed - TESTING ONLY')

dmriprep/cli/run.py

@@ -27,7 +27,7 @@ def main():
     # CRITICAL Save the config to a file. This is necessary because the execution graph
     # is built as a separate process to keep the memory footprint low. The most
     # straightforward way to communicate with the child process is via the filesystem.
-    config_file = config.execution.work_dir / '.fmriprep.toml'
+    config_file = config.execution.work_dir / '.dmriprep.toml'
     config.to_filename(config_file)
 
     # CRITICAL Call build_workflow(config_file, retval) in a subprocess.
@@ -45,7 +45,7 @@ def main():
 
     # CRITICAL Load the config from the file. This is necessary because the ``build_workflow``
     # function executed constrained in a process may change the config (and thus the global
-    # state of fMRIPrep).
+    # state of dMRIPrep).
     config.load(config_file)
 
     if config.execution.reports_only:
@@ -85,15 +85,15 @@ def main():
     except Exception as e:
         if not config.execution.notrack:
             popylar.track_event(__ga_id__, 'run', 'error')
-        config.loggers.workflow.critical('fMRIPrep failed: %s', e)
+        config.loggers.workflow.critical('dMRIPrep failed: %s', e)
         raise
     else:
         config.loggers.workflow.log(25, 'dMRIPrep finished successfully!')
 
         # Bother users with the boilerplate only iff the workflow went okay.
         if (config.execution.output_dir / 'dmriprep' / 'logs' / 'CITATION.md').exists():
             config.loggers.workflow.log(
-                25, 'Works derived from this fMRIPrep execution should '
+                25, 'Works derived from this dMRIPrep execution should '
                 'include the following boilerplate:\n\n%s',
                 (config.execution.output_dir / 'dmriprep' / 'logs' / 'CITATION.md').read_text()
             )

dmriprep/config/__init__.py

@@ -58,7 +58,7 @@
 
 Other responsibilities
 ----------------------
-The :py:mod:`config` is responsible for other conveniency actions.
+The :py:mod:`config` is responsible for other convenience actions.
 
   * Switching Python's :obj:`multiprocessing` to *forkserver* mode.
   * Set up a filter for warnings as early as possible.