Merge pull request #1909 from mgxd/maint/cl-args

MAINT: Remove deprecated command-line arguments

.circleci/config.yml

@@ -678,8 +678,8 @@ jobs:
                 --config $PWD/nipype.cfg -w /tmp/ds210/work \
                 /tmp/data/ds210 /tmp/ds210/derivatives participant \
                 --fs-no-reconall --t2s-coreg --use-syn-sdc \
-                --template-resampling-grid native --dummy-scans 1 \
-                --sloppy --write-graph --mem_mb 4096 --nthreads 2 -vv
+                --dummy-scans 1 --sloppy --write-graph \
+                --mem_mb 4096 --nthreads 2 -vv
       - run:
           name: Checking outputs of fMRIPrep
           command: |

fmriprep/cli/run.py

@@ -108,11 +108,6 @@ def get_parser():
                          help='run anatomical workflows only')
     g_perfm.add_argument('--boilerplate', action='store_true',
                          help='generate boilerplate only')
-    g_perfm.add_argument('--ignore-aroma-denoising-errors', action='store_true',
-                         default=False,
-                         help='DEPRECATED (now does nothing, see --error-on-aroma-warnings) '
-                              '- ignores the errors ICA_AROMA returns when there are no '
-                              'components classified as either noise or signal')
     g_perfm.add_argument('--md-only-boilerplate', action='store_true',
                          default=False,
                          help='skip generation of HTML and LaTeX formatted citation with pandoc')
@@ -122,8 +117,6 @@ def get_parser():
                               '(e.g., if all the components are classified as signal or noise)')
     g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
                          help="increases log verbosity for each occurence, debug level is -vvv")
-    g_perfm.add_argument('--debug', action='store_true', default=False,
-                         help='DEPRECATED - Does not do what you want.')
 
     g_conf = parser.add_argument_group('Workflow configuration')
     g_conf.add_argument(
@@ -157,26 +150,6 @@ def get_parser():
             ', '.join('"%s"' % s for s in templates()), ', '.join(NONSTANDARD_REFERENCES),
             currentv.base_version if is_release else 'latest'))
 
-    g_conf.add_argument(
-        '--output-space', required=False, action='store', type=str, nargs='+',
-        choices=['T1w', 'template', 'fsnative', 'fsaverage', 'fsaverage6', 'fsaverage5'],
-        help='DEPRECATED: please use ``--output-spaces`` instead.'
-    )
-    g_conf.add_argument(
-        '--template', required=False, action='store', type=str,
-        choices=['MNI152NLin2009cAsym'],
-        help='volume template space (default: MNI152NLin2009cAsym). '
-             'DEPRECATED: please use ``--output-spaces`` instead.')
-    g_conf.add_argument(
-        '--template-resampling-grid', required=False, action='store',
-        help='Keyword ("native", "1mm", or "2mm") or path to an existing file. '
-             'Allows to define a reference grid for the resampling of BOLD images in template '
-             'space. Keyword "native" will use the original BOLD grid as reference. '
-             'Keywords "1mm" and "2mm" will use the corresponding isotropic template '
-             'resolutions. If a path is given, the grid of that image will be used. '
-             'It determines the field of view and resolution of the output images, '
-             'but is not used in normalization. '
-             'DEPRECATED: please use ``--output-spaces`` instead.')
     g_conf.add_argument('--bold2t1w-dof', action='store', default=6, choices=[6, 9, 12], type=int,
                         help='Degrees of freedom when registering BOLD to T1w images. '
                              '6 degrees (rotation and translation) are used by default.')
@@ -261,11 +234,9 @@ def get_parser():
     g_surfs_xor = g_surfs.add_mutually_exclusive_group()
     g_surfs_xor.add_argument('--cifti-output', action='store_true', default=False,
                              help='output BOLD files as CIFTI dtseries')
-    g_surfs_xor.add_argument('--fs-no-reconall', '--no-freesurfer',
+    g_surfs_xor.add_argument('--fs-no-reconall',
                              action='store_false', dest='run_reconall',
-                             help='disable FreeSurfer surface preprocessing.'
-                             ' Note : `--no-freesurfer` is deprecated and will be removed in 1.2.'
-                             ' Use `--fs-no-reconall` instead.')
+                             help='disable FreeSurfer surface preprocessing.')
 
     g_other = parser.add_argument_group('Other options')
     g_other.add_argument('-w', '--work-dir', action='store', type=Path, default=Path('work'),
@@ -340,10 +311,6 @@ def main():
         from ..utils.sentry import sentry_setup
         sentry_setup(opts, exec_env)
 
-    if opts.debug:
-        print('WARNING: Option --debug is deprecated and has no effect',
-              file=sys.stderr)
-
     # Validate inputs
     if not opts.skip_bids_validation:
         print("Making sure the input data is BIDS compliant (warnings can be ignored in most "
@@ -730,34 +697,9 @@ def parse_spaces(opts):
     """Ensures the spaces are correctly parsed"""
     from sys import stderr
     from collections import OrderedDict
-    from templateflow.api import templates as get_templates
     # Set the default template to 'MNI152NLin2009cAsym'
     output_spaces = opts.output_spaces or OrderedDict([('MNI152NLin2009cAsym', {})])
 
-    if opts.template:
-        print("""\
-The ``--template`` option has been deprecated in version 1.4.0. Your selected template \
-"%s" will be inserted at the front of the ``--output-spaces`` argument list. Please update \
-your scripts to use ``--output-spaces``.""" % opts.template, file=stderr)
-        deprecated_tpl_arg = [(opts.template, {})]
-        # If output_spaces is not set, just replate the default - append otherwise
-        if opts.output_spaces is not None:
-            deprecated_tpl_arg += list(output_spaces.items())
-        output_spaces = OrderedDict(deprecated_tpl_arg)
-
-    if opts.output_space:
-        print("""\
-The ``--output_space`` option has been deprecated in version 1.4.0. Your selection of spaces \
-"%s" will be inserted at the front of the ``--output-spaces`` argument list. Please update \
-your scripts to use ``--output-spaces``.""" % ', '.join(opts.output_space), file=stderr)
-        missing = set(opts.output_space)
-        if 'template' in missing:
-            missing.remove('template')
-            if not opts.template:
-                missing.add('MNI152NLin2009cAsym')
-        missing = missing - set(output_spaces.keys())
-        output_spaces.update({tpl: {} for tpl in missing})
-
     FS_SPACES = set(['fsnative', 'fsaverage', 'fsaverage6', 'fsaverage5'])
     if opts.run_reconall and not list(FS_SPACES.intersection(output_spaces.keys())):
         print("""\
@@ -787,15 +729,6 @@ def parse_spaces(opts):
 ``fsaverage`` space. The argument ``fsaverage:den-10k`` (a.k.a ``fsaverage5``) has been \
 automatically added to the list of output spaces (option ``--output-space``).""", file=stderr)
 
-    if opts.template_resampling_grid is not None:
-        print("""Option ``--template-resampling-grid`` is deprecated, please specify \
-resampling grid options as modifiers to templates listed in ``--output-spaces``. \
-The configuration value will be applied to ALL output standard spaces.""")
-        if opts.template_resampling_grid != 'native':
-            for key in output_spaces.keys():
-                if key in get_templates():
-                    output_spaces[key]['res'] = opts.template_resampling_grid[0]
-
     return output_spaces
 
 

fmriprep/workflows/base.py

@@ -637,7 +637,7 @@ def init_single_subject_wf(
               ('outputnode.joint_template', 'inputnode.joint_template'),
               ('outputnode.joint_anat2std_xfm', 'inputnode.joint_anat2std_xfm'),
               ('outputnode.joint_std2anat_xfm', 'inputnode.joint_std2anat_xfm'),
-              # Undefined if --no-freesurfer, but this is safe
+              # Undefined if --fs-no-reconall, but this is safe
               ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
               ('outputnode.subject_id', 'inputnode.subject_id'),
               ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),

fmriprep/workflows/bold/base.py

@@ -589,7 +589,7 @@ def init_func_preproc_wf(
         (inputnode, bold_reg_wf, [
             ('t1w_brain', 'inputnode.t1w_brain'),
             ('t1w_dseg', 'inputnode.t1w_dseg'),
-            # Undefined if --no-freesurfer, but this is safe
+            # Undefined if --fs-no-reconall, but this is safe
             ('subjects_dir', 'inputnode.subjects_dir'),
             ('subject_id', 'inputnode.subject_id'),
             ('fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),

wrapper/fmriprep_docker.py

@@ -18,7 +18,6 @@
 import os
 import re
 import subprocess
-from warnings import warn
 
 __version__ = '99.99.99'
 __copyright__ = 'Copyright 2019, Center for Reproducible Neuroscience, Stanford University'
@@ -31,6 +30,30 @@
 Image '{}' is missing
 Would you like to download? [Y/n] """
 PKG_PATH = '/usr/local/miniconda/lib/python3.7/site-packages'
+TF_TEMPLATES = (
+    'MNI152Lin',
+    'MNI152NLin2009cAsym',
+    'MNI152NLin6Asym',
+    'MNI152NLin6Sym',
+    'MNIInfant',
+    'MNIPediatricAsym',
+    'NKI',
+    'OASIS30ANTs',
+    'PNC',
+    'UNCInfant',
+    'fsLR',
+    'fsaverage',
+    'fsaverage5',
+    'fsaverage6',
+)
+NONSTANDARD_REFERENCES = (
+    'anat',
+    'T1w',
+    'run',
+    'func',
+    'sbref',
+    'fsnative'
+)
 
 # Monkey-patch Py2 subprocess
 if not hasattr(subprocess, 'DEVNULL'):
@@ -141,7 +164,7 @@ def merge_help(wrapper_help, target_help):
 
     # Make sure we're not clobbering options we don't mean to
     overlap = set(w_flags).intersection(t_flags)
-    expected_overlap = set(['h', 'version', 'w', 'template-resampling-grid',
+    expected_overlap = set(['h', 'version', 'w', 'output-spaces',
                             'fs-license-file', 'fs-subjects-dir', 'use-plugin'])
 
     assert overlap == expected_overlap, "Clobbering options: {}".format(
@@ -226,17 +249,19 @@ def get_parser():
     g_wrap.add_argument('-w', '--work-dir', action='store', type=os.path.abspath,
                         help='path where intermediate results should be stored')
     g_wrap.add_argument(
-        '--output-grid-reference', required=False, action='store', type=os.path.abspath,
-        help='Deprecated after FMRIPREP 1.0.8. Please use --template-resampling-grid instead.')
-    g_wrap.add_argument(
-        '--template-resampling-grid', required=False, action='store', type=str,
-        help='Keyword ("native", "1mm", or "2mm") or path to an existing file. '
-             'Allows to define a reference grid for the resampling of BOLD images in template '
-             'space. Keyword "native" will use the original BOLD grid as reference. '
-             'Keywords "1mm" and "2mm" will use the corresponding isotropic template '
-             'resolutions. If a path is given, the grid of that image will be used. '
-             'It determines the field of view and resolution of the output images, '
-             'but is not used in normalization.')
+        '--output-spaces', nargs="+",
+        help="""\
+Standard and non-standard spaces to resample anatomical and functional images to. \
+Standard spaces may be specified by the form \
+``<TEMPLATE>[:res-<resolution>][:cohort-<label>][...]``, where ``<TEMPLATE>`` is \
+a keyword (valid keywords: %s) or path pointing to a user-supplied template, and \
+may be followed by optional, colon-separated parameters. \
+Non-standard spaces (valid keywords: %s) imply specific orientations and sampling \
+grids. \
+Important to note, the ``res-*`` modifier does not define the resolution used for \
+the spatial normalization.""" % (', '.join('"%s"' % s for s in TF_TEMPLATES),
+                                 ', '.join(NONSTANDARD_REFERENCES)))
+
     g_wrap.add_argument(
         '--fs-license-file', metavar='PATH', type=os.path.abspath,
         default=os.getenv('FS_LICENSE', None),
@@ -395,16 +420,16 @@ def main():
                                         'ro'))])
         unknown_args.extend(['--use-plugin', '/tmp/plugin.yml'])
 
-    template_target = opts.template_resampling_grid or opts.output_grid_reference
-    if template_target is not None:
-        if opts.output_grid_reference is not None:
-            warn('Option --output-grid-reference is deprecated, please use '
-                 '--template-resampling-grid', DeprecationWarning)
-        if template_target not in ['native', '2mm' '1mm']:
-            target = '/imports/' + os.path.basename(template_target)
-            command.extend(['-v', ':'.join((os.path.abspath(
-                template_target), target, 'ro'))])
-        unknown_args.extend(['--template-resampling-grid', template_target])
+    if opts.output_spaces:
+        spaces = []
+        for space in opts.output_spaces:
+            if space.split(':')[0] not in (TF_TEMPLATES + NONSTANDARD_REFERENCES):
+                target = '/imports/' + os.path.basename(space)
+                command.extend(['-v', ':'.join((os.path.abspath(space), target, 'ro'))])
+                spaces.append(target)
+            else:
+                spaces.append(space)
+        unknown_args.extend(['--output-spaces'] + spaces)
 
     if opts.shell:
         command.append('--entrypoint=bash')