Merge pull request #2018 from oesteban/maint/config-file

ENH: Config module to replace long list of downstreamed arguments

.circleci/config.yml

@@ -334,10 +334,10 @@ jobs:
             - data-v7-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - ds005-anat-v17-{{ .Branch }}-{{ .Revision }}
-            - ds005-anat-v17-{{ .Branch }}
-            - ds005-anat-v17-master
-            - ds005-anat-v17-
+            - ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
+            - ds005-anat-v18-{{ .Branch }}
+            - ds005-anat-v18-master
+            - ds005-anat-v18-
       - run:
           name: Set-up a Docker registry
           command: |
@@ -380,7 +380,7 @@ jobs:
             rm -rf /tmp/ds005/work/reportlets
             rm -rf /tmp/ds005/derivatives/fmriprep
       - save_cache:
-         key: ds005-anat-v17-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+         key: ds005-anat-v18-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
          paths:
             - /tmp/ds005/work
 
@@ -404,6 +404,8 @@ jobs:
                 --output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
                 --use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
                 --nthreads 2 --cifti-output -vv
+      - store_artifacts:
+          path: /tmp/ds005/derivatives
       - run:
           name: Move intermediate results for second run
           command: |
@@ -414,7 +416,7 @@ jobs:
           name: Checking outputs of full fMRIPrep run
           command: |
             mkdir -p /tmp/ds005/test
-            find /tmp/ds005/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -437,7 +439,7 @@ jobs:
           command: |
             mkdir -p /tmp/ds005/test
             sudo rm -rf /tmp/ds005/derivatives_partial/freesurfer
-            find /tmp/ds005/derivatives_partial -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_partial_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -458,7 +460,7 @@ jobs:
                 -exec sh -c 'rm -f {}; touch {}' \;
 
       - store_artifacts:
-          path: /tmp/ds005
+          path: /tmp/ds005/work
 
   ds054:
     machine:
@@ -562,7 +564,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds054/test
-            find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
+            find /tmp/ds054/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
             exit $?
       - run:
@@ -700,7 +702,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds210/test
-            find /tmp/ds210/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
+            find /tmp/ds210/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds210_outputs.txt /tmp/ds210/test/outputs.out
             exit $?
       - run:

.travis.yml

@@ -10,7 +10,7 @@ python:
 
 before_install:
   - python -m pip install --upgrade pip
-  - pip install "flake8<3.0" flake8-putty
+  - pip install flake8
 
 script:
   - flake8 fmriprep wrapper

docs/api.rst

@@ -3,6 +3,11 @@
 ================
 Developers - API
 ================
+Internal configuration system
+-----------------------------
+
+.. automodule:: fmriprep.config
+   :members: from_dict, load, get, dumps, to_filename, init_spaces
 
 Workflows
 ---------

docs/usage.rst

@@ -31,7 +31,7 @@ Example: ::
 Command-Line Arguments
 ----------------------
 .. argparse::
-   :ref: fmriprep.cli.run.get_parser
+   :ref: fmriprep.cli.parser._build_parser
    :prog: fmriprep
    :nodefault:
    :nodefaultconst:

docs/workflows.rst

@@ -17,52 +17,10 @@ is presented below:
     :graph2use: orig
     :simple_form: yes
 
-    from collections import namedtuple
-    from niworkflows.utils.spaces import Reference, SpatialReferences
+    from fmriprep.workflows.tests import mock_config
     from fmriprep.workflows.base import init_single_subject_wf
-    BIDSLayout = namedtuple('BIDSLayout', ('root'))
-    wf = init_single_subject_wf(
-        anat_only=False,
-        aroma_melodic_dim=-200,
-        bold2t1w_dof=9,
-        cifti_output=False,
-        debug=False,
-        dummy_scans=None,
-        echo_idx=None,
-        err_on_aroma_warn=False,
-        fmap_bspline=False,
-        fmap_demean=True,
-        force_syn=True,
-        freesurfer=True,
-        hires=True,
-        ignore=[],
-        layout=BIDSLayout('.'),
-        longitudinal=False,
-        low_mem=False,
-        medial_surface_nan=False,
-        name='single_subject_wf',
-        omp_nthreads=1,
-        output_dir='.',
-        reportlets_dir='.',
-        regressors_all_comps=False,
-        regressors_dvars_th=1.5,
-        regressors_fd_th=0.5,
-        skull_strip_fixed_seed=False,
-        skull_strip_template=Reference('OASIS30ANTs'),
-        spaces=SpatialReferences(
-            spaces=[('MNI152Lin', {}),
-                    ('fsaverage', {'density': '10k'}),
-                    ('T1w', {}),
-                    ('fsnative', {})],
-            checkpoint=True),
-        subject_id='test',
-        t2s_coreg=False,
-        task_id='',
-        use_aroma=False,
-        use_bbr=True,
-        use_syn=True,
-        bids_filters=None,
-    )
+    with mock_config():
+        wf = init_single_subject_wf('01')
 
 Preprocessing of structural MRI
 -------------------------------
@@ -96,7 +54,7 @@ single reference template (see `Longitudinal processing`_).
         skull_strip_fixed_seed=False,
     )
 
-See also *sMRIPrep*'s 
+See also *sMRIPrep*'s
 :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`.
 
 .. _t1preproc_steps:
@@ -218,7 +176,7 @@ would be processed by the following command::
         -autorecon1 \
         -noskullstrip
 
-The second phase imports the brainmask calculated in the 
+The second phase imports the brainmask calculated in the
 `Preprocessing of structural MRI`_ sub-workflow.
 The final phase resumes reconstruction, using the T2w image to assist
 in finding the pial surface, if available.
@@ -279,44 +237,13 @@ BOLD preprocessing
     :graph2use: orig
     :simple_form: yes
 
-    from collections import namedtuple
-    from niworkflows.utils.spaces import SpatialReferences
+    from fmriprep.workflows.tests import mock_config
+    from fmriprep import config
     from fmriprep.workflows.bold.base import init_func_preproc_wf
-    BIDSLayout = namedtuple('BIDSLayout', ['root'])
-    wf = init_func_preproc_wf(
-        aroma_melodic_dim=-200,
-        bold2t1w_dof=9,
-        bold_file='/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
-        cifti_output=False,
-        debug=False,
-        dummy_scans=None,
-        err_on_aroma_warn=False,
-        fmap_bspline=True,
-        fmap_demean=True,
-        force_syn=True,
-        freesurfer=True,
-        ignore=[],
-        low_mem=False,
-        medial_surface_nan=False,
-        omp_nthreads=1,
-        output_dir='.',
-        regressors_all_comps=False,
-        regressors_fd_th=0.5,
-        regressors_dvars_th=1.5,
-        reportlets_dir='.',
-        t2s_coreg=False,
-        spaces=SpatialReferences(
-            spaces=[('MNI152Lin', {}),
-                    ('fsaverage', {'density': '10k'}),
-                    ('T1w', {}),
-                    ('fsnative', {})],
-            checkpoint=True),
-        use_aroma=False,
-        use_bbr=True,
-        use_syn=True,
-        layout=BIDSLayout('.'),
-        num_bold=1,
-    )
+    with mock_config():
+        bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
+            / 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+        wf = init_func_preproc_wf(str(bold_file))
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
 split into multiple sub-workflows described below.
@@ -396,7 +323,7 @@ Slice time correction
     wf = init_bold_stc_wf(
         metadata={'RepetitionTime': 2.0,
                   'SliceTiming': [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]},
-        )
+    )
 
 If the ``SliceTiming`` field is available within the input dataset metadata,
 this workflow performs slice time correction prior to other signal resampling
@@ -501,7 +428,7 @@ Resampling BOLD runs onto standard spaces
 This sub-workflow concatenates the transforms calculated upstream (see
 `Head-motion estimation`_, `Susceptibility Distortion Correction (SDC)`_ --if
 fieldmaps are available--, `EPI to T1w registration`_, and an anatomical-to-standard
-transform from `Preprocessing of structural MRI`_) to map the 
+transform from `Preprocessing of structural MRI`_) to map the
 :abbr:`EPI (echo-planar imaging)`
 image to the standard spaces given by the ``--output-spaces`` argument
 (see :ref:`output-spaces`).

fmriprep/__about__.py

@@ -1,8 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Base module variables
-"""
+"""Base module variables."""
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions

fmriprep/__init__.py

@@ -1,26 +1,17 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-This pipeline is developed by the Poldrack lab at Stanford University
-(https://poldracklab.stanford.edu/) for use at
-the Center for Reproducible Neuroscience (http://reproducibility.stanford.edu/),
-as well as for open-source software distribution.
-"""
+"""Top-module metadata."""
 
-from .__about__ import (  # noqa
-    __version__,
+from .__about__ import (
     __copyright__,
     __credits__,
     __packagename__,
+    __version__,
 )
 
-import warnings
-
-# cmp is not used by fmriprep, so ignore nipype-generated warnings
-warnings.filterwarnings('ignore', r'cmp not installed')
-warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
-warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
-warnings.simplefilter('ignore', DeprecationWarning)
-warnings.simplefilter('ignore', ResourceWarning)
+__all__ = [
+    '__copyright__',
+    '__credits__',
+    '__packagename__',
+    '__version__',
+]