fix: documentation build

Author: oesteban

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,
-    )
+    mock_config()
+    wf = init_single_subject_wf()
 
 Preprocessing of structural MRI
 -------------------------------
@@ -279,44 +237,14 @@ BOLD preprocessing
     :graph2use: orig
     :simple_form: yes
 
+    from fmriprep.workflows.tests import mock_config
+    from fmriprep.workflows.bold.base import init_func_preproc_wf
+    mock_config()
+
     from collections import namedtuple
     from niworkflows.utils.spaces import SpatialReferences
-    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,
-    )
+    wf = init_func_preproc_wf('sub-01_task-nback_bold.nii.gz')
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
 split into multiple sub-workflows described below.
@@ -396,7 +324,7 @@ 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

fmriprep/config.py

@@ -499,7 +499,7 @@ def init_layout():
         execution._layout = BIDSLayout(
             str(execution.bids_dir),
             validate=False,
-            database_path=str(work_dir),
+            # database_path=str(work_dir),
             ignore=("code", "stimuli", "sourcedata", "models",
                     "derivatives", re.compile(r'^\.')))
     execution.layout = execution._layout
@@ -522,10 +522,13 @@ def set_logger_level():
 def init_spaces(checkpoint=True):
     """Get a spatial references."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
-    if getattr(workflow, 'spaces'):
+    if (
+        getattr(workflow, 'spaces')
+        and isinstance(workflow.spaces, SpatialReferences)
+    ):
         return
 
-    spaces = getattr(execution, 'output_spaces')
+    spaces = execution.output_spaces
     if spaces is not None and not isinstance(spaces, _SRs):
         spaces = SpatialReferences(
             [ref for s in execution.output_spaces.split(' ')
@@ -537,7 +540,7 @@ def init_spaces(checkpoint=True):
     if checkpoint:
         spaces.checkpoint()
 
-    internal = getattr(workflow, 'internal_spaces')
+    internal = workflow.internal_spaces
     if internal is not None and internal.strip():
         spaces += [ref for s in internal.split(' ')
                    for ref in Reference.from_string(s)]

fmriprep/data/tests/config.toml

@@ -0,0 +1,64 @@
+[environment]
+cpu_count = 8
+exec_env = "posix"
+free_mem = 2.2
+overcommit_policy = "heuristic"
+overcommit_limit = "50%"
+nipype_version = "1.5.0"
+templateflow_version = "0.4.2"
+version = "20.0.1"
+
+[execution]
+bids_dir = "ds000005/"
+bids_description_hash = "5d42e27751bbc884eca87cb4e62b9a0cca0cd86f8e578747fe89b77e6c5b21e5"
+boilerplate_only = false
+fs_license_file = "/opt/freesurfer/license.txt"
+fs_subjects_dir = "/opt/freesurfer/subjects"
+log_dir = "/home/oesteban/tmp/fmriprep-ds005/out/fmriprep/logs"
+log_level = 40
+low_mem = false
+md_only_boilerplate = false
+notrack = true
+output_dir = "/tmp"
+output_spaces = "MNI152NLin2009cAsym:res-2 MNI152NLin2009cAsym:res-native fsaverage:den-10k fsaverage:den-30k"
+reports_only = false
+run_uuid = "20200306-105302_d365772b-fd60-4741-a722-372c2f558b50"
+participant_label = [ "01",]
+templateflow_home = "~/.cache/templateflow"
+work_dir = "work/"
+write_graph = false
+
+[workflow]
+anat_only = false
+aroma_err_on_warn = false
+aroma_melodic_dim = -200
+bold2t1w_dof = 6
+fmap_bspline = false
+force_syn = false
+hires = true
+ignore = []
+internal_spaces = "fsaverage:den-164k MNI152NLin6Asym:res-2"
+longitudinal = false
+medial_surface_nan = false
+regressors_all_comps = false
+regressors_dvars_th = 1.5
+regressors_fd_th = 0.5
+run_reconall = true
+skull_strip_fixed_seed = false
+skull_strip_template = "OASIS30ANTs"
+t2s_coreg = false
+use_aroma = false
+
+[nipype]
+crashfile_format = "txt"
+get_linked_libs = false
+memory_gb = 32
+nprocs = 8
+omp_nthreads = 8
+plugin = "MultiProc"
+resource_monitor = false
+stop_on_first_crash = false
+
+[nipype.plugin_args]
+maxtasksperchild = 1
+raise_insufficient = false

fmriprep/data/tests/ds000005/CHANGES

@@ -0,0 +1,12 @@
+2.0.1 2016-10-21
+  
+  - Added authors to dataset_discription.json
+
+1.0.1 2016-02-18
+
+  -  Update orientation information in nifti header for improved left-right determination
+
+
+1.0.0 2011-10-06
+
+  -  initial release

fmriprep/data/tests/ds000005/README

@@ -0,0 +1,22 @@
+This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).
+Accession #: ds005
+Description: Mixed-gambles task
+
+Please cite the following references if you use these data:
+
+Tom, S.M., Fox, C.R., Trepel, C., Poldrack, R.A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315(5811):515-8
+
+
+Release history:
+10/06/2011: initial release
+3/21/2013: Updated release with QA information
+2/18/2016: Update orientation information in nifti header for improved left-right determination
+
+This dataset is made available under the Public Domain Dedication and License 
+v1.0, whose full text can be found at 
+http://www.opendatacommons.org/licenses/pddl/1.0/. 
+We hope that all users will follow the ODC Attribution/Share-Alike 
+Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); 
+in particular, while not legally required, we hope that all users 
+of the data will acknowledge the OpenfMRI project and NSF Grant 
+OCI-1131441 (R. Poldrack, PI) in any publications.

fmriprep/data/tests/ds000005/dataset_description.json

@@ -0,0 +1,7 @@
+{
+    "BIDSVersion": "1.0.0rc4",
+    "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
+    "Name": "Mixed-gambles task",
+    "Authors": ["Tom, S.M.", "Fox, C.R.", "Trepel, C.", "Poldrack, R.A."],
+    "ReferencesAndLinks": "Tom, S.M., Fox, C.R., Trepel, C., Poldrack, R.A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315(5811):515-8"
+}

fmriprep/data/tests/ds000005/participants.tsv

@@ -0,0 +1,17 @@
+participant_id	sex	age
+sub-01	M	28
+sub-02	F	21
+sub-03	F	27
+sub-04	M	25
+sub-05	F	20
+sub-06	M	20
+sub-07	F	24
+sub-08	M	25
+sub-09	F	19
+sub-10	M	20
+sub-11	M	20
+sub-12	M	21
+sub-13	F	22
+sub-14	F	19
+sub-15	F	20
+sub-16	M	22