Merge pull request #1459 from poldracklab/fix/docs

FIX: ReadTheDocs builds

Author: effigies

.readthedocs.yml

@@ -1,12 +1,14 @@
 # conda:
 #     file: docs/environment.yml
 # requirements_file: requirements.txt - this option seems to be ignored by RTD
-formats:
-    - none
+build:
+    image: latest
+
 python:
-    setup_py_install: false
+    version: 3.6
     pip_install: true
-    version: 3.5
+    use_system_site_packages: true
     extra_requirements:
         - doc
 
+formats: []

docs/environment.yml

@@ -28,5 +28,5 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.5.2.post5,<0.5.3
+    - git+https://github.com/poldracklab/niworkflows.git@master#egg=niworkflows
     - tedana>=0.0.5

fmriprep/__about__.py

@@ -98,10 +98,13 @@
     'scikit-image',
     'statsmodels',
     'tedana>=0.0.5',
+    'psutil>=5.4',
 ]
 
 
 LINKS_REQUIRES = [
+    'git+https://github.com/poldracklab/niworkflows.git@'
+    'master#egg=niworkflows',
 ]
 
 TESTS_REQUIRES = [
@@ -121,7 +124,7 @@
         'sphinx_rtd_theme',
     ],
     'duecredit': ['duecredit'],
-    'resmon': ['psutil>=5.4.0'],
+    'resmon': [],
     'sentry': ['sentry-sdk>=0.5.3'],
     'tests': TESTS_REQUIRES,
 }

fmriprep/data/flirtsch/bbr.sch

@@ -0,0 +1,44 @@
+# 1mm scale
+setscale 1 force
+setoption costfunction bbr
+setoption optimisationtype brent
+setoption tolerance 0.0005 0.0005 0.0005 0.02 0.02 0.02 0.002 0.002 0.002 0.001 0.001 0.001
+#setoption tolerance 0.005 0.005 0.005 0.2 0.2 0.2 0.02 0.02 0.02 0.01 0.01 0.01
+setoption boundguess 1
+setoption bbrstep 200
+clear UA
+clear UU
+clear UV
+clear U
+setrowqsform UU
+setrow UU 1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1
+measurecost 6 UU:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+gridmeasurecost 6 UU:1-2  -0.07 0.07 0.07  -0.07 0.07 0.07  -0.07 0.07 0.07  -4.0 4.0 4.0  -4.0 4.0 4.0  -4.0 4.0 4.0  0.0 0.0 0.0  abs 8
+sort U
+copy U UA
+clear U
+optimise 6 UA:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype powell
+optimise 6 U:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype brent
+optimise 6 U:2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4
+sort U
+setoption tolerance 0.0002 0.0002 0.0002 0.02 0.02 0.02 0.002 0.002 0.002 0.001 0.001 0.001
+setoption bbrstep 2
+clear UU
+copy U UU
+clear U
+gridmeasurecost 6 UU:1  -0.0017 0.0017 0.0017  -0.0017 0.0017 0.0017  -0.0017 0.0017 0.0017  -0.1 0.1 0.1  -0.1 0.1 0.1  -0.1 0.1 0.1  0.0 0.0 0.0  abs 8
+sort U
+clear UB
+copy U UB
+clear U
+setoption optimisationtype brent
+optimise 6 UB:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype powell
+optimise 12 U:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype brent
+optimise 12 U:2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4
+sort U
+print U:1
+

fmriprep/workflows/bold/registration.py

@@ -16,7 +16,10 @@
 import os
 import os.path as op
 
+import pkg_resources as pkgr
+
 from nipype.pipeline import engine as pe
+from nipype import logging
 from nipype.interfaces import utility as niu, fsl, c3
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 # See https://github.com/poldracklab/fmriprep/issues/768
@@ -37,6 +40,8 @@
 
 DEFAULT_MEMORY_MIN_GB = 0.01
 
+LOGGER = logging.getLogger('nipype.workflow')
+
 
 def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, mem_gb, omp_nthreads,
                      use_compression=True, write_report=True, name='bold_reg_wf'):
@@ -658,10 +663,17 @@ def init_fsl_bbr_wf(use_bbr, bold2t1w_dof, name='fsl_bbr_wf'):
         return workflow
 
     flt_bbr = pe.Node(
-        FLIRTRPT(cost_func='bbr', dof=bold2t1w_dof, generate_report=True,
-                 schedule=op.join(os.getenv('FSLDIR'), 'etc/flirtsch/bbr.sch')),
+        FLIRTRPT(cost_func='bbr', dof=bold2t1w_dof, generate_report=True),
         name='flt_bbr')
 
+    FSLDIR = os.getenv('FSLDIR')
+    if FSLDIR:
+        flt_bbr.inputs.schedule = op.join(FSLDIR, 'etc/flirtsch/bbr.sch')
+    else:
+        # Should mostly be hit while building docs
+        LOGGER.warning("FSLDIR unset - using packaged BBR schedule")
+        flt_bbr.inputs.schedule = pkgr.resource_filename('fmriprep', 'data/flirtsch/bbr.sch')
+
     workflow.connect([
         (inputnode, wm_mask, [('t1_seg', 'in_seg')]),
         (inputnode, flt_bbr, [('in_file', 'in_file'),

fmriprep/workflows/bold/util.py

@@ -290,7 +290,8 @@ def init_enhance_and_skullstrip_bold_wf(
             name='init_aff',
             n_procs=omp_nthreads)
 
-        if parseversion(Registration().version) > Version('2.2.0'):
+        # Registration().version may be None
+        if parseversion(Registration().version or '0.0.0') > Version('2.2.0'):
             init_aff.inputs.search_grid = (40, (0, 40, 40))
 
         # Set up spatial normalization

requirements.txt

@@ -1,3 +1,3 @@
-niworkflows>=0.5.2.post5,<0.5.3
 grabbit==0.2.3
 pybids==0.6.5
+git+https://github.com/poldracklab/niworkflows.git@master#egg=niworkflows

setup.py

@@ -38,6 +38,7 @@ def main():
             'data/*.mat',
             'data/boilerplate.bib',
             'data/itkIdentityTransform.txt',
+            'data/flirtsch/bbr.sch',
             'viz/*.tpl',
             'viz/*.json',
         ]