Merge pull request #3067 from effigies/mnt/workflows_to_niflows

RF: Redirect nipype.workflows to niflow.nipype1.workflows

Author: effigies

docker/generate_dockerfiles.sh

@@ -93,8 +93,8 @@ function generate_main_dockerfile() {
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
                                libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
-                               pandas psutil scikit-learn scipy traits' \
-                pip_install="pytest-xdist" \
+                               pandas psutil scikit-learn scipy traits rdflib' \
+                pip_install="pytest-xdist niflow-nipype1-workflows" \
                 activate=true \
     --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
            docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \

nipype/interfaces/fsl/dti.py

@@ -424,7 +424,7 @@ class BEDPOSTX5(FSLXCommand):
 
 
     .. note:: Consider using
-      :func:`nipype.workflows.fsl.dmri.create_bedpostx_pipeline` instead.
+      :func:`niflow.nipype1.workflows.fsl.dmri.create_bedpostx_pipeline` instead.
 
 
     Example

nipype/interfaces/fsl/epi.py

@@ -1100,7 +1100,7 @@ class EPIDeWarp(FSLCommand):
     <http://surfer.nmr.mgh.harvard.edu/fswiki/epidewarp.fsl>`_.
 
     .. warning:: deprecated in FSL, please use
-      :func:`nipype.workflows.dmri.preprocess.epi.sdc_fmb` instead.
+      :func:`niflow.nipype1.workflows.dmri.preprocess.epi.sdc_fmb` instead.
 
     Examples
     --------

nipype/interfaces/mrtrix/convert.py

@@ -15,13 +15,34 @@
 
 from ... import logging
 from ...utils.filemanip import split_filename
-from ...workflows.misc.utils import get_data_dims, get_vox_dims
 from ..base import TraitedSpec, File, isdefined
 from ..dipy.base import DipyBaseInterface, HAVE_DIPY as have_dipy
 
 iflogger = logging.getLogger('nipype.interface')
 
 
+def get_vox_dims(volume):
+    import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
+    if isinstance(volume, list):
+        volume = volume[0]
+    nii = nb.load(volume, mmap=NUMPY_MMAP)
+    hdr = nii.header
+    voxdims = hdr.get_zooms()
+    return [float(voxdims[0]), float(voxdims[1]), float(voxdims[2])]
+
+
+def get_data_dims(volume):
+    import nibabel as nb
+    from nipype.utils import NUMPY_MMAP
+    if isinstance(volume, list):
+        volume = volume[0]
+    nii = nb.load(volume, mmap=NUMPY_MMAP)
+    hdr = nii.header
+    datadims = hdr.get_data_shape()
+    return [int(datadims[0]), int(datadims[1]), int(datadims[2])]
+
+
 def transform_to_affine(streams, header, affine):
     from dipy.tracking.utils import move_streamlines
     rotation, scale = np.linalg.qr(affine)

nipype/workflows/__init__.py

@@ -1,3 +1,25 @@
 # -*- 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:
+
+_msg = ["Nipype 1 workflows have been moved to the niflow-nipype1-workflows package."]
+try:
+    from niflow.nipype1.workflows import data, dmri, fmri, misc, rsfmri, smri
+except ImportError:
+    _msg.append("pip install niflow-nipype1-workflows to continue using them.")
+else:
+    import sys
+    # Hack to make `from nipype.workflows.X import Y` work
+    sys.modules['nipype.workflows.data'] = data
+    sys.modules['nipype.workflows.dmri'] = dmri
+    sys.modules['nipype.workflows.fmri'] = fmri
+    sys.modules['nipype.workflows.misc'] = misc
+    sys.modules['nipype.workflows.rsfmri'] = rsfmri
+    sys.modules['nipype.workflows.smri'] = smri
+    _msg.append("nipype.workflows.* provides a reference for backwards compatibility. "
+                "Please use niflow.nipype1.workflows.* to avoid this warning.")
+    del sys
+
+import warnings
+warnings.warn(' '.join(_msg))
+del warnings, _msg