Merge pull request #3134 from oesteban/fix/old-workflows-missing

FIX: Can't seem to import workflows from niflows in CircleCI

Author: oesteban

docker/generate_dockerfiles.sh

@@ -94,7 +94,7 @@ function generate_main_dockerfile() {
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
                                libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko
                                pandas psutil scikit-learn scipy traits rdflib' \
-                pip_install="pytest-xdist niflow-nipype1-workflows" \
+                pip_install="pytest-xdist" \
                 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/ \
@@ -110,6 +110,8 @@ function generate_main_dockerfile() {
     --miniconda use_env=neuro \
                 pip_opts="-e" \
                 pip_install="/src/nipype[all] https://github.com/bids-standard/pybids/tarball/0.7.0" \
+    --miniconda use_env=neuro \
+                pip_install='"niflow-nipype1-workflows>=0.4.0"' \
     --workdir /work \
     --label org.label-schema.build-date='$BUILD_DATE' \
             org.label-schema.name="NIPYPE" \

examples/dmri_connectivity_advanced.py

@@ -58,12 +58,12 @@
 import inspect
 import os
 import os.path as op  # system functions
-from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
-from nipype.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
+from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
+from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import select_aparc_annot
 from nipype.utils.misc import package_check
 import warnings
-from nipype.workflows.dmri.connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline
-from nipype.workflows.smri.freesurfer import create_tessellation_flow
+from niflow.nipype1.workflows.dmri.connectivity.nx import create_networkx_pipeline, create_cmats_to_csv_pipeline
+from niflow.nipype1.workflows.smri.freesurfer import create_tessellation_flow
 
 try:
     package_check('cmp')

examples/dmri_dtk_dti.py

@@ -26,7 +26,7 @@
 import nipype.interfaces.utility as util  # utility
 import nipype.pipeline.engine as pe  # pypeline engine
 import os  # system functions
-from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
+from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
 """
 Confirm package dependencies are installed.  (This is only for the
 tutorial, rarely would you put this in your own code.)

examples/dmri_dtk_odf.py

@@ -26,7 +26,7 @@
 import nipype.interfaces.utility as util  # utility
 import nipype.pipeline.engine as pe  # pypeline engine
 import os  # system functions
-from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
+from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
 """
 Confirm package dependencies are installed.  (This is only for the
 tutorial, rarely would you put this in your own code.)

examples/dmri_fsl_dti.py

@@ -25,7 +25,7 @@
 import nipype.interfaces.utility as util  # utility
 import nipype.pipeline.engine as pe  # pypeline engine
 import os  # system functions
-from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline,\
+from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline,\
     create_bedpostx_pipeline
 """
 Confirm package dependencies are installed.  (This is only for the

examples/dmri_group_connectivity_camino.py

@@ -57,8 +57,8 @@
 import nipype.interfaces.freesurfer as fs  # freesurfer
 import os.path as op  # system functions
 import cmp
-from nipype.workflows.dmri.camino.group_connectivity import create_group_connectivity_pipeline
-from nipype.workflows.dmri.connectivity.group_connectivity import (
+from niflow.nipype1.workflows.dmri.camino.group_connectivity import create_group_connectivity_pipeline
+from niflow.nipype1.workflows.dmri.connectivity.group_connectivity import (
     create_merge_networks_by_group_workflow,
     create_merge_group_networks_workflow,
     create_average_networks_by_group_workflow)

examples/dmri_group_connectivity_mrtrix.py

@@ -57,8 +57,8 @@
 import nipype.interfaces.freesurfer as fs  # freesurfer
 import os.path as op  # system functions
 import cmp
-from nipype.workflows.dmri.mrtrix.group_connectivity import create_group_connectivity_pipeline
-from nipype.workflows.dmri.connectivity.group_connectivity import (
+from niflow.nipype1.workflows.dmri.mrtrix.group_connectivity import create_group_connectivity_pipeline
+from niflow.nipype1.workflows.dmri.connectivity.group_connectivity import (
     create_merge_network_results_by_group_workflow,
     create_merge_group_network_results_workflow,
     create_average_networks_by_group_workflow)

examples/dmri_preprocessing.py

@@ -32,13 +32,13 @@
 from nipype.interfaces import ants
 """
 Load specific nipype's workflows for preprocessing of dMRI data:
-:class:`nipype.workflows.dmri.preprocess.epi.all_peb_pipeline`,
+:class:`niflow.nipype1.workflows.dmri.preprocess.epi.all_peb_pipeline`,
 as data include a *b0* volume with reverse encoding direction
 (*P>>>A*, or *y*), in contrast with the general acquisition encoding
 that is *A>>>P* or *-y* (in RAS systems).
 """
 
-from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline, remove_bias
+from niflow.nipype1.workflows.dmri.fsl.artifacts import all_fsl_pipeline, remove_bias
 """
 Map field names into individual subject runs
 """

examples/dmri_tbss_nki.py

@@ -10,8 +10,8 @@
 
 """
 
-from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
-from nipype.workflows.dmri.fsl.tbss import create_tbss_non_FA, create_tbss_all
+from niflow.nipype1.workflows.dmri.fsl.dti import create_eddy_correct_pipeline
+from niflow.nipype1.workflows.dmri.fsl.tbss import create_tbss_non_FA, create_tbss_all
 """
 Tell python where to find the appropriate functions.
 """

examples/fmri_ants_openfmri.py

@@ -38,7 +38,7 @@
 from nipype.interfaces.io import FreeSurferSource
 import nipype.interfaces.utility as niu
 from nipype.interfaces.utility import Merge, IdentityInterface
-from nipype.workflows.fmri.fsl import (create_featreg_preproc,
+from niflow.nipype1.workflows.fmri.fsl import (create_featreg_preproc,
                                        create_modelfit_workflow,
                                        create_fixed_effects_flow)