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

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

Author: oesteban

Diff for: 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" \

Diff for: 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')

Diff for: 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.)

Diff for: 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.)

Diff for: 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

Diff for: 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)

Diff for: 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)

Diff for: 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
 """

Diff for: 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.
 """

Diff for: 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)
 

Diff for: examples/fmri_fsl_feeds.py

@@ -22,7 +22,7 @@
 from nipype.interfaces import fsl  # fsl
 from nipype.pipeline import engine as pe  # pypeline engine
 from nipype.algorithms import modelgen as model  # model generation
-from nipype.workflows.fmri.fsl import (
+from niflow.nipype1.workflows.fmri.fsl import (
     create_featreg_preproc, create_modelfit_workflow, create_reg_workflow)
 from nipype.interfaces.base import Bunch
 """

Diff for: examples/fmri_fsl_reuse.py

@@ -28,7 +28,7 @@
 import nipype.algorithms.modelgen as model  # model generation
 import nipype.algorithms.rapidart as ra  # artifact detection
 
-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)
 """

Diff for: examples/fmri_spm_dartel.py

@@ -21,7 +21,7 @@
 
 import nipype.interfaces.io as nio  # Data i/o
 import nipype.interfaces.spm as spm  # spm
-import nipype.workflows.fmri.spm as spm_wf  # spm
+import niflow.nipype1.workflows.fmri.spm as spm_wf  # spm
 import nipype.interfaces.fsl as fsl  # fsl
 from nipype.interfaces import utility as niu  # Utilities
 import nipype.pipeline.engine as pe  # pypeline engine

Diff for: examples/frontiers_paper/smoothing_comparison.py

@@ -16,7 +16,7 @@
 import nipype.interfaces.utility as util
 import nipype.pipeline.engine as pe  # pypeline engine
 import nipype.algorithms.modelgen as model  # model specification
-import nipype.workflows.fmri.fsl as fsl_wf
+import niflow.nipype1.workflows.fmri.fsl as fsl_wf
 from nipype.interfaces.base import Bunch
 import os  # system functions
 

Diff for: examples/nipype_tutorial.ipynb

@@ -1615,7 +1615,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "from nipype.workflows.fmri.fsl.preprocess import create_susan_smooth\n",
+      "from niflow.nipype1.workflows.fmri.fsl.preprocess import create_susan_smooth\n",
       "\n",
       "smooth = create_susan_smooth()\n",
       "smooth.inputs.inputnode.in_files = opap('output/realigned/_subject_id_sub044/rbold_out.nii')\n",

Diff for: examples/smri_ants_build_template.py

@@ -23,7 +23,7 @@
 import nipype.interfaces.io as io
 import nipype.pipeline.engine as pe  # pypeline engine
 
-from nipype.workflows.smri.ants import ANTSTemplateBuildSingleIterationWF
+from niflow.nipype1.workflows.smri.ants import ANTSTemplateBuildSingleIterationWF
 """
 2. Download T1 volumes into home directory
 """

Diff for: examples/smri_antsregistration_build_template.py

@@ -22,7 +22,7 @@
 import nipype.interfaces.io as io
 import nipype.pipeline.engine as pe  # pypeline engine
 
-from nipype.workflows.smri.ants import antsRegistrationTemplateBuildSingleIterationWF
+from niflow.nipype1.workflows.smri.ants import antsRegistrationTemplateBuildSingleIterationWF
 """
 2. Download T1 volumes into home directory
 """

Diff for: examples/smri_fsreconall.py

@@ -20,7 +20,7 @@
 
 import nipype.pipeline.engine as pe
 import nipype.interfaces.io as nio
-from nipype.workflows.smri.freesurfer import create_reconall_workflow
+from niflow.nipype1.workflows.smri.freesurfer import create_reconall_workflow
 from nipype.interfaces.freesurfer.utils import MakeAverageSubject
 from nipype.interfaces.utility import IdentityInterface
 """

Diff for: examples/tessellation_tutorial.py

@@ -7,7 +7,7 @@
 Introduction
 ============
 
-This script, tessellation_tutorial.py, demonstrates the use of create_tessellation_flow from nipype.workflows.smri.freesurfer, and it can be run with::
+This script, tessellation_tutorial.py, demonstrates the use of create_tessellation_flow from niflow.nipype1.workflows.smri.freesurfer, and it can be run with::
 
     python tessellation_tutorial.py
 
@@ -39,7 +39,7 @@
 import nipype.interfaces.io as nio  # Data i/o
 import os
 import os.path as op
-from nipype.workflows.smri.freesurfer import create_tessellation_flow
+from niflow.nipype1.workflows.smri.freesurfer import create_tessellation_flow
 """
 Directories
 ===========

Diff for: nipype/interfaces/fsl/epi.py

@@ -1417,7 +1417,7 @@ def __init__(self, **inputs):
         warnings.warn(
             (
                 "Deprecated: Please use "
-                "nipype.workflows.dmri.preprocess.epi.sdc_fmb instead"
+                "niflow.nipype1.workflows.dmri.preprocess.epi.sdc_fmb instead"
             ),
             DeprecationWarning,
         )

Diff for: nipype/sphinxext/plot_workflow.py

@@ -21,7 +21,7 @@
       :graph2use: flat
       :simple_form: no
 
-      from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
+      from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
       wf = create_connectivity_pipeline()
 
 
@@ -32,7 +32,7 @@
   :graph2use: flat
   :simple_form: no
 
-  from nipype.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
+  from niflow.nipype1.workflows.dmri.camino.connectivity_mapping import create_connectivity_pipeline
   wf = create_connectivity_pipeline()