Merge pull request #1392 from FCP-INDI/upgrade/nipype-1.5.1

⬆️ Upgrade Nipype to v1.5.1 (from 1.1.2)

Author: sgiavasis

.circleci/config.yml

@@ -15,14 +15,15 @@ commands:
       - run:
           name: "Setting Python Version"
           command: |
-            pyenv install 3.6.3
-            pyenv global 3.6.3
+            cd /opt/circleci/.pyenv/plugins/python-build/../.. && git pull && cd -
+            pyenv install -v 3.9.0
+            pyenv global 3.9.0
   install-singularity-requirements:
     steps:
       - run:
           name: "Installing Singularity requirements"
           command: |
-           sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.0.0 libarchive-dev libgpgme11-dev libseccomp-dev -y
+           sudo apt-get update && sudo apt-get install flawfinder squashfs-tools uuid-dev libuuid1 libffi-dev libssl-dev libssl1.1 libarchive-dev libgpgme11-dev libseccomp-dev -y
   set-up-singularity:
     steps:
       - run:
@@ -87,7 +88,8 @@ commands:
 
 jobs:
   pytest-docker:
-    machine: true
+    machine:
+      image: ubuntu-2004:202010-01
     steps:
       - attach_workspace:
           # Must be absolute path or relative path from working_directory
@@ -111,7 +113,8 @@ jobs:
           path: htmlcov
           no_output_timeout: 5h
   pytest-singularity:
-    machine: true
+    machine:
+      image: ubuntu-2004:202010-01
     steps:
       - attach_workspace:
           # Must be absolute path or relative path from working_directory
@@ -126,7 +129,8 @@ jobs:
             pip install -r dev/circleci_data/requirements.txt
             coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors  dev/circleci_data/test_install.py
   build:
-    machine: true
+    machine:
+      image: ubuntu-2004:202010-01
     steps:
       - checkout
       - set-python-version
@@ -135,32 +139,20 @@ jobs:
           name: "Checking if version needs updated"
           # update version if version needs updated, otherwise just move on
           command: |
-            if [[ ! $(git log -1 --pretty=%B) == *"Update version to"* ]]
+            COMMIT_MESSAGE=$(git log -1 --pretty=%B)
+            if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]]
             then
               cd $HOME/project/CPAC
-              VERSION=$(python -c "from info import __version__; print(__version__)")
+              VERSION=$(python -c "from info import __version__; print('.'.join(('.'.join(__version__[::-1].split('-')[1].split('.')[1:])[::-1], __version__.split('-')[1])) if '-' in __version__ else __version__)")
               cd ..
-              if ! [[ $CIRCLE_BRANCH = 'master' ]]
-                then
-                  git fetch --all
-                  if [[ -n ${CIRCLE_PR_NUMBER} && -n ${GITHUB_PR_BASE_TOKEN} ]]
-                    then
-                      curl -L "https://github.com/stedolan/jq/releases/download/jq-1.5/jq-linux64" -o jq
-                      chmod +x jq
-                      REBASE_BASE=origin/$(curl -u shnizzedy:$GITHUB_PR_BASE_TOKEN "https://api.github.com/repos/$CIRCLE_PROJECT_USERNAME/$CIRCLE_PROJECT_REPONAME/pulls/$CIRCLE_PR_NUMBER" | jq '.base.ref' | tr -d '"')
-                  else
-                    REBASE_BASE=$(git rev-parse --short HEAD~30)
-                  fi
-                GIT_SEQUENCE_EDITOR=dev/circleci_data/drop_version_bump_commits git rebase -X ours -i $REBASE_BASE --empty drop
-              fi
               echo "v${VERSION}" > version
               sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" dev/docker_data/default_pipeline.yml
               find ./CPAC/resources/configs -name "*.yml" -exec sed -i -r "s/^(# [Vv]ersion ).*$/# Version ${VERSION}/g" {} \;
               git add version CPAC/resources/configs dev/docker_data/default_pipeline.yml
               if [[ ! -z $(git diff origin/${CIRCLE_BRANCH}) ]]
               then
-                git commit -m ":bookmark: Update version to ${VERSION}"
-                git push origin HEAD:${CIRCLE_BRANCH} -f || true
+                git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)"
+                git push origin HEAD:${CIRCLE_BRANCH} || true
                 circleci step halt
               fi
               cd ..
@@ -177,4 +169,4 @@ workflows:
             - build
       - pytest-singularity:
           requires:
-            - build
+            - build

CPAC/info.py

@@ -10,8 +10,8 @@
 # version
 _version_major = 1
 _version_minor = 7
-_version_micro = 1
-_version_extra = ''
+_version_micro = 3
+_version_extra = 'dev'
 
 
 def get_cpac_gitversion():
@@ -146,7 +146,7 @@ def get_cpac_gitversion():
     "networkx==2.4",
     "nibabel==2.3.3",
     "nilearn==0.4.1",
-    "nipype==1.1.2",
+    "nipype==1.5.1",
     "nose==1.3.7",
     "numpy==1.16.4",
     "pandas==0.23.4",

CPAC/nuisance/nuisance.py

@@ -2,43 +2,30 @@
 import os
 import numpy as np
 import nibabel as nb
-
 import nipype.pipeline.engine as pe
 import nipype.interfaces.utility as util
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.ants as ants
-import nipype.interfaces.c3 as c3
+import CPAC
+
+from nipype.interfaces import fsl
+from nipype.interfaces import ants
+from nipype.interfaces import c3
 from nipype.interfaces import afni
 from nipype.interfaces.afni import utils as afni_utils
-
-import CPAC
-import CPAC.utils as utils
+from scipy.fftpack import fft, ifft
+from CPAC import utils
 from CPAC.utils.interfaces.function import Function
 from CPAC.utils.interfaces.masktool import MaskTool
 from CPAC.utils.interfaces.pc import PC
-
 from CPAC.nuisance.utils import (
     find_offending_time_points,
     generate_summarize_tissue_mask,
-    temporal_variance_mask,
-    calc_compcor_components
-)
-
+    temporal_variance_mask)
 from CPAC.nuisance.utils.compcor import (
     calc_compcor_components,
     cosine_filter,
     TR_string_to_float)
-
-
 from CPAC.utils.datasource import check_for_s3
-
-from scipy.fftpack import fft, ifft
-
 from .bandpass import bandpass_voxels
-import nipype.pipeline.engine as pe
-import nipype.interfaces.utility as util
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.ants as ants
 
 
 def gather_nuisance(functional_file_path,
@@ -1212,10 +1199,10 @@ def create_regressor_workflow(nuisance_selectors,
 
                         nuisance_wf.connect(
                             union_masks_paths, 'out_file',
-                            mean_node, 'mask'
+                            mean_node, 'mask_file'
                         )
 
-                        summary_method_input = (mean_node, 'stats')
+                        summary_method_input = (mean_node, 'out_file')
 
                     if 'PC' in summary_method:
 

CPAC/pipeline/cpac_pipeline.py

@@ -401,9 +401,9 @@ def run_workflow(sub_dict, c, run, pipeline_timing_info=None, p_name=None,
             log_nodes_initial(workflow)
 
             # Add status callback function that writes in callback log
-            if nipype.__version__ not in ('1.1.2'):
+            if nipype.__version__ not in ('1.5.1'):
                 err_msg = "This version of Nipype may not be compatible with " \
-                            "CPAC v%s, please install Nipype version 1.1.2\n" \
+                            "CPAC v%s, please install Nipype version 1.5.1\n" \
                             % (CPAC.__version__)
                 logger.error(err_msg)
             else:

CPAC/resources/configs/data_config_S3-BIDS-ABIDE.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-ADHD200.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-ADHD200_only2.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_S3-BIDS-NKI-RocklandSample.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_config_cpac_benchmark.yml

@@ -1,5 +1,5 @@
 # CPAC Data Configuration File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #

CPAC/resources/configs/data_settings_template.yml

@@ -1,5 +1,5 @@
 # CPAC Data Settings File
-# Version 1.7.1
+# Version 1.7.3.dev
 #
 # http://fcp-indi.github.io for more info.
 #