PIN: nipype 1.1.0, niworkflows

.circleci/config.yml

@@ -111,13 +111,13 @@ jobs:
     environment:
       - TZ: "/usr/share/zoneinfo/America/Los_Angeles"
       - TEST_DATA_NAME: "circle-tests"
-      - TEST_DATA_URL: "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/590ce4a96c613b025147c568"
+      - TEST_DATA_URL: "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b6c9950fed49e001a7885b6"
     working_directory: /home/circleci/data
     steps:
       - restore_cache:
           keys:
-            - data-v1-{{ epoch }}
-            - data-v1-
+            - data-v2-{{ epoch }}
+            - data-v2-
       - run:
           name: Get test data
           command: |
@@ -144,7 +144,7 @@ jobs:
             - t1w/nipype.cfg
             - bold/nipype.cfg
       - save_cache:
-         key: data-v1-{{ epoch }}
+         key: data-v2-{{ epoch }}
          paths:
             - /tmp/data
             - /tmp/t1w

mriqc/__about__.py

@@ -56,8 +56,9 @@
 SETUP_REQUIRES = []
 
 REQUIRES = [
-    'niworkflows>=0.4.0',
-    'pybids>=0.5.0',
+    'nipype>=1.1.1',
+    'niworkflows>=0.4.2',
+    'pybids>=0.6.4',
     'numpy>=1.12.0',
     'scikit-learn>=0.19.0',
     'scikit-image',

mriqc/bin/mriqc_run.py

@@ -243,9 +243,9 @@ def main():
     })
 
     # Set nipype logging level
-    nlog.getLogger('workflow').setLevel(log_level)
-    nlog.getLogger('interface').setLevel(log_level)
-    nlog.getLogger('utils').setLevel(log_level)
+    nlog.getLogger('nipype.workflow').setLevel(log_level)
+    nlog.getLogger('nipype.interface').setLevel(log_level)
+    nlog.getLogger('nipype.utils').setLevel(log_level)
 
     plugin_settings = {'plugin': 'Linear'}
     if opts.use_plugin is not None:

mriqc/interfaces/anatomical.py

@@ -26,7 +26,7 @@
 from ..qc.anatomical import (snr, snr_dietrich, cnr, fber, efc, art_qi1,
                              art_qi2, volume_fraction, rpve, summary_stats,
                              cjv, wm2max)
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class StructuralQCInputSpec(BaseInterfaceInputSpec):

mriqc/interfaces/bids.py

@@ -19,7 +19,7 @@
 )
 from ..utils.misc import BIDS_COMP, BIDS_EXPR
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class ReadSidecarJSONInputSpec(BaseInterfaceInputSpec):

mriqc/interfaces/common.py

@@ -18,7 +18,7 @@
 from nipype.interfaces.ants import ApplyTransforms
 
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class ConformImageInputSpec(BaseInterfaceInputSpec):

mriqc/interfaces/functional.py

@@ -19,7 +19,7 @@
 from ..utils.misc import _flatten_dict
 from ..qc.anatomical import snr, fber, efc, summary_stats
 from ..qc.functional import gsr
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 
 class FunctionalQCInputSpec(BaseInterfaceInputSpec):

mriqc/interfaces/webapi.py

@@ -11,7 +11,7 @@
 )
 from urllib.parse import urlparse
 
-IFLOGGER = logging.getLogger('interface')
+IFLOGGER = logging.getLogger('nipype.interface')
 
 SECRET_KEY = '<secret_token>'
 

requirements.txt

@@ -1,3 +1 @@
-numpy>=1.12.0
-scikit-learn>=0.19
-niworkflows>=0.4.0
+niworkflows>=0.4.2