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[MRG] fix: update provenance creation to use released prov library #1279

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Merged
merged 26 commits into from
Dec 14, 2015
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1a10c21
fix: update provenance creation to use released prov library
satra Nov 19, 2015
8cacff0
fix: account for sets
satra Nov 19, 2015
1ac4025
Merge remote-tracking branch 'upstream/pr/1278' into fix/use_current_…
satra Nov 19, 2015
1e205a7
fix: remove prov/rdf lib and add make check fixes
satra Nov 19, 2015
48b7b6b
fix: ensure encoding happens before hashing
satra Nov 19, 2015
601b8a3
fix: changing extra_attributes call
satra Nov 19, 2015
1c38232
fix: ordered dict to str
satra Nov 19, 2015
db87813
fix: changing commit format to support py3
satra Nov 23, 2015
6f86bd9
fix: string decoding for prov literal and few pipeline job submission…
satra Dec 3, 2015
233f05d
Merge remote-tracking branch 'origin/fix/use_current_prov' into fix/u…
satra Dec 3, 2015
ca2be1f
tst: add prov test
satra Dec 3, 2015
e9c96a7
Merge remote-tracking branch 'origin/fix/use_current_prov' into fix/u…
satra Dec 3, 2015
728585c
tst: added missing auto tests
satra Dec 4, 2015
db51634
fix: updated provenance support to use pypi prov package
satra Dec 4, 2015
7fe6251
fix: removed decode call
satra Dec 4, 2015
2eaecfa
fix: removed iflogger statement
satra Dec 4, 2015
c34bcef
Merge remote-tracking branch 'upstream/master' into fix/use_current_prov
satra Dec 4, 2015
526571d
Merge remote-tracking branch 'upstream/master' into fix/use_current_prov
satra Dec 12, 2015
74cd3bd
fix: use text_type to control unicode output
satra Dec 12, 2015
1b83253
fix: use text_type on str for exceptions
satra Dec 12, 2015
191937f
tst: add a test that fails with unicode strings
satra Dec 12, 2015
60b36a2
Merge remote-tracking branch 'origin/fix/use_current_prov' into fix/u…
satra Dec 12, 2015
b66c850
fix: unicode/str accounting on py3/2
satra Dec 13, 2015
e33e99c
fix: updated changes, fixed circle feeds
satra Dec 13, 2015
8860758
Merge remote-tracking branch 'upstream/master' into fix/use_current_prov
satra Dec 13, 2015
8cbf91d
tst: enable provenance for testing on circle
satra Dec 13, 2015
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2 changes: 0 additions & 2 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,6 @@ install:
- pip install python-coveralls
- pip install nose-cov
- pip install -r requirements.txt # finish remaining requirements
- pip install https://github.com/RDFLib/rdflib/archive/master.zip
- pip install https://github.com/trungdong/prov/archive/rdf.zip
- python setup.py install
script:
- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-cov --cover-package nipype --cov-config .coveragerc --logging-level=INFO
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2 changes: 2 additions & 0 deletions CHANGES
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
Next release
============

* FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
* ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
* ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
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2 changes: 1 addition & 1 deletion circle.yml
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ dependencies:
- if [[ ! -d ~/fsl ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz"; tar zxvf fsl-5.0.9-centos6_64.tar.gz; mv fsl ~/fsl; fi
- if [[ ! -d ~/examples/data ]]; then wget "http://tcpdiag.dl.sourceforge.net/project/nipy/nipype/nipype-0.2/nipype-tutorial.tar.bz2"; tar jxvf nipype-tutorial.tar.bz2; mkdir ~/examples; mv nipype-tutorial/* ~/examples/; fi
# we download this manually because CircleCI does not cache apt
- if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-feeds.tar.gz"; tar zxvf fsl-5.0.8-feeds.tar.gz; mv feeds ~/examples/; fi
- if [[ ! -d ~/examples/feeds ]]; then wget "http://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-feeds.tar.gz"; tar zxvf fsl-5.0.9-feeds.tar.gz; mv feeds ~/examples/; fi
- if [[ ! -d ~/examples/fsl_course_data ]]; then wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz" ; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz"; wget -c "http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz"; mkdir ~/examples/fsl_course_data; tar zxvf fdt1.tar.gz -C ~/examples/fsl_course_data; tar zxvf fdt2.tar.gz -C ~/examples/fsl_course_data; tar zxvf tbss.tar.gz -C ~/examples/fsl_course_data; fi
- bash ~/nipype/tools/install_spm_mcr.sh
- mkdir -p ~/.nipype && echo "[logging]" > ~/.nipype/nipype.cfg && echo "workflow_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "interface_level = DEBUG" >> ~/.nipype/nipype.cfg && echo "filemanip_level = DEBUG" >> ~/.nipype/nipype.cfg
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2 changes: 1 addition & 1 deletion nipype/COMMIT_INFO.txt
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# This is an ini file that may contain information about the code state
[commit hash]
# The line below may contain a valid hash if it has been substituted during 'git archive'
archive_subst_hash=$Format:%h$
archive_subst_hash=$Format:%%h$
# This line may be modified by the install process
install_hash=
35 changes: 0 additions & 35 deletions nipype/algorithms/tests/test_auto_ErrorMap.py

This file was deleted.

47 changes: 0 additions & 47 deletions nipype/algorithms/tests/test_auto_Overlap.py

This file was deleted.

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