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chrisgorgochrisgorgo
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‎circle.yml

Lines changed: 24 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -21,38 +21,38 @@ dependencies:
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- if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
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- docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
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timeout: 1600
24-
# - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
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# timeout: 1600
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# - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
27-
# timeout: 1600
24+
- docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
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timeout: 1600
26+
- mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
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timeout: 1600
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test:
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override:
31-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
32-
- export ci_env=`bash <(curl -s https://codecov.io/env)` && docker run $ci_env -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
31+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh
32+
- docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 :
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timeout: 2600
34-
# - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
35-
# timeout: 2600
36-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
37-
# timeout: 1600
38-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
39-
# timeout: 1600
40-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
41-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
42-
# timeout: 1600
43-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
44-
# timeout: 1600
45-
# - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
46-
# - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
47-
# - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
48-
# - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
34+
- docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 :
35+
timeout: 2600
36+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d :
37+
timeout: 1600
38+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d :
39+
timeout: 1600
40+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_feeds Linear /root/examples/ l1pipeline
41+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ level1 :
42+
timeout: 1600
43+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_dartel Linear /root/examples/ l2pipeline :
44+
timeout: 1600
45+
- docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_fsl_reuse Linear /root/examples/ level1_workflow
46+
- docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
47+
- docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
48+
- docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
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post:
5151
- bash docker/circleci/teardown.sh
52-
# - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/coverage*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
53-
# - bash <(curl -s https://codecov.io/bash) -f "/home/ubuntu/scratch/smoketest*.xml" -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
52+
- bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests
53+
- bash <(curl -s https://codecov.io/bash) -f ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests
5454

5555
general:
5656
artifacts:
57-
# - "~/docs"
57+
- "~/docs"
5858
- "~/logs"

‎docker/circleci/run_nosetests.sh

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -3,8 +3,6 @@ set -e
33
set -x
44
set -u
55

6-
env
7-
86
PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" )
97

108
# Create necessary directories
@@ -26,16 +24,13 @@ fi
2624
cd /root/src/nipype/
2725
make clean
2826
nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml"
29-
bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
3027

3128
# Workaround: run here the profiler tests in python 3
3229
if [[ "${PYTHON_VERSION}" -ge "30" ]]; then
3330
echo '[execution]' >> /root/.nipype/nipype.cfg
3431
echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg
3532
nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml"
36-
bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
3733
nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml"
38-
bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
3934
fi
4035

4136
# Copy crashfiles to scratch

‎docker/circleci/teardown.sh

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -7,9 +7,9 @@ set -u
77
set -e
88

99
mkdir -p ${CIRCLE_TEST_REPORTS}/nose
10-
sudo cp ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
11-
# mkdir -p ~/docs
12-
# sudo mv ~/scratch/docs/* ~/docs/
10+
sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose
11+
mkdir -p ~/docs
12+
sudo mv ~/scratch/docs/* ~/docs/
1313
mkdir -p ~/logs
1414
sudo mv ~/scratch/builddocs.log ~/logs/builddocs.log
1515
sudo mv ~/scratch/logs/* ~/logs/

‎tools/run_examples.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -37,8 +37,7 @@ def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
3737
os.makedirs(log_dir)
3838
wf.config = {'execution': {'hash_method': 'timestamp',
3939
'stop_on_first_rerun': 'true',
40-
'write_provenance': 'true',
41-
'poll_sleep_duration': 2},
40+
'write_provenance': 'true'},
4241
'logging': {'log_directory': log_dir, 'log_to_file': True}}
4342
try:
4443
wf.inputs.inputnode.in_data = os.path.abspath(data_path)

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