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miykaelmiykael
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Merge pull request miykael#94 from miykael/circleci_workflow
ENH: run CircleCi in parallel/workflow
2 parents e607d3e + bf7ac41 commit ddd2060

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‎.circleci/config.yml

Lines changed: 59 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -2,20 +2,72 @@ version: 2
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jobs:
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build:
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docker:
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- image: docker:17.10.0-ce-git
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- image: docker:18.05.0-ce-git
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steps:
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- checkout
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test_1:
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docker:
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- image: docker:18.05.0-ce-git
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steps:
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- checkout
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- setup_remote_docker:
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docker_layer_caching: true
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- run:
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name: docker build 1
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no_output_timeout: 60m
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command: |
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docker build -t miykael/nipype_tutorial:$CIRCLE_BRANCH .
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- run:
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name: run tests 1
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no_output_timeout: 120m
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command: |
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docker run -it --rm miykael/nipype_tutorial:$CIRCLE_BRANCH python /home/neuro/nipype_tutorial/test_notebooks.py 1
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test_2:
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docker:
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- image: docker:18.05.0-ce-git
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steps:
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- checkout
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- setup_remote_docker:
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docker_layer_caching: true
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- run:
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name: docker build 2
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no_output_timeout: 60m
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command: |
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docker build -t miykael/nipype_tutorial:$CIRCLE_BRANCH .
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- run:
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name: run tests 2
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no_output_timeout: 120m
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command: |
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docker run -it --rm miykael/nipype_tutorial:$CIRCLE_BRANCH python /home/neuro/nipype_tutorial/test_notebooks.py 2
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test_3:
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docker:
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- image: docker:18.05.0-ce-git
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steps:
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- checkout
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- setup_remote_docker:
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docker_layer_caching: true
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- run:
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name: docker build
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name: docker build 3
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no_output_timeout: 60m
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command: |
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for i in {1..5}; do
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docker build -t miykael/nipype_tutorial:$CIRCLE_BRANCH . && break || sleep 15
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done
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docker build -t miykael/nipype_tutorial:$CIRCLE_BRANCH .
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- run:
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name: docker run
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name: run tests 3
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no_output_timeout: 120m
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command: |
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docker run -it --rm miykael/nipype_tutorial:$CIRCLE_BRANCH python /home/neuro/nipype_tutorial/test_notebooks.py
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docker run -it --rm miykael/nipype_tutorial:$CIRCLE_BRANCH python /home/neuro/nipype_tutorial/test_notebooks.py 3
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workflows:
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version: 2
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build_and_test:
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jobs:
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- build
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- test_1:
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requires:
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- build
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- test_2:
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requires:
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- build
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- test_3:
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requires:
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- build

‎test_notebooks.py

Lines changed: 35 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
11
import os
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import sys
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import time
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from glob import glob
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@@ -55,21 +56,41 @@ def reduce_notebook_load(path):
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test_version()
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notebooks = sorted(glob("/home/neuro/nipype_tutorial/notebooks/introduction_*.ipynb")) + \
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sorted(glob("/home/neuro/nipype_tutorial/notebooks/basic*.ipynb")) + \
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sorted(glob("/home/neuro/nipype_tutorial/notebooks/advanced*.ipynb"))
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# Notebooks that should be tested
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notebooks = []
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for n in ["/home/neuro/nipype_tutorial/notebooks/example_preprocessing.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_1stlevel.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_normalize.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_2ndlevel.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/handson_preprocessing.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/handson_analysis.ipynb"]:
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# Test mode that should be run
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test_mode = int(sys.argv[1])
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print('Reducing: %s' % n)
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notebooks.append(reduce_notebook_load(n))
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# Specifies which tests should be run
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if test_mode == 1:
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# Test introduction, basic and advanced notebooks
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notebooks += sorted(glob("/home/neuro/nipype_tutorial/notebooks/introduction*.ipynb"))
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notebooks += sorted(glob("/home/neuro/nipype_tutorial/notebooks/basic*.ipynb"))
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notebooks += sorted(glob("/home/neuro/nipype_tutorial/notebooks/advanced*.ipynb"))
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elif test_mode == 2:
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# Test example notebooks
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for n in ["/home/neuro/nipype_tutorial/notebooks/example_preprocessing.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_1stlevel.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_normalize.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/example_2ndlevel.ipynb"]:
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print('Reducing: %s' % n)
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notebooks.append(reduce_notebook_load(n))
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elif test_mode == 3:
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# Test hands-on notebooks
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for n in ["/home/neuro/nipype_tutorial/notebooks/handson_preprocessing.ipynb",
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"/home/neuro/nipype_tutorial/notebooks/handson_analysis.ipynb"]:
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print('Reducing: %s' % n)
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notebooks.append(reduce_notebook_load(n))
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for test in notebooks:
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t0 = time.time()
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os.system('pytest --nbval-lax --nbval-cell-timeout 7200 -v -s %s' % test)
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print("time", time.time() - t0)
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pytest_cmd = 'pytest --nbval-lax --nbval-cell-timeout 7200 -v -s %s' % test
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print(pytest_cmd)
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os.system(pytest_cmd)

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