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# Python CircleCI 2.0 configuration file | ||
# | ||
# Check https://circleci.com/docs/2.0/language-python/ for more details | ||
# | ||
version: 2 | ||
jobs: | ||
build: | ||
docker: | ||
# specify the version you desire here | ||
# use `-browsers` prefix for selenium tests, e.g. `3.6.1-browsers` | ||
- image: circleci/python:3.6.1 | ||
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# Specify service dependencies here if necessary | ||
# CircleCI maintains a library of pre-built images | ||
# documented at https://circleci.com/docs/2.0/circleci-images/ | ||
# - image: circleci/postgres:9.4 | ||
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working_directory: ~/repo | ||
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steps: | ||
- checkout | ||
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# Download and cache dependencies | ||
- restore_cache: | ||
keys: | ||
- v1-dependencies-{{ checksum "requirements.txt" }} | ||
# fallback to using the latest cache if no exact match is found | ||
- v1-dependencies- | ||
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- run: | ||
name: Install dependencies | ||
command: | | ||
python3 -m venv venv | ||
. venv/bin/activate | ||
pip install -r requirements.txt | ||
- save_cache: | ||
paths: | ||
- ./venv | ||
key: v1-dependencies-{{ checksum "requirements.txt" }} | ||
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- restore_cache: | ||
keys: | ||
- test-data | ||
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- run: | ||
name: Download test data | ||
command: | | ||
bash .circleci/test_data_downloader.sh | ||
- save_cache: | ||
paths: | ||
- ./test_data | ||
key: test-data | ||
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# run tests! | ||
- run: | ||
name: Smoke test - print help | ||
command: | | ||
. venv/bin/activate | ||
./run_denoise.py --help | ||
- run: | ||
name: Smoke test - basic denoising | ||
command: | | ||
. venv/bin/activate | ||
mkdir -p test_outputs/basic | ||
./run_denoise.py test_data/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz test_data/sub-01_task-rhymejudgment_bold_confounds.tsv test_outputs/basic | ||
- run: | ||
name: Smoke test - select subsest of columns | ||
command: | | ||
. venv/bin/activate | ||
mkdir -p test_outputs/subset | ||
./run_denoise.py test_data/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz test_data/sub-01_task-rhymejudgment_bold_confounds.tsv test_outputs/subset --col_names FramewiseDisplacement GlobalSignal | ||
- run: | ||
name: Smoke test - high pass | ||
command: | | ||
. venv/bin/activate | ||
mkdir -p test_outputs/hp | ||
./run_denoise.py test_data/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz test_data/sub-01_task-rhymejudgment_bold_confounds.tsv test_outputs/hp --hp_filter 0.009 | ||
- run: | ||
name: Smoke test - low pass | ||
command: | | ||
. venv/bin/activate | ||
mkdir -p test_outputs/lp | ||
./run_denoise.py test_data/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz test_data/sub-01_task-rhymejudgment_bold_confounds.tsv test_outputs/lp --lp_filter 0.1 | ||
- store_artifacts: | ||
path: test_outputs | ||
destination: test_outputs |
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src/data/02-denoiser/denoiser/.circleci/test_data_downloader.sh
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#!/usr/bin/env bash | ||
set -x | ||
set -e | ||
if [ ! -e test_data ]; then | ||
mkdir test_data | ||
wget http://openneuro.outputs.s3.amazonaws.com/091b91a257f6b517790f2fb82a784c8e/3e22d7c1-c7e8-4cc7-bfdd-c89dd6681982/fmriprep/sub-01/func/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz -O test_data/sub-01_task-rhymejudgment_bold_space-MNI152NLin2009cAsym_preproc.nii.gz | ||
wget http://openneuro.outputs.s3.amazonaws.com/091b91a257f6b517790f2fb82a784c8e/3e22d7c1-c7e8-4cc7-bfdd-c89dd6681982/fmriprep/sub-01/func/sub-01_task-rhymejudgment_bold_confounds.tsv -O test_data/sub-01_task-rhymejudgment_bold_confounds.tsv | ||
fi |
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
env/ | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
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# PyInstaller | ||
# Usually these files are written by a python script from a template | ||
# before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
*.manifest | ||
*.spec | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
.hypothesis/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# pyenv | ||
.python-version | ||
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# celery beat schedule file | ||
celerybeat-schedule | ||
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# SageMath parsed files | ||
*.sage.py | ||
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# dotenv | ||
.env | ||
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# virtualenv | ||
.venv | ||
venv/ | ||
ENV/ | ||
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
.idea/ |
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