Saving modified denoiser module

src/data/02-denoiser/denoiser/.circleci/config.yml

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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
+
+      # 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
+
+    working_directory: ~/repo
+
+    steps:
+      - checkout
+
+      # 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-
+
+
+      - 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" }}
+
+      - restore_cache:
+          keys:
+          - test-data
+
+      - run:
+          name: Download test data
+          command: |
+            bash .circleci/test_data_downloader.sh
+
+      - save_cache:
+          paths:
+            - ./test_data
+          key: test-data
+
+      # 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

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

src/data/02-denoiser/denoiser/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.idea/