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Merge remote-tracking branch 'upstream/master' into interface/cat12
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‎.git-blame-ignore-revs

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# Commits with messages like "STY: black" or "run black"
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12deb959cccc431fb8222cc5854f1c92a0080021
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f64bf338f630a9ee5cbe7a3ec98c68292897e720
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83358d7f17aac07cb90d0330f11ea2322e2974d8
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faef7d0f93013a700c882f709e98fb3cd36ebb03
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d50c1858564c0b3073fb23c54886a0454cb66afa
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417b8897a116fcded5000e21e2b6ccbe29452a52
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aaf677a87f64c485f3e305799e4a5dc73b69e5fb
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f763008442d88d8ce00ec266698268389415f8d6
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b1eccafd4edc8503b02d715f5b5f6f783520fdf9
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70db90349598cc7f26a4a513779529fba7d0a797
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6c1d91d71f6f0db0e985bd2adc34206442b0653d
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97bdbd5f48ab242de5288ba4715192a27619a803
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78fa360f5b785224349b8b85b07e510d2233bb63
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7f85f43a34de8bff8e634232c939b17cee8e8fc5
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9c50b5daa797def5672dd057155b0e2c658853e2
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47194993ae14aceeec436cfb3769def667196668
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75653feadc6667d5313d83e9c62a5d5819771a9c
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497b44d680eee0892fa59c6aaaae22a17d70a536

‎.github/workflows/contrib.yml

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name: Contribution checks
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# This checks validate contributions meet baseline checks
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#
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# * specs - Ensure make
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on:
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push:
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branches:
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- master
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- maint/*
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pull_request:
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branches:
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- master
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- maint/*
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-18.04']
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python-version: [3.8]
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nipype-extras: ['dev']
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check: ['specs', 'style']
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env:
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DEPENDS: ""
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CHECK_TYPE: ${{ matrix.check }}
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NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
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EXTRA_PIP_FLAGS: ""
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INSTALL_DEB_DEPENDENCIES: false
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-18.04' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v1
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with:
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file: coverage.xml
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if: ${{ always() }}
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.github/workflows/tests.yml

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name: Stable tests
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# This file tests the claimed support range of nipype including
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#
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# * Operating systems: Linux, OSX
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# * Dependencies: minimum requirements, optional requirements
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# * Installation methods: setup.py, sdist, wheel, archive
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on:
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push:
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branches:
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- master
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- maint/*
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pull_request:
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branches:
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- master
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- maint/*
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defaults:
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run:
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shell: bash
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jobs:
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stable:
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# Check each OS, all supported Python, minimum versions and latest releases
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-18.04']
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python-version: [3.6, 3.7, 3.8, 3.9]
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check: ['test']
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pip-flags: ['']
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depends: ['REQUIREMENTS']
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deb-depends: [false]
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nipype-extras: ['doc,tests,profiler']
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include:
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- os: ubuntu-18.04
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python-version: 3.8
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check: test
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pip-flags: ''
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depends: REQUIREMENTS
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deb-depends: true
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nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
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env:
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DEPENDS: ${{ matrix.depends }}
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CHECK_TYPE: ${{ matrix.check }}
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EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
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INSTALL_DEB_DEPENDENCIES: ${{ matrix.deb-depends }}
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NIPYPE_EXTRAS: ${{ matrix.nipype-extras }}
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INSTALL_TYPE: pip
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CI_SKIP_TEST: 1
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Create virtual environment
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run: tools/ci/create_venv.sh
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- name: Build archive
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run: |
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source tools/ci/build_archive.sh
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echo "ARCHIVE=$ARCHIVE" >> $GITHUB_ENV
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- name: Install Debian dependencies
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run: tools/ci/install_deb_dependencies.sh
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if: ${{ matrix.os == 'ubuntu-18.04' }}
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- name: Install dependencies
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run: tools/ci/install_dependencies.sh
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- name: Install Nipype
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run: tools/ci/install.sh
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- name: Run tests
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run: tools/ci/check.sh
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if: ${{ matrix.check != 'skiptests' }}
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- uses: codecov/codecov-action@v1
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with:
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file: coverage.xml
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if: ${{ always() }}
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- name: Upload pytest test results
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uses: actions/upload-artifact@v2
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.pre-commit-config.yaml

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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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rev: v3.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 19.3b0
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rev: 20.8b1
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hooks:
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- id: black

‎.zenodo.json

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"name": "Mihai, Paul Glad",
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"orcid": "0000-0001-5715-6442"
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},
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{
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"name": "Jalan, Raunak",
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},
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{
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"affiliation": "Department of Psychology, Stanford University",
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"name": "Gorgolewski, Krzysztof J.",

‎doc/users/install.rst

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116116
Installation for developers
117117
---------------------------
118118

119-
Developers should start `here <../devel/testing_nipype.html>`_.
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Developers should start `here <../devel/testing_nipype.rst>`_.
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Developers can also use this docker container: `docker pull nipype/nipype:master`
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‎nipype/algorithms/confounds.py

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@@ -577,7 +577,7 @@ class CompCor(SimpleInterface):
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]
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579579
def __init__(self, *args, **kwargs):
580-
""" exactly the same as compcor except the header """
580+
"""exactly the same as compcor except the header"""
581581
super(CompCor, self).__init__(*args, **kwargs)
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self._header = "CompCor"
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"""
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def __init__(self, *args, **kwargs):
777-
""" exactly the same as compcor except the header """
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"""exactly the same as compcor except the header"""
778778
super(ACompCor, self).__init__(*args, **kwargs)
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self._header = "aCompCor"
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output_spec = TCompCorOutputSpec
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def __init__(self, *args, **kwargs):
828-
""" exactly the same as compcor except the header """
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"""exactly the same as compcor except the header"""
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super(TCompCor, self).__init__(*args, **kwargs)
830830
self._header = "tCompCor"
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self._mask_files = []

‎nipype/algorithms/mesh.py

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class TVTKBaseInterface(BaseInterface):
26-
""" A base class for interfaces using VTK """
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"""A base class for interfaces using VTK"""
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_redirect_x = True
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‎nipype/algorithms/metrics.py

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class Distance(BaseInterface):
66-
"""Calculates distance between two volumes.
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"""
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"""Calculates distance between two volumes."""
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6968
input_spec = DistanceInputSpec
7069
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543542

544543
class ErrorMap(BaseInterface):
545-
""" Calculates the error (distance) map between two input volumes.
544+
"""Calculates the error (distance) map between two input volumes.
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548547
-------

‎nipype/algorithms/misc.py

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class SimpleThreshold(BaseInterface):
144-
"""Applies a threshold to input volumes
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"""
144+
"""Applies a threshold to input volumes"""
146145

147146
input_spec = SimpleThresholdInputSpec
148147
output_spec = SimpleThresholdOutputSpec
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241240

242241
class CreateNifti(BaseInterface):
243-
"""Creates a nifti volume
244-
"""
242+
"""Creates a nifti volume"""
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input_spec = CreateNiftiInputSpec
247245
output_spec = CreateNiftiOutputSpec

‎nipype/algorithms/modelgen.py

Lines changed: 13 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -40,13 +40,13 @@ def spm_hrf(RT, P=None, fMRI_T=16):
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% p - parameters of the response function (two gamma
4141
% functions)
4242
% defaults (seconds)
43-
% p(0) - delay of response (relative to onset) 6
44-
% p(1) - delay of undershoot (relative to onset) 16
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% p(2) - dispersion of response 1
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% p(3) - dispersion of undershoot 1
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% p(4) - ratio of response to undershoot 6
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% p(5) - onset (seconds) 0
49-
% p(6) - length of kernel (seconds) 32
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% p(0) - delay of response (relative to onset) 6
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% p(1) - delay of undershoot (relative to onset) 16
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% p(2) - dispersion of response 1
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% p(3) - dispersion of undershoot 1
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% p(4) - ratio of response to undershoot 6
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% p(5) - onset (seconds) 0
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% p(6) - length of kernel (seconds) 32
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%
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% hrf - hemodynamic response function
5252
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135135

136136

137137
def bids_gen_info(
138-
bids_event_files, condition_column="", amplitude_column=None, time_repetition=False,
138+
bids_event_files, condition_column="", amplitude_column=None, time_repetition=False
139139
):
140140
"""
141141
Generate a subject_info structure from a list of BIDS .tsv event files.
@@ -471,8 +471,7 @@ def _generate_standard_design(
471471
return sessinfo
472472

473473
def _generate_design(self, infolist=None):
474-
"""Generate design specification for a typical fmri paradigm
475-
"""
474+
"""Generate design specification for a typical fmri paradigm"""
476475
realignment_parameters = []
477476
if isdefined(self.inputs.realignment_parameters):
478477
for parfile in self.inputs.realignment_parameters:
@@ -517,8 +516,7 @@ def _generate_design(self, infolist=None):
517516
)
518517

519518
def _run_interface(self, runtime):
520-
"""
521-
"""
519+
""" """
522520
self._sessioninfo = None
523521
self._generate_design()
524522
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@@ -739,7 +737,7 @@ class SpecifySparseModelOutputSpec(SpecifyModelOutputSpec):
739737

740738

741739
class SpecifySparseModel(SpecifyModel):
742-
""" Specify a sparse model that is compatible with SPM/FSL designers [1]_.
740+
"""Specify a sparse model that is compatible with SPM/FSL designers [1]_.
743741
744742
Examples
745743
--------
@@ -770,8 +768,7 @@ class SpecifySparseModel(SpecifyModel):
770768
output_spec = SpecifySparseModelOutputSpec
771769

772770
def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans):
773-
"""Generates a regressor for a sparse/clustered-sparse acquisition
774-
"""
771+
"""Generates a regressor for a sparse/clustered-sparse acquisition"""
775772
bplot = False
776773
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
777774
bplot = True
@@ -901,8 +898,7 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans):
901898
return reg
902899

903900
def _cond_to_regress(self, info, nscans):
904-
"""Converts condition information to full regressors
905-
"""
901+
"""Converts condition information to full regressors"""
906902
reg = []
907903
regnames = []
908904
for i, cond in enumerate(info.conditions):

‎nipype/algorithms/rapidart.py

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -686,8 +686,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
686686
save_json(statsfile, stats)
687687

688688
def _run_interface(self, runtime):
689-
"""Execute this module.
690-
"""
689+
"""Execute this module."""
691690
funcfilelist = ensure_list(self.inputs.realigned_files)
692691
motparamlist = ensure_list(self.inputs.realignment_parameters)
693692
for i, imgf in enumerate(funcfilelist):
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814813
return outmatrix
815814

816815
def _run_interface(self, runtime):
817-
"""Execute this module.
818-
"""
816+
"""Execute this module."""
819817
import scipy.io as sio
820818

821819
motparamlist = self.inputs.realignment_parameters

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