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Merge pull request #91 from rmarkello/corrnan
[ENH] Updates stats.efficient_pearsonr to handle NaNs
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‎.github/workflows/tests.yml‎

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name: netneurotools tests
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on: [push, pull_request]
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jobs:
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check_skip:
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runs-on: ubuntu-latest
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outputs:
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skip: ${{ steps.result_step.outputs.ci-skip }}
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- id: result_step
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uses: mstachniuk/ci-skip@master
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with:
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commit-filter: '[skip ci];[ci skip];[skip github]'
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commit-filter-separator: ';'
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checks:
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needs: check_skip
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if: ${{ needs.check_skip.outputs.skip == 'false' }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
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python-version: ['3.6', '3.7', '3.8', '3.9']
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install: ['setup']
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check: ['test']
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optional-depends: ['']
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include:
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: style
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optional-depends: ''
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: doc
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optional-depends: ''
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- os: ubuntu-latest
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python-version: 3.8
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install: setup
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check: test
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optional-depends: numba
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- os: ubuntu-latest
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python-version: 3.8
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install: sdist
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check: test
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optional-depends: ''
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- os: ubuntu-latest
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python-version: 3.8
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install: bdist_wheel
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check: test
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optional-depends: ''
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exclude:
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- os: ubuntu-latest
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architecture: x86
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- os: macos-latest
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architecture: x86
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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CHECK_TYPE: ${{ matrix.check }}
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OPTIONAL_DEPENDS: ${{ matrix.optional-depends }}
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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: 'Install dependencies'
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run: ./tools/install_dependencies.sh
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- name: 'Install netneurotools'
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run: ./tools/install_package.sh
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- name: 'Run tests'
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run: ./tools/run_checks.sh
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- uses: codecov/codecov-action@v1
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with:
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file: for_testing/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: for_testing/test-results.xml
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if: ${{ always() && matrix.check == 'test' }}

‎.travis.yml‎

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language: python
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os: linux
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arch: arm64
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dist: xenial
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language: python
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cache: pip
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notifications:
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email: change
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python:
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- 3.6
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- 3.7
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- 3.8
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- 3.9
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env:
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jobs:
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- CHECK_TYPE=linting
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- CHECK_TYPE=docdoctest
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- CHECK_TYPE=test
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- CHECK_TYPE=test INSTALL_NUMBA=true
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global:
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- INSTALL_TYPE=setup
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jobs:
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include:
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- python: 3.6
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env:
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- INSTALL_TYPE=sdist
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- CHECK_TYPE=test
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- python: 3.6
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env:
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- INSTALL_TYPE=wheel
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- CHECK_TYPE=test
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- python: 3.6
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env:
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- INSTALL_TYPE=conda
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- CHECK_TYPE=test
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- INSTALL_TYPE="setup"
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- CHECK_TYPE="test"
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- OPTIONAL_DEPENDS=
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before_install:
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- python -m pip install --upgrade pip
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- if [ "${INSTALL_TYPE}" == "conda" ]; then
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wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
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bash miniconda.sh -b -p $HOME/miniconda;
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export PATH="$HOME/miniconda/bin:$PATH";
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hash -r;
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conda config --set always_yes yes --set changeps1 no;
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conda update -q conda;
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conda env create -f environment.yml;
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source activate netneurotools;
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fi
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- if [ "${CHECK_TYPE}" == "linting" ]; then
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pip install flake8;
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fi
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- if [ "${CHECK_TYPE}" == "test" ]; then
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pip install "pytest>=4.6" pytest-cov coverage codecov;
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fi
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- if [ ! -z "${INSTALL_NUMBA}"]; then
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pip install numba;
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fi
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- travis_retry tools/install_dependencies.sh
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install:
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- |
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if [ "${INSTALL_TYPE}" == "setup" ]; then
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python setup.py install;
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elif [ "${INSTALL_TYPE}" == "sdist" ]; then
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python setup.py sdist;
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pip install dist/*.tar.gz;
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elif [ "${INSTALL_TYPE}" == "wheel" ]; then
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python setup.py bdist_wheel;
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pip install dist/*.whl;
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elif [ "${INSTALL_TYPE}" == "conda" ]; then
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pip install --no-deps .;
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else
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false;
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fi
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- travis_retry tools/install_package.sh
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script:
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- |
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if [ "${CHECK_TYPE}" == "linting" ]; then
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flake8 netneurotools;
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elif [ "${CHECK_TYPE}" == "docdoctest" ]; then
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cd docs;
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pip install -r ./requirements.txt;
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make html;
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make doctest;
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elif [ "${CHECK_TYPE}" == "test" ]; then
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py.test --doctest-modules --cov-report term-missing --cov=netneurotools netneurotools;
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else
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false;
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fi
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- tools/run_checks.sh
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after_success:
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# codecov with numba installed doesn't make sense, so don't do that
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- if [ "${CHECK_TYPE}" == "test" ] && [ -z "${INSTALL_NUMBA}" ]; then
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codecov;
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fi
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- travis_retry python -m pip install codecov

‎MANIFEST.in‎

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include README.md LICENSE environment.yml
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recursive-include netneurotools_matlab *.m
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recursive-include netneurotools data/*
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include README.rst LICENSE environment.yml requirements.txt
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recursive-include netneurotools/data *
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include versioneer.py
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include netneurotools/_version.py

‎README.rst‎

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netneurotools: Tools for network neuroscience
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=============================================
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This toolbox is a collection of functions written in Python (and some Matlab!)
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that get frequent usage in the `Network Neuroscience Lab <www.misiclab.com>`_,
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housed in the `Brain Imaging Centre <https://www.mcgill.ca/bic/home>`_ at
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This toolbox is a collection of functions written in Python that get frequent
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usage in the `Network Neuroscience Lab <netneurolab.github.io/>`_, housed in
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the `Brain Imaging Centre <https://www.mcgill.ca/bic/home>`_ at
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`McGill University <https://www.mcgill.ca/>`_.
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.. image:: https://travis-ci.org/netneurolab/netneurotools.svg?branch=master

‎dev_environment.yml‎

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- "pytest>=3.6"
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- pytest-cov
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- scikit-learn
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- scipy
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- "scipy>=1.4.0"
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- "sphinx>=1.2"
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- sphinx-gallery
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- sphinx_rtd_theme

‎docs/installation.rst‎

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git clone https://github.com/netneurolab/netneurotools.git
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cd netneurotools
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python setup.py install
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pip install .
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Alternatively, you can install ``netneurotools`` directly from PyPi with:
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.. code-block:: bash
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pip install netneurotools
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.. _matlab_installation:
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Matlab installation
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-------------------
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The Matlab functions should work on R2012B or later (though that is an estimate
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based on the versions of Matlab that were around when the code was written).
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To use the Matlab functions, download the repository and add the
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`netneurotools_matlab` directory to your Matlab path.

‎environment.yml‎

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- defaults
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- conda-forge
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dependencies:
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- python==3.7
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- python>=3.6
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- matplotlib
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- nibabel
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- nilearn
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- "numpy>=1.16"
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- pip
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- scikit-learn
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- scipy
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- "scipy>=1.4.0"
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- pip:
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- git+https://github.com/aestrivex/bctpy.git#egg=bctpy

‎netneurotools/__init__.py‎

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__all__ = [
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'__author__', '__description__', '__email__', '__license__',
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'__maintainer__', '__packagename__', '__url__', '__version__',
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'__version__',
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]
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from ._version import get_versions
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__version__ = get_versions()['version']
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del get_versions
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from .info import (
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__author__,
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__description__,
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__email__,
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__license__,
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__maintainer__,
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__packagename__,
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__url__,
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)

‎netneurotools/info.py‎

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‎netneurotools/modularity.py‎

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z_rand : float
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Z-rand index
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See Also
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--------
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netneurotools_matlab/randz.m
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References
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----------
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Amanda L. Traud, Eric D. Kelsic, Peter J. Mucha, and Mason A. Porter.

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