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Merge pull request #379 from cosanlab/ejolly/dev
Entire code base reformat with black. Added github workflow for ci. Drop Python 2 artifacts.
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| name: Deploy Docs and PyPI | ||
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| on: release | ||
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| jobs: | ||
| # Job (1): Build and deploy docs. | ||
| docs: | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| name: Build & deploy docs | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout Code | ||
| uses: actions/checkout@v2 | ||
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| - name: Setup Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: "3.8" | ||
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| - name: Upgrade pip | ||
| run: | | ||
| # install pip=>20.1 to use "pip cache dir" | ||
| python3 -m pip install --upgrade pip | ||
| - name: Setup pip-cache | ||
| id: pip-cache | ||
| run: echo "::set-output name=dir::$(pip cache dir)" | ||
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| - name: Cache deps | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: ${{ steps.pip-cache.outputs.dir }} | ||
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | ||
| restore-keys: | | ||
| ${{ runner.os }}-pip- | ||
| - name: Install deps | ||
| run: | | ||
| python3 -m pip install . -r requirements.txt | ||
| python3 -m pip install . -r requirements-dev.txt | ||
| python3 -m pip install . -r optional-dependencies.txt | ||
| - name: Build docs | ||
| run: | | ||
| cd docs | ||
| make clean | ||
| make html | ||
| touch _build/html/.nojekyll | ||
| - name: Deploy docs | ||
| if: success() | ||
| uses: crazy-max/ghaction-github-pages@v2 | ||
| with: | ||
| target_branch: gh-pages | ||
| build_dir: docs/_build/html | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
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| # Job (2): Build package and upload to pypi | ||
| deploy: | ||
| if: "!contains(github.event.head_commit.message, 'skip ci')" | ||
| name: Build & deploy package | ||
| runs-on: ubuntu-latest | ||
| needs: docs | ||
| steps: | ||
| - name: Checkout Code | ||
| uses: actions/checkout@v2 | ||
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| - name: Setup Python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: "3.8" | ||
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| - name: Pypa build | ||
| run: | | ||
| python3 -m pip install build --user | ||
| - name: Wheel and source build | ||
| run: | | ||
| python3 -m build --sdist --wheel --outdir dist/ | ||
| - name: Publish to PyPI | ||
| uses: pypa/gh-action-pypi-publish@master | ||
| with: | ||
| password: ${{ secrets.PYPI_API_TOKEN }} |
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| { | ||
| "recommendations": [ | ||
| "kevinrose.vsc-python-indent", | ||
| "njpwerner.autodocstring" | ||
| ] | ||
| } |
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| { | ||
| "editor.formatOnSave": true, | ||
| "python.testing.pytestEnabled": true, | ||
| "python.testing.unittestEnabled": false, | ||
| "python.testing.nosetestsEnabled": false, | ||
| "python.testing.pytestArgs": [ | ||
| "nltools" | ||
| ], | ||
| "python.testing.autoTestDiscoverOnSaveEnabled": true, | ||
| "editor.insertSpaces": true | ||
| } |
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| [](https://pypi.org/project/nltools/) | ||
| [](https://travis-ci.org/cosanlab/nltools/) | ||
| [] | ||
| [](https://codecov.io/gh/cosanlab/nltools) | ||
| [](https://www.codacy.com/app/ljchang/nltools?utm_source=github.com&utm_medium=referral&utm_content=ljchang/nltools&utm_campaign=Badge_Grade) | ||
| [](http://neurolearn.readthedocs.io/en/latest/?badge=latest) | ||
| [ | ||
| [](https://doi.org/10.5281/zenodo.2229813) | ||
|  | ||
|  | ||
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| # NLTools | ||
| Python toolbox for analyzing neuroimaging data. It is particularly useful for conducting multivariate analyses. It is originally based on Tor Wager's object oriented matlab [canlab core tools](http://wagerlab.colorado.edu/tools) and relies heavily on [nilearn](http://nilearn.github.io) and [scikit learn](http://scikit-learn.org/stable/index.html). Nltools is compatible with Python 3.6+. Python 2.7 was only supported through 0.3.11. We will no longer be supporting Python2 starting with version 0.3.12. | ||
| Python toolbox for analyzing neuroimaging data. It is particularly useful for conducting multivariate analyses. It is originally based on Tor Wager's object oriented matlab [canlab core tools](http://wagerlab.colorado.edu/tools) and relies heavily on [nilearn](http://nilearn.github.io) and [scikit learn](http://scikit-learn.org/stable/index.html). Nltools is only compatible with Python 3.7+. | ||
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| ### Installation | ||
| 1. Method 1 | ||
| ## Documentation | ||
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| Documentation and tutorials are available at https://nltools.org | ||
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| ## Installation | ||
| 1. Method 1 (stable) | ||
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| ``` | ||
| pip install nltools | ||
| ``` | ||
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| 2. Method 2 (Recommended) | ||
| 2. Method 2 (bleeding edge) | ||
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| ``` | ||
| pip install git+https://github.com/cosanlab/nltools | ||
| ``` | ||
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| 3. Method 3 | ||
| 3. Method 3 (for development) | ||
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| ``` | ||
| git clone https://github.com/cosanlab/nltools | ||
| python setup.py install | ||
| ``` | ||
| or | ||
| ``` | ||
| pip install -e 'path_to_github_directory' | ||
| pip install -e nltools | ||
| ``` | ||
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| ### Dependencies | ||
| nltools requires several dependencies. All are available in pypi. Can use `pip install 'package'` | ||
| - nibabel>=2.0.1 | ||
| - scikit-learn>=0.19.1 | ||
| - nilearn>=0.4 | ||
| - pandas>=0.20 | ||
| - numpy>=1.9 | ||
| - seaborn>=0.7.0 | ||
| - matplotlib>=2.1 | ||
| - scipy | ||
| - six | ||
| - pynv | ||
| - joblib | ||
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| ### Optional Dependencies | ||
| - mne | ||
| - requests | ||
| - networkx | ||
| - ipywidgets >=5.2.2 | ||
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| ### Documentation | ||
| Current Documentation can be found at [readthedocs](http://neurolearn.readthedocs.org/en/latest). | ||
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| Please see our [tutorials](http://neurolearn.readthedocs.io/en/latest/auto_examples/index.html), which provide numerous examples for how to use the toolbox. | ||
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| ### Preprocessing | ||
| Please see our [cosanlab_preproc](https://github.com/cosanlab/cosanlab_preproc) library for nipype pipelines to perform preprocessing on neuroimaging data. | ||
| ## Preprocessing | ||
| Nltools has minimal routines for pre-processing data. For more complete pre-processing pipelines please see our [cosanlab_preproc](https://github.com/cosanlab/cosanlab_preproc) library built with `nipype`. |
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