Initial commit - boilerplate

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+*.c
+
+# Distribution / packaging
+.Python
+env/
+# build/ # commented due to some strangeness with Docker/circle setup
+develop-eggs/
+dist/
+build/lib*
+build/temp*
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.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
+
+# Sphinx documentation
+docs/_build/
+build/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+auth/
+secrets.py
+local_settings.py
+
+*.swp

.travis.yml

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+# vim ft=yaml
+language: python
+sudo: false
+cache:
+  directories:
+    - $HOME/.cache/pip
+
+python:
+  - 3.6
+
+before_install:
+  - python -m pip install --upgrade pip
+  - pip install "flake8<3.0" flake8-putty
+
+script:
+  - flake8 fmriprep wrapper

.zenodo.json

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+{
+  "creators": [
+    {
+      "name": "Markiewicz, Christopher J.",
+      "affiliation": "Department of Psychology, Stanford University",
+      "orcid": "0000-0002-6533-164X"
+    },
+    {
+      "name": "Poldrack, Russell A.",
+      "affiliation": "Department of Psychology, Stanford University",
+      "orcid": "0000-0001-6755-0259"
+    },
+    {
+      "name": "Gorgolewski, Krzysztof J.",
+      "affiliation": "Department of Psychology, Stanford University",
+      "orcid": "0000-0003-3321-7583"
+    }
+  ],
+  "keywords": [
+    "neuroimaging",
+    "workflow",
+    "pipeline",
+    "statistics",
+    "fMRI",
+    "BIDS"
+  ],
+  "license": "BSD-3-Clause",
+  "upload_type": "software"
+}

CONTRIBUTING.md

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+# Contributing
+
+**Are you new to open source and GitHub?**
+If so, reading the "[How to submit a contribution](
+https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution)"
+guide will provide a great introduction to contributing to MODELFIT and other
+Open Source projects.
+All the MODELFIT-specific contributing instructions listed below will make much
+more sense after reading this guide.
+
+If you are new to the project don't forget to add your name and affiliation to
+the `.zenodo.json` file.
+
+## Code style guide
+
+### Function and variable names
+
+Whenever possible, instances of Nodes and Workflows should use the same names
+as the variables they are assigned to.
+This makes it easier to relate the content of the working directory to the code
+that generated it when debugging.
+
+Workflow variables should end in `_wf` to indicate that they refer to Workflows
+and not Nodes.
+For instance, a workflow whose basename is `myworkflow` might be defined as
+follows:
+
+```Python
+from nipype.pipeline import engine as pe
+
+myworkflow_wf = pe.Workflow(name='myworkflow_wf')
+```
+
+If a workflow is generated by a function, the name of the function should take
+the form `init_<basename>_wf`:
+
+```Python
+def init_myworkflow_wf(name='myworkflow_wf):
+    workflow = pe.Workflow(name=name)
+    ...
+    return workflow
+
+myworkflow_wf = init_workflow_wf(name='myworkflow_wf')
+```
+
+If multiple instances of the same workflow might be instantiated in the same
+namespace, the workflow names and variables should include either a numeric
+identifier or a one-word description, such as:
+
+```Python
+myworkflow0_wf = init_workflow_wf(name='myworkflow0_wf')
+myworkflow1_wf = init_workflow_wf(name='myworkflow1_wf')
+
+# or
+
+myworkflow_lh_wf = init_workflow_wf(name='myworkflow_lh_wf')
+myworkflow_rh_wf = init_workflow_wf(name='myworkflow_rh_wf')
+```

LICENSE

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+Copyright (c) 2017, the CRN developers team.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of fmriprep nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fitlins/info.py

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+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Base module variables
+"""
+
+__version__ = '0.0.1-dev'
+__author__ = 'The CRN developers'
+__copyright__ = 'Copyright 2017, Center for Reproducible Neuroscience, Stanford University'
+__credits__ = ['Christopher J. Markiewicz', 'Chris Gorgolewski', 'Russell A. Poldrack']
+__license__ = '3-clause BSD'
+__maintainer__ = 'Christopher J. Markiewicz'
+__email__ = '[email protected]'
+__status__ = 'Prototype'
+__url__ = 'https://github.com/poldracklab/fitlins'
+__packagename__ = 'fitlins'
+__description__ = ''
+__longdesc__ = ''
+
+DOWNLOAD_URL = (
+    'https://github.com/effigies/{name}/archive/{ver}.tar.gz'.format(
+        name=__packagename__, ver=__version__))
+
+
+SETUP_REQUIRES = [
+    'setuptools>=18.0',
+]
+
+REQUIRES = [
+    'nistats',
+    'pybids>=0.3',
+    'niworkflows>=0.1.8',
+]
+
+LINKS_REQUIRES = [
+]
+
+TESTS_REQUIRES = [
+]
+
+EXTRA_REQUIRES = {
+    'doc': ['sphinx>=1.5.3', 'pydotplus', 'pydot>=1.2.3', 'sphinx_rtd_theme', 'sphinx-argparse'],
+    'tests': TESTS_REQUIRES,
+    'duecredit': ['duecredit'],
+}
+
+# Enable a handle to install all extra dependencies at once
+EXTRA_REQUIRES['all'] = [val for _, val in list(EXTRA_REQUIRES.items())]
+CLASSIFIERS = [
+    'Development Status :: 2 - Pre-Alpha',
+    'Intended Audience :: Science/Research',
+    'Topic :: Scientific/Engineering',
+    'License :: OSI Approved :: BSD License',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+]