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General configuration of the infrastructure
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Stefano Moia committed May 11, 2020
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5 changes: 2 additions & 3 deletions .all-contributorsrc
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"contributions": [
"data",
"infra",
"projectManagement",
"doc"
"projectManagement"
]
}
],
"contributorsPerLine": 5,
"contributorsPerLine": 8,
"projectName": "phys2denoise",
"projectOwner": "physiopy",
"repoType": "github",
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86 changes: 86 additions & 0 deletions .autorc
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{
"plugins": [
"git-tag",
"all-contributors",
"conventional-commits",
"first-time-contributor",
"released"
],
"release": {
"prerelease": true
},
"owner": "physiopy",
"repo": "phys2bids",
"name": "Stefano Moia",
"email": "[email protected]",
"labels": [
{
"name": "Majormod",
"changelogTitle": "💥 Breaking Change",
"description": "This PR breaks compatibility, and increments the major version (+1.0.0)",
"releaseType": "major",
"overwrite": true
},
{
"name": "Minormod",
"changelogTitle": "🚀 Enhancement",
"description": "This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0)",
"releaseType": "minor",
"overwrite": true
},
{
"name": "Minormod-breaking",
"changelogTitle": "💥 Breaking Change during development",
"description": "For development only, this PR increments the minor version (0.+1.0) but breaks compatibility",
"releaseType": "minor",
"overwrite": true
},
{
"name": "BugFIX",
"changelogTitle": "🐛 Bug Fix",
"description": "This PR generally closes a `Bug` issue, and increments the patch version (0.0.+1)",
"releaseType": "patch",
"overwrite": true
},
{
"name": "Documentation",
"changelogTitle": "📝 Documentation",
"description": "This issue or PR is about the documentation ",
"releaseType": "none",
"overwrite": true
},
{
"name": "Testing",
"changelogTitle": "⚠️ Tests",
"description": "This is for testing features, writing tests or producing testing code",
"releaseType": "none",
"overwrite": true
},
{
"name": "Internal",
"changelogTitle": "🏠 Internal",
"description": "Changes affect the internal API. It doesn't increase the version, but produces a changelog",
"releaseType": "none",
"overwrite": true
},
{
"name": "Outreach",
"changelogTitle": "🖋️ Outreach",
"description": "Issue about outreaching of any form",
"releaseType": "none",
"overwrite": true
},
{
"name": "Skip release",
"description": "This PR preserves the current version when merged, and doesn't appear in the changelog",
"releaseType": "skip",
"overwrite": true
},
{
"name": "Release",
"description": "For PR only, trigger a release at the merge",
"releaseType": "release",
"overwrite": true
}
]
}
34 changes: 34 additions & 0 deletions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md
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---
name: Bug issue
about: Use this template to report bugs.
title: ''
labels: Bug
assignees:
---

<!--- Provide a general summary of the issue in the Title above -->

## Expected Behavior
<!--- NECESSARY -->
<!--- Describe what one would expect from the buggy code -->

## Actual Behavior
<!--- NECESSARY -->
<!--- Describe what the buggy code is actually doing/returning -->
<!--- Do not hesitate and share screenshots and code snippets that could help understand the issue -->

## Steps to Reproduce the Problem
<!--- Briefly point out the steps we should take to reproduce the problem -->

1.
2.
3.

## Specifications
<!--- Point out the version of phys2bids you are running and your OS version -->
- Python version:
- phys2bids version:
- Platform:

## Possible solution
<!--- Describe a possible approach to solve the issue -->
27 changes: 27 additions & 0 deletions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md
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---
name: Discussion
about: Use this template to start a discussion issue, i.e. an issue that
title: ''
labels: Discussion
assignees: ''
---

<!--- Provide the detailed description of the idea to discuss
This section should present:
- What is the topic
- Why you want to spark such a discussion (what is the problem you're trying to solve)
- If you thought about them, what are the possible positions on the topic you came up with - invite others to add some!
It could contain questions. Don't be afraid to ping users that could be more interested in this topic! -->

I'm opening this discussion because/I think that/I noticed that...




## Outstanding questions
<!--- Repeat the concept in a very few, short (max 3) questions -->
<!--- Remember that the aim is not to give a "tldr", but to help address salient points. -->

-
-
-
20 changes: 20 additions & 0 deletions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_FEATURE_REQUEST.md
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---
name: Feature request
about: Use this template to request new features.
title: ''
labels: Enhacement
assignees: ''
---

<!--- Provide a general summary of the issue in the Title above -->

## Detailed Description
<!--- Provide a detailed description of the change or addition you are proposing -->

## Context / Motivation
<!--- Why is this change important to you? How would you use it? -->
<!--- How can it benefit other users? -->

## Possible Implementation
<!--- Not obligatory, but suggest an idea for implementing addition or change -->
<!--- If you already have worked on the idea, please share a link to the branch in your forked project -->
23 changes: 23 additions & 0 deletions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md
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---
name: General issue
about: Use this template for any issues not related to bugs or feature requests
title: ''
labels:
assignees: ''
---

<!--- Provide a general summary of the issue in the Title above -->
<!--- Please label the issue with one of the following: Documentation, Outreach or Question -->

## Summary
<!--- Describe the motivation behind the issue -->

## Additional detail
<!--- Provide a additional details that could help developers understand the issue -->

## Next Steps
<!--- Provide possible steps to take in order to address the issue -->

*
*
*
8 changes: 8 additions & 0 deletions .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md
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---
name: Dev call
about: Only for PM
title: 'phys2bids YYY developer call (dd.mm.yyyy @ time)
labels: Community
assignees:
---
7 changes: 7 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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Closes #

## Proposed Changes

-
-
-
32 changes: 32 additions & 0 deletions .github/workflows/pythonpublish.yml
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# This workflows will upload a Python Package using Twine when a release is created
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

name: Upload Python Package

on:
release:
types: [created]

jobs:
deploy:

runs-on: ubuntu-18.04

steps:
- name: Checkout source
uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v1
with:
python-version: 3.7
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install setuptools wheel twine
- name: Build and publish
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
run: |
python -m python setup.py sdist bdist_wheel
python -m twine upload dist/*
28 changes: 28 additions & 0 deletions .zenodo.json
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{
"metadata": {
"license": {
"id": "Apache-2.0"
},
"title": "physiopy/phys2denoise: Creation of physiological regressors for fMRI",
"creators": [
{
"affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
"name": "C\u00e9sar Caballero Gaudes"
},
{
"affiliation": "McGill University",
"name": "Ross Markello"
},
{
"orcid": "0000-0002-2553-3327",
"affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
"name": "Stefano Moia"
}
],
"access_right": "open",
"resource_type": {
"type": "software",
"title": "Software"
},
}
}
1 change: 0 additions & 1 deletion MANIFEST.in
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include README.* LICENSE setup* MANIFEST.in requirements.txt
recursive-include phys2denoise/data *
recursive-include phys2denoise/heuristics *
recursive-include phys2denoise/tests/data *

include versioneer.py
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35 changes: 2 additions & 33 deletions README.md
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<a name="readme"></a>
<!-- <img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->
<!-- <img alt="physiopy" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150"> -->

phys2denoise
============

<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3653153.svg)](https://doi.org/10.5281/zenodo.3653153) -->
<!-- [![Build Status](https://travis-ci.org/physiopy/phys2bids.svg?branch=master)](https://travis-ci.org/physiopy/phys2bids) -->
<!-- [![Join the chat at https://gitter.im/phys2bids/community](https://badges.gitter.im/phys2bids/community.svg)](https://gitter.im/phys2bids/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) -->
<!-- [![Documentation Status](https://readthedocs.org/projects/phys2bids/badge/?version=latest)](https://phys2bids.readthedocs.io/en/latest/?badge=latest) -->
<!-- [![Requirements Status](https://requires.io/github/physiopy/phys2bids/requirements.svg?branch=master)](https://requires.io/github/physiopy/phys2bids/requirements/?branch=master) -->
<!-- [![codecov](https://codecov.io/gh/physiopy/phys2bids/branch/master/graph/badge.svg)](https://codecov.io/gh/physiopy/phys2bids) -->
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
<!-- [![All Contributors](https://img.shields.io/badge/all_contributors-11-orange.svg?style=flat)](#contributors-) -->
<!-- ALL-CONTRIBUTORS-BADGE:END -->

<!-- ``phys2denoise`` is a python3 library meant to format physiological files in BIDS. -->
<!-- It was born for AcqKnowledge files (BIOPAC), and at the moment it supports -->
<!-- ``.acq`` files as well as ``.txt`` files obtained by labchart -->
<!-- (ADInstruments). -->
<!-- It doesn't support physiological files recorded with the MRI, as you can find a software for it [here](https://github.com/tarrlab/physio2bids). -->
<!-- -->
<!-- If you use ``phy2bids`` in your work, please cite it with the zenodo DOI as: -->
<!-- -->
<!-- >The phys2bids contributors, Daniel Alcalá, Apoorva Ayyagari, Molly Bright, César Caballero-Gaudes, Vicente Ferrer Gallardo, Soichi Hayashi, Ross Markello, Stefano Moia, Rachael Stickland, Eneko Uruñuela, & Kristina Zvolanek (2020, February 6). physiopy/phys2bids: BIDS formatting of physiological recordings v1.3.0-beta (Version v1.3.0-beta). Zenodo. http://doi.org/10.5281/zenodo.3653153 -->
<!-- -->
<!-- [Read the latest documentation](https://phys2bids.readthedocs.io/en/latest/) for more information on phys2bids! -->
<!-- -->
<!-- Shortcuts: -->
<!-- - [Requirements](https://phys2bids.readthedocs.io/en/latest/installation.html#requirements) -->
<!-- - [Installation](https://phys2bids.readthedocs.io/en/latest/installation.html#linux-and-mac-installation) -->
<!-- - [Usage](https://phys2bids.readthedocs.io/en/latest/cli.html) -->
<!-- - [How to use phys2bids](https://phys2bids.readthedocs.io/en/latest/howto.html) -->
<!-- - [Contributing to phys2bids](https://phys2bids.readthedocs.io/en/latest/contributing.html) -->
<!-- - [Developer installation](https://phys2bids.readthedocs.io/en/latest/contributing.html#linux-and-mac-developer-installation) -->
<!-- - [**Contributor guide**](https://phys2bids.readthedocs.io/en/latest/contributorfile.html) -->
<!-- - [**Code of Conduct**](https://phys2bids.readthedocs.io/en/latest/conduct.html) -->

**The project is currently under development**.
Any suggestion/bug report is welcome! Feel free to open an issue.
Expand All @@ -58,7 +27,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
License
-------

Copyright 2019, The Phys2BIDS community.
Copyright 2019, The phys2denoise community.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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1 change: 0 additions & 1 deletion codecov.yml
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Expand Up @@ -27,7 +27,6 @@ ignore:
- "**/__init__.py"
- "**/**/__init__.py"
- "phys2denoise/tests"
- "phys2denoise/heuristics"

comment:
layout: "reach,diff,flags,tree"
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Empty file added phys2denoise/cli/__init__.py
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3 changes: 2 additions & 1 deletion setup.cfg
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Expand Up @@ -22,7 +22,6 @@ provides =
[options]
python_requires = >=3.6.1
install_requires =
bioread >=1.0.4
numpy >=1.9.3
matplotlib >=3.1.1
tests_require =
Expand All @@ -39,7 +38,9 @@ doc =
sphinx_rtd_theme
style =
flake8 >=3.7
flake8-docstrings >=1.5
test =
pytest >=5.3
pytest-cov
all =
%(doc)s
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