Skip to content

Commit

Permalink
Merge pull request #1 from smoia/Rachael-docs
Browse files Browse the repository at this point in the history
Rachael docs
  • Loading branch information
RayStick authored Mar 6, 2020
2 parents 763c3b9 + 842cc78 commit 8ef2b6e
Show file tree
Hide file tree
Showing 40 changed files with 190,364 additions and 4,125,173 deletions.
1 change: 1 addition & 0 deletions .all-contributorsrc
Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,7 @@
"profile": "https://github.com/eurunuela",
"contributions": [
"bug",
"code",
"infra",
"review",
"test"
Expand Down
26 changes: 0 additions & 26 deletions .codecov.yml

This file was deleted.

3 changes: 2 additions & 1 deletion .gitattributes
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
phys2bids/_version.py export-subst

* eol=lf
*.py eol=lf
*.rst eol=lf
7 changes: 7 additions & 0 deletions .requires.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
version: 1.0
requirements:
- requirements.txt
- setup.py
- tox.ini
- path: /requirements.txt
parser: python/pip
2 changes: 1 addition & 1 deletion .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ before_install:
pip install flake8;
fi
- if [ "${CHECK_TYPE}" == "test" ]; then
pip install "pytest>=3.6" pytest-cov coverage coveralls codecov;
pip install "pytest>=3.6" pytest-cov coverage coveralls codecov wget;
fi
- if [ "${CHECK_TYPE}" == "docdoctest" ]; then
pip install "sphinx>2.0" sphinx_rtd_theme pandas sphinx-argparse;
Expand Down
86 changes: 0 additions & 86 deletions Code_of_Conduct.md

This file was deleted.

17 changes: 13 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,31 +1,40 @@
<a name="readme"></a>
<img alt="Phys2BIDS" src="https://github.com/physiopy/phys2bids/blob/master/docs/_static/phys2bids_logo1280×640.png" height="150">

phys2bids
=========

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3586045.svg)](https://doi.org/10.5281/zenodo.3586045)
[![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)
[![codecov](https://codecov.io/gh/smoia/phys2bids/branch/master/graph/badge.svg)](https://codecov.io/gh/smoia/phys2bids)
[![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 -->

Phys2bids is a python3 library meant to format physiological files in BIDS.
``phys2bids`` 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 @@ -52,7 +61,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
<tr>
<td align="center"><a href="https://github.com/smoia"><img src="https://avatars3.githubusercontent.com/u/35300580?v=4" width="100px;" alt=""/><br /><sub><b>Stefano Moia</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/commits?author=smoia" title="Code">💻</a> <a href="#data-AyyagariA" title="Data">🔣</a> <a href="#ideas-smoia" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-smoia" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#projectManagement-smoia" title="Project Management">📆</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Asmoia" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=smoia" title="Documentation">📖</a> <a href="#content-smoia" title="Content">🖋</a></td>
<td align="center"><a href="https://github.com/RayStick"><img src="https://avatars3.githubusercontent.com/u/50215726?v=4" width="100px;" alt=""/><br /><sub><b>Rachael Stickland</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Araystick" title="Bug reports">🐛</a> <a href="#data-AyyagariA" title="Data">🔣</a> <a href="https://github.com/physiopy/phys2bids/commits?author=raystick" title="Documentation">📖</a> <a href="#userTesting-raystick" title="User Testing">📓</a></td>
<td align="center"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4" width="100px;" alt=""/><br /><sub><b>Eneko Uruñuela</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Aeurunuela" title="Bug reports">🐛</a> <a href="#infra-eurunuela" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Aeurunuela" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Tests">⚠️</a></td>
<td align="center"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4" width="100px;" alt=""/><br /><sub><b>Eneko Uruñuela</b></sub></a><br /><a href="https://github.com/physiopy/phys2bids/issues?q=author%3Aeurunuela" title="Bug reports">🐛</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Code">💻</a> <a href="#infra-eurunuela" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/physiopy/phys2bids/pulls?q=is%3Apr+reviewed-by%3Aeurunuela" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/physiopy/phys2bids/commits?author=eurunuela" title="Tests">⚠️</a></td>
<td align="center"><a href="https://github.com/kristinazvolanek"><img src="https://avatars3.githubusercontent.com/u/54590158?v=4" width="100px;" alt=""/><br /><sub><b>Kristina Zvolanek</b></sub></a><br /><a href="#data-AyyagariA" title="Data">🔣</a> <a href="https://github.com/physiopy/phys2bids/commits?author=kristinazvolanek" title="Documentation">📖</a> <a href="#content-kristinazvolanek" title="Content">🖋</a></td>
</tr>
</table>
Expand Down
35 changes: 35 additions & 0 deletions codecov.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
codecov:
branch: master
strict_yaml_branch: master
require_ci_to_pass: yes
bot: "codecov-io"
ci:
- "travis.org"
max_report_age: 48
disable_default_path_fixes: no

coverage:
precision: 2
round: down
range: "60...90"

parsers:
gcov:
branch_detection:
conditional: yes
loop: yes
method: no
macro: no

ignore:
- "docs"
- "phys2bids/_version.py"
- "**/__init__.py"
- "**/**/__init__.py"
- "phys2bids/tests"
- "phys2bids/heuristics"

comment:
layout: "reach,diff,flags,tree"
behavior: default
require_changes: no
Binary file added docs/_static/tutorial_file.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/_static/tutorial_file_trigger_time.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
154 changes: 154 additions & 0 deletions docs/conduct.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,154 @@
.. _conduct:

Physiopy Code of Conduct
=========================

*Based on the* |covenant|_.

.. _covenant: https://www.contributor-covenant.org/

.. |covenant| replace:: *Contributor Covenant Code of Conduct*

Our Pledge
----------

We as members, contributors, and leaders pledge to make participation in
our community a harassment-free experience for everyone, regardless of
age, body size, visible or invisible disability, ethnicity, sex
characteristics, gender identity and expression, level of experience,
education, socio-economic status, nationality, personal appearance,
race, religion, or sexual identity and orientation.

We pledge to act and interact in ways that contribute to an open,
welcoming, diverse, inclusive, and healthy community.

Our Standards
-------------

Examples of behavior that contributes to a positive environment for our
community include:

- Demonstrating empathy and kindness toward other people
- Being respectful of differing opinions, viewpoints, and experiences
- Giving and gracefully accepting constructive feedback
- Accepting responsibility and apologizing to those affected by our
mistakes, and learning from the experience
- Focusing on what is best not just for us as individuals, but for the
overall community

Examples of unacceptable behavior include:

- The use of sexualized language or imagery, and sexual attention or
advances of any kind
- Trolling, insulting or derogatory comments, and personal or political
attacks
- Public or private harassment
- Publishing others' private information, such as a physical or email
address, without their explicit permission
- Other conduct which could reasonably be considered inappropriate in a
professional setting

Enforcement Responsibilities
----------------------------

Community leaders are responsible for clarifying and enforcing our
standards of acceptable behavior and will take appropriate and fair
corrective action in response to any behavior that they deem
inappropriate, threatening, offensive, or harmful.

Community leaders have the right and responsibility to remove, edit, or
reject comments, commits, code, wiki edits, issues, and other
contributions that are not aligned to this Code of Conduct, and will
communicate reasons for moderation decisions when appropriate.

Scope
-----

This Code of Conduct applies within all community spaces, and also
applies when an individual is officially representing the community in
public spaces. Examples of representing our community include using an
official e-mail address, posting via an official social media account,
creating and diffusing outreaching material (e.g. abstracts, posters,
papers, demonstrations, ...), or acting as an appointed representative
at an online or offline event.

Enforcement
-----------

Instances of abusive, harassing, or otherwise unacceptable behavior may
be reported to the community leaders responsible for enforcement at
[email protected]. All complaints will be reviewed and investigated
promptly and fairly.

All community leaders are obligated to respect the privacy and security
of the reporter of any incident.

Enforcement Guidelines
----------------------

Community leaders will follow these Community Impact Guidelines in
determining the consequences for any action they deem in violation of
this Code of Conduct:

1. Correction
~~~~~~~~~~~~~

**Community Impact**: Use of inappropriate language or other behavior
deemed unprofessional or unwelcome in the community.

**Consequence**: A private, written warning from community leaders,
providing clarity around the nature of the violation and an explanation
of why the behavior was inappropriate. A public apology may be
requested.

2. Warning
~~~~~~~~~~

**Community Impact**: A violation through a single incident or series of
actions.

**Consequence**: A warning with consequences for continued behavior. No
interaction with the people involved, including unsolicited interaction
with those enforcing the Code of Conduct, for a specified period of
time. This includes avoiding interactions in community spaces as well as
external channels like social media. Violating these terms may lead to a
temporary or permanent ban.

3. Temporary Ban
~~~~~~~~~~~~~~~~

**Community Impact**: A serious violation of community standards,
including sustained inappropriate behavior.

**Consequence**: A temporary ban from any sort of interaction or public
communication with the community for a specified period of time. No
public or private interaction with the people involved, including
unsolicited interaction with those enforcing the Code of Conduct, is
allowed during this period. Violating these terms may lead to a
permanent ban.

4. Permanent Ban
~~~~~~~~~~~~~~~~

**Community Impact**: Demonstrating a pattern of violation of community
standards, including sustained inappropriate behavior, harassment of an
individual, or aggression toward or disparagement of classes of
individuals.

**Consequence**: A permanent ban from any sort of public interaction
within the project community.

Attribution
-----------

This Code of Conduct is adapted from the `Contributor
Covenant <https://www.contributor-covenant.org>`_, version 2.0,
available at
https://www.contributor-covenant.org/version/2/0/code\_of\_conduct.html.

Community Impact Guidelines were inspired by `Mozilla's code of conduct
enforcement ladder <https://github.com/mozilla/diversity>`_.

For answers to common questions about this code of conduct, see the FAQ
at https://www.contributor-covenant.org/faq. Translations are available
at https://www.contributor-covenant.org/translations.
2 changes: 1 addition & 1 deletion docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@

# Add project name, copyright holder, and author(s)
project = 'phys2bids'
author = '{} developers'.format(project)
author = 'the {} developers'.format(project)
copyright = '2019-{}, {}'.format(datetime.now().year, author)

# Import project to get version info
Expand Down
Loading

0 comments on commit 8ef2b6e

Please sign in to comment.