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1 change: 1 addition & 0 deletions .all-contributorsrc
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"projectOwner": "physiopy",
"repoType": "github",
"repoHost": "https://github.com",
"skipCi": true,
"files": [
"README.md"
],
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93 changes: 93 additions & 0 deletions .autorc
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{
"plugins": [
"git-tag",
"all-contributors",
"conventional-commits",
"first-time-contributor",
"released"
],
"owner": "physiopy",
"repo": "phys2bids",
"name": "Stefano Moia",
"email": "s.moia@bcbl.eu",
"labels": [
{
"name": "Majormod",
"changelogTitle": "💥 Breaking Change",
"description": "This PR breaks compatibility, and increments the major version (+1.0.0)",
"releaseType": "major",
"overwrite": true,
"color": "#05246d"
},
{
"name": "Minormod",
"changelogTitle": "🚀 Enhancement",
"description": "This PR generally closes an `Enhancement` issue. It increments the minor version (0.+1.0)",
"releaseType": "minor",
"overwrite": true,
"color": "#05246d"
},
{
"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,
"color": "#05246d"
},
{
"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,
"color": "#d73a4a"
},
{
"name": "Documentation",
"changelogTitle": "📝 Documentation",
"description": "This issue or PR is about the documentation ",
"releaseType": "none",
"overwrite": true,
"color": "#1D70CF"
},
{
"name": "Testing",
"changelogTitle": "⚠️ Tests",
"description": "This is for testing features, writing tests or producing testing code",
"releaseType": "none",
"overwrite": true,
"color": "#ffb5b4"
},
{
"name": "Internal",
"changelogTitle": "🏠 Internal",
"description": "Changes affect the internal API. It doesn't increase the version, but produces a changelog",
"releaseType": "none",
"overwrite": true,
"color": "#ffffff"
},
{
"name": "Outreach",
"changelogTitle": "🖋️ Outreach",
"description": "Issue about outreaching of any form",
"releaseType": "none",
"overwrite": true,
"color": "#0e8a16"
},
{
"name": "Skip release",
"description": "This PR preserves the current version when merged, and doesn't appear in the changelog",
"releaseType": "skip",
"overwrite": true,
"color": "#ffffff"
},
{
"name": "Release",
"description": "For PR only, trigger a release at the merge",
"releaseType": "release",
"overwrite": true,
"color": "#FFFFFF"
}
]
}
2 changes: 1 addition & 1 deletion .circleci/artifact_path
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0/tmp/src/phy2sbids/docs/_build/html/index.html
0/tmp/src/phys2bids/docs/_build/html/index.html
43 changes: 43 additions & 0 deletions .github/workflows/auto-release.yml
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# This workflows will create a release using auto when a PR is merged in master.

name: Auto-release on PR merge

on:
# ATM, this is the closest trigger to a PR merging
push:
branches:
- master

jobs:
auto-release:
runs-on: ubuntu-18.04
# Set skip ci to avoid loops
if: "!contains(github.event.head_commit.message, 'ci skip') && !contains(github.event.head_commit.message, 'skip ci')"
# Set bash as default shell for jobs
defaults:
run:
shell: bash
steps:
- name: Checkout source
uses: actions/checkout@v2
with:
# Fetch all history for all branches and tags
fetch-depth: 0
# Use token with write access to the repo
token: ${{ secrets.GH_TOKEN }}
- name: Download and install latest auto
env:
# OS can be linux, macos, or win
OS: linux
# Retrieve URL of latest auto, download it, unzip it, and give exec permissions.
run: |
curl -vkL -o - $( curl -s https://api.github.com/repos/intuit/auto/releases/latest \
| grep browser_download_url | grep ${OS} | awk -F'"' '{print $4}') \
| gunzip > ~/auto
chmod a+x ~/auto
- name: Create release without version prefix
env:
GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
# Run auto release, don't use 'v' prefix, and be verbose
run: |
~/auto shipit --no-version-prefix -v
4 changes: 4 additions & 0 deletions .zenodo.json
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"affiliation": "Northwestern University",
"name": "Rachael Stickland"
},
{
"affiliation": "Florida International University",
"name": "Taylor Salo"
},
{
"affiliation": "BCBL - Basque Center on Cognition, Brain and Language",
"name": "Eneko Uru\u00f1uela"
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107 changes: 107 additions & 0 deletions CHANGELOG.md
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# 2.2.3 (Fri Oct 23 2020)

#### 🐛 Bug Fix

- Update PyYAML minimal requirements to avoid "FullLoader" attribute errors. [#330](https://github.com/physiopy/phys2bids/pull/330) ([@smoia](https://github.com/smoia))

#### Authors: 1

- Stefano Moia ([@smoia](https://github.com/smoia))

---

# 2.2.2 (Mon Oct 19 2020)

#### 🐛 Bug Fix

- Fix auto release workflow settings [#323](https://github.com/physiopy/phys2bids/pull/323) ([@smoia](https://github.com/smoia))

#### Authors: 1

- Stefano Moia ([@smoia](https://github.com/smoia))

---

# 2.2.1 (Mon Oct 19 2020)

#### 🐛 Bug Fix

- Make sure we delete testing files after finishing tests [#307](https://github.com/physiopy/phys2bids/pull/307) ([@vinferrer](https://github.com/vinferrer))
- Add label colours to set auto labels [#318](https://github.com/physiopy/phys2bids/pull/318) ([@smoia](https://github.com/smoia))
- Reduce `auto` verbosity [#317](https://github.com/physiopy/phys2bids/pull/317) ([@smoia](https://github.com/smoia))

#### 📝 Documentation

- Update badges in README and documentation [#322](https://github.com/physiopy/phys2bids/pull/322) ([@smoia](https://github.com/smoia))
- Update zenodo info [#321](https://github.com/physiopy/phys2bids/pull/321) ([@smoia](https://github.com/smoia))

#### 🏠 Internal

- Setup auto release workflow [#313](https://github.com/physiopy/phys2bids/pull/313) ([@smoia](https://github.com/smoia))

#### Authors: 2

- Stefano Moia ([@smoia](https://github.com/smoia))
- Vicente Ferrer ([@vinferrer](https://github.com/vinferrer))

---

# v2.2.0 (Wed Oct 14 2020)

#### 🚀 Enhancement

- Make trigger-based time-offset correction more generalisable (resample time before comparing it to trigger) [#308](https://github.com/physiopy/phys2bids/pull/308) (s.moia@bcbl.eu)
- Format logger to make terminal (stdout) more human readable [#312](https://github.com/physiopy/phys2bids/pull/312) ([@vinferrer](https://github.com/vinferrer))
- Add (resampled) trigger to all output files [#288](https://github.com/physiopy/phys2bids/pull/288) ([@vinferrer](https://github.com/vinferrer))

#### 🐛 Bug Fix

- Skip CI on all-contributors (s.moia@bcbl.eu)
- Explicitly ignore rc files and github folder (s.moia@bcbl.eu)
- Add autorc (s.moia@bcbl.eu)
- Add auto badge to documentation (s.moia@bcbl.eu)
- Add auto badge (s.moia@bcbl.eu)
- Add workflow for auto publishing (s.moia@bcbl.eu)
- Change build shield from Travis to CircleCI [#297](https://github.com/physiopy/phys2bids/pull/297) ([@eurunuela](https://github.com/eurunuela))
- Fix linting errors [#294](https://github.com/physiopy/phys2bids/pull/294) ([@eurunuela](https://github.com/eurunuela))
- Start of sampling time is now the same for all frequencies [#283](https://github.com/physiopy/phys2bids/pull/283) ([@vinferrer](https://github.com/vinferrer))
- Add travis wait command [#284](https://github.com/physiopy/phys2bids/pull/284) ([@eurunuela](https://github.com/eurunuela))
- Correct trigger channel indexing while reading AcqKnowledge files. [#275](https://github.com/physiopy/phys2bids/pull/275) (s.moia@bcbl.eu)

#### ⚠️ Pushed to `master`

- Merge branch 'int/auto' (s.moia@bcbl.eu)
- Update README.md (s.moia@bcbl.eu)
- Update ISSUE_TEMPLATE_MEETING.md (s.moia@bcbl.eu)
- Fix message shown when skipping integration test ([@eurunuela](https://github.com/eurunuela))
- Update .travis.yml ([@eurunuela](https://github.com/eurunuela))
- Update setup.cfg ([@eurunuela](https://github.com/eurunuela))

#### 📝 Documentation

- Update all-contributors [#310](https://github.com/physiopy/phys2bids/pull/310) (s.moia@bcbl.eu)
- Update documentation to reflect change from Travis CI to CircleCI [#290](https://github.com/physiopy/phys2bids/pull/290) ([@eurunuela](https://github.com/eurunuela))

#### ⚠️ Tests

- Add tests for exceptions [#291](https://github.com/physiopy/phys2bids/pull/291) ([@eurunuela](https://github.com/eurunuela))
- Add CircleCI for automatic testing and correct integration test parameters [#286](https://github.com/physiopy/phys2bids/pull/286) ([@eurunuela](https://github.com/eurunuela))
- Switch from Travis to CircleCI for automatic testing [#285](https://github.com/physiopy/phys2bids/pull/285) ([@eurunuela](https://github.com/eurunuela))
- Add integration test for the multi run pipeline [#266](https://github.com/physiopy/phys2bids/pull/266) ([@eurunuela](https://github.com/eurunuela))

#### 🏠 Internal

- Refactor txt.py chtrig parameter to improve code readability [#305](https://github.com/physiopy/phys2bids/pull/305) ([@vinferrer](https://github.com/vinferrer))

#### 🖋️ Outreach

- Add link to Google Calendar [#302](https://github.com/physiopy/phys2bids/pull/302) ([@eurunuela](https://github.com/eurunuela))

#### Authors: 3

- Eneko Uruñuela ([@eurunuela](https://github.com/eurunuela))
- Stefano Moia ([@smoia](https://github.com/smoia))
- Vicente Ferrer ([@vinferrer](https://github.com/vinferrer))

---

# v2.1.0 (Tue Jun 23 2020)

:tada: This release contains work from new contributors! :tada:
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23 changes: 14 additions & 9 deletions README.md
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phys2bids
=========

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3653153.svg)](https://doi.org/10.5281/zenodo.3653153)
[![Join the chat at Gitter: https://gitter.im/physiopy/phys2bids](https://badges.gitter.im/physiopy/phys2bids.svg)](https://gitter.im/physiopy/phys2bids?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=body_badge)
[![codecov](https://codecov.io/gh/physiopy/phys2bids/branch/master/graph/badge.svg)](https://codecov.io/gh/physiopy/phys2bids)
[![Latest version](https://img.shields.io/pypi/v/phys2bids)](https://pypi.org/project/phys2bids/)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3470091.svg)](https://doi.org/10.5281/zenodo.3470091)
[![Licensed Apache 2.0](https://img.shields.io/github/license/physiopy/phys2bids)](https://github.com/physiopy/phys2bids/blob/master/LICENSE)

[![codecov](https://codecov.io/gh/physiopy/phys2bids/branch/master/graph/badge.svg)](https://codecov.io/gh/physiopy/phys2bids)
[![CircleCI](https://circleci.com/gh/physiopy/phys2bids.svg?branch=master&style=shield)](https://circleci.com/gh/physiopy/phys2bids)
[![Build Status. Windows](https://dev.azure.com/physiopy/phys2bids/_apis/build/status/physiopy.phys2bids?branchName=master)](https://dev.azure.com/physiopy/phys2bids/_build/latest?definitionId=1&branchName=master)
[![See the documentation at: https://phys2bids.readthedocs.io](https://readthedocs.org/projects/phys2bids/badge/?version=latest)](https://phys2bids.readthedocs.io/en/latest/?badge=latest)

[![Join the chat at Gitter: https://gitter.im/physiopy/phys2bids](https://badges.gitter.im/physiopy/phys2bids.svg)](https://gitter.im/physiopy/phys2bids?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=body_badge)
[![Auto Release](https://img.shields.io/badge/release-auto.svg?colorA=888888&colorB=9B065A&label=auto)](https://github.com/intuit/auto)
[![Supports python version](https://img.shields.io/pypi/pyversions/phys2bids)](https://pypi.org/project/phys2bids/)
[![Requirements Status](https://requires.io/github/physiopy/phys2bids/requirements.svg?branch=master)](https://requires.io/github/physiopy/phys2bids/requirements/?branch=master)

<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
[![All Contributors](https://img.shields.io/badge/all_contributors-14-orange.svg?style=flat)](#contributors)
[![All Contributors](https://img.shields.io/badge/all_contributors-15-orange.svg?style=flat)](#contributors)
<!-- ALL-CONTRIBUTORS-BADGE:END -->

``phys2bids`` is a python3 library meant to format physiological files in BIDS.
Expand All @@ -24,7 +29,9 @@ It was born for AcqKnowledge files (BIOPAC), and at the moment it supports
(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 ``phys2bids`` in your work, please cite it with the zenodo DOI. You can check it [here](https://zenodo.org/record/3903920)
> If you use ``phys2bids`` in your work, please cite it with the zenodo DOI of the version you used. You can find the latest version [here](https://doi.org/10.5281/zenodo.3470091)
> We also support gathering all relevant citations via [DueCredit](http://duecredit.org).
[Read the latest documentation](https://phys2bids.readthedocs.io/en/latest/) for more information on phys2bids!

Expand All @@ -39,12 +46,12 @@ Shortcuts:
- [**Code of Conduct**](https://phys2bids.readthedocs.io/en/latest/conduct.html)
- [Developer calls calendar](https://calendar.google.com/calendar/u/0?cid=amoycDQ1MTdhMWdpaHNuNzlnOW1ucHJkMjRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ)

## Hacktoberfest
<!-- ## Hacktoberfest
Hacktoberfest participants, welcome!
We have some issues for you [here](https://github.com/physiopy/phys2bids/issues?q=is%3Aissue+is%3Aopen+label%3Ahacktoberfest)!
However, feel free to tackle any issue you'd like. Depending on the issue and extent of contribution, Hacktoberfest related PRs might not count toward being listed as contributors and authors (unless there is the specific interest). You can ask about it in the issue itself!
Feel free to ask help to the contributors over gitter, happy coding and (hopefully) enjoy hour tee (or tree)!

-->
## The BrainWeb
BrainWeb participants, welcome!
We have a milestone [here](https://github.com/physiopy/phys2bids/milestone/5) as a collection of issues you could work on with our help.
Expand Down Expand Up @@ -83,8 +90,6 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
<tr>
<td align="center"><a href="https://github.com/eurunuela"><img src="https://avatars0.githubusercontent.com/u/13706448?v=4?s=100" 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?s=100" width="100px;" alt=""/><br /><sub><b>Kristina Zvolanek</b></sub></a><br /><a href="#data-kristinazvolanek" title="Data">🔣</a> <a href="#content-kristinazvolanek" title="Content">🖋</a> <a href="https://github.com/physiopy/phys2bids/commits?author=kristinazvolanek" title="Documentation">📖</a></td>
</tr>
</table>

<!-- markdownlint-restore -->
<!-- prettier-ignore-end -->
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2 changes: 2 additions & 0 deletions codecov.yml
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- "phys2bids/tests"
- "phys2bids/heuristics"
- "phys2bids/due.py"
- ".*rc"
- ".github"

comment:
layout: "reach,diff,flags,tree"
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