From 51ab22ba174e86457c2c1d47d35ae02e4cf02384 Mon Sep 17 00:00:00 2001
From: Stefano Moia <s.moia@bcbl.eu>
Date: Mon, 11 May 2020 17:43:23 +0200
Subject: [PATCH] General configuration of the infrastructure

---
 .all-contributorsrc                           |  5 +-
 .autorc                                       | 86 +++++++++++++++++++
 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md | 34 ++++++++
 .../ISSUE_TEMPLATE_DISCUSSION.md              | 27 ++++++
 .../ISSUE_TEMPLATE_FEATURE_REQUEST.md         | 20 +++++
 .../ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md  | 23 +++++
 .../ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md  |  8 ++
 .github/PULL_REQUEST_TEMPLATE.md              |  7 ++
 .github/workflows/pythonpublish.yml           | 32 +++++++
 .zenodo.json                                  | 28 ++++++
 MANIFEST.in                                   |  1 -
 README.md                                     | 35 +-------
 codecov.yml                                   |  1 -
 phys2denoise/cli/__init__.py                  |  0
 phys2denoise/metrics/__init__.py              |  0
 setup.cfg                                     |  3 +-
 16 files changed, 271 insertions(+), 39 deletions(-)
 create mode 100644 .autorc
 create mode 100644 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md
 create mode 100644 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md
 create mode 100644 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_FEATURE_REQUEST.md
 create mode 100644 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md
 create mode 100644 .github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md
 create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
 create mode 100644 .github/workflows/pythonpublish.yml
 create mode 100644 .zenodo.json
 create mode 100644 phys2denoise/cli/__init__.py
 create mode 100644 phys2denoise/metrics/__init__.py

diff --git a/.all-contributorsrc b/.all-contributorsrc
index 839c338..95c7e0b 100644
--- a/.all-contributorsrc
+++ b/.all-contributorsrc
@@ -33,12 +33,11 @@
       "contributions": [
         "data",
         "infra",
-        "projectManagement",
-        "doc"
+        "projectManagement"
       ]
     }
   ],
-  "contributorsPerLine": 5,
+  "contributorsPerLine": 8,
   "projectName": "phys2denoise",
   "projectOwner": "physiopy",
   "repoType": "github",
diff --git a/.autorc b/.autorc
new file mode 100644
index 0000000..a967574
--- /dev/null
+++ b/.autorc
@@ -0,0 +1,86 @@
+{
+  "plugins": [
+    "git-tag",
+    "all-contributors",
+    "conventional-commits",
+    "first-time-contributor",
+    "released"
+  ],
+  "release": {
+    "prerelease": true
+  },
+  "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
+    },
+    {
+      "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
+    }
+  ]
+}
\ No newline at end of file
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md
new file mode 100644
index 0000000..ad02986
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_BUGS.md
@@ -0,0 +1,34 @@
+---
+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 -->
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md
new file mode 100644
index 0000000..35a198c
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_DISCUSSION.md
@@ -0,0 +1,27 @@
+---
+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. -->
+
+    - 
+    - 
+    - 
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_FEATURE_REQUEST.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_FEATURE_REQUEST.md
new file mode 100644
index 0000000..098ac0d
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_FEATURE_REQUEST.md
@@ -0,0 +1,20 @@
+---
+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 -->
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md
new file mode 100644
index 0000000..c52035f
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_GENERAL.md
@@ -0,0 +1,23 @@
+---
+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 -->
+
+    * 
+    * 
+    * 
diff --git a/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md
new file mode 100644
index 0000000..bb78256
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/ISSUE_TEMPLATE_MEETING.md
@@ -0,0 +1,8 @@
+---
+name: Dev call
+about: Only for PM
+title: 'phys2bids YYY developer call (dd.mm.yyyy @ time)
+labels: Community
+assignees:
+---
+
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..7e25258
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,7 @@
+Closes #
+
+## Proposed Changes
+
+  -
+  -
+  -
\ No newline at end of file
diff --git a/.github/workflows/pythonpublish.yml b/.github/workflows/pythonpublish.yml
new file mode 100644
index 0000000..9e24640
--- /dev/null
+++ b/.github/workflows/pythonpublish.yml
@@ -0,0 +1,32 @@
+# 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/*
\ No newline at end of file
diff --git a/.zenodo.json b/.zenodo.json
new file mode 100644
index 0000000..2bef93d
--- /dev/null
+++ b/.zenodo.json
@@ -0,0 +1,28 @@
+{
+  "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"
+    },
+  }
+}
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
index e847aa7..443d4b1 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,6 +1,5 @@
 include README.* LICENSE setup* MANIFEST.in requirements.txt
 recursive-include phys2denoise/data *
-recursive-include phys2denoise/heuristics *
 recursive-include phys2denoise/tests/data *
 
 include versioneer.py
diff --git a/README.md b/README.md
index 832984d..dbc1a4b 100644
--- a/README.md
+++ b/README.md
@@ -1,40 +1,9 @@
 <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.
@@ -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.
diff --git a/codecov.yml b/codecov.yml
index b804094..da58677 100644
--- a/codecov.yml
+++ b/codecov.yml
@@ -27,7 +27,6 @@ ignore:
   - "**/__init__.py"
   - "**/**/__init__.py"
   - "phys2denoise/tests"
-  - "phys2denoise/heuristics"
 
 comment:
   layout: "reach,diff,flags,tree"
diff --git a/phys2denoise/cli/__init__.py b/phys2denoise/cli/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/phys2denoise/metrics/__init__.py b/phys2denoise/metrics/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/setup.cfg b/setup.cfg
index f76d594..b36689a 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -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 =
@@ -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