Merge pull request #2 from maestroque/migrate-physio

Migrate Physio class from peakdet

.autorc

@@ -0,0 +1,92 @@
+{
+  "plugins": [
+    "git-tag",
+    "conventional-commits",
+    "first-time-contributor",
+    "released"
+  ],
+  "owner": "physiopy",
+  "repo": "physutils",
+  "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,
+      "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"
+    }
+  ]
+}

.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 peakdet you are running and your OS version -->
+    - Python version:
+    - peakdet version:
+    - Platform:
+
+## Possible solution
+<!--- Describe a possible approach to solve the issue -->

.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 meant to open a community debate over a topic
+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. -->
+
+    -
+    -
+    -

.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: Enhancement
+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 -->

.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 -->
+
+    *
+    *
+    *

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,4 @@
+contact_links:
+    - name: Usage question
+      url: https://neurostars.org/tag/physiopy
+      about: Please ask questions about using physiopy libraries here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,40 @@
+<!-- Write all of the issues that are linked to this pull request. -->
+<!-- If this PR is enough to close them you can write something like "Closes #314 and closes #42" -->
+<!-- If you just want to reference them without closing them, you can add something like "References #112" -->
+Closes #
+
+<!-- Add a short description of the PR content here-->
+
+
+## Proposed Changes
+<!-- List major points of changes here, so that the reviewers can have a bit more context while looking at your work! -->
+  -
+  -
+  -
+
+## Change Type
+<!-- Indicate the type of change you think your pull request is -->
+- [ ] `bugfix` (+0.0.1)
+- [ ] `minor` (+0.1.0)
+- [ ] `major`  (+1.0.0)
+- [ ] `refactoring` (no version update)
+- [ ] `test` (no version update)
+- [ ] `infrastructure` (no version update)
+- [ ] `documentation` (no version update)
+- [ ] `other`
+
+## Checklist before review
+<!-- If this section is not clear, please read this part of the docs: https://phys2bids.readthedocs.io/en/latest/contributorfile.html#pr -->
+<!-- You're invited to open a draft PR ASAP, but before marking it "ready for review", check that you have done the following: -->
+- [ ] I added everything I wanted to add to this PR.
+- [ ] \[Code or tests only\] I wrote/updated the necessary docstrings.
+- [ ] \[Code or tests only\] I ran and passed tests locally.
+- [ ] \[Documentation only\] I built the docs locally.
+- [ ] My contribution is harmonious with the rest of the code: I'm not introducing repetitions.
+- [ ] My code respects the adopted style, especially linting conventions.
+- [ ] The title of this PR is explanatory on its own, enough to be understood as part of a changelog.
+- [ ] I added or indicated the right labels.
+<!-- If relevant, you can add a milestone label or indicate an ideal timeline for this PR, including whether the progress of this PR is linked to other PRs being completed before or after it. -->
+- [ ] I added information regarding the timeline of completion for this PR.
+<!-- If you want, you can ask for reviews on a draft PR -->
+- [ ] Please, comment on my PR while it's a draft and give me feedback on the development!

.github/labeler.yml

@@ -0,0 +1,11 @@
+Documentation:
+  - changed-files:
+      - any-glob-to-any-file: ['docs/*', '.readthedocs.yml', 'README.md', 'LICENSE', 'MANIFEST.in']
+
+Internal:
+  - changed-files:
+      - any-glob-to-any-file: ['.*', 'codecov.yml', 'setup.cfg', 'setup.py', 'versioneer.py', '.github/*', '.circleci/*', 'physutils/_version.py', 'requirements.txt', 'pyproject.toml']
+
+Testing:
+  - changed-files:
+      - any-glob-to-any-file: ['physutils/tests/*', '.circleci/*']

.github/workflows/auto-author-assign.yml

@@ -0,0 +1,17 @@
+name: Auto Author Assign
+
+on:
+  issues:
+    types: [ opened, reopened ]
+  pull_request_target:
+    types: [ opened, reopened ]
+
+permissions:
+  pull-requests: write
+  issues: write
+
+jobs:
+  assign-author:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: toshimaru/[email protected]

.github/workflows/auto-label.yml

@@ -0,0 +1,15 @@
+name: auto-label
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request_target
+
+jobs:
+  pr:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@v5

.github/workflows/auto-release.yml

@@ -0,0 +1,43 @@
+# 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-22.04
+    # 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

.github/workflows/python-publish.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-22.04
+
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.6'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*