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‎.coveragerc

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[run]
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omit = setup.py

‎.github/dependabot.yml

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "github-actions" # See documentation for possible values
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directory: "/" # Location of package manifests
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schedule:
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interval: "daily"
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- package-ecosystem: "pip"
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directory: "/"
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schedule:
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interval: "daily"

‎.github/rename_project.sh

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#!/usr/bin/env bash
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while getopts a:n:u:d: flag
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do
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case "${flag}" in
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a) author=${OPTARG};;
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n) name=${OPTARG};;
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u) urlname=${OPTARG};;
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d) description=${OPTARG};;
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esac
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done
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echo "Author: $author";
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echo "Project Name: $name";
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echo "Project URL name: $urlname";
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echo "Description: $description";
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echo "Renaming project..."
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original_author="author_name"
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original_name="project_name"
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original_urlname="project_urlname"
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original_description="project_description"
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# for filename in $(find . -name "*.*")
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for filename in $(git ls-files)
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do
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sed -i "s/$original_author/$author/g" $filename
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sed -i "s/$original_name/$name/g" $filename
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sed -i "s/$original_urlname/$urlname/g" $filename
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sed -i "s/$original_description/$description/g" $filename
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echo "Renamed $filename"
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done
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mv project_name $name
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mv $name/project_name.json $name/$name.json
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# This command runs only once on GHA!
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rm -rf .github/template.yml

‎.github/template.yml

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author: jernsting
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Inspired by https://github.com/rochacbruno/python-project-template

‎.github/workflows/deploy_to_pypi.yml

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name: Release deployment on PyPI
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on:
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release:
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types: [published]
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jobs:
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deploy:
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if: ${{ !contains (github.repository, '/photonai_module_template') }}
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name: Build and publish to PyPI
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: "3.10.8"
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- name: Install pypa/build
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run: pip install build pbr wheel
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- name: Build a binary wheel and a source tarball
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run: python -m build -n --sdist --wheel --outdir dist/ .
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- name: Publish distribution to Test PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/lindandtest.yml

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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python application
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on: push
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jobs:
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build:
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name: Test
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: "3.10.8"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install flake8 pytest_cov coveralls
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
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- name: Test with pytest
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run: |
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pytest --cov=. test/
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- name: Coveralls
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run: coveralls
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env:
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COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/rename_project.yml

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name: Rename the project from template
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on: [push]
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permissions: write-all
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jobs:
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rename-project:
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if: ${{ !contains (github.repository, '/photonai_module_template') }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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# by default, it uses a depth of 1
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# this fetches all history so that we can read each commit
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fetch-depth: 0
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ref: ${{ github.head_ref }}
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- run: echo "REPOSITORY_NAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}' | tr '-' '_' | tr '[:upper:]' '[:lower:]')" >> $GITHUB_ENV
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shell: bash
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- run: echo "REPOSITORY_URLNAME=$(echo '${{ github.repository }}' | awk -F '/' '{print $2}')" >> $GITHUB_ENV
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shell: bash
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- run: echo "REPOSITORY_OWNER=$(echo '${{ github.repository }}' | awk -F '/' '{print $1}')" >> $GITHUB_ENV
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shell: bash
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- name: Is this still a template
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id: is_template
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run: echo "::set-output name=is_template::$(ls .github/template.yml &> /dev/null && echo true || echo false)"
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- name: Rename the project
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if: steps.is_template.outputs.is_template == 'true'
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run: |
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echo "Renaming the project with -a(author) ${{ env.REPOSITORY_OWNER }} -n(name) ${{ env.REPOSITORY_NAME }} -u(urlname) ${{ env.REPOSITORY_URLNAME }}"
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.github/rename_project.sh -a ${{ env.REPOSITORY_OWNER }} -n ${{ env.REPOSITORY_NAME }} -u ${{ env.REPOSITORY_URLNAME }} -d "Awesome ${{ env.REPOSITORY_NAME }} created by ${{ env.REPOSITORY_OWNER }}"
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- uses: stefanzweifel/git-auto-commit-action@v5
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with:
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commit_message: "✅ Ready to clone and code."
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# commit_options: '--amend --no-edit'
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push_options: --force

‎.github/workflows/update_documentation.yml

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name: Update documentation
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on: push
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jobs:
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build:
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name: Build docs
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runs-on: ubuntu-latest
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if: ${{ github.ref != 'refs/heads/main' }}
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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- name: Install Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10.8'
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- name: Install mkdocs requirements
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run: pip install mkdocs mkdocs-material pymdown-extensions mkdocstrings-python mkdocs-jupyter jupyter
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- name: Install project requirements
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run: pip install -r requirements.txt
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- name: Install project
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run: pip install .
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- name: Build docs
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run: |
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mkdocs build
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deploy:
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name: Deploy docs
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runs-on: ubuntu-latest
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if: ${{ github.ref == 'refs/heads/main' }}
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steps:
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- name: Checkout main
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uses: actions/checkout@v4
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- name: Install Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.10.8'
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- name: Install mkdocs requirements
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run: pip install mkdocs mkdocs-material pymdown-extensions mkdocstrings-python mkdocs-jupyter jupyter
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- name: Install project requirements
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run: pip install -r requirements.txt
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- name: Install project
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run: pip install .
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- name: Deploy docs
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run: |
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mkdocs gh-deploy --force

‎.gitignore

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.idea/
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project_name/registered
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*.pyc

‎LICENSE

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MIT License
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Copyright (c) 2020 Medical Machine Learning Lab at the University of Münster
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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[![Python application](https://github.com/wwu-mmll/photonai_module_template/actions/workflows/lindandtest.yml/badge.svg)](https://github.com/wwu-mmll/photonai_module_template/actions/workflows/lindandtest.yml)
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[![Coverage Status](https://coveralls.io/repos/github/wwu-mmll/photonai_module_template/badge.svg?branch=master)](https://coveralls.io/github/wwu-mmll/photonai_module_template?branch=master)
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![GitHub](https://img.shields.io/github/license/wwu-mmll/photonai_module_template)
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[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=wwu-mmll_photonai_module_template&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=wwu-mmll_photonai_module_template)
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# How to use this template
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This repository is a quick start template for new photonai modules. To get started simply follow these steps:
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1. Klick "Use this template" button
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2. Fill in details for the new photonai module
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3. Wait for the repository to be created
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4. Wait for the Github Actions to run once
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5. As soon as the "✅ Ready to clone and code." commit appears in your repository you are ready to start coding
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6. (optional) Remove "rename_project.yml" workflow from .github/workflows
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7. (optional) Remove "rename_project.sh" from .github
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8. Remove this how to section from readme
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## Included features
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- [X] Code testing and coverage calculation (if coveralls secret **COVERALLS_REPO_TOKEN** is set)
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- [X] Continous Integration for testing and documentation updates based on Github Actions.
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- [X] MkDocs-Material based documentation template
21+
- [X] Photonai compatible **init.py** with boilerplate code for registration of new module
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- [X] pbr based auto-versioning for python releases
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- [X] blueprint action for pypi publishing (on github release)
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# How to implement a photonai module
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Take a look at some of our modules like [photonai neuro](https://github.com/wwu-mmll/photonai_neuro)
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or [photonai graph](https://github.com/wwu-mmll/photonai_graph).
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Most importantly: Feel free to reach out via issues in case of problems, e.g. by creating an issue at the [photonai repo](https://github.com/wwu-mmll/photonai)
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## Development workflow: Add new algorithms
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In order to add a new Algorithm / Feature to your project you can follow the steps below. By providing unit tests, a documentation and an example you maximize code quality and usability of your module.
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- [ ] Develop your learning algorithm / transformer / utility code (remember to adhere to the scikit-learn object API as [documented here](https://wwu-mmll.github.io/photonai/getting_started/custom_algorithm/))
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- [ ] Test your algorithms in a respective test file in the `test` folder
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- [ ] Document algorithms in the `docs` folder by copying and adapting the provided .md file
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- [ ] Provide an example on how to use your algorithms in an appropriately named file in the examples folder.
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- [ ] Expose the algorithm to photonai by adding it to the the `project_name/project_name.json` file with the full path. An example is provided within this repository. Thereby, the algorithm can be imported via its name, as defined in the json file. Make sure to pick a unique name.
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**In order to access your algorithms and functions in photonai you have to import your module once in your final script. This triggers the registration process in the photonai core module!**
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## Release a version of your software (on pypi)
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We suggest releasing via the github website. Simply create a release and an according tag.
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The tag is then used as version number and (if configured) the desired version is immediately build and released on pypi.
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Documentation avaiable at: [Documentation](https://wwu-mmll.github.io/photonai_module_template/)

‎docs/api/DummyTransformer.md

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# DummyTransformer
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A module for performing dummy transformations
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!!! info
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This is only a dummy transformer
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::: project_name.dummy.DummyTransformer.DummyTransformer.__init__
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rendering:
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show_root_toc_entry: False

‎docs/examples

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../examples

‎docs/index.md

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[![Python application](https://github.com/wwu-mmll/photonai_module_template/actions/workflows/lindandtest.yml/badge.svg)](https://github.com/wwu-mmll/photonai_module_template/actions/workflows/lindandtest.yml)
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[![Coverage Status](https://coveralls.io/repos/github/wwu-mmll/photonai_module_template/badge.svg?branch=master)](https://coveralls.io/github/wwu-mmll/photonai_module_template?branch=master)
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![GitHub](https://img.shields.io/github/license/wwu-mmll/photonai_module_template)
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[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=wwu-mmll_photonai_module_template&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=wwu-mmll_photonai_module_template)
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# How to use this template
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This repository is a quick start template for new photonai modules. To get started simply follow these steps:
7+
8+
1. Klick "Use this template" button
9+
2. Fill in details for the new photonai module
10+
3. Wait for the repository to be created
11+
4. Wait for the Github Actions to run once
12+
5. As soon as the "✅ Ready to clone and code." commit appears in your repository you are ready to start coding
13+
6. (optional) Remove "rename_project.yml" workflow from .github/workflows
14+
7. (optional) Remove "rename_project.sh" from .github
15+
8. Remove this how to section from readme
16+
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## Included features
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19+
- Code testing and coverage calculation (if coveralls secret **COVERALLS_REPO_TOKEN** is set)
20+
- Continous Integration for testing and documentation updates based on Github Actions.
21+
- MkDocs-Material based documentation template
22+
- Photonai compatible **init.py** with boilerplate code for registration of new module
23+
24+
# How to implement a photonai module
25+
26+
Take a look at some of our modules like [photonai neuro](https://github.com/wwu-mmll/photonai_neuro)
27+
or [photonai graph](https://github.com/wwu-mmll/photonai_graph).
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Most importantly: Feel free to reach out via issues in case of problems, e.g. by creating an issue at the [photonai repo](https://github.com/wwu-mmll/photonai)
29+
30+
## Development workflow: Add new algorithms
31+
32+
In order to add a new Algorithm / Feature to your project you can follow the steps below. By providing unit tests, a documentation and an example you maximize code quality and usability of your module.
33+
34+
- Develop your learning algorithm / transformer / utility code (remember to adhere to the scikit-learn object API as [documented here](https://wwu-mmll.github.io/photonai/getting_started/custom_algorithm/))
35+
- Test your algorithms in a respective test file in the `test` folder
36+
- Document algorithms in the `docs` folder by copying and adapting the provided .md file
37+
- Provide an example on how to use your algorithms in an appropriately named file in the examples folder.
38+
- Expose the algorithm to photonai by adding it to the the `project_name/project_name.json` file with the full path. An example is provided within this repository. Thereby, the algorithm can be imported via its name, as defined in the json file. Make sure to pick a unique name.
39+
40+
**In order to access your algorithms and functions in photonai you have to import your module once in your final script. This triggers the registration process in the photonai core module!**

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