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‎.github/actions/setup-poetry/action.yml‎

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name: "Set up Poetry"
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description: "Sets up Python and Poetry"
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inputs:
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python-version:
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required: false
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description: "Version of Python to use"
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default: "3.13"
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poetry-version:
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required: false
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description: "Version of Poetry to use"
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default: "2.1.0"
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runs:
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using: "composite"
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steps:
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- name: Install Poetry
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run: pipx install poetry==${{ inputs.poetry-version }}
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shell: bash
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ inputs.python-version }}
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cache: "poetry"

‎.github/actions/workflows/lint.yml‎

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name: Lint
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on:
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push:
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branches:
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- main
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pull_request:
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types:
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- opened
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- synchronize
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jobs:
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lint:
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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 Poetry
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uses: ./.github/actions/setup-poetry
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- name: Install dependencies
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run: poetry install --with dev
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- name: Lint
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run: poetry run ruff check .
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check-format:
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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 Poetry
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uses: ./.github/actions/setup-poetry
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- name: Install dependencies
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run: poetry install --with dev
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- name: Lint
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run: poetry run ruff format --check .

‎.github/actions/workflows/test.yml‎

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name: Test
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on:
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push:
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branches:
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- main
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pull_request:
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types:
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- opened
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- synchronize
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version:
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- "3.13"
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- "3.12"
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- "3.11"
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- "3.10"
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fail-fast: false
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steps:
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- uses: actions/checkout@v4
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- name: Set up Poetry
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uses: ./.github/actions/setup-poetry
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: poetry install --with dev
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- name: Test
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run: poetry run pytest

‎.gitignore‎

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### VisualStudioCode template
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.vscode/*
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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!.vscode/*.code-snippets
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# Local History for Visual Studio Code
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.history/
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# Built Visual Studio Code Extensions
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*.vsix
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### JetBrains template
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# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
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# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
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# User-specific stuff
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.idea/**/workspace.xml
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.idea/**/tasks.xml
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.idea/**/usage.statistics.xml
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.idea/**/dictionaries
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.idea/**/shelf
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# AWS User-specific
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.idea/**/aws.xml
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# Generated files
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.idea/**/contentModel.xml
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# Sensitive or high-churn files
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.idea/**/dataSources/
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.idea/**/dataSources.ids
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.idea/**/dataSources.local.xml
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.idea/**/sqlDataSources.xml
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.idea/**/dynamic.xml
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.idea/**/uiDesigner.xml
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.idea/**/dbnavigator.xml
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# Gradle
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.idea/**/gradle.xml
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.idea/**/libraries
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# Gradle and Maven with auto-import
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# When using Gradle or Maven with auto-import, you should exclude module files,
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# since they will be recreated, and may cause churn. Uncomment if using
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# auto-import.
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# .idea/artifacts
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# .idea/compiler.xml
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# .idea/jarRepositories.xml
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# .idea/modules.xml
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# .idea/*.iml
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# .idea/modules
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# *.iml
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# *.ipr
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# CMake
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cmake-build-*/
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# Mongo Explorer plugin
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.idea/**/mongoSettings.xml
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# File-based project format
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*.iws
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# IntelliJ
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out/
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# mpeltonen/sbt-idea plugin
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.idea_modules/
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# JIRA plugin
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atlassian-ide-plugin.xml
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# Cursive Clojure plugin
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.idea/replstate.xml
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# SonarLint plugin
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.idea/sonarlint/
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# Crashlytics plugin (for Android Studio and IntelliJ)
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com_crashlytics_export_strings.xml
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crashlytics.properties
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crashlytics-build.properties
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fabric.properties
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# Editor-based Rest Client
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.idea/httpRequests
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# Android studio 3.1+ serialized cache file
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.idea/caches/build_file_checksums.ser
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### VirtualEnv template
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# Virtualenv
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# http://iamzed.com/2009/05/07/a-primer-on-virtualenv/
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.Python
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[Bb]in
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[Ii]nclude
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[Ll]ib
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[Ll]ib64
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[Ll]ocal
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[Ss]cripts
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pyvenv.cfg
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.venv
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pip-selfcheck.json
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### Python template
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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.idea/

‎LICENSE‎

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MIT License
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Copyright (c) 2025 University Medical Center Leipzig, Dept. Medical Data Science
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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.

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