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Merge pull request #1 from SmartMonkey-git/rr/setup
Basic Setup
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‎.github/actions/setup_env/action.yaml‎

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name: Setup/Cache Env
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description: 'Sets up and caches a python env. Will only install dependencies if no cache was hit.'
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runs:
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using: composite
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steps:
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- name: Get project version with yq
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id: get_python_version
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uses: mikefarah/yq@v4.46.1
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with:
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cmd: yq '.project.requires-python' pyproject.toml
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- name: Set up Python
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uses: actions/setup-python@v5.6.0
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with:
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python-version: ${{ steps.get_python_version.outputs.result }}
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- name: Cache Env
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uses: actions/cache@v4.2.3
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id: env-cache
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with:
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path: ${{ env.pythonLocation }}
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key: ${{ hashFiles('./requirements/requirements.txt') }}-${{ hashFiles('./requirements/requirements_scripts.txt') }}-${{ hashFiles('./requirements/requirements_test.txt') }}
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- name: Install Dependencies
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if: ${{ steps.env-cache.outputs.cache-hit != 'true' }}
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements/requirements.txt
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pip install -r requirements/requirements_test.txt
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shell: bash

‎.github/workflows/cd.yaml‎

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name: CD
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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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publish-to-pypi:
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name: Build distribution 📦
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runs-on: ubuntu-latest
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permissions:
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id-token: write
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steps:
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- name: Check out Repo
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uses: actions/checkout@v4
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with:
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persist-credentials: false
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fetch-depth: 0
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- name: Get project version with yq
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id: get_python_version
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uses: mikefarah/yq@v4.46.1
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with:
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cmd: yq '.project.requires-python' pyproject.toml
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- name: Initialize Python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ steps.get_python_version.outputs.result }}
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- name: Install build
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run: >-
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pip install build==1.2.2.post1
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- name: Build a binary wheel and a source tarball
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run: python3 -m build
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- name: Publish distribution 📦 to PyPI
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env:
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SETUPTOOLS_SCM_PRETEND_VERSION: ${{ github.event.release.tag_name }}
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with:
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packages-dir: dist/
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repository-url: https://pypi.org/legacy/
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/ci.yaml‎

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name: CI
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on:
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pull_request:
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permissions:
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id-token: write
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contents: read
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env:
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PYTEST_ADDOPTS: "--color=yes"
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jobs:
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test:
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name: Test
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timeout-minutes: 15
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runs-on: ubuntu-latest
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steps:
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- name: Check out Repo
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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: Setup Env
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uses: ./.github/actions/setup_env
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- name: Test with pytest
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id: tests
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run: |
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pytest --disable-warnings ./
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formatting:
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name: Formatting
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- name: Check out Repo
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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: Setup Env
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uses: ./.github/actions/setup_env
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- name: Ruff Formatting
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run: ruff format --check
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linting:
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name: Linting
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runs-on: ubuntu-latest
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timeout-minutes: 15
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steps:
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- name: Check out Repo
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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: Setup Env
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uses: ./.github/actions/setup_env
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- name: Ruff Linting
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run: ruff check

‎.github/workflows/master_cache.yaml‎

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name: Create Master Cache
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on:
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pull_request:
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types: [closed]
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branches:
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- main
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- master
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permissions:
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id-token: write
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contents: read
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env:
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PYTEST_ADDOPTS: "--color=yes"
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jobs:
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create_master_cache:
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name: Caching
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timeout-minutes: 15
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runs-on: ubuntu-latest
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steps:
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- name: Check out Repo
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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: Setup Env
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uses: ./.github/actions/setup_env

‎.gitignore‎

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# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
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# refer to https://docs.cursor.com/context/ignore-files
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.cursorignore
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.cursorindexingignore
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.cursorindexingignore
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.vscode/
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.idea/
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_version.py

‎README.md‎

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# robinson-group-python-template
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## Robinson Group Python Template
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This repo serves as a template for python projects in the [Robinson Group](https://robinsongroup.github.io/) of the BIH.
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To get started copy or fork this project and follow the steps below.
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### Install conda
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If you not already have conda, miniconda or Anaconda installed. Check out the [miniconda installation guide](https://www.anaconda.com/docs/getting-started/miniconda/install#quickstart-install-instructions).
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#### Setup env
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Open `requirements/environment.yml` and adjust `<Project-Name>`.
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To create and activate the env execute:
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```
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conda env create -f requirements/environment.yml
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conda activate <Project-Name>
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```
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### Renaming
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As this is a template project, some of the directories and setting have generic names. To ensure the project is set up, that it aligns with your intended name please:
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1. Rename the folder inside of src
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2. Open the pyproject.toml
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- Rename all variables in the sections ``[project]`` and ``[project.urls]``
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### Ruff Linting and Formatting
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Ruff helps to maintain the same code style and prevent the most common bugs in our code base. Keeping the code style uniform simplifies the collaboration - it is much easier to review a pull request without hundreds of whitespace changes.
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Please take a moment to learn how to use the IDE plugins. In PyCharm, the formatting action can be invoked with right-clicking at any code location and the same applies for VS Code. The keyboard shortcuts are also available. However, it is recommended to format and lint on saving a file.
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Besides the IDE, Ruff can also be run as a command line tool. Assuming that the virtual environment is active, the following command will format/lint the entire project:
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**Formatting**
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```bash
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ruff format
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```
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**Linting**
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```bash
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ruff check
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```
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We recommend to run commit the resulting changes before opening a PR, because the unformatted code will fail the Continuous Integration (CI) pipeline. A PR cannot be merged until the code passes the CI.
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#### Ruff Plugins
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- [Pycharm - Ruff Plugin](https://plugins.jetbrains.com/plugin/20574-ruff)
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- [VSCode - Ruff Plugin](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff)
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### Continuous Delivery
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You've done it, your package is at a state, where you want other to use it. Luckily, this repository features a CD-Pipeline,
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that will build and upload your packages to Pypi for you. To get the CD running you need to first follow these [instructions](https://docs.pypi.org/trusted-publishers/adding-a-publisher/). The pipeline uses [OIDC](https://openid.net/developers/how-connect-works/) to authenticate on Pypi. Make sure your [pyproject.toml](pyproject.toml) is set up correctly.
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Then open your repository page on Github. To the right you should find **Create new Release**. Press it!
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You will find this page:
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![img.png](release_page.png)
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Create a new Tag for your release, add a title and a description. Press **Publish release**, watch the CD launch in the **Actions Tab** and enjoy your well deserved coffee. ☕

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=80.9.0", "wheel==0.45.1", "setuptools_scm==8.3.1"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "robinson-group-python-template"
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description = "A template for python projects build in the robinson group"
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authors = [{ name = "Rouven Reuter" }]
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requires-python = ">=3.10"
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dynamic = ["dependencies", "version"]
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license = { file = "LICENSE" }
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readme = "README.md"
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[project.urls]
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homepage = "https://github.com/SmartMonkey-git/robinson-group-python-template"
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repository = "https://github.com/SmartMonkey-git/robinson-group-python-template.git"
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documentation = "https://github.com/SmartMonkey-git/robinson-group-python-template"
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bugtracker = "https://github.com/SmartMonkey-git/robinson-group-python-template/issues"
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[tool.setuptools]
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packages.find = { where = ["src"] }
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[tool.setuptools_scm]
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version_file = "src/project_name/_version.py"
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[tool.setuptools.dynamic]
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version = { attr = "project_name._version.version" }
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dependencies = {file = ["requirements/requirements.txt"]}

‎pytest.ini‎

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[pytest]
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minversion = 7.0
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pythonpath = src
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testpaths =
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tests

‎release_page.png‎

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‎requirements/environment.yml‎

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name: <Project-Name>
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dependencies:
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- python>=3.10
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- pip
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- pip:
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- -r requirements.txt
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- -r requirements_test.txt

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