New version Python Project template

.pre-commit-config.yaml

@@ -1,13 +1,26 @@
+# pre-commit-config.yaml
+# See https://pre-commit.com for docs and https://pre-commit.com/hooks.html for available hooks
+
+# ======================================================
+# =======            repository hooks           ========
+# ======================================================
 repos:
+# Official pre-commit-hooks for general checks
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
     -   id: pretty-format-json
         args: [--no-sort-keys, --indent=4, --autofix]
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
+# Format TOML and YAML files with pretty-format hooks
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
     rev: v2.14.0
     hooks:
     -   id: pretty-format-yaml
-        args: [--autofix, --indent=4]
+        args:
+        -   --autofix
+        -   --indent
+        -   '4'
+        stages: [pre-commit]
+        files: \.ya?ml$

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2022-2023, Saez Lab
+Copyright (c) 2022-2025, Saez Lab
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -0,0 +1,90 @@
+# Python project template (Saez-Rodriguez Group)
+
+## Description
+
+This is a Cookiecutter template to create Python projects. It has been tailored by the [Saez-Rodriguez Group](https://saezlab.org/) at Universität Heidelberg.
+
+This template provides tools to streamline setup and maintenance, letting you focus on your project instead of getting bogged down by technical details. It includes:
+
+- Documentation
+  - [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/): A sleek, responsive theme for MkDocs documentation sites.
+
+- Code Quality/Automation
+  - [Pre-commit hooks](https://pre-commit.com/): A framework for managing and running code quality hooks before commits.
+
+- Release Management
+  - [Bump2version](https://github.com/c4urself/bump2version):  A tool to automate version number management in your project.
+
+- Testing
+  - [Pytest](https://docs.pytest.org/en/stable/):  A powerful testing framework for writing and running Python tests.
+
+
+## Pre-requisites
+> **Note:**   We strongly recommend you have the following pre-requisites before using this template.
+
+| Pre-requisite                                                 | Description                                                                      |
+| ------------------------------------------------------------- | -------------------------------------------------------------------------------- |
+| [uv](https://docs.astral.sh/uv/getting-started/installation/) | A high-performance tool for managing Python packages and virtual environments.   |
+| [Cruft](https://cruft.github.io/cruft/#installation)          | A CLI tool to scaffold new projects using customizable templates.                |
+| [GitHub CLI](https://github.com/cli/cli#installation)         | A command-lIne tool to interact with GitHub repositories, issues, and workflows. |
+
+## How-to use this template?
+
+In six easy steps you will have a ready to use Python project with batteries included.
+
+**1.  Generate Your Project from the Template**
+
+  Run the following command and follow the prompts in your terminal:
+  ```bash
+  cruft create https://github.com/saezlab/python-project.git --checkout master
+  ```
+
+**2. Navigate to Your New Project Directory**
+```bash
+cd <my-project> # replace with the name of your project
+```
+
+**3. Set Up and Activate a Virtual Environment using `uv`**
+```bash
+uv venv .venv
+source .venv/bin/activate
+```
+> This creates and activates a lightweight virtual environment in `.venv`.
+
+**4. Install Project Dependencies listed in the `pyproject.toml` file**
+
+  Install all required and optional dependencies (development, testing, docs):
+  ```bash
+  uv pip install ".[dev,tests,docs]"
+  ```
+
+**5. Install and update pre-commit hooks**
+```bash
+git init
+pre-commit install
+pre-commit autoupdate
+```
+
+**6. Initialize Git and Push to GitHub**
+```bash
+
+git add .
+git commit -m "Initial commit"
+gh repo create <GitHub-organization>/<my-project>  --public --source=. --push
+```
+
+
+🎉 Congratulations! Wishing you every success as you begin your project journey 🚀
+
+Saez-Rodriguez Group Team!
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first
+to discuss what you would like to change.
+
+Please make sure to update tests as appropriate.
+
+## License
+
+Python-project template has a [BSD3](https://opensource.org/license/bsd-3-clause) license, as found in the [LICENSE](./LICENSE) file.