Merge pull request #210 from KumarLabJax/switch-from-poetry-to-uv

Adding uv.lock, updating readme, and adding future build system change

Author: bergsalex

README.md

@@ -33,7 +33,7 @@ packages. These packages are available from the Python Package Index (PyPI).
 
 Currently, JABS supports Python 3.10 through 3.13.
 
-## Python Env Setup
+## Python Environment Setup
 
 We recommend creating a Python Virtualenv for JABS:
 
@@ -105,27 +105,46 @@ startup times should be significantly reduced.**
 The following instructions are for Linux or macOS Developers. Commands for JABS developers using Windows might be 
 slightly different.
 
-This project uses Poetry for packaging and dependency management. JABS developers will need to install Poetry by 
-following the instructions on [Poetry's official website](https://python-poetry.org/docs/#installation).
+This project now uses **uv** for dependency management and building. Poetry is no longer required.
 
-You can use Poetry to manage your virtualenv, or manage your virtualenv externally to Poetry and use Poetry only for 
-installing dependencies. The following instructions assume that you've already created and activated a Python 
-environment for JABS using whichever method you prefer.
+JABS developers will need to install uv by following the instructions on 
+[uv's official website](https://docs.astral.sh/uv/getting-started/installation/).
 
-Clone the JABS git repository, and with your JABS virtualenv activated, run the following command in the project root:
+1) **Clone** the repository and enter the project directory.
 
-```commandline
-poetry install
+2) **Create/activate** a virtual environment (uv recommended):
+
+Note, if you don't want to activate the virtualenv, you can use `uv run <command>` to run commands in the virtualenv.
+If you don't want to activate the virtualenv, you can skip this step.
+
+```bash
+uv venv
+source .venv/bin/activate   # Linux/macOS
+# .venv\Scripts\Activate.ps1 # Windows PowerShell
+```
+
+3) **Install dependencies** in editable mode:
+
+```bash
+uv sync
 ```
 
 This will install all dependencies and JABS will be installed in "editable" mode, meaning that the JABS Python modules 
 installed in the virtualenv will be links to the files in the cloned git repository. JABS code changes will be 
 reflected immediately in the Python environment.
 
 Note to Developers: JABS uses package metadata to determine the version number. If you change the version number in the 
-pyproject.toml file, you will need to run `poetry install` to update the version number in the installed package so 
+pyproject.toml file, you will need to run `uv sync` to update the version number in the installed package so 
 that the GUI will display the correct version.
 
+
+#### Adding Dependencies
+```
+uv add <package>            # runtime dependency
+uv add --dev <package>      # dev-only dependency
+```
+
+
 #### Code Style
 
 JABS uses [ruff](https://docs.astral.sh/ruff/) for linting and formatting. Developers should run `ruff check` and `ruff format` before 
@@ -146,10 +165,18 @@ ruff format src/packagepath/modulename.py
 
 #### Building Python Packages
 
-Developers can build a Python package using the `poetry build` command. This will produce both a .tar.gz and a Python 
-Wheel file (.whl) in the dist directory. The wheel file can be installed with pip:
+Build wheels and source distributions with uv:
+
+```bash
+uv build
+```
+
+This will produce both a .tar.gz and a Python Wheel file (.whl) in the dist directory. 
 
-```pip install jabs_behavior_classifier-<version>-py3-none-any.whl```
+The wheel file can be installed with pip:
+```
+pip install jabs_behavior_classifier-<version>-py3-none-any.whl
+```
 
 Since the Wheel does not contain any compiled code it is platform independent.
 

pyproject.toml

@@ -34,10 +34,16 @@ dependencies = [
 
 [dependency-groups]
 dev = [
-  "matplotlib>=3.9.3,<4.0.0",
+  {include-group = "lint"},
+  {include-group = "test"},
+  "pre-commit>=4.2.0,<5.0.0",
+]
+test = [
   "pytest>=8.3.4,<9.0.0",
+  "matplotlib>=3.9.3,<4.0.0",
+]
+lint = [
   "ruff>=0.11.5,<0.12.0",
-  "pre-commit>=4.2.0,<5.0.0",
 ]
 
 [project.urls]
@@ -60,5 +66,8 @@ packages = [
 ]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["uv_build>=0.7.19,<0.8.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "jabs"