Update README and pyproject.toml

Author: phuongho43

README.md

@@ -1,67 +1,21 @@
 # ezplot
 
-[![Release](https://img.shields.io/github/v/release/phuongho43/ezplot)](https://img.shields.io/github/v/release/phuongho43/ezplot)
-[![Build status](https://img.shields.io/github/actions/workflow/status/phuongho43/ezplot/main.yml?branch=main)](https://github.com/phuongho43/ezplot/actions/workflows/main.yml?query=branch%3Amain)
-[![codecov](https://codecov.io/gh/phuongho43/ezplot/branch/main/graph/badge.svg)](https://codecov.io/gh/phuongho43/ezplot)
-[![Commit activity](https://img.shields.io/github/commit-activity/m/phuongho43/ezplot)](https://img.shields.io/github/commit-activity/m/phuongho43/ezplot)
-[![License](https://img.shields.io/github/license/phuongho43/ezplot)](https://img.shields.io/github/license/phuongho43/ezplot)
-
 Visualizing data from biology experiments.
 
-- **Github repository**: <https://github.com/phuongho43/ezplot/>
-- **Documentation** <https://phuongho43.github.io/ezplot/>
-
-## Getting started with your project
-
-### 1. Create a New Repository
+## Getting Started
 
-First, create a repository on GitHub with the same name as this project, and then run the following commands:
+### 1. Install [UV](https://docs.astral.sh/uv/getting-started/installation/)
 
 ```bash
-git init -b main
-git add .
-git commit -m "init commit"
-git remote add origin git@github.com:phuongho43/ezplot.git
-git push -u origin main
+$ curl -LsSf https://astral.sh/uv/install.sh | sh
 ```
 
-### 2. Set Up Your Development Environment
-
-Then, install the environment and the pre-commit hooks with
-
-```bash
-make install
-```
-
-This will also generate your `uv.lock` file
-
-### 3. Run the pre-commit hooks
+### 2. Specify file paths and plotting parameters
 
-Initially, the CI/CD pipeline might be failing due to formatting issues. To resolve those run:
+ezplot/plot\_[type].py
 
-```bash
-uv run pre-commit run -a
-```
-
-### 4. Commit the changes
-
-Lastly, commit the changes made by the two steps above to your repository.
+### 3. Run plotting functions
 
 ```bash
-git add .
-git commit -m 'Fix formatting issues'
-git push origin main
+$ uv run plot_[type]
 ```
-
-You are now ready to start development on your project!
-The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
-
-To finalize the set-up for publishing to PyPI, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/publishing/#set-up-for-pypi).
-For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/mkdocs/#enabling-the-documentation-on-github).
-To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-uv/features/codecov/).
-
-## Releasing a new version
-
----
-
-Repository initiated with [fpgmaas/cookiecutter-uv](https://github.com/fpgmaas/cookiecutter-uv).

pyproject.toml

@@ -17,11 +17,22 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
+dependencies = [
+    "fcsparser>=0.2.8",
+    "matplotlib>=3.9.4",
+    "natsort>=8.4.0",
+    "numpy>=1.26.4",
+    "pandas>=2.2.3",
+    "seaborn>=0.13.2",
+]
 
 [project.urls]
-Homepage = "https://phuongho43.github.io/ezplot/"
 Repository = "https://github.com/phuongho43/ezplot"
-Documentation = "https://phuongho43.github.io/ezplot/"
+
+[project.scripts]
+plot_dynamics = "fluoressential.plot_dynamics:main"
+plot_groups = "fluoressential.plot_groups:main"
+plot_cytometry = "fluoressential.plot_cytometry:main"
 
 [dependency-groups]
 dev = [
@@ -30,9 +41,7 @@ dev = [
     "tox-uv>=1.11.3",
     "deptry>=0.20.0",
     "mypy>=0.991",
-
     "ruff>=0.6.9",
-
 ]
 
 [build-system]
@@ -57,7 +66,7 @@ testpaths = ["tests"]
 
 [tool.ruff]
 target-version = "py39"
-line-length = 120
+line-length = 200
 fix = true
 
 [tool.ruff.lint]