diff --git a/LICENSE b/LICENSE index 7903d62..614a8cb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ BSD 3-Clause License -Copyright (c) 2023, Chaste - Cancer Heart and Soft Tissue Environment +Copyright (c) 2025, Chaste - Cancer Heart and Soft Tissue Environment Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: diff --git a/README.md b/README.md index 7988791..d24c10b 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,44 @@ -# Chaste code generation from SBML +# SBML → Chaste -The `chaste_codegen_sbml` module takes [SBML](https://synonym.caltech.edu/) models as input and uses [libSBML](https://synonym.caltech.edu/software/libsbml/) to parse the models and output C++ code for Chaste. +`chaste_codegen_sbml` converts [SBML](https://synonym.caltech.edu/) models to C++ Chaste code. It relies on [libSBML](https://synonym.caltech.edu/software/libsbml/) for parsing SBML. ## Installation -### User install Installation via [`pipx`](https://pipx.pypa.io/) is recommended ``` pipx install git+https://github.com/Chaste/chaste-codegen-sbml@develop ``` -Alternatively, install via `pip` (optionally in a virtual environment) +Alternatively, install via `pip` ``` -# Create and activate a virtual environment +# Create and activate a virtual environment (optional) python -m venv sbml-venv +source sbml-venv/bin/activate # Install pip install git+https://github.com/Chaste/chaste-codegen-sbml@develop ``` -### Developer install -Clone the repository and install the package in editable mode along with the `dev` dependencies: +## Usage +``` +chaste_codegen_sbml [-h] +``` + +## Development +### Getting the code ``` +# Clone the repository git clone https://github.com/Chaste/chaste-codegen-sbml cd chaste-codegen-sbml -pip install -e .[dev] + +# Create and activate a virtual environment +python -m venv venv +source venv/bin/activate + +# Install in editable mode along with dev dependencies +pip install -e ."[dev]" ``` -## Usage +### Running tests ``` -chaste_codegen_sbml [-h] +python -m pytest ``` - -## Testing