diff --git a/.gitignore b/.gitignore index 8ef6839e..23c482eb 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,6 @@ volestipy.egg-info .ipynb_checkpoints/ .vscode venv +lp_solve_5.5/ +.devcontainer/ +.github/dependabot.yml \ No newline at end of file diff --git a/README.md b/README.md index ae3a81b8..3dae1dab 100644 --- a/README.md +++ b/README.md @@ -15,11 +15,22 @@ metabolic network, namely Flux Balance Analysis and Flux Variability Analysis. [![Tutorial In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GeomScale/dingo/blob/develop/tutorials/dingo_tutorial.ipynb) [![Chat](https://badges.gitter.im/geomscale.png)](https://gitter.im/GeomScale/community?utm_source=share-link&utm_medium=link&utm_campaign=share-link) + ## Installation +**Note:** Python version should be 3.8.x. You can check this by running the following command in your terminal: +```bash +python --version +``` +If you have a different version of Python installed, you'll need to install it ([start here](https://linuxize.com/post/how-to-install-python-3-8-on-ubuntu-18-04/)) and update-alternatives ([start here](https://linuxhint.com/update_alternatives_ubuntu/)) + +**Note:** If you are using `GitHub Codespaces`. Start [here](https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/adding-a-dev-container-configuration/setting-up-your-python-project-for-codespaces) to set the python version. Once your Python version is `3.8.x` you can start following the below instructions. + + + To load the submodules that dingo uses, run -````unix +````bash git submodule update --init ```` @@ -39,12 +50,14 @@ rm lp_solve_5.5.2.11_source.tar.gz Then, you need to install the dependencies for the PySPQR library; for Debian/Ubuntu Linux, run -``` -apt-get install libsuitesparse-dev +```bash +sudo apt-get update -y +sudo apt-get install -y libsuitesparse-dev ``` -To install the Python dependencies, install [Poetry](https://python-poetry.org/). Then, run +To install the Python dependencies, `dingo` is using [Poetry](https://python-poetry.org/), ``` +curl -sSL https://install.python-poetry.org | python3 - --version 1.3.2 poetry shell poetry install ```