diff --git a/README.md b/README.md index f11e46c..d838910 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ -> **⚠️ Disclaimer**: This is an early preview of the CORNETO library. **CORNETO is under active development and has not yet reached a stable release for end users**. Contributions and feedback are not yet open until the first stable release. Please stay tuned for updates. +> **⚠️ Disclaimer**: This is an early preview of the CORNETO library. **CORNETO is under active development and has not yet reached a stable release for end users**. Contributions are not yet open until the first stable release. Please stay tuned for updates. --- @@ -27,17 +27,40 @@ CORNETO (Constrained Optimization for the Recovery of Networks from Omics) is a CORNETO abstract

+## Installation +We're currently working towards having a first, stable release for end-users with all the features described in the preprint. In the meantime, you can play with CORNETO using the latest dev. version. -## Installation +### Development version -A pre-release version of the lib, which is used by LIANA+ and NetworkCommons, is already available at Pypi and can be installed with `pip install corneto`. However, this version lacks many of the developments discussed in the preprint. You can install it along with CVXPY, Scipy (for open source solver support) and Gurobipy for using GUROBI solver: +To install the development version with support for the Gurobi solver and plotting capabilities using graphviz, please use conda or mamba to create an environment: -```bash -pip install corneto cvxpy-base scipy gurobipy ``` +conda activate your-environment +conda install -c conda-forge python-graphviz scipy +pip install cvxpy-base gurobipy +``` + +Then, install the dev version of CORNETO: +``` +git clone -b dev https://github.com/saezlab/corneto.git +cd corneto +pip install -e . +``` + +### Installing Gurobi solver + +CORNETO supports many different mathematical solvers for optimization. However, for real world problems, we typically use GUROBI. **GUROBI is a commercial solver which offers free academic licenses**. If you have an academic email, this step is very easy to do in just few minutes. Follow these steps: -Please note that **GUROBI is a commercial solver which offers free academic licenses**. If you have an academic email, this step is very easy to do in just few minutes: https://www.gurobi.com/features/academic-named-user-license/. You need to register GUROBI in your machine with the `grbgetkey` tool from GUROBI. +1. Request the "Academic Named-User License" here: https://www.gurobi.com/features/academic-named-user-license/. +2. Register the license in your machine with the `grbgetkey` tool from GUROBI. For this, download the corresponding license tool for your system here: https://support.gurobi.com/hc/en-us/articles/360059842732-How-do-I-set-up-a-license-without-installing-the-full-Gurobi-package +3. Run the `grbgetkey` tool and introduce your license key. + +If you find any issue, please check this article: https://support.gurobi.com/hc/en-us/articles/13207658935185-How-do-I-retrieve-an-Academic-Named-User-license + +Please note that other high performance solvers like CPLEX, COPT, Mosek, etc are also supported. Please check the solver's table from https://www.cvxpy.org/tutorial/solvers/index.html to see which solvers are supported by the CVXPY backend. + +### Installing open-source solvers Alternatively, it is possible to use CORNETO with any free solver, such as HIGHS, included in Scipy. For this you don't need to install Gurobi. Please note that if `gurobipy` is installed but not registered with a valid license, CORNETO will choose it but the solver will fail due to license issues. If SCIPY is installed, when optimizing a problem, select SCIPY as the solver @@ -46,23 +69,17 @@ Alternatively, it is possible to use CORNETO with any free solver, such as HIGHS P.solve(solver="SCIPY") ``` -### Development version +### Pre-release version -To install the development version with support for ploting using graphviz, please use conda or mamba to create an environment: +A pre-release version of the lib, which is used by [LIANA+](https://liana-py.readthedocs.io/) and [NetworkCommons](https://networkcommons.readthedocs.io/), is already available at Pypi and can be installed with `pip install corneto`. However, this version lacks many of the developments discussed in the preprint. -``` -conda activate your-environment -conda install -c conda-forge python-graphviz -pip install cvxpy-base gurobipy -``` +You can install it along with CVXPY, Scipy (for open source solver support) and Gurobipy for using GUROBI solver: -Then, install the dev version of CORNETO: -``` -git clone -b dev https://github.com/saezlab/corneto.git -cd corneto -pip install -e . +```bash +pip install corneto cvxpy-base scipy gurobipy ``` + ## How to cite ```