pySCUBA is Python bindings to the SCUBA library. These can be built from the SCUBA source code.

Here we show how to install pySCUBA(version 1.0) and use the SCUBA-sketch program.

Getting Started Using pySCUBA

1. Requirements

• Operating System: Linux (Recommended)
• No non-standard hardware is required.

1.1. Install Dependencies

Before installing, make sure the following dependencies are installed:

• cmake
• lapack
• python3.8

Here is how to install cmake:

sudo apt install cmake gfortran

To install lapack, we suggest build from source code. For example, you can download lapack-3.10.1 and compile it following the instructions in lapack-3.10.1/README.md:

   mkdir build
   cd build
   cmake -DCMAKE_INSTALL_LIBDIR=$HOME/.local/lapack ..
   cmake --build . -j --target install

We assume that the dynamic libraries liblapacke.so installed in ~/.local/lapack/ if you follow the previous steps. However, if lapack installed in other path, your can to change the line in our CMakeLists.txt to your path:

# if install lapack in other enviroment ,change the lines
find_package(LAPACK REQUIRED)
set(PythonLibs_LIBRARIES ${YOURPATH}/liblapacke.so)

and make sure the file lapacke.h(Under the path /lapack-3.10.1/LAPACKE/include/) in /usr/local/include.

Python 3.8 dynamic libraries are also necessary for our project. We assume you have created a Python 3.8 environment using Anaconda.

conda create --name pySCUBA python=3.8
conda activate pySCUBA
conda install numpy

The following files, libpython3.8.so and libpython3.8.so.1.0, should be located in ~/anaconda3/envs/pySCUBA/lib/. If your python3.8 enviroment is installed in other directory. You have to change the line in our CMakeLists.txt to your path.

# if install python3.8 in other enviroment ,change the line
set(PythonLibs_LIBRARIES ${YOURPATH}/libpython3.8.so)

2. Install pySCUBA

Enter our project directory and run the installation program:

python setup.py develop

After a few minutes of compiling, the pySCUBA package is installed

Then activate the environment:

source ~/.bashrc
conda activate pySCUBA

To test if pySCUBA is successfully installed, run

cd ./demo/SCUBASketch/
python SCUBAsketch.py

If there are no error messages, it indicates that the pySCUBA has been installed successfully. More demos are in the /demo/SCUBASketch/ folder. It takes about 2 minutes to run the entire demo.