Introduction

This is the Python MsSpec version with support for Python 3.x and dynamic memory allocation for Phagen and Spec

To work with the git repository

You can clone this repository onto your local computer using git

git clone https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git

This will create a folder named "msspec_python3" with all the source code inside.

You can also clone the development branch:

git clone --branch devel https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git

It is higly recommended to work in a Python virtual environment. To create one, you can use:

virtualenv --python=python3 msspec_venv

or

virtualenv --python=python3 --system-site-packages msspec_venv

to activate the virtual environment (if you are in the folder where you created "msspec_venv"):

source ./msspec_venv/bin/activate

Now you can build the program, go in the source folder

cd msspec_python3/src

Install the python package dependencies.

pip install -r setup_requirements.txt
pip install -r requirements.txt

You need to compile the fortran libs. This is done by the scons (Software Construction) program

scons

Finally, install the package in develop mode:

pip install -e .

That's all. All you need to do each time you want to work with msspec is activating the virtual environment