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

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

To get the python package dependencies, you can install the requirements with the provided requirements.txt file.

pip install --upgrade -r requirements.txt

You also need to export the path to the msspec package in the PYTHONPATH variable (replace the whereisthegitrepo part of the string with the actual absolute path of your repo.

export PYTHONPATH=/whereisthegitrepo/src:$PYTHONPATH

Finally you need to compile the fortran libs:

make pybinding

That's all. All you need to do each time you want to work with msspec is:

• To activate the virtual environment
• Export the path to msspec package in the PYTHONPATH variable

To create a self-extracible archive

If you want to create a setup program to install msspec:

At the root of the repo, type in

make selfex

This will compile the code and create the results of unit tests, then it will create a self-extractible archive in the package folder

To install the *.setup file

Just execute the file with a shell

sh ./MsSpec-###.setup

Replace ### with the version number.

To automatically accept the defaults you could type in

sh ./MsSpec-###.setup --accept -- -y

and to make the install process verbose:

sh ./MsSpec-###.setup -- -d