msspec_python3/README.md

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

```Bash
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:

```Bash
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:


```Bash
virtualenv --python=python3 msspec_venv
```

or 

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

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

```Bash
source ./msspec_venv/bin/activate
```

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

```Bash
cd msspec_python3/src
```

Install the python package dependencies.

```Bash
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

```Bash
scons
```

Finally, install the package in develop mode:

```Bash
pip install -e .
```

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