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
===============================

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
```

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

```Bash
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.

```Bash
export PYTHONPATH=/whereisthegitrepo/src:$PYTHONPATH
```

Finally you need to compile the fortran libs:

```Bash
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

```Bash
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

```Bash
sh ./MsSpec-###.setup
```

Replace ### with the version number.

To automatically accept the defaults you could type in

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

and to make the install process verbose:

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