Updated installation instructions.

The README.md file contains now more information on how to
install MsSpec (compilation and Python package) either in
standard or devel mode.

README.md

@@ -4,8 +4,8 @@ Introduction
 This is the Python MsSpec version with support for Python 3.x and dynamic memory allocation for Phagen and Spec
 
 
-Installation of the devel package
-=================================
+Installation
+============
 
 Requirements
 ------------
@@ -42,13 +42,14 @@ you need to install it.
 Fetching the code
 -----------------
 
-You first need to clone the devel branch with either 2 commands below:
+You first need to clone the repository with the command below:
 
 ```Bash
 git clone https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
-git checkout devel
 ```
 
+If you want to pull the devel branch (unstable):
+
 ```Bash
 git clone --branch devel https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
 ```
@@ -61,21 +62,22 @@ One step install
 ----------------
 
 The command below will do all the stuff to install msspec in its dedicated Python
-virtual environment provided all the above requirements are fullfilled
+virtual environment provided all the above requirements are fullfilled:
 
 
 ```Bash
 cd msspec_python3
-make devel
+make install
 ```
 
 This will:
 
-- Create a Python virtual environment in the "\_venv" folder inside the msspec\_python3 folder.
+- Create a Python virtual environment in your '~/.local/src' folder
 - Install all the required Python packages in this virtual environment.
 - Install (or even maybe build) wxPython for your OS and Python version in this virtual environment.
 - Build the msspec shared librarires.
-- Install msspec in *edit mode* in this virtual environment.
+- Install the Python msspec package in this virtual environment.
+- Install a frontend script called 'msspec' in the '~/.local/bin' folder.
 
 You can tweak the process by specifying space separated  key=value pairs on the command line.
 Allowed keys are:
@@ -89,35 +91,61 @@ Allowed keys are:
 - FC, the Fortran compiler to use (gfortran)
 - F2PY
 
-
-Work with msspec
-----------------
-
-All you need to do each time you want to work with msspec is activating the virtual environment.
-
-For example, if *virtualenv* was used to create the virtual environment:
-
+To install msspec in developpment mode, use:
 ```Bash
-source msspec_python3/_venv/bin/activate
+cd msspec_python3
+make devel
 ```
 
-Then you can launch your script with 
+This will do the same steps as above except that the virtual environment will be located in 
+the "\_venv" folder inside the "msspec\_python3" folder and the frontend script will not be
+installed.
+
+
+Working with msspec
+-------------------
+
+Use the frontend command to process a Python script with msspec.
 
 ```Bash
-python myscript.py
+msspec -p myscript.py
 ```
 
+This will execute the myscript.py inside the msspec virtual environment.
+
+You can also load a hdf5 file with the '-l' option:
+
+```Bash
+msspec -l results.hdf5
+```
+
+You can load an iPython console with "msspec -i". It is a good way to modify the virtual environment
+of MsSpec since you can add or remove packages withe the "%pip" command.
+
+If you want to activate the MsSpec virtual environment in your current shell session:
+
+```Bash
+eval $(msspec -e)
+```
+
+You can then run scripts using the 'python' command directly.
+Type in 'deactivate' to go back to your standard shell.
+
 See the online [tutorials](https://msspec.cnrs.fr/tutorials/index.html) for more information on how to use msspec.
 
-When you're done, you can deactivate the virtual environment with
-
-```Bash
-deactivate
-```
 
 Uninstall MsSpec
 ----------------
 
+To remove MsSpec, use the command:
+
+```Bash
+msspec -u
+```
+
+This will simply remove the virtual environment folder in '~/.local/src' and the frontend script in '~/.local/bin'.
+
+
 When Installed in "devel mode", nothing is created outside the msspec\_python3 folder, so you just have to remove 
 that folder to get rid of msspec on your computer