Improved installation instructions.

Author: StuntsPT

docs/install.md

@@ -1,75 +1,94 @@
 # Installation
-Although you can run *Structure_threader* by simply cloning the repository (or
+
+## Preferred method
+
+Since v0.1.8 *Structure_threader* is available in
+[Pypi](https://pypi.python.org/pypi/structure_threader/0.1.8), which means that
+currently, installing *Structure_threader* is as simple as running
+`pip3 install structure_threader`. Don't forget the `--user` option if you can't
+or don't want to install the program as `root` user.
+
+## Alternative methods
+
+You can also run *Structure_threader* by simply cloning the repository (or
 downloading one of the releases), and placing the contents of the directory
-"structure_threader", $PATH, there is now a better, simpler way.   
-Since version 0.1.6 `setup.py` is implemented, and therefore all that is
-required is running `python3 setup.py install` (or even better,
-`pip install .`) from the distribution's root directory (where `setup.py` is
-located).
+"structure_threader", on any location on your `$PATH` env var.
+
+Another alternative, that can be used since version 0.1.6 is the `setup.py`
+method. This can be used either by running `python3 setup.py install` (or even
+better, `pip3 install .`) from the distribution's root directory (where
+`setup.py` is located).
+
 Please note that while dependencies like numpy and matplotlib are handled by
-this method, and if using the `pip` method for installing, binary distributions
-of STRUCTURE and fastStructure are also installed.
+this method, the preferred method for installing via Pypi will also install
+binary versions of both STRUCTURE and fastStructure for your platform.
 These binaries are installed in the "standard" `setup.py`
-[locations](https://docs.python.org/2/install/), eg. `/usr/bin` is installed
-with `sudo` or `~/.local/bin` if installed with the option `--user`, etc...
-Regardless, if you wish to compile your own binaries, you may wish to rely on
-our
+[locations](https://docs.python.org/2/install/), eg. `/usr/bin/` if installed
+with `sudo` or `~/.local/bin/` if installed with the option `--user`, etc...
+
+If you wish to compile your own binaries for these programs, you may wish to
+rely on our
 ["helper_scripts"](https://github.com/StuntsPT/Structure_threader/tree/master/helper_scripts)
 which contain commands to compile and install *Structure* **and**
-*fastStructure* (along with any required dependencies).
-Since v0.1.8 *Structure_threader* is available in
-[Pypi](https://pypi.python.org/pypi/structure_threader/0.1.8), which means that
-currently, installing *Structure_threader* is as simple as running
-`pip install structure_threader`. Don't forget the `--user` option if you can't
-or don't want to install the program as `root` user.
+*fastStructure* (along with any required dependencies). For more details check
+the next few sections.
 
 
 ## Structure_threader helper scripts
+
 The directory "helper_scripts" contains two scripts that will install STRUCTURE and fastStructre, respectively in a *semi* automatic way.
 
 Both scripts default the programs' install locations to ~/Software/<program_name>. You can change this in the scripts themselves should you wish to change this location.
 
 
 ### install_structure.sh
+
 This script will download and install STRUCTURE.
 
 
 #### Requirements:
 * a C compiler, such as GCC, with fortran support.
 * Cmake is required to build LAPACK
 
-In every HPC this should be available.
+This should be available in every HPC environment.
 
-In Ubuntu, all you should need is the package "build-essential" (if it is not already installed for some reason). In other distros, the package name should be similar. It can be installed like this:
+In Ubuntu, all you should need is the package "build-essential" (if it is not
+already installed for some reason). It can be installed like this:
 
 ```
 sudo apt-get install build-essential
 ```
 
+In other distros, the package name should be similar.
 
 ### install_faststructure.sh
-This script will download and install faststructure and its dependencies.
+This script will download and install fastStructure and its dependencies.
 
-Faststructure depends on quite a few software packages:
+fastStructure depends on quite a few software packages:
 * cython
 * numpy
 * scipy
 * GNU scientific library
 
-If these are already installed in your system, feel free to comment the script section that will install them. Otherwise it will install a new local copy of these programs. Otherwise, you can install them in Ubuntu with the following command:
+If these are already installed in your system, feel free to comment the script
+section that will install them. Otherwise it will install a new local copy of
+these programs. You can install these packages in Ubuntu with the following
+command:
 
 ```
 sudo apt-get install cython python-numpy python-scipy gsl-bin
 ```
 
 ###Important note:
 
-If you are relying on the GNU Scientific Library that was installed using the `install_faststructure` script, you will need to make your system aware of where these libraries are.
+If you are relying on the GNU Scientific Library that was installed using the
+`install_faststructure` script, you will need to make your system aware of
+where these libraries are.
 for that, add the following to your `~/.bashrc`:
 
 ```bash
 LD_LIBRARY_PATH=$install_dir/lib
 export LD_LIBRARY_PATH
 ```
 
-Where `$install_dir` is the directory defined in `install_faststructure`.
+Where `$install_dir` is the directory defined in `install_faststructure.sh`.