Update manual (installation)

cosymlib/__init__.py

@@ -84,7 +84,6 @@ class Cosymlib:
     Main cosymlib class
 
     :param structures: List of :class:`~cosymlib.molecule.geometry.Geometry` or :class:`~cosymlib.molecule.Molecule`
-    type objects
     :type structures: list
     :param ignore_atoms_labels: Ignore atomic element labels is symmetry calculations
     :type ignore_atoms_labels: bool
@@ -800,7 +799,6 @@ def print_minimum_distortion_path_shape(self, shape_label1, shape_label2, centra
         output2.write(file_io.get_file_xyz_txt(test_structures))
 
         if output1 is sys.stdout:
-            import matplotlib.pyplot as plt
             plt.plot(path[0], path[1], 'k', linewidth=2.0)
             plt.scatter(np.array(csm[label1_name])[filter_mask],
                         np.array(csm[label2_name])[filter_mask], linewidths=0.01)

cosymlib/molecule/electronic_structure/__init__.py

@@ -9,8 +9,6 @@ class ElectronicStructure:
     :type basis: dict
     :param orbital_coefficients: Molecular orbital coefficients
     :type orbital_coefficients: list
-    # :param charge: The charge
-    # :type charge: int
     :param multiplicity: The multiplicity
     :type multiplicity: int
     :param alpha_energies: Alpha molecular orbital energies in Hartree

docs/install.rst

@@ -3,29 +3,46 @@
 Install
 =======
 
-Download the code and use :file:`setup.py` to install the code using :program:`setuptools`
-python module ::
+:program:`cosymlib` is available in both GitHub and PyPI repositories (https://pypi.org/project/cosymlib/).
+Installation via PyPI is simpler and it is recommended for most users.
 
-   $ python setup.py install --user
+Install from PyPI
+_________________
 
-for python3 ::
+This installation requires :program:`pip`  ( https://pip.pypa.io/en/stable/installing/) to be installed
+in your system. Once pip is properly installed you can install :program:`cosymlib` by typing the following
+command in the terminal: ::
 
-   $ python3 setup.py install --user
+    pip install cosymlib --user
 
-the code will be installed as a python module. To check that it is properly installed you can
-run the :program:`python` interpret and execute ::
+if your system contains both :program:`python2` and :program:`python3` installed and you intend to install :program:`cosymlib`
+for :program:`python3` use: ::
 
-   import cosymlib
+    pip3 install cosymlib --user
 
-Install via pip
-_______________
+Install from GitHub
+___________________
 
-If pip is already installed in your computer, you can download and install the cosymlib module as any other
-module in python ::
+Alternatively you can download the latest version of :program:`cosymlib` from github using :program:`git` (https://git-scm.com)
+and install it manually through :file:`setup.py` file using :program:`setuptools` (https://setuptools.readthedocs.io/).
 
-    pip install cosymlib --user
+First, download the code using :program:`git` in your computer by typing: ::
 
-for python3 ::
+    git clone https://github.com/GrupEstructuraElectronicaSimetria/cosymlib.git
 
-    pip3 install cosymlib --user
+This creates a copy of the repository in your computer. You can keep it updated by synchronizing it
+with GitHub repository by using the command: ::
+
+    git pull
+
+Once this is done, move to the repository root directory (where :file:`setup.py` is found) and type the
+following command to install :program:`cosymlib` : ::
+
+    python setup.py install --user
+
+In both cases (PyPI & Github installations) the code will be installed as a :program:`python` module. To check that it is properly
+installed you can run the :program:`python` interpreter and execute: ::
+
+   import cosymlib
 
+if the execution do not show any errors :program:`cosymlib` has been installed successfully.