Manual update

docs/install.rst

@@ -10,43 +10,50 @@ from PyPI (recommended)
 -----------------------
 
 This installation requires :program:`pip`  ( https://pip.pypa.io/en/stable/installing/) to be installed
-in your system. We strongly recommend the use of python environments (https://docs.python.org/3/library/venv.html).
-For most users the basic installation instructions are:
+in your system. We strongly recommend the use of python environments, for more details refer to
+https://docs.python.org/3/library/venv.html . For most users the basic installation proceed as follows:
 
 1. Create a virtual environment at path <venv>::
 
-    python3 -m venv <venv>
+    $ python3 -m venv <venv>
 
 2. Activate environment ::
 
-    # on MAC / Linux (bash shell)
-    source <venv>/bin/activate
+    # on MAC / Linux
+    $ source <venv>/bin/activate
 
-    # on windows (powershell)
+    # on windows (powershell) [see note below]
     C:\> <venv>\Scripts\Activate.ps1
 
 3. Install cosymlib ::
 
-    pip install numpy
-    pip install cosymlib
+    $ pip install numpy
+    $ pip install cosymlib
 
 4. Deactivate environmen ::
 
-    deactivate
+    $ deactivate
 
-.. note::
-    To use :program:`cosymlib` it is necessary to activate the environment every time a new shell is open.
-    All the scripts contained in :program:`cosymlib` will be accessible in this environment. On windows
-    it is necessary to type *python* before the script name ::
 
-        python <script_name> <script_options>
+To use :program:`cosymlib` it is necessary to activate the environment every time a new shell is open.
+On Linux/MAC all the scripts contained in :program:`cosymlib` will be accessible in this environment. ::
+
+    $ source <venv>/bin/activate
+    $ <script_name> <script_options>
+    $ deactivate
+
+
+On windows, to execute the scripts it is necessary to type *python* followed by the full path of the script name ::
+
+    C:\> python <venv>\Scripts\<script_name> <script_options>
 
 .. note::
-   On windows it may be necessary to add user execution permissions to activate the environment.
+    On windows it may be necessary to add user execution permissions to activate the environment.
     To do this open a poweshell as administrator and type ::
 
       Set-ExecutionPolicy -ExecutionPolicy RemoteSigned -Scope CurrentUser
 
+    this has to be done only once to gain execution permissions.
 
 from source code
 ----------------

scripts/cosym

@@ -23,7 +23,7 @@ def write_reference_structures(vertices, central_atom, directory):
         output_references.write(file_io.get_file_xyz_txt(ref_structure))
 
 
-parser = argparse.ArgumentParser(description='Cosym')
+parser = argparse.ArgumentParser(description='cosym')
 parser.add_argument(type=str, dest='input_file', nargs='?', default=None, help='input file name(+extension)')
 parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None,
                     help='Perform the calculations with the command file')
@@ -52,7 +52,7 @@ parser.add_argument('-c3_c4', dest='c3_c4', action='store_true', default=False,
                     help='axis is a c3 rotational axis instead of a c4')
 
 # Shape input flags
-group_shape = parser.add_argument_group('Shape')
+group_shape = parser.add_argument_group('shape')
 group_shape.add_argument('-shp_m', '--shp_measure',
                          dest='shp_measure',
                          action='store',
@@ -90,7 +90,7 @@ group_pointgroup.add_argument('-pointgroup',
                               help='Gives the point group of an input structure')
 
 # Symgroup input flags
-group_symgroup = parser.add_argument_group('Symgroup')
+group_symgroup = parser.add_argument_group('symgroup')
 group_symgroup.add_argument('-sym_m', '--sym_measure',
                             dest='sym_measure',
                             action='store',
@@ -113,7 +113,7 @@ group_symgroup.add_argument('-sym_chirality',
                             help='search for a possible chirality in molecule')
 
 # Qsym input flags
-group_qsym = parser.add_argument_group('Qsym')
+group_qsym = parser.add_argument_group('qsym')
 group_qsym.add_argument('-qsym_wfn',
                         dest='qsym_wfn',
                         action='store',

scripts/mosym

@@ -11,7 +11,7 @@ import yaml
 import numpy as np
 
 
-parser = argparse.ArgumentParser(description='esym')
+parser = argparse.ArgumentParser(description='mosym')
 
 # positional arguments
 parser.add_argument(type=str,

scripts/shape

@@ -22,7 +22,7 @@ def write_reference_structures(vertices, central_atom, directory):
 
 
 # positional arguments
-parser = argparse.ArgumentParser(description='Shape', allow_abbrev=False)
+parser = argparse.ArgumentParser(description='shape', allow_abbrev=False)
 parser.add_argument(type=str,
                     dest='input_file',
                     nargs='?',

scripts/shape_classic

@@ -9,7 +9,7 @@ import argparse
 import os
 import sys
 
-parser = argparse.ArgumentParser(description='Shape')
+parser = argparse.ArgumentParser(description='shape')
 parser.add_argument(type=str, dest='input_file', nargs='?', help='input file name(+extension)')
 parser.add_argument('-n', dest='n', action='store', default=None,
                     type=int, help='show the reference labels for a given structure')