- The config file is now created when the module is imported for the …

…first time. Everything whould work fine when installing from pypi.

- Changed the name of pyscholar.py to scopus.py.
- Updated the documentation source files to reflect this name change.
- Moved the examples part of the docstrings in scopus.py to the respective docs source (in progress).
- Added intersphinx info for pandas and networkx.
- Fixed some typos in the docstrings.

MANIFEST.in

@@ -1,2 +1,2 @@
 include README.rst
-include pyscholar/keys.cfg
+include ~/.pyscholar

README.rst

@@ -10,7 +10,7 @@ A library to create collaboration science networks.
 Requirements
 -------------
 
-- `Python <https://www.python.org/download/releases/2.7/>`_  >= 2.7
+- `Python <https://www.python.org/download/releases/2.7/>`_  ≥ 2.7
 - `Networkx <http://networkx.github.io/documentation/networkx-1.7/install.html>`_
 - `Matplotlib <http://matplotlib.org/users/installing.html>`_
 

docs/source/conf.py

@@ -18,7 +18,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.abspath('../../src'))
+sys.path.insert(0, os.path.abspath('../../pyscholar'))
 
 # -- General configuration ------------------------------------------------
 
@@ -267,4 +267,6 @@
 
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'http://docs.python.org/': None}
+intersphinx_mapping = {'http://docs.python.org/': None,
+                       'pandas': ('http://pandas.pydata.org/pandas-docs/stable/', None),
+                       'networkx': ('https://networkx.readthedocs.io/en/stable/', None)}

docs/source/index.rst

@@ -7,16 +7,16 @@
 Welcome to Pyscholar's documentation!
 =====================================
 
-Pyscholar gives you easy, Pythonic access to Scopus's API. 
+Pyscholar gives you easy, pythonic access to Scopus' API. 
 
-Some of the functionalities implemented in Pyscholar are as follows:
+Some of the functionalities implemented in Pyscholar are:
 
-* Retrieve information about the affiliated authors to Scopus.
-* Retrieve information about the articles registered in Scopus.
-* Retrieve information about the Institutions registered in Scopus.
+* Retrieve information about authors affiliated to Scopus.
+* Retrieve information about articles registered in Scopus.
+* Retrieve information about institutions registered in Scopus.
 
 
-From the information obtained in the above points, Pyscholar can with this information  build citation graphs and coauthor graphs, since it has features that allow you to perform this task.
+Pyscholar can also build citation and coauthor graphs with this information.
 
 Contents:
 
@@ -25,7 +25,7 @@ Contents:
 
 
    Installation <installation>
-   Pyscholar Module <pyscholar>
+   Scopus Module <scopus>
    Tutorial <tutorial>
 
 
@@ -35,5 +35,4 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
-
+* :ref:`search`

docs/source/installation.rst

@@ -1,7 +1,8 @@
 .. _installation:
-================
- Installation
-================
+
+============
+Installation
+============
 
 Requirements
 ================

docs/source/scopus.rst

@@ -0,0 +1,122 @@
+.. _scopus:
+
+================
+scopus module
+================
+
+.. currentmodule:: scopus
+
+Scopus Author/Co-Authors
+==========================
+.. autofunction:: find_author_scopus_id_by_name
+.. autofunction:: get_authors_by_id_affiliation
+
+.. autofunction:: get_coauthors (id_author,min_year="",max_year="")
+
+.. autofunction:: get_ids_authors_by_id_paper
+.. autofunction:: load_authors_from_file
+
+    :param path: The directory where the file is located.
+    :type path: :class:`str`
+    :returns: A list with the authors ids.
+    :rtype: :class:`list`
+
+    :Example:
+
+    >>> import pyscholar
+    >>> pyscholar.load_authors_from_file("/home/dir/authors.txt")
+    >>> ['56013555800', '12645109800', '12645615700', '12646275800', '15740951000', '23388216300', '23398643600', '24171073600', '24512697200', '26032291700', '34870304900', '35566511400', '36117667600', '36117782600', '36118513000', '36141027800', '37107692000', '37111010900', '54792735300', '55439178900', '55468916100', '55669785100', '55918277800', '55943170800', '55993686500', '56002701400', '56013629200', '56013731100', '56013734400', '56240672400', '56263920000', '56279187000']
+    >>>
+
+.. autofunction:: search_author
+
+
+Scopus Paper
+==============
+.. autofunction:: count_citations_by_id_paper
+.. autofunction:: get_common_papers
+.. autofunction:: get_papers
+.. autofunction:: get_references_by_paper
+.. autofunction:: get_title_abstract_by_idpaper
+.. autofunction:: get_title_abstract_by_idpaper
+.. autofunction:: load_papers_from_file
+
+    :param path: The directory where the file is located.
+    :type path: :class:`str`
+    :returns: A list with the papers ids.
+    :rtype: :class:`list`
+
+    :Example:
+
+    >>> import pyscholar
+    >>> pyscholar.load_papers_from_file("/home/dir/papers.txt")
+    >>> ['78149425675', '79959254005', '84883029526', '84887837079', '84892691931', '84893836569', '84897620666', '84904102369', '84908190310', '84919922003', '84924004559', '84925067887', '84928486421', '84928490197', '84928742486', '84939945186', '84939973084', '84945466401', '84961373040']
+
+
+
+Scopus Affiliation
+====================
+.. autofunction:: find_affiliation_scopus_id_by_name
+
+    :param organization: The name of the affiliation to search.
+    :type organization: :class:`str`
+    :returns: A data frame with the following attributes: id,city,country,name_variant,eid,affiliation_name,identifier,document_count.
+    :rtype: :class:`pandas.DataFrame`
+
+    :Example:
+
+    >>> import pyscholar
+    >>> pyscholar.find_affiliation_scopus_id_by_name("CINVESTAV")
+               id                 city      country                 name_variant                        eid                   affiliation_name                              identifier          document_count
+        0    60017323          Mexico City  Mexico        [CINVESTAV-IPN, CINVESTAV]             10-s2.0-60017323  Centro de Investigacion y de Estudios Avanzados    AFFILIATION_ID:60017323       19254  
+        1    60010531        Mérida  Mexico              [CINVESTAV-IPN]                  10-s2.0-60010531           CINVESTAV Unidad Merida                   AFFILIATION_ID:60010531        1811
+        2    60018216          Guadalajara  Mexico  [CINVESTAV, CINVESTAV Unidad Guadalajara]    10-s2.0-60018216           CINVESTAV Unidad Guadalajara              AFFILIATION_ID:60018216        1010  
+        .
+        .
+        .
+        .
+
+.. autofunction:: search_affiliation_by_id
+
+
+Graph Generators
+===================
+.. autofunction:: get_citation_graph
+.. autofunction:: get_coauthors_graph
+
+
+Reading and Writing Graphs
+=============================
+.. autofunction:: save_graph_pickle
+
+    :param G: The graph object to be saved.
+    :param path: The directory where the graph will be saved.
+    :param name_graph: The name of the graph.
+    :type G: :ref:`networkx.graph <networkx:Graph>`
+    :type path: :class:`str`
+    :type name_graph:  :class:`str`
+    :returns: :class:`NoneType`
+
+    :Example:
+
+    >>> import pyscholar
+    >>> psycholar.save_graph_pickle(G,"~/dir/","my_graph")
+
+.. autofunction:: load_graph_pickle
+
+    :param path: The directory where the pickle object is located.
+    :type path: :class:`str`
+    :returns: A graph G.
+    :rtype: :ref:`networkx.graph <networkx:Graph>`
+
+    :Example:
+
+    >>> import pyscholar
+    >>> my_graph = psycholar.load_graph_pickle("~/dir/graph.pickle")
+    >>> my_graph
+
+
+Other Functions
+=================
+.. autofunction:: disable_graphical_interface
+.. autofunction:: enable_graphical_interface

pyscholar/__init__.py

@@ -1 +1,19 @@
-import pyscholar
+import os, ConfigParser
+#Check if .pyscholar exists and create it if necessary
+pyscholarDir = os.path.join(os.path.expanduser("~"), ".pyscholar")
+if not os.path.exists(pyscholarDir):
+    os.makedirs(pyscholarDir)
+
+#Same for .pyscholar/keys.cfg
+if not os.path.exists(os.path.join(pyscholarDir, "keys.cfg")):
+    keysParser = ConfigParser.ConfigParser()
+    keysParser.add_section("Keys")
+    keysParser.set('Keys', 'Scopus', "")
+    originalMask = os.umask(0)
+    keysDescriptor = os.open(os.path.join(pyscholarDir, 'keys.cfg'), os.O_WRONLY | os.O_CREAT, 0666)
+    keysFile = os.fdopen(keysDescriptor, 'w')
+    os.umask(originalMask)
+    keysParser.write(keysFile)
+    keysFile.close()
+
+import scopus