Finalize docs for 0.2

LICENSE

@@ -1,5 +1,5 @@
 abipy is free software: you can redistribute it and/or modify
-it under the terms of the GNU Lesser General Public License version 2 as published by
+it under the terms of the GNU General Public License version 2 as published by
 the Free Software Foundation
 
 abipy is distributed in the hope that it will be useful,
@@ -8,4 +8,4 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public License along with abipy.  
-If not, see <http://www.gnu.org/licenses/>.
+If not, see http://www.gnu.org/licenses/.

README.rst

@@ -1,14 +1,14 @@
 .. :Repository: https://github.com/abinit/abipy
 .. :Author: Matteo Giantomassi (http://github.com/abinit)
 
-.. image:: https://pypip.in/v/abipy/badge.png
-        :target: https://pypi.python.org/pypi/abipy
+.. image:: https://badge.fury.io/py/abipy.svg
+        :target: https://badge.fury.io/py/abipy
 
-.. image:: https://img.shields.io/travis/abinit/abipy/master.svg
+.. image:: https://travis-ci.org/abinit/abipy.svg?branch=develop
         :target: https://travis-ci.org/abinit/abipy
 
-.. image:: https://coveralls.io/repos/github/abinit/abipy/badge.svg?branch=master
-        :target: https://coveralls.io/github/abinit/abipy?branch=master
+.. image:: https://coveralls.io/repos/github/abinit/abipy/badge.svg?branch=develop
+        :target: https://coveralls.io/github/abinit/abipy?branch=develop
 
 .. image:: https://img.shields.io/badge/license-GPL-blue.svg
 

abipy/examples/README.md

@@ -1,8 +1,7 @@
-==============
-abipy examples
+AbiPy examples
 ==============
 
-There are a variety of ways to use abipy, and most of them are
+There are a variety of ways to use AbiPy, and most of them are
 illustrated in the examples in this directory.
 
 Below is a brief description of the different directories found here:

abipy/examples/_runplots.py

@@ -16,6 +16,7 @@
 from subprocess import call, Popen
 from abipy.core.testing import change_matplotlib_backend, revert_matplotlib_backend
 
+
 def str_examples():
     examples = """
       Usage example:\n\n
@@ -36,7 +37,8 @@ def show_examples_and_exit(err_msg=None, error_code=1):
 def main():
     parser = argparse.ArgumentParser(epilog=str_examples(),formatter_class=argparse.RawDescriptionHelpFormatter)
 
-    parser.add_argument('-b', '--backend', type=str, default="", help="matplotlib backend")
+    parser.add_argument('-b', '--backend', type=str, default="",
+                        help="matplotlib backend e.g. Agg for non-graphical display.")
 
     parser.add_argument('-m', '--mode', type=str, default="automatic",
                         help="execution mode. Either s (sequential) or a (automatic)")
@@ -46,6 +48,11 @@ def main():
 
     options = parser.parse_args()
 
+    #import matplotlib
+    #if options.backend:
+    #    print("Using ", matplotlib.backend, "matplotlib backend")
+    #    matplotlib.use(matplotlib.backend)
+
     change_matplotlib_backend(new_backend=options.backend)
 
     # Find scripts.

abipy/examples/tests/test_plots.py

@@ -13,9 +13,19 @@
 
 class TestPlots(AbipyTest):
 
-    def test_plots(self):
+    #def test_plots_with_runtests(self):
+    #    """Running _runplots script."""
+    #    if not self.has_matplotlib():
+    #        raise unittest.SkipTest("matplotlib is not installed")
+
+    #    script = os.path.abspath(os.path.join(root, "..", "_runplots.py"))
+    #    assert os.path.exists(script)
+    #    assert os.system(script + " --backend Agg")
+
+    def test_plots_with_exec(self):
+        """Running plot script with exec."""
         if not self.has_matplotlib():
-            raise unittest.SkipTest("sympy is not installed")
+            raise unittest.SkipTest("matplotlib is not installed")
 
         #0 file /home/travis/build/abinit/abipy/abipy/examples/tests/../plot/plot_qpconverge.py
         # Traceback (most recent call last):

docs/devel/coding_guide.rst

@@ -15,9 +15,9 @@ When committing changes to AbiPy, there are a few things to bear in mind.
 
 * Are your changes python2.7 compatible?
 
-* Can you pass the automatic tests? (:file:`README-tests.rst` describes how to run the tests)
+* Can you pass the automatic tests? 
 
-* Can you add a test to :file:`abipy/tests` to test your changes?
+* Can you add a test to test your changes?
 
 * if you have added new files or directories, or reorganized existing
   ones, are the new files included in the match patterns in :file:`MANIFEST.in`.  
@@ -60,9 +60,6 @@ Prefer the shortest names that are still readable.
 Configure your editor to use spaces, not hard tabs. 
 The standard indentation unit is always four spaces; 
 if there is a file with tabs or a different number of spaces it is a bug -- please fix it.
-To detect and fix these and other whitespace errors (see below),
-use :file:`tools/reindent.py` as a command-line script.  
-Unless you are sure your editor always does the right thing, please use reindent.py before committing your changes.
 
 Keep docstrings uniformly indented as in the example below, with nothing to the left of the triple quotes.  
 

docs/devel/documenting_guide.rst

@@ -1,23 +1,20 @@
 .. _documenting-abipy:
 
 *****************
-Documenting abipy
+Documenting AbiPy
 *****************
 
 Getting started
 ===============
 
-The documentation for abipy is generated from ReStructured Text using the Sphinx_ documentation generation tool. 
-Sphinx-1.0 or later is required.
-
+The documentation for AbiPy is generated from ReStructured Text using the Sphinx_ documentation generation tool. 
 The documentation sources are found in the :file:`docs/` directory in the trunk.  
 To build the users guide in html format, cd into :file:`docs/` and do::
 
   make html 
 
 The output produced by Sphinx can be configured by editing the :file:`conf.py` file located in the :file:`docs/`.
 
-
 Organization of AbiPy's documentation
 =====================================
 

docs/index.rst

@@ -1,11 +1,11 @@
-.. image:: https://pypip.in/v/abipy/badge.png
-        :target: https://pypi.python.org/pypi/abipy
+.. image:: https://badge.fury.io/py/abipy.svg
+        :target: https://badge.fury.io/py/abipy
 
-.. image:: https://img.shields.io/travis/abinit/abipy/master.svg
+.. image:: https://travis-ci.org/abinit/abipy.svg?branch=master
         :target: https://travis-ci.org/abinit/abipy
 
-.. image:: https://coveralls.io/repos/github/abinit/abipy/badge.svg?branch=master
-        :target: https://coveralls.io/github/abinit/abipy?branch=master
+.. image:: https://coveralls.io/repos/github/abinit/abipy/badge.svg?branch=develop
+        :target: https://coveralls.io/github/abinit/abipy?branch=develop
 
 .. image:: https://img.shields.io/badge/license-GPL-blue.svg