Fix typos ; minor style improvements. (#163)

* Insert one sentence to explain why conda install --file ./requirements-optional.txt is suggested.

* More explanations in the README.rst .

* Fix typos. Specify how to get a PMG_MAPI_KEY.

* Several minor modifs

* Minor modif, slightly more accurate wording.

README.rst

@@ -162,7 +162,7 @@ To solve the problem, use conda to update scipy to a version >= 1.0.1 with::
 
     conda install "scipy>=1.0.1"
 
-then issue again python setup.py develop.
+then issue again python setup.py develop. If this fails, supposing you were upgrading abipy inside an already existing conda environment, try to restart by creating from scratch a fresh conda environment, see above.
 
 Use::
 
@@ -188,11 +188,17 @@ To run the suite of unit tests, make sure you have pytest_ installed and then ty
 
     pytest
 
-in the AbiPy root directory.
+in the AbiPy root directory. A quicker check might be obtained with 
+
+    pytest abipy/core/tests -v
+
 Unit tests require ``scripttest`` that can be installed with::
 
     pip install scripttest
 
+Two tests rely on the availability of a 
+`pymatgen PMG_MAPI_KEY <http://pymatgen.org/usage.html#setting-the-pmg-mapi-key-in-the-config-file>` in ~/.pmgrc.yaml.
+
 Note that several unit tests check the integration between AbiPy and Abinit. 
 In order to run the tests, you need a working set of Abinit executables and  a ``manager.yml`` configuration file.
 A pre-compiled sequential version of Abinit for Linux and OSx can be installed directly from the 
@@ -201,7 +207,7 @@ abinit-channel_ with::
     conda install abinit -c abinit
 
 For further information on the syntax of the configuration file, please consult the 
-`workflows <http://abinit.github.io/abipy/workflows/taskmanager.html>`_ section.
+`workflows docs <http://abinit.github.io/abipy/workflows/taskmanager.html>`_ section.
 
 Contributing to AbiPy is relatively easy.
 Just send us a `pull request <https://help.github.com/articles/using-pull-requests/>`_.
@@ -248,7 +254,7 @@ The following scripts can be invoked directly from the terminal:
 
 Use ``SCRIPT --help`` to get the list of supported commands and 
 ``SCRIPT COMMAND --help`` to get the documentation for ``COMMAND``.
-For further information, please consult the `official documentation <http://abinit.github.io/abipy/scripts/index.html>`_.
+For further information, please consult the `scripts docs <http://abinit.github.io/abipy/scripts/index.html>` section.
 
 License
 =======

abipy/abio/inputs.py

@@ -565,7 +565,7 @@ class AbinitInput(six.with_metaclass(abc.ABCMeta, AbiAbstractInput, MSONable, Ha
         String representation.
 
         Args:
-            sortmode: "section" if variables should be gruped by sections.
+            sortmode: "section" if variables should be grouped by sections.
                 "a" for alphabetical order, None if no sorting is wanted.
             with_mnemonics: True if mnemonics should be added.
             mode: Either `text` or `html` if HTML output with links is wanted.
@@ -740,7 +740,7 @@ class AbinitInput(six.with_metaclass(abc.ABCMeta, AbiAbstractInput, MSONable, Ha
     def set_phdos_qmesh(self, nqsmall, method="tetra", ph_qshift=(0, 0, 0)):
         """
         Set the variables (ngkpt, shift, kptopt) for the computation of the Phonon DOS in Abinit.
-        Remember that the Phdos is computed via Fourier interpolation so there's no costraint
+        Remember that the Phdos is computed via Fourier interpolation so there's no constraint
         of the q-mesh.
 
         Args:

abipy/abio/timer.py

@@ -1,6 +1,6 @@
 """
 This module provides objects for extracting timing data from the ABINIT output files
-It also provides tools to analye and to visualize the parallel efficiency.
+It also provides tools to analyze and to visualize the parallel efficiency.
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
 
@@ -21,7 +21,7 @@ class AbinitTimerParser(_Parser, NotebookWriter):
 
     def write_notebook(self, nbpath=None):
         """
-        Write an ipython notebook to nbpath. If nbpath is None, a temporay file in the current
+        Write an ipython notebook to nbpath. If nbpath is None, a temporary file in the current
         working directory is created. Return path to the notebook.
         """
         nbformat, nbv, nb = self.get_nbformat_nbv_nb(title=None)

docs/README.rst

@@ -10,17 +10,21 @@ Organization of documentation
 -----------------------------
 
 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 repository.  
+The documentation sources are found in the :file:`~/docs/` directory in the repository. Major items : 
 
 * index.rst - the top level include document for AbiPy docs
 * api - placeholders to automatically generate the api documentation
+* scripts - documentation for scripts
+* workflows - documentation for workflows 
+* README.rst - the present file
 * conf.py - the sphinx configuration
 * _static - used by the sphinx build system
 * _templates - used by the sphinx build system
 
 The main entry point is :file:`docs/index.rst`, which pulls in 
 the files for the users guide, developers guide, api reference. 
-The actual ReStructured Text files for the API are kept in :file:`docs/api`. 
+The actual ReStructured Text files for the APIs of the subpackages, for the scripts and for the workflows (resp.) are kept 
+in :file:`docs/api`, :file:`docs/scripts` and :file:`docs/workflows` (resp.). 
 
 Additional files can be added to the various guides by including their base
 file name (the ``.rst`` extension is not necessary) in the table of contents.

docs/coding_guide.rst

@@ -70,7 +70,7 @@ Naming, spacing, and formatting conventions
 -------------------------------------------
 
 In general, we want to stay as closely as possible to the standard
-coding guidelines for python written by Guido in `PEP0008 <http://www.python.org/dev/peps/pep-0008>`_.
+coding guidelines for python written by Guido van Rossum in `PEP0008 <http://www.python.org/dev/peps/pep-0008>`_.
 
 * functions and class methods: ``lower`` or ``lower_underscore_separated``
 * attributes and variables: ``lower`` 
@@ -112,4 +112,4 @@ Testing
 Abipy has a testing infrastructure based on :mod:`unittest` and pytest_.
 
 Common test support is provided by :mod:`abipy.core.testing`, 
-data files are storeed in :file:`abipy/tests/data`.
+data files are stored in :file:`abipy/tests/data`.

docs/postprocessing_howto.rst

@@ -139,7 +139,7 @@ Get a quick look to a file
 --------------------------
 
 The :ref:`abiview.py` script is especially designed for this task.
-The syntax is ``abistruct.py COMMAND FILE`` where ``COMMAND`` is either 
+The syntax is ``abiview.py COMMAND FILE`` where ``COMMAND`` is either 
 the Abinit file extension (without ``.nc``, if any) or the AbiPy object we want to visualize.
 
 To get a quick look at the DDB file, use::
@@ -152,7 +152,7 @@ If ``FILE`` contains electronic band energies, use e.g.::
 
     abiview.py ebands out_GSR.nc
 
-to plot the KS eigenvalues (the same command works for other files such as ``WFK.nc``, ``DEN.nc`` etcetera. 
+to plot the KS eigenvalues (the same command works for other files such as ``WFK.nc``, ``DEN.nc`` etc. 
 
 Note that :ref:`abiview.py` uses a predefined logic to visualize the data.
 There are options to tune some parameters and/or export data in different formats
@@ -174,7 +174,7 @@ Visualize a structure
 ---------------------
 
 The visualization of the structure is delegated to external graphical applications
-that must be istalled on your machine. 
+that must be installed on your machine. 
 AbiPy will extract the structure from ``FILE``, convert it to one of the formats 
 supported by the graphical application and finally invoke the executable.
 If you have vesta_ installed in one of the standard 
@@ -355,7 +355,7 @@ to print the warnings/comments/errors reported in the Abinit log file ``run.log`
 Export bands to xmgrace format 
 ------------------------------
 
-But |ElectronBands| and |PhononBands| provide a ``to_xmgrace`` method to produce xmgrace_ files.
+Both |ElectronBands| and |PhononBands| provide a ``to_xmgrace`` method to produce xmgrace_ files.
 To export the data to xmgrace, use :ref:`abiview.py` with the ``--xmgrace`` option.
 For electrons, use::
 

docs/workflows/manager_examples.rst

@@ -559,6 +559,7 @@ Travis
 	        mpi_runner: mpirun
 	        pre_run:
 	            - source activate test-environment
+	            - ulimit -s unlimited
 	      limits:
 	         min_cores: 1
 	         max_cores: 2