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10
docs/features.rst
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@ -5,9 +5,9 @@ Feature Overview
AbiPy is a Python library to analyze the results produced by `ABINIT <http://www.abinit.org>`_,
an open-source program for the ab-initio calculations of the physical properties of materials
within Density Functional Theory and Many-Body perturbation theory.
It also provides tools to generate input files and workflows to automate
AbiPy also provides tools to generate input files and workflows to automate
ab-initio calculations and typical convergence studies.
AbiPy is interfaced with `Pymatgen <http://www.pymatgen.org>`_ and this allows users to
AbiPy is interfaced with `Pymatgen <http://www.pymatgen.org>`_ allowing users to
benefit from the different tools and python objects available in the pymatgen ecosystem.
AbiPy can be used in conjunction with `matplotlib <http://matplotlib.org>`_, `pandas <http://pandas.pydata.org>`_,
@ -20,10 +20,10 @@ and the
`AbiPy lessons <http://nbviewer.ipython.org/github/abinit/abipy/blob/master/abipy/examples/notebooks/lessons/index.ipynb>`_.
AbiPy supports both Python 2.7 as well as Python >= 3.4.
Note however that Python 2.7 is more intensively tested than py3k especially at the level of workflows
so we still recommend py2.7 if you plan to run automatic calculations with AbiPy.
Note however that Python 2.7 is more intensively tested than py3k, especially at the level of workflows.
We hence still recommend py2.7 if you plan to run automatic calculations with AbiPy.
Note also that the majority of the post-processing tools available in AbiPy require output files in
Note also that the majority of the post-processing tools available in AbiPy require the Abinit output files in
``netcdf`` format so we strongly suggest to compile Abinit with netcdf support
(use ``--with_trio_flavor="netcdf-fallback"`` at configure time to activate the internal netcdf library,
to link Abinit against an external netcdf library please consult the configuration examples

29
docs/installation.rst
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@ -55,7 +55,8 @@ Optional libraries that are required if you need certain features:
Required to generate jupyter notebooks.
Install these two packages with ``conda install jupyter nbformat`` or use ``pip``.
Recommended but you will also need a web browser to open the notebook.
To use notebooks you will also need a web browser to open the notebook.
(recommended)
``wxPython`` and ``wxmplot`` for the GUI
@ -76,6 +77,7 @@ You may want to use the ``wget`` utility to download the anaconda script directl
Run the bash script in the terminal and follow the instructions.
By default, the installer creates the ``anaconda`` directory in your home.
Anaconda will add one line to your bashrc to enable acces to the anaconda executables.
Once the installation is completed, execute::
$ source ~/anaconda/bin/activate root
@ -99,7 +101,7 @@ Now you can install the stable version of ``abipy`` with::
$ pip install abipy
If you want to use the developmental version, clone (or fork) the repositories on github
If you want to use the developmental version, clone (or fork and clone) the repositories on github
(see also the :ref:`developmental_version` section).
Once you have completed the installation of AbiPy and pymatgen, open the ``ipython`` shell and type::
@ -117,7 +119,7 @@ to install the ``wxpython`` graphical toolkit required for the GUIs.
Note that one can use ``conda`` to create different environments with different
versions of the python interpreter or different libraries.
Further information are available on the `conda official website <http://conda.pydata.org/docs/test-drive.html>`_.
Using different environments is very useful to keep different version and branches separate.
.. _developmental_version:
@ -141,13 +143,19 @@ or alternately::
$ python setup.py develop
to install the package in developmental mode
(this is the recommended approach, especially if you are planning to implement new features).
(Develop mode is the recommended approach if you are planning to implement new features.
In this case you may also opt to first fork AbiPy on Git and then clone your own fork.
This will a low you to push any changes to you own fork and also get them merged in the main branch.).
The documentation of the **developmental** version is hosted on `github pages <http://abinit.github.io/abipy>`_.
The Github version include test files for complete unit testing.
To run the suite of unit tests, make sure you have ``py.test`` (recommended)
or ``nose`` installed and then just type::
or ``nose`` installed. Unit tests require two additional packages that can be installed with::
$ pip install nose-exclude scripttest
once this is in place just type::
$ py.test
@ -156,11 +164,8 @@ or::
$ nosetests
in the AbiPy root directory.
Unit tests require two additional packages that can be installed with::
$ pip install nose-exclude scripttest
Note that several unit tests check the integration between AbiPy and Abinit.
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.
For further information on the syntax of the configuration file, please consult the :ref:`workflows` section.
@ -176,6 +181,8 @@ AbiPy uses the `Git Flow <http://nvie.com/posts/a-successful-git-branching-model
The ``develop`` branch contains the latest contributions, and ``master`` is always tagged and points
to the latest stable release.
If you choose to share your developments please also take some time to also develop some unit tests of at least the
basic functionalities of you code
.. _howto_compile_python_and_bootstrap_pip:
@ -212,7 +219,9 @@ Configure the package with the ``--prefix`` option and compile the code
$ ./configure --prefix=$HOME/local
$ make -j4
At the end, you should get the list of modules that could not be built because
If you whish to use any graphical tools it is needed that one of the supported graphical backend supported by python
is installed and functional at the time of compilation of python.
At the end, you should get the list of modules that could not be built because
your system does not provide the required libraries.
The installation should be OK for AbiPy if you get::