diff --git a/docs/features.rst b/docs/features.rst index ce245076..52760113 100644 --- a/docs/features.rst +++ b/docs/features.rst @@ -5,9 +5,9 @@ Feature Overview AbiPy is a Python library to analyze the results produced by `ABINIT `_, 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 `_ and this allows users to +AbiPy is interfaced with `Pymatgen `_ allowing users to benefit from the different tools and python objects available in the pymatgen ecosystem. AbiPy can be used in conjunction with `matplotlib `_, `pandas `_, @@ -20,10 +20,10 @@ and the `AbiPy lessons `_. 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 diff --git a/docs/installation.rst b/docs/installation.rst index 105055bc..9c899fb6 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -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 `_. - +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 `_. 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