Quick and Simple¶
From a terminal install the latest stable version with pip:
pip install pychemia --user
It will install pychemia and all its dependencies in your $HOME folder. If you want a central installation you can install directly with:
sudo pip install pychemia
Installing PyChemia with pip¶
This is probably the easiest way, pip will download the code, check and eventually install dependencies and installing the package on a system-wide place or the home directory. All you have to do is execute this command:
sudo pip install pychemia
or for python 3.x:
sudo pip3 install pychemia
If you are on a machine where you do not have superuser privileges you can install pychemia on your home directory by adding the command ‘–user’:
pip install pychemia --user
or for python 3.x:
pip3 install pychemia --user
Uninstall or upgrade pychemia is also very simple with pip:
pip uninstall pychemia pip install pychemia --upgrade
Installing PyChemia with virtualenv¶
PyChemia requieres a relative recent version of Python (Python 2.7 appeared on July 3, 2010). However, it is common for some HPC infraestructures to use Linux installations such as RHEL 6 that only provides python 2.6 dating back to 2008. You can contour this situation by using Software Collections:
Install a more recent version of python and virtualenv. After that you can install PyChemia and its dependencies contained on a virtual environment following this commands:
- Create a new virtual environment, lets call it “venv_pcm”
- Activate the environment by sourcing the activate script
3. You will notive that the prompt changes and you get your path pointing to a containerized python environment where you can install PyChemia and its dependencies
pip install pychemia
4. Shortly after that, you will get all the dependencies installed and the software ready for use without touching the libraries and modules installed by your Linux distribution. You can leave the virtual environment with the command:
To re-enable the environment all you have to do is execute step 2 and you get the environment ready to work.
Installing PyChemia from github¶
The current stable repository for PyChemia is on Github, you can download the master branch with the command:
git clone https://github.com/MaterialsDiscovery/PyChemia.git
If you get a message such as:
$ git clone https://github.com/MaterialsDiscovery/PyChemia.git -bash: git: command not found
You need to install
git first. On machines from the Debian ‘lineage’ (Ubuntu, Mint, and many others) you can use
sudo apt-get install git
On systems with
yum you can use:
sudo yum install git
Now that you have ‘cloned’ the PyChemia repository you have two options. Install the package by using the set of commands:
cd PyChemia python setup build python setup install --user
python3 for the commands above, if you want to use python 3.x instead.
Another alternative is add path where you downloaded the repository to the variable $PYTHONPATH. You can do that
by editing your
.bashrc file. Supposing that you execute the
git clone command directly on your home directory
you can add the path for PyChemia adding this line to your .bashrc:
If you want the changes on .bashrc take inmediate effect execute:
PyChemia relies on the presence of at least this libraries:
numpy >= 1.12.0 scipy >= 0.18.0 future >= 0.16.0 spglib >= 1.9.9 pymongo >= 3.4.0
Most Linux distributions will probably include older versions of those dependencies. HPC Linux clusters usually have a very conservative approach related to packages and even older versions of those dependencies will be installed the system or completely absent from it.
scipy are well known python packages for Linear Algebra and general scientific computing.
PyChemia is able to run on Python 2 and 3 using the same sources.
The python package
future is a small package that helps keeping compatibility with python 2 and python 3 on the same
source code. The package
spglib is a C-library with python wrappers for computing space groups and related functionality.
pymongo offers connectivity with a MongoDB database. MongoDB is a document-based NoSQL database engine.
PyChemia uses MongoDB databases for storing collections of structures or properties and parameters associated to them.
We try to keep the dependencies of PyChemia to a very minimum. Some other libraries provides extra functionality that could be necessary for some tasks. Consider install nose and matplotlib. You can do that using pip with the command:
sudo pip install nose matplotlib
Remember that you can use
--user if you want to install on your home directory without special privileges.
Matplotlib is the ‘standard de-facto’
for 2D plots on python. Many of the functionalities on ‘pychemia.visual’ subpackage depends on it. Nose is a python
package for executing automatize tests for PyChemia. If you want to use it more information is below.
Importing the library¶
No matter how you installed PyChemia, you should be able to load the library. You can use the traditional python terminal, for example:
$ python3.5 Python 3.5.1 (default, Mar 2 2016, 03:38:02) [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pychemia >>> pychemia.info() PyChemia -------- Version: 0.1.2 Path: /Users/guilleaf/PyChemia/pychemia Date: May 13, 2016 Python version=3.5.1 (default, Mar 2 2016, 03:38:02) [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)] pymongo Not Found numpy 1.11.0 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/numpy scipy 0.17.1 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/scipy mayavi Not Found Scientific Not Found matplotlib 1.5.1 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/matplotlib future 0.15.2 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/future nose 1.3.7 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/nose coverage 4.0.3 /opt/local/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/coverage spglib 1.9.4 /Users/guilleaf/Library/Python/3.5/lib/python/site-packages/spglib pyhull Not Found pymatgen Not Found qmpy Not Found ase Not Found
pcyhemia.info() will inform about the several libraries that PyChemia uses, both mandatory and optional,
their versions and path. That could be informative in case of something not working as expected.
Testing with nose¶
It is always important to test a library, not only from the developer point of view, but also for an user. Nose is a python package that offers a simple command to execute predefined test for a python package and report any errors or inconsistencies from the expected resuts.
Direct the terminal to the place where PyChemia is located. Lets suppose that you have pychemia on
/Users/guilleaf/PyChemia, test PyChemia using the command:
cd /Users/guilleaf/PyChemia nosetests -v
The name of the command could have small variations according to your distribution. On a MacOS using macports
the name could be for example
nosetests-3.5 for python 2 and 3 respectively.
nosetests will search for tests on the entire package and subpackages. If everything is fine (and you use
for verbose output) you will get something like:
... Example of a simple calc : ... ok Example of a multiple calc : ... ok ---------------------------------------------------------------------- Ran 38 tests in 5.469s OK
That is an indication that all tests were successful and eventually you are ready to use the library.