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Downloading and Installing pyPcazip

For many users, installing pyPcazip is as simple as giving the single command: 

pip install --user pyPcazip
You can then test your installation: 
pyPcazip --tests
However if you need or want to do it the harder way, here is a guide.

Prerequisites and Dependencies

A few prerequisites need to be installed before pyPcazip: numpy (minimum version 1.0.3), scipy (minimum version 0.10.0), and cython (minimum version 0.19.0). Although all further dependencies should be downloaded and installed automatically if missing, we find it is better to manually install mdtraj (minimum version 1.7.2) in advance, as well.

We recommend you install these packages in the following order:

#!python

pip install numpy --user
pip install scipy --user
pip install cython --user
pip install mdtraj --user
If you plan to work with netCDF-format trajectory files (e.g. those produced by AMBER), you will require the netCDF4 package. If you want to use pyPczplot, you will need matplotlib.

##Installing pyPcazip ##

  1. Use git to download the pyPcazip package:

#!python

git clone https://bitbucket.org/ramonbsc/pyPcazip.git
2. After the download is complete, change into the pyPcazip directory and run the setup script:

#!python

cd pyPcazip
python setup.py install --user
The command line interface executables should now be installed, most probably in ~username/.local/bin. Make sure this location is in your PATH.

Alternatively, if you have root privileges, you can omit the --user option, and the command line interface executables will be generally installed in /usr/bin/.

How to run tests

In ./test you will find a shell script run_tests.sh that checks the general correctness of the installation. 

#!python

./run_tests.sh
Each test should give a "PASSED" message, or, depending on which extension packages you have installed, a "SKIPPED" message. Depending on details of your python installation the output may include the occasional warning message, but all tests should complete successfully.

How to run examples

The ./test folder also contains a number of shell scripts and associated data files that put the pyPcazip suite through its paces, exemplifying some of the most common usages and providing further checks that the installation has been successful:

#!python

./run_basic_examples.sh > basic_examples.log
./run_ncdf_examples.sh > ncdf_examples.log # only applicable if you have netcdf support installed

Who do I talk to?

  • charles.laughton@nottingham.ac.uk
  • ardita.shkurti@nottingham.ac.uk (Repo admin)
  • rgoni@mmb.pcb.ub.es (Repo owner/admin)
  • e.breitmoser@epcc.ed.ac.uk
  • ibethune@epcc.ed.ac.uk

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