PyReshaper 1.1.1

Python Time-Slice to Time-Series NetCDF Converter

The PyReshaper

A package for converting NetCDF files from time-slice (history) format to time-series (single-variable) format.

AUTHORS:

John Dennis, Sheri Mickelson, Kevin Paul, Haiying Xu

COPYRIGHT:

2019 University Corporation for Atmospheric Research

LICENSE:

Apache 2.0

Send questions and comments to Kevin Paul ([e-mail]).

Overview

The PyReshaper is a tool for converting time-slice (or history-file or synoptically) formatted NetCDF files into time-series (or single-field) format. The PyReshaper package is designed to run in parallel (MPI) to maximize performance, with the parallelism implemented over variables (i.e., task parallelism). This means that the maximum parallelism achieveable for a given operation is one core/processor per variables in the time-slice NetCDF files.

Dependencies

The PyReshaper directly depends upon the ASAP Python Toolbox (ASAPTools) and either PyNIO or netcdf4-python. Access and manipulation of the NetCDF files is done through PyNIO or netcdf4-python, and the parallelism is implimented using the ASAPTools SimpleComm, which uses mpi4py. Implicit dependencies exist as a result of these direct dependencies.

The PyReshaper explicitly depends upon the following Python packages:

• PyNIO (v1.5+) or netCDF4-python (v1.2+)

• ASAPPyTools (v0.4+)

These packages imply a dependency on the NumPy (v1.4+) and mpi4py (v1.3+) packages, and the libraries NetCDF and MPI/MPI-2.

The version requirements have not been rigidly tested, so earlier versions may actually work. No version requirement is made during installation, though, so problems might occur if an earlier versions of these packages have been installed.

Easy Installation with PIP

The easiest way to install the ASAP Python Toolbox is from the Python Package Index (PyPI) with the pip package manager:

$  pip install [--user] PyReshaper

The optional ‘–user’ argument can be used to install the package in the local user’s directory, which is useful if the user doesn’t have root privileges.

One should be careful, however, as the PyPI packages may not always be up to date. We recommend obtaining the most recent versions of the PyReshaper from the GitHub site shown in the section below.

Obtaining the Source Code

Currently, the most up-to-date development source code is available via git from the site:

https://github.com/NCAR/PyReshaper

You may then check out the most recent stable tag. The source is available in read-only mode to everyone. Developers are welcome to update the source and submit Pull Requests via GitHub.

Building & Installing from Source

Installation of the PyReshaper is very simple. After checking out the source from the above svn link, via:

$ git clone https://github.com/NCAR/PyReshaper

Enter the newly cloned directory:

$ cd PyReshaper

Then, run the Python setuptools setup script. On unix, this involves:

$  python setup.py install [--prefix=/path/to/install/location]

The prefix is optional, as the default prefix is typically /usr/local on linux machines. However, you must have permissions to write to the prefix location, so you may want to choose a prefix location where you have write permissions. Like most distutils installations, you can alternatively install the PyReshaper with the ‘–user’ option, which will automatically select (and create if it does not exist) the $HOME/.local directory in which to install. To do this, type (on unix machines):

$  python setup.py install --user

This can be handy since the site-packages directory will be common for all user installs, and therefore only needs to be added to the PYTHONPATH once.

Before Using the PyReshaper Package

Before the PyReshaper package can be used, you must make sure that the site-packages directory containing the ‘pyreshaper’ source directory is in your PYTHONPATH. Depending on the PREFIX used during installation, this path will be:

$PREFIX/lib/python2.X/site-packages

where X will be 6 or 7 (or other) depending on the version of Python that you are using to install the package.

To use the PyReshaper scripts (e.g., ‘s2smake’ and ‘s2srun’), you must add the script binary directory to your PATH. Depending on the PREFIX used during installation, this path will be:

$PREFIX/bin/

Once the script binary directory has been added to your PATH and the site-packages directory has been added to your PYTHONPATH, you may use the PyReshaper package without issue.

Instructions & Use

Please see the more detailed instructions found in the docs/ directory for usage and examples. See the ‘Building & Installing from Source’ section for how to build the documentation with Sphinx.