stagpy 0.1.0

Tool for StagYY output files processing

StagPy

StagPy is a Python 3 command line tool to read and process StagYY output files to produce high-quality figures.

The aim is to have different cases in one file (Cartesian, Spherical Annulus, etc).

The code to read the binary output files has been adapted from a matlab version initially developed by Boris Kaus.

Installation

if you want to use (and modify) the development version, see the “For developers” section at the end of this page

You will need Python 3.3 or higher to use StagPy.

If you don’t have pip for Python3 on your system, download the official script <https://bootstrap.pypa.io/get-pip.py> and run it with python3.

StagPy is available via pip. You can install it with the following command:

python3 -m pip install --user stagpy

Make sure that the directory where pip install package entry-points (usually ~/.local/bin) is in your PATH environment variable. You can run python3 -m pip show stagpy to obtain some hint about this location (this command will show you were the compiled sources are installed, e.g. ~/.local/lib/python3.5/site-packages, from which you can deduce the entry-point location, e.g. ~/.local/bin).

Once this is done, you can enable command-line auto-completion if you use either bash or zsh.

Add this to your ~/.bashrc file:

eval "$(register-python-argcomplete stagpy)"

Or this to your ~/.zshrc file:

autoload bashcompinit
bashcompinit
eval "$(register-python-argcomplete stagpy)"

Finally, run the following once to create your config file (at ~/.config/stagpy/):

stagpy config --create

Enjoy!

Available commands

The available subcommands are the following:

• field: computes and/or plots scalar fields such as temperature or stream function;

• rprof: computes and/or plots radial profiles;

• time: computes and/or plots time series;

• plates: plate analysis;

• var: displays a list of available variables;

• config: configuration handling.

You can run stagpy --help (or stagpy -h) to display a help message describing those subcommands. You can also run stagpy <subcommand> --help to have some help on the available options for one particular sub command.

StagPy looks for a StagYY par file in the current directory. It then reads the value of the output_file_stem option to determine the location and name of the StagYY output files (set to test if no par file can be found). You can change the directory in which StagYY looks for a par file by two different ways:

• you can change the default behavior in a global way by editing the config file (stagpy config --edit) and change the core.path variable;

• or you can change the path only for the current run with the -p option.

The time step option -s allows you to specify a range of time steps in a way which mimic the slicing syntax: begin:end:gap (both ends included). If the first step is not specified, it is set to 0. If the final step is not specified, all available time steps are processed. Here are some examples:

• -s 100:350 will process every time steps between 100 and 350;

• -s 201:206:2 will process time steps 201, 203 and 205;

• -s 201:205:2 same as previous;

• -s 5682: will process every time steps from the 5682nd to the last one;

• -s :453 will process every time steps from the 0th to the 453rd one;

• -s ::2 will process every even time steps.

By default, the temperature, pressure and stream function fields are plotted. You can change this with the -o option (e.g. ./main.py field -o ps to plot only the pressure and stream function fields).

For developers

A Makefile in the git repository allows you to install StagPy in a virtual environment.

StagPy uses the following non-standard modules: numpy, scipy, f90nml, matplotlib, and seaborn (the latter is optional and can be turned off with the core.useseaborn option). These dependencies will be checked and needed installation performed in a virtual environment. If you use Python3.2 or encouter problems with the installation, see the troubleshooting section at the end of this README.

However, installation of numpy and scipy involve heavy building operations, it might be better that you (or your system administrator) install it with a package manager such as homebrew on Mac OS or your favorite Linux package manager.

The installation process is then fairly simple:

git clone https://github.com/mulvrova/StagPy.git
cd StagPy
make

A soft link named stagpy is created in your ~/bin directory, allowing you to launch StagPy directly by running stagpy in a terminal (provided that ~/bin is in your PATH environment variable).

Two files .comp.zsh and .comp.sh are created. Source them respectively in ~/.zshrc and ~/.bashrc to enjoy command line completion with zsh and bash. Run make info to obtain the right sourcing commands.

To check that everything work fine, go to the data directory of the repository and run:

stagpy field

Three PDF files with a plot of the temperature, pressure and stream function fields should appear.

Troubleshooting

• Matplotlib related error in MacOS

  This might be due to the matplotlib backend that is not correctly set. See this Stack Overflow question: <http://stackoverflow.com/questions/21784641/installation-issue-with-matplotlib-python>

• Installation fails with ImportError: No module named 'encodings'

  This seems to be due to a bug in the venv module with some Python installation setups. If installing Python properly with your package manager doesn’t solve the issue, you can try installing StagPy without any virtual environment by using make novirtualenv.