FindSim package on PyPi

Created by: dilawar

Closes #18. The package is on nightly channel, to install it using pip, one should use --pre with pip.

$ pip install FindSim --user --pre

Works with both python2 and python3.

Install

To install last stable release (NOTE This uses moose version 3.1.4 (outdated with this release))

 $ pip install FindSim   #  not uploaded yet.

Or, to install the nightly built,

 $ pip install FinSim --pre   # recommended and available

Alternatively, you can download the source code and install it yourself.

1. Install MOOSE which can be found here https://moose.ncbs.res.in/readthedocs/install/install.html
2. Install FindSim

git clone https://github.com/BhallaLab/FindSim
cd FindSim
python setup.py install  

After successful installation, two new commands are available at your disposal findsim and findsim_parallel. To see the help message, pass -h option to either of these commands. For example, findsim -h will show you following message.

usage: findsim [-h] [-m MODEL] [-d DUMP_SUBSET] [-p PARAM_FILE] [-t] [-hp]
               [-hs] [-o] [-s SCALE_PARAM SCALE_PARAM SCALE_PARAM]
               [-settle_time SETTLE_TIME]
               script

FindSim argument parser This program loads a kinetic model, and runs it with
the specified stimuli. The output is then compared with expected output
specified in the same file, to generate a model score.

positional arguments:
  script                Required: filename of experiment spec, in tsv format.

optional arguments:
  -h, --help            show this help message and exit
  -m MODEL, --model MODEL
                        Optional: model filename, .g or .xml
  -d DUMP_SUBSET, --dump_subset DUMP_SUBSET
                        Optional: dump selected subset of model into named
                        file
  -p PARAM_FILE, --param_file PARAM_FILE
                        Optional: Generate file of tweakable params belonging
                        to selected subset of model
  -t, --tabulate_output
                        Flag: Print table of plot values. Default is NOT to
                        print table
  -hp, --hide_plot      Hide plot output of simulation along with expected
                        values. Default is to show plot.
  -hs, --hide_subplots  Hide subplot output of simulation. By default the
                        graphs include dotted lines to indicate individual
                        quantities (e.g., states of a molecule) that are being
                        summed to give a total response. This flag turns off
                        just those dotted lines, while leaving the main plot
                        intact.
  -o, --optimize_elec   Optimize electrical computation. By default the
                        electrical computation runs for the entire duration of
                        the simulation. With this flag the system turns off
                        the electrical engine except during the times when
                        electrical stimuli are being given. This can be *much*
                        faster.
  -s SCALE_PARAM SCALE_PARAM SCALE_PARAM, --scale_param SCALE_PARAM SCALE_PARAM SCALE_PARAM
                        Scale specified object.field by ratio.
  -settle_time SETTLE_TIME, --settle_time SETTLE_TIME
                        Run model for specified settle time and return dict of
                        {path,conc}.
						

Command findsim_parellel is a helper utility: it runs multiple simulations using findsim in parellel.