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README.md

Multilang

A way to write code in Python, R, Matlab, and/or bash in the same file

Why

In computational biology, there are many tools that exist in either only Python or only R. Even within the same project, I was having to switch from Python (my workhorse) to R for some steps and then back to Python where I'm more comfortable. I decided that I wanted to be able to interact with an R environment from within Python, and that being able to write a file that could execute in both languages was really appealing.

Install

pip install multilang Import as import multilang

Requirements

  1. Termainal command $ R that launches the R CLI
  2. Terminal command $ matlab -nojvm -nodisplay -nosplash that launches the Matlab CLI

Development

Current build is 0.1.3
Developed solely by me in pursuit of my graduate studies at MIT
If you find any bugs, please place an Issue on github.

Features

The 2 main use cases are:

  1. python -m multilang path/to/file.mul
ml = multilang.Master()
ml.r('...')
# or
multilang.as_multilang('path/to/file.mul')
# or
multilang.as_multilang(open('path/to/file.mul', 'r')) # or 'rb'
# or
multilang.as_multilang('''#! multilang
	code here...''')

The first shows how the module can be used to run Multilang .mul scripts directly. It calls multilang.as_multilang() on the given file.
The second shows the interact form of Multilang, using its Master class. This allows for an interactive experience writing in 2 to 4 languages.

Either way, you get full access to the Python, R, Matlab, and shell environments; can use any library or built-in function; and can build on top of these frameworks to do crazy things and bodge things quickly.

Command Line

usage: python -m multilang [-h] [-v [{0,1,2,3}]] [-s] [-t [TIMEOUT]] file

positional arguments:
  1. file
    the file name to run
optional arguments:
  1. -h, --help
    show this help message and exit

  2. -v [{0,1,2,3}], --verbosity [{0,1,2,3}]
    the level of things to print
    0 is silent,
    1 is default,
    2 also prints switching environments,
    3 is max

  3. -s, --silent
    same as --verbosity 0

  4. -t [TIMEOUT], --timeout [TIMEOUT]
    the number of seconds to wait for R or matlab to respond
    default 600

Syntax Highlighting

By putting the .tmPreferences and .sublime-syntax in the .config/sublime-text-3/Packages/User folder, Sublime will automatically highlight the syntax correctly for each language in a .mul file and understand how to properly comment in Multilang.
You may need to do View > Syntax > Open all with current extension as... > User > Multilang

Example code

Examples will be placed in the examples folder

Changelog

v0.1.3:

  • added options to command line
  • added _verbosity to as_multilang
  • capture output for R and Matlab
  • timeout parameter added across the board

v0.1.2:

  • expanded documentation
  • better handling of errors from pexpect
  • Windows handling in __init__ instead of __main__

v0.1.1:

  • name change
  • Suggested extension changed from .ry to .mul
  • added bash support
  • calling python -m multilang on Windows calls as_multilang_windows

matrython==0.1.0:

  • name change to upload to PyPI
  • bug fixes

rython==0:

  • Python/R/Matlab support
  • Unit tests

MIT License

Copyright (C) 2018 SC van Nostrand

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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