Yoav Ram yoavram

Guidelines for contribution

This document described guidelines for contributions for projects led by members of the [Poisot lab of computational ecology][pl], Université de Montréal. It should be followed by lab members (at all times), as well as people with suggested added features, or willing to contribute enhancement or bug fixes.

Authorship

Any contribution to the code of a software grants authorship on the next paper

To transform the currently opened Graphviz source file (in DOT Language) into a PNG:

{
    "cmd": [ "dot", "-Tpng", "-o", "$file_base_name.png", "$file"],
    "selector": "source.dot"
}

Usage

For ETS's SKLL project, we found out the hard way that Travis-CI's support for numpy and scipy is pretty abysmal. There are pre-installed versions of numpy for some versions of Python, but those are seriously out of date, and scipy is not there are at all. The two most popular approaches for working around this are to (1) build everything from scratch, or (2) use apt-get to install more recent (but still out of date) versions of numpy and scipy. Both of these approaches lead to longer build times, and with the second approach, you still don't have the most recent versions of anything. To circumvent these issues, we've switched to using Miniconda (Anaconda's lightweight cousin) to install everything.

A template for installing a simple Python package that relies on numpy and scipy using Miniconda is provided below. Since it's a common s

	import os

	import ipywidgets as widgets


	class FileBrowser(object):
	def __init__(self):
	self.path = os.getcwd()
	self._update_files()

	[//]: # (Claas Heuer, November 2015)
	[//]: # (Run pandoc like this)
	[//]: # (pandoc --filter pandoc-crossref -s -S --bibliography references.bib paper_skeleton.txt -o test.docx)
	[//]: # (pandoc --filter pandoc-crossref -s -S --bibliography references.bib paper_skeleton.txt -o test.pdf)


	# First Section {#sec:first_section}

	This is the first section and we are writing an equation that we want to reference to later in
	the document:

	start on filesystem or runlevel [2345]
	stop on shutdown

	description "Jupyter / IPython Notebook Upstart script"

	script
	export HOME="/home/phil/Notebooks"; cd $HOME
	echo $$ > /var/run/ipython_start.pid
	exec su -s /bin/sh -c 'exec "$0" "$@"' phil -- /home/phil/Enthought/Canopy_64bit/User/bin/jupyter-notebook --config='/home/phil/.jupyter/jupyter_notebook_config.py'
	end script

	"""
	This script produces a video analysis proving for the first time in history
	that bacterial populations grow exponentially. See the result here:
	http://i.imgur.com/uoITKiA.gif

	We proceed as follows:

	- Download a video of bacteria growing under a microscope.
	- Cut the video to keep only the first 7 seconds.
	- Threshold each frame to find where the bacteria are, and compute the

	#!/usr/bin/env python
	"""
	nbconcat: concatenate notebooks

	Usage:

	nbconcat nb1.py nb2.py [nb3.py...] > allmynbs.ipynb

	requires IPython >= 3.0
	"""

	# -- coding: utf-8 --

	u"""
	Beta regression for modeling rates and proportions.

	References
	----------
	Grün, Bettina, Ioannis Kosmidis, and Achim Zeileis. Extended beta regression
	in R: Shaken, stirred, mixed, and partitioned. No. 2011-22. Working Papers in
	Economics and Statistics, 2011.

	app.directive('autosize', function($document) {
	return {
	require: 'ngModel',
	link: function(scope, element, attrs, ctrl) {
	var placeholder, span, resize;

	placeholder = element.attr('placeholder') \|\| '';

	span = angular.element('<span></span>');
	span[0].style.cssText = getComputedStyle(element[0]).cssText;