brantfaircloth

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

dashed

/*! normalize.css v2.1.3 | MIT License | git.io/normalize */

/* ==========================================================================
   HTML5 display definitions
   ========================================================================== */

/**
 * Correct `block` display not defined in IE 8/9.
 */

dan-blanchard

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 There are pre-installed versions of numpy for some versions of Python, but those are seriously out of date, and scipy is not there are at all.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for working around this are to (1) build everything from scratch, or (2) use apt-get to install more recent (but still out of date) versions of numpy and scipy.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

slowkow

#!/usr/bin/env python
"""
GTF.py
Kamil Slowikowski
December 24, 2013

Read GFF/GTF files. Works with gzip compressed files and pandas.

    http://useast.ensembl.org/info/website/upload/gff.html

jjhelmus

# Plot polar data using Bokeh
# Author: Jonathan J. Helmus

import numpy as np
from bokeh.plotting import *

# Data in polar coordinates
azimuths = np.linspace(0, 2 * np.pi, 20)
ranges = np.array([2, 4, 6, 8])

subfuzion

There are certain files created by particular editors, IDEs, operating systems, etc., that do not belong in a repository. But adding system-specific files to the repo's .gitignore is considered a poor practice. This file should only exclude files and directories that are a part of the package that should not be versioned (such as the node_modules directory) as well as files that are generated (and regenerated) as artifacts of a build process.

All other files should be in your own global gitignore file:

• Create a file called .gitignore in your home directory and add any filepath patterns you want to ignore.
• Tell git where your global gitignore file is.

Note: The specific name and path you choose aren't important as long as you configure git to find it, as shown below. You could substitute .config/git/ignore for .gitignore in your home directory, if you prefer.

mrocklin

brendancol

from __future__ import division
from functools import partial

import pyproj
from shapely.ops import transform
import numpy as np

from rasterio import features
from affine import Affine
import fiona

klmr

A little experiment using restarts.

(And while we’re at it, let’s torture R’s syntax a little.)

![screenshot][]

In the following we will be using R’s “restarts” feature to implement the state machine that drives generators in languages such as Python. Generators allow lazily generating values on demand: a consumer invokes a generator, and consumes values as they are produced. A new value is only produced once the previous one has been consumed.

aiguofer

Find out how much memory each of the jupyter notebooks running on a server is using. Helpful for knowing which ones to shut down.

Original code from http://stackoverflow.com/questions/34685825/jupyter-notebook-memory-usage-for-each-notebook

You'll need to

pip install tabulate psutil pandas requests