psudmant’s gists

psudmant / gist:45fd7c2b10bc4ea60710b207de0b970e

Created March 26, 2017 21:29

flat convolution

	"""
	flat convolution of width n on an array x in O(n) time
	padded out to maintain shape
	"""

	def do_convolve(X, n):
	csum = np.cumsum(X)
	conv = np.r_[np.repeat(csum[n-1],n), csum[n:]-csum[:-n]]
	return conv

psudmant / getNonZeroRanges

Created July 16, 2014 23:28

	"""
	get position of adjactent 1st in a vector
	"""
	def getNonZeroRanges( A, zeroDefVal=0 ):
	dA=np.diff(A)
	N=A.shape[0]
	nzdA,=np.nonzero(dA)
	liRangesAll=np.c_[ np.r_[0,nzdA+1],
	np.r_[nzdA,N-1] +1]
	iiR = A.take(liRangesAll[:,0]) != zeroDefVal

psudmant / flat_convolution

Last active August 29, 2015 14:01

flat convolution

	"""
	flat convolution of width n on an array x in O(n) time
	padded out to maintain shape
	"""

	def do_convolve(X, n):
	csum = np.cumsum(X)
	conv = np.r_[np.repeat(csum[n-1],n), csum[n:]-csum[:-n]]
	return conv

psudmant / index.html

Created May 13, 2014 03:29

Test Sankey Diagram: Obama schedule

	<!doctype HTML>
	<meta charset = 'utf-8'>
	<html>
	<head>
	<link rel='stylesheet' href='http://timelyportfolio.github.io/rCharts_d3_sankey/css/sankey.css'>

	<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
	<script src='http://timelyportfolio.github.io/rCharts_d3_sankey/js/sankey.js' type='text/javascript'></script>

	<style>

psudmant / index.html

Created May 13, 2014 03:28

Test Sankey Diagram

	<!doctype HTML>
	<meta charset = 'utf-8'>
	<html>
	<head>
	<link rel='stylesheet' href='http://timelyportfolio.github.io/rCharts_d3_sankey/css/sankey.css'>

	<script src='http://d3js.org/d3.v3.min.js' type='text/javascript'></script>
	<script src='http://timelyportfolio.github.io/rCharts_d3_sankey/js/sankey.js' type='text/javascript'></script>

	<style>

psudmant / install_openblas.sh

Created January 29, 2014 17:23 — forked from nkrumm/install_openblas.sh

	#!/bin/bash


	# Get and install openblas
	mkdir -p ~/bin/openblas
	cd ~/bin/openblas
	wget https://github.com/xianyi/OpenBLAS/archive/v0.2.9.rc1.zip
	unzip v0.2.9.rc1
	cd OpenBLAS-0.2.9.rc1/
	make

psudmant / jobscript.sh

Created November 12, 2013 00:02 — forked from hyeshik/jobscript.sh

	#!/bin/sh
	#rule: {job}
	#input: {job.input}
	#output: {job.output}
	#threads: {job.threads}
	{self.workflow.snakemakepath} --snakefile {self.workflow.snakefile} \
	--force -j{self.cores} \
	--directory {workdir} --nocolor --notemp --quiet --nolock {job.output} \
	> /dev/null && touch "{jobfinished}" \|\| touch "{jobfailed}"
	exit 0

psudmant / sgesnake.sh

Created November 12, 2013 00:02 — forked from hyeshik/sgesnake.sh

	#!/bin/sh
	#
	# Adopts and submit a snakemake cluster job script to SGE queue
	#
	# by Hyeshik Chang
	#

	JOBSCRIPT_SNAKEMAKE=$1
	JOBSCRIPT_SGE="`dirname $1`/sge`basename $1`"

psudmant / gist:7031044

Created October 17, 2013 19:46 — forked from nkrumm/gist:7031035

	# set this to your head node hostname (run hostname)
	HEAD_NODE_NAME=master


	if [ `hostname` = $HEAD_NODE_NAME ]; then
	NODES=`qconf -sel \| grep -v $HEAD_NODE_NAME`
	for NODE in $NODES; do
	SCRIPT_PATH=$(dirname `which $0`)
	qsub -l h=$NODE $SCRIPT_PATH
	done

psudmant / github_cli.bash

Created October 16, 2013 23:33 — forked from nkrumm/github_cli.bash

	Improve the log (https://coderwall.com/p/euwpig?i=3&p=1&t=git)

	git config --global alias.lg "log --color --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)<%an>%Creset' --abbrev-commit --"

	Enable color in git:
	git config --global --add color.ui true

	Make git push only push the current branch
	git config --global push.default current

Peter Sudmant psudmant