Genevieve Buckley GenevieveBuckley

Install

Either copy the aliases from the .gitconfig or run the commands in add-pr-alias.sh

Usage

Easily checkout local copies of pull requests from remotes:

git pr 4 - creates local branch pr/4 from the github upstream(if it exists) or origin remote and checks it out
git pr 4 someremote - creates local branch pr/4 from someremote remote and checks it out

Rules for good testing

Look at the following image...

...it shows an object being tested.

You can't see inside the object. All you can do is send it messages. This is an important point to make because we should be "testing the interface, and NOT the implementation" - doing so will allow us to change the implementation without causing our tests to break.

Whether you're trying to give back to the open source community or collaborating on your own projects, knowing how to properly fork and generate pull requests is essential. Unfortunately, it's quite easy to make mistakes or not know what you should do when you're initially learning the process. I know that I certainly had considerable initial trouble with it, and I found a lot of the information on GitHub and around the internet to be rather piecemeal and incomplete - part of the process described here, another there, common hangups in a different place, and so on.

In an attempt to coallate this information for myself and others, this short tutorial is what I've found to be fairly standard procedure for creating a fork, doing your work, issuing a pull request, and merging that pull request back into the original project.

Creating a Fork

Just head over to the GitHub page and click the "Fork" button. It's just that simple. Once you've done that, you can use your favorite git client to clone your repo or j

Re-installing Git on Mac OSX with Brew

This is helpful if you've previously installed git from source on OSX, and other compilers can't find the correct path. You need to remove the current version of git, then re-install with brew.

Uninstall git if installed manually

Check which git you're running:
```
which git
```

	# read in and display ImagePlus object(s)
	from loci.plugins import BF
	file = "/Users/curtis/data/tubhiswt4D.ome.tif"
	imps = BF.openImagePlus(file)
	for imp in imps:
	imp.show()

	# read in and display ImagePlus(es) with arguments
	from loci.common import Region
	from loci.plugins.in import ImporterOptions

	#Mounting the share is a 2 stage process:
	# 1. Create a directory that will be the mount point
	# 2. Mount the share to that directory

	#Create the mount point:
	mkdir share_name

	#Mount the share:
	mount_smbfs //username:[email protected]/share_name share_name/

-# delete local tag '12345'
-git tag -d 12345
-# delete remote tag '12345' (eg, GitHub version too)
-git push origin :refs/tags/12345
-# alternative approach
-git push --delete origin tagName
-git tag -d tagName

	#!/usr/bin/env bash

	# obtains all data tables from database
	TS=`sqlite3 $1 "SELECT tbl_name FROM sqlite_master WHERE type='table' and tbl_name not like 'sqlite_%';"`

	# exports each table to csv
	for T in $TS; do

	sqlite3 $1 <<!
	.headers on

	# Compiled source #
	###################
	*.com
	*.class
	*.dll
	*.exe
	*.o
	*.so

	# Packages #

	# -- coding: utf-8 --

	"""
	This script loads a Brain Tumor DICOM dataset into Glue.
	The data comes from http://www.osirix-viewer.com/datasets/DATA/BRAINIX.zip

	To run this locally, download and unzip that file, and run this script
	from the directory that you dowloaded the ZIP file to

	This requires the dicom library, which you can install via