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The page displays a screen with three major parts:
    * The left side holds today's notes: please edit these as we go along.
    * The top right side shows the names of users who are logged in: please add your name and pick the color that best reflects your mood and personality.
    * The bottom right is a real time chat window for asking questions of the instructor and your fellow learners.

To start, please add yourself to the attendee list below:
    * Instructor (discipline, institution)
      - Benjamin Laken (RSD , UCL)
      - David Pérez-Suárez (RSD/astrophysics, UCL)
      - Tom Couch (RITS, UCL)
      - Mladen Georgiev (ISD, UCL)
    * Helpers (discipline, institution)
      -
    * Attendee
      -Robert Wacholc
      -Pete Dockrill

*Software Carpentry Etherpad: June 22-23 2016, UCL
*
*Main lesson page: http://rits.github-pages.ucl.ac.uk/2016-06-22-UCL_software_carpentry/
*Survey Code: 2016-06-22-UCL
*Please use this etherpad as a place to track notes and chatter, and please do:
	    1. Ask (and answer) questions communally in the pad
	    2. Update the pad with commands, links, notes and annotations for youself and your fellow students as the lesson progresses
	
*12
*The Unix Shell
*Getting ready
Before we start you'll need to download some files:
    1. Download the zip file from this location: http://swcarpentry.github.io/shell-novice/shell-novice-data.zip
    2. Unzip/Extract the file and copy the data-shell folder to your desktop

*Socrative exercises
During this module, we'll be using Socrative to ask you some questions. To take part:
    1. Visit https://b.socrative.com/login/student/
    2. Join this room: UqlwDDj6
    
*Commands

pwd - print working directory - tells you your current location in the filesystem

whoami - returns current username

pwd - Print Working Directory, where are you in your filesystem.

ls - lists all files and folders in working directory
	* -F appends an indicator to tell directories from files
	* ls [directory]  - lists all files and folders in the specified sub-directory
	* -a lists all files, including the hidden files (those that start with a dot)
	* -r lists the files in reverse order

cd - change directory

clear - clears shell's window

special symbols:
	* . represents the current directory
	* .. represents the parent directory of the current directory
	* ~ represents the home directory
	* * wildcard representing 0 or more characters
	* ? wildcard representing exactly one or zero character(s)
	* | ("pipe") - sends output of one command to a second command
	* $ specifies the next thing you type is a variable name and not to be read literally

[up arrow] - cycles through previous commands in the command line. Can then be executed by pressing enter as usual
GIT, git it all!

mkdir - makes a new directory

nano draft.txt- makes a new text file and opens in nano
In nano, ^ = ctrl

rm - removes file (a text file, not a folder/directory)
	* rm -r thesis - removes folder/directory
	* rm -ri thesis- goes through each subfolder in directory asking if want to remove

mv [from_path/current_filename] [to_path/new_filename] - moves file current_filename in from_path to to_path and names it new_filename.

cp - copy - same as mv, except it leaves a copy of the file in the original location

[Ctrl+C] - when a command is running, this cancels it

wc [filename] - (word count) tells you the number of lines, words, characters in [filename]
	* -l , counts the number of lines
	* -w , counts the number of words
	* -c , counts the number of characters 


cat - prints contents of file to screen

sort - sorts a list alphabetically
	* -n sorts a list numerically (ascending order)


Looping:
    $ for var in foo_list   enter
    > do   enter
    > some_command with $var   enter
    > done   enter

alternately:
     for var in foo_list; do [some_command]; do [some_other_command]; done

echo - simple print command; prints whatever you type after it. Accepts variables with $

touch - creates an empty file with the specified file name, can also change the timestamp of the file should you execute without creating a new file: touch -c ...

bash - executes the commands contained in a specified file, accepts variables as inputs

GIT, git it all!!!
Socrative code:  0Xx3NcSV

Set up Git:
    git config --global user.name "My Name"
    git config --global user.email "me@ucl.ac.uk"
    git config --global color.ui "auto"
    git config --global core.editor "nano -w"
    
See the Git config
	git config --list

Initialise a repository in a certain folder
	git init

Check the status of the repository 
	git status 

See whats changed:
    git diff
    
Make a change to a document
	git add filename
	git commit -m "Write a message to track the changes"
	
See what commits you've made to the file
	git log
	
If you want to see previous versions of the file:
    git diff HEAD~1 filename
    
If want to revert back to a previous version
	git checkout HEAD filename
	git reset HEAD filename
	git checkout -- filename
	
	https://github.com/notifications to accept the invitation
	
	
	
*Day 2: Python

Socrative Room: 755T5UATS

(If you have python 2.7 you can update using Conda:)
$ conda create --name py3 python=3.5 ipython
$ source activate py3

Getting started:
You need to download some files to follow this lesson (from http://swcarpentry.github.io/python-novice-inflammation/python-novice-inflammation-data.zip )
1. Make a new folder in your Desktop called python-novice-inflammation.
2. Download python-novice-inflammation-data.zip and move the file to this folder.
3. If it’s not unzipped yet, double-click on it to unzip it. You should end up with a new folder called data.
4. You can access this folder from the Unix shell with:
*$ cd && cd Desktop/python-novice-inflammation/data
	
	
	In the py notebook:
	
	C?         ...works as a manual page of command C
	print(X)     ...return a print out of variable X
	%who       ...to show the list of variables and modules loaded
	%whos      ...as per %who with more details 
	type(X)      ...return the type of variable X
	
	

*Databases and SQL
*Getting ready

Download the database file:
    http://files.software-carpentry.org/survey.db
    
$ sqlite3 survey.db
sqlite> .tables

*Socrative

Here are the notes:
    http://swcarpentry.github.io/sql-novice-survey/index.html

Here are the instructions to get to the quizzes.
    1. Visit https://b.socrative.com/login/student/
    2. Join this room: G4NNY4GU

*Test Query

sqlite> SELECT * FROM site;

To get the list of tables
.tables

To see the fields of a table 
.schema tablename

*Python Notebook Code

import sqlite3
connection = sqlite3.connect("survey.db")
cursor = connection.cursor()
cursor.execute("SELECT reading FROM Survey WHERE quant = 'sal';")
results = cursor.fetchall()

n = 0
sum = 0
for r in results:
     sum += r[0]
     n += 1
avg = sum/n
result = 0
for r in results:
     print r
     result += (r[0] - avg)**2

print "I computed: ", result/(n-1)

cursor.close()
connection.close()