Add stack trace for createSpecies first stage error
Fixed XMLParser error when speciesDefault is not specified in markup
Minor fix on RunIdyno.py

Reverted srcpath to its original value
Added a message alerting the user to the need to change this
Merge pull request #35 from fophillips/bugfix/speciesDefault

Bugfix: New speciesDefault XMLParser error
Utils.ExtraMath cleaned up

Many small changes made to ExtraMath, the most notable being:
- the use of Double instead of double, Integer instead of int, etc.
- splitting deviateFrom() into deviateFromCV() and deviateFromSD() to
cater for the alternate methods of deviation from a value.
- more robust determination of the sign of a value.

Changes to other files are those required to deal with changes to
ExtraMath: further work on these will be commited soon.
Merge pull request #37 from roughhawkbit/master

Utils.ExtraMath cleaned up. Checked Through 221013
Warning message if array empty

Following fophillips comment on pull request #37, I've added warning
messages in the case that the array given to mean() or stddev() is
empty or contains only values that are NaN/infinite
Fix XML syntax error in env_Sum file
Merge pull request #39 from fophillips/bugfix/xml-error

Fix XML syntax error in env_Sum file
Merge pull request #38 from roughhawkbit/master

Warning message if array empty
Changes to ContinuousVector required for eGUT epithelium. 1. Now
implements Comparable so that two CVs can be compared. 2. Implements the
required "compareTo" method.
Merge pull request #41 from kalden/master

Changes to ContinuousVector required for eGUT epithelium.
Merge pull request #1 from kreft/master

Fetching upstream changes
Delete .DS_store
Tidied ContinuousVector.compareTo()
Initialising Double[] arrays

Small bug noticed by Kieran: arrays changed from double[] to Double[]
(see pull request #37) were being initialised with null's rather than
zero's as before. A new command, ExtraMath.newDoubleArray(), is useful
for initialising Double[] arrays correctly, and this is now called in
those instances that were changed in pull request #37
Merge pull request #42 from roughhawkbit/master

Fix to initialising Double[] arrays
Merge pull request #1 from kreft/master

Update iDynoMiCS with Double Array Initialiser
Changes to initial setup of species such that these can be declared in
terms of area rather than as a number of cells. Now the user has the
option to specify the number of cells per millimetre cubed. This is then
used to calculate the number of cells that should be introduced to the
simulation initially. However the update goes a little further than this
- in all the examples, the cell initial setup area is the whole length
of the Y and Z domains, with a height of 1 (to ensure the cells are
initially near the substratum). Now the user will have the opportunity
of not declaring an initial area at all: if they do this, iDynoMiCS
assumes the area to be the length of the Y and Z domains, with a height
of 1. This detail has been specified in detail, with examples, in the
new example protocol file that is included in this commit
Changes to make the differences between 2D and 3D more clearer - basing
3D on area and 2D on length. Also added information into the log file
output statements that states how the distribution was formed