optEnvelope

[Kretaks]

Please include a short description of enhancement here

Added a design tool called optEnvelope: https://doi.org/10.1371/journal.pone.0294313
Added a test for optEnvelope

I hereby confirm that I have:

• Tested my code on my own machine
• Followed the guidelines in the Contributing Guide
• Selected develop as a target branch (top left drop-down menu)

(Note: You may replace [ ] with [X] to check the box)

[rmtfleming]

Numerous functions without headers.
milpOEReinserts

Try this to start with
which printFunctionIO

[Kretaks]

@rmtfleming
Added headers to functions

[rmtfleming]

Follow the style of printFunctionIO
https://opencobra.github.io/cobratoolbox/latest/contributing.html#code
headers should show what type of input is expected, e.g., cell arrray, numeric, etc. with dimensions

[Kretaks]

@rmtfleming
Changes have been made.

[farid-zare]

Could you please address these reviews?

[farid-zare]

Could you please change this section to define 'gurobi' as a required solver first and then use prepareTest function as here in the template:
https://github.com/opencobra/cobratoolbox/blob/master/docs/source/guides/testTemplate.m
By using this method the test would be skipped where gurobi is not installed instead of failing

[Kretaks]

@farid-zare
defined gurobi as required and
added prepareTest function

[farid-zare]

Please also include a USAGE section in your documentation as:
% the end of the description
%
% USAGE:
%
% [output1, output2, output3] = someFunction(input1, input2, input3)
%
% here the other section can begin

examples of this is available in other cobra toolbox codes

[Kretaks]

@farid-zare
I am using "EXAMPLE:" in other functions so I changed this one to include "EXAMPLE:" just before "AUTHORS:"
Let me know if I need to change all "EXAMPLE:" to "USAGE:" for all functions

[farid-zare]

Thanks for your reply. Function documents must contain USAGE section but EXAMPLE is optional. Including both is recommended. Here is an example of how a standard documentation should look alike, please follow such structure for all of your functions:
https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/FVA/fastFVA/fastFVA.m

[Kretaks]

@farid-zare
Added "USAGE" for functions

[farid-zare]

Ok, thanks, I just updated two of the USAGE sections. The EXAMPLE section is a specific example whereas the USAGE section must illustrate a general function call format.
Looks good now.