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Merge pull request opencobra#2322 from opencobra/master
rmtfleming
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rmtfleming
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Numerous functions without headers.
milpOEReinserts
Try this to start with
which printFunctionIO
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@rmtfleming |
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Follow the style of printFunctionIO |
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@rmtfleming |
farid-zare
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farid-zare
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Could you please address these reviews?
| tol = 1e-6; | ||
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| % define the solver packages to be used to run this test | ||
| solversPkgs = {'gurobi'}; |
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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
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@farid-zare
defined gurobi as required and
added prepareTest function
| % This function is going through inactive reactions sequentially and | ||
| % reinserting them one by one to get best possible set of knockouts while | ||
| % retaining optimal envelope. With numTries parameter this can be done | ||
| % multiple times by randomizing list of inactive reactions |
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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
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@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
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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
farid-zare
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@farid-zare |
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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. |
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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:
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