refactor: char, string and cell array input

[edkerk]

Main improvements in this PR:

• feat:

  • allow both character vectors ('example') and string arrays ("example") as input when text strings are expected (solves refactor: allow string parameters to be given as string array #397)
  • when a function expects a cell array as input, also allow character vector and string arrays instead of forcing a 1x1 cell array (and make the necessary conversion)
  • numerous tests (updating feat: unit tests for functions #414)

• fix:

  • MAFFT: explicitly force mafft.bat to be handled as binary, to prevent end-of-line character changes when checking out on Windows

I hereby confirm that I have:

• Tested my code on my own machine
• Followed the development guidelines.
• Selected devel as a target branch
• If needed, asked first in the Gitter chat room about this PR

[github-actions]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 Running blastPlusTests . Done blastPlusTests 
 Running cdhitTests . Done cdhitTests 
 Running diamondTests . Done diamondTests 
 Running fillGapsLargeTests . 
 Error occurred in fillGapsLargeTests/testLargeCobra and it did not run to completion. 
 Error ID: 
 '' 
 Error Details: 
 Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsLargeTests>testLargeCobra (line 85) setRavenSolver('cobra'); 
 . Done fillGapsLargeTests 
 Running fillGapsSmallTests .. 
 Error occurred in fillGapsSmallTests/testSmallCobra and it did not run to completion. 
 Error ID: 
 '' 
 Error Details: 
 Error using setRavenSolver (line 19) COBRA toolbox is not initialized, run 'initCobraToolbox()' Error in fillGapsSmallTests>testSmallCobra (line 85) setRavenSolver('cobra'); 
 . Done fillGapsSmallTests 
 Running hmmerTests . Done hmmerTests 
 Running importExportTests .... Done importExportTests 
 Running mafftTests . Done mafftTests 
 Running miriamTests . Done miriamTests 
 Running modelAbilitiesTests .. testOut = struct with fields: np: [16x1 double] npn: {16x1 cell} nfpm: [16x16 logical] mtc: {9x1 cell} testOut = struct with fields: np: [16x1 double] npn: {16x1 cell} nfpm: [16x16 logical] mtc: {9x1 cell} testOut = struct with fields: np: [16x1 double] npn: {16x1 cell} nfpm: [16x16 logical] mtc: {9x1 cell} testOut = struct with fields: np: [16x1 double] npn: {16x1 cell} nfpm: [16x16 logical] mtc: {9x1 cell} ...... Done modelAbilitiesTests 
 Running modelConversionTests . Done modelConversionTests 
 Running modelCurationTests .......... ....... Done modelCurationTests 
 Running solverTests .. 
 Error occurred in solverTests/testCobra and it did not run to completion. 
 Error ID: 
 '' 
 Error Details: 
 Error using solverTests>testCobra (line 95) Solver not working 
 . Done solverTests 
 Running sortIdentifiers_and_permuteModelTests . Done sortIdentifiers_and_permuteModelTests 
 Running tinitTests . Done tinitTests 
 Failure Summary: Name Failed Incomplete Reason(s) 
 fillGapsLargeTests/testLargeCobra X X Errored. 
 fillGapsSmallTests/testSmallCobra X X Errored. 
 solverTests/testCobra X X Errored.

Note: In the case of multiple test runs, this post will be edited.

[edkerk]

cd to the testing\unit_tests folder and run runtests(struct2table(dir('*.m')).name);

[johan-gson]

Tested the test cases on my computer using
"runtests(struct2table(dir('*.m')).name)" - all but the mafft tests worked, which according to Ed was fine.