chore: update libSBML to 5.20.2 (#535)

* chore: update to libSBML 5.20.2

* Revert "chore: update to libSBML 5.20.2" mexmaci64

This partially reverts commit cbfe73f.
Keep the old .mexmaci64 from release 5.18.3.

* fix: checkInstallation makeBinaryExecutable

Bug introduced by #528

* doc: software versions.txt

installation/checkInstallation.m

@@ -29,7 +29,6 @@
 %Get the RAVEN path
 [ST, I]=dbstack('-completenames');
 [ravenDir,~,~]=fileparts(fileparts(ST(I).file));
-    status = makeBinaryExecutable();
 
 % Do not print first few lines if only version should be reported
 if ~versionOnly
@@ -105,7 +104,7 @@
 
 if isunix
     fprintf([myStr('   > Make binaries executable',40) '%f'])
-    status = makeBinaryExecutable();
+    status = makeBinaryExecutable(ravenDir);
     if status == 0
         fprintf('Pass\n')
     else
@@ -313,12 +312,12 @@
 end
 end
 
-function status = makeBinaryExecutable()
+function status = makeBinaryExecutable(ravenDir)
 if ispc
     status = 0; % No need to run on Windows
     return;
 end
-binDir = fullfile(findRAVENroot(),'software');
+binDir = fullfile(ravenDir,'software');
 
 binList = {fullfile(binDir,'blast+','blastp');                  fullfile(binDir,'blast+','blastp.mac');
            fullfile(binDir,'blast+','makeblastdb');             fullfile(binDir,'blast+','makeblastdb.mac');

software/libSBML/ConvertFormulaToMathML.m

@@ -119,7 +119,7 @@
     j = j+1;
     x = SubFormula(j:length(SubFormula)-1);
 
-    if (exist('OCTAVE_VERSION', 'var'))
+    if (exist('OCTAVE_VERSION'))
       ReplaceFormula = myRegexprep(SubFormula, n, x, 'once');
       ReplaceFormula = myRegexprep(ReplaceFormula,regexptranslate('escape',x),n,2);
       ReplaceFormula = myRegexprep(ReplaceFormula, 'nthroot', 'root', 'once');

software/libSBML/OutputSBML.m

@@ -0,0 +1,95 @@
+% OutputSBML(model, (filename), (extensionsAllowed), (applyUserValidation), (fbcGeneProductOptions))) 
+% outputs an xml file
+%
+% The function OutputSBML is the converse of TranslateSBML: 
+% it writes an MATLAB_SBML structure to an XML file. It accepts two arguments:
+%
+%   * model: This argument must be a MATLAB_SBML structure representing the 
+%            model to be written out to a file. Note that the structure will 
+%            not be validated to check if it is fully correct SBML; OutputSBML 
+%            will only verify the basic integrity of the structure (i.e., to 
+%            make sure it has the form expected of a MATLAB_SBML structure), 
+%            but nothing more.
+%
+%   * filename: The name of the file where the SBML content should be written.
+%
+%        NOTE: This argument is optional where a graphical user interface is
+%                      available, in which case a missing argument will open a browse window.
+%                      relative to the current working directory). 
+%
+%   * extensionsAllowed: An optional argument indicating that when 
+%             determining whether the MATLAB_SBML structure represents 
+%             a valid structure any additional fields are ignored. The default value is 1.
+%             If this argument is set to 0, a structure will be considered 
+%             valid if it contains only the expected fields and no additional fields.
+%
+%   * applyUserValidation: An optional argument indicating that when 
+%             determining whether the MATLAB_SBML structure represents 
+%             a valid structure user defined validation is applied. The default
+%             value is 0 which disables custom validation. A value of 1 
+%             indicates that when using the function 'isSBML_Model' to assess 
+%             whether the MATLAB_SBML structure is correct the 
+%             'applyUserValidation' function should be invoked. This allows a 
+%             user to add their own custom validation criteria to the export of SBML.
+%
+%   * fbcGeneProductOptions: This optional argument is an array of two values that
+%               allows the user to change the behavior relating to
+%               geneProduct elements in the fbc package.
+%                  - The first value in the array impacts of the infix respresentation of a 
+%                     GeneProductAssociation.
+%                     A value of [0, n] (the default) indicates that OutputSBML 
+%                     should interpret the geneProductAssociation using the label
+%                     attribute to refer to the geneProduct.  A value of [1,n]
+%                     indicates the id attribute should be used.
+%
+%                  - The second entry in the array indicates whether OutputSBML
+%                     should add geneProduct elements if it encounters a
+%                     label/id in an association element that does not
+%                     correspond to an existing geneProduct.  
+%                     A value of [n, 1] (the default) will add missing geneProducts. A value of
+%                     [n, 0] turns off this behavior.
+%
+
+%  Filename    : OutputSBML.m
+%  Description : MATLAB help file for OutputSBML
+%  Author(s)   : SBML Development Group <[email protected]>
+%
+%<!---------------------------------------------------------------------------
+% This file is part of libSBML.  Please visit http://sbml.org for more
+% information about SBML, and the latest version of libSBML.
+%
+% Copyright (C) 2013-2018 jointly by the following organizations:
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%     3. University of Heidelberg, Heidelberg, Germany
+%
+% Copyright (C) 2009-2013 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%  
+% Copyright (C) 2006-2008 by the California Institute of Technology,
+%     Pasadena, CA, USA 
+%  
+% Copyright (C) 2002-2005 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. Japan Science and Technology Agency, Japan
+% 
+% This library is free software; you can redistribute it and/or modify it
+% under the terms of the GNU Lesser General Public License as published by
+% the Free Software Foundation.  A copy of the license agreement is provided
+% in the file named "LICENSE.txt" included with this software distribution
+% and also available online as http://sbml.org/software/libsbml/license.html
+%
+% The original code contained here was initially developed by:
+%
+%      Sarah Keating
+%      Science and Technology Research Centre
+%      University of Hertfordshire
+%      Hatfield, AL10 9AB
+%      United Kingdom
+%
+%      http://www.sbml.org
+%      mailto:[email protected]
+%
+% Contributor(s):
+%

software/libSBML/TranslateSBML.m

@@ -0,0 +1,92 @@
+% [model, (errors), (version)] = TranslateSBML((filename), (validateFlag), (verboseFlag), (fbcGeneProductOptions))
+% reads an SBML document and converts it to a MATLAB_SBML structure.
+%
+% It accepts four optional arguments:
+%
+%   * filename: This is the name of the file to be imported. 
+%               If the file is not in the current directory, then the 
+%               argument must be a full pathname (either absolute or 
+%               relative to the current working directory). 
+%
+%        NOTE: In Octave the filename is a required argument.
+%
+%   * validateFlag: This flag tells libSBML whether to perform full 
+%               validation of the SBML file being read. The default 
+%               value is 0, which signifies not to perform validation. 
+%               (Note libSBML will still check for and report basic 
+%               XML parsing errors regardless of the value of this flag.)
+%
+%   * verboseFlag: A value of 1 (the default) indicates that TranslateSBML 
+%               should perform the validation process interactively, 
+%               displaying errors and prompting the user for feedback 
+%               if the model is invalid. A value of 0 will suppress user 
+%               interaction, and is useful when calling TranslateSBML 
+%               from within another function/script.
+%
+%   * fbcGeneProductOptions: This optional argument is an array of two values that
+%               allows the user to change the behavior relating to
+%               geneProduct elements in the fbc package.
+%                  - The first value in the array impacts of the infix respresentation of a 
+%                     GeneProductAssociation.
+%                     A value of [0, 1] (the default) indicates that TranslateSBML 
+%                     should display the geneProductAssociation using the label
+%                     attribute to refer to the geneProduct.  A value of [1,1]
+%                     indicates the id attribute should be used.
+%        
+%                  - NOTE: the second value has no impact on TranslateSBML.
+%
+% There are three possible outputs:
+%
+%   * model: The MATLAB_SBML Structure representing the imported model.
+%
+%   * errors: A structure representing any validation errors within the imported model.
+%
+%   * version: A structure representing version information about libSBML.
+%
+
+
+
+
+% Filename    : TranslateSBML.m
+% Description : MATLAB help file for TranslateSBML
+% Author(s)   : SBML Team <[email protected]>
+% Created     : 2003-09-15
+%
+% This file is part of libSBML.  Please visit http://sbml.org for more
+% information about SBML, and the latest version of libSBML.
+%
+% Copyright (C) 2013-2018 jointly by the following organizations:
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%     3. University of Heidelberg, Heidelberg, Germany
+%
+% Copyright (C) 2009-2013 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+%  
+% Copyright (C) 2006-2008 by the California Institute of Technology,
+%     Pasadena, CA, USA 
+%  
+% Copyright (C) 2002-2005 jointly by the following organizations: 
+%     1. California Institute of Technology, Pasadena, CA, USA
+%     2. Japan Science and Technology Agency, Japan
+% 
+% This library is free software; you can redistribute it and/or modify it
+% under the terms of the GNU Lesser General Public License as published by
+% the Free Software Foundation.  A copy of the license agreement is provided
+% in the file named "LICENSE.txt" included with this software distribution
+% and also available online as http://sbml.org/software/libsbml/license.html
+%
+% The original code contained here was initially developed by:
+%
+%      Sarah Keating
+%      Science and Technology Research Centre
+%      University of Hertfordshire
+%      Hatfield, AL10 9AB
+%      United Kingdom
+%
+%      http://www.sbml.org
+%      mailto:[email protected]
+%
+% Contributor(s):
+%

software/libSBML/VERSION.txt

@@ -1 +1,2 @@
-5.18.3
+5.20.2
+.mexmaci64 => use 5.18.3 version instead of .mexmaci from 5.20.2