Fold getToolboxVersion into exportForGit; report GECKO instead of COBRA (#635)

* Fold getToolboxVersion into exportForGit and report GECKO not COBRA

getToolboxVersion was only used by exportForGit, so it becomes a local
subfunction there and the standalone file (and its doc) are removed. The
dependency report now covers RAVEN and, for enzyme-constrained models
(those with an "ec" field), GECKO; the COBRA Toolbox version is no longer
reported. GECKO is located via GECKOInstaller.m.

The tIO test that called getToolboxVersion directly now checks that
exportForGit writes a RAVEN_toolbox entry to dependencies.txt instead.

* Report toolbox version from version.txt only, otherwise 'unknown'

Drop the git describe/commit-hash fallback in the folded getToolboxVersion:
the reported version now comes solely from the toolbox version.txt, and is
'unknown' when that file is absent (e.g. a development checkout between
releases).

Author: edkerk

doc/io/getToolboxVersion.html

@@ -23,8 +23,8 @@
 %     should be exported (default all formats as {'mat', 'txt', 'xlsx',
 %     'xml', 'yml'}).
 % mainBranchFlag : logical
-%     if true, function will error if RAVEN (and COBRA if detected) is/are
-%     not on the main branch (default false).
+%     if true, function will error if RAVEN (and GECKO for enzyme-
+%     constrained models) is/are not on the main branch (default false).
 % subDirs : logical
 %     whether model files for each file format should be written in their
 %     own subdirectory, with 'model' as parent directory, in accordance to
@@ -77,12 +77,13 @@
 %Sort reactions, metabolites and genes alphabetically
 model=sortIdentifiers(model);
 
-%Get versions or commits of toolboxes:
+%Get versions or commits of toolboxes. GECKO is only relevant for
+%enzyme-constrained models (those with an "ec" field).
 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
-if exist('initCobraToolbox.m','file')
-    COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
+if isfield(model,'ec')
+    GECKOver = getToolboxVersion('GECKO','GECKOInstaller.m',mainBranchFlag);
 else
-    COBRAver = [];
+    GECKOver = [];
 end
 %Retrieve libSBML version:
 [ravenDir,prevDir]=findRAVENroot();
@@ -159,8 +160,8 @@
 fprintf(fid,['MATLAB\t' version '\n']);
 fprintf(fid,['libSBML\t' libSBMLver '\n']);
 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']);
-if ~isempty(COBRAver)
-    fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']);
+if ~isempty(GECKOver)
+    fprintf(fid,['GECKO_toolbox\t' GECKOver '\n']);
 end
 if isfield(model,'modelVersion')
     fields = fieldnames(model.modelVersion);
@@ -171,3 +172,63 @@
 end
 fclose(fid);
 end
+
+function version = getToolboxVersion(toolbox,fileID,mainBranchFlag)
+% getToolboxVersion  Return the version of RAVEN or GECKO.
+%
+% Returns the version of the toolbox as stated in its version.txt, or
+% 'unknown' if that file cannot be found.
+%
+% toolbox        name of the toolbox (e.g. 'RAVEN' or 'GECKO').
+% fileID         a file only found in that toolbox, used to locate its root
+%                (e.g. 'ravenCobraWrapper.m' or 'GECKOInstaller.m').
+% mainBranchFlag if true, error if the toolbox is not on the main branch.
+currentPath = pwd;
+version     = '';
+
+%Try to find root of toolbox:
+try
+    toolboxPath = which(fileID);                %full file path
+    slashPos    = getSlashPos(toolboxPath);
+    toolboxPath = toolboxPath(1:slashPos(end)); %folder path
+    %Go up until the root is found:
+    D = dir(toolboxPath);
+    while ~ismember({'.git'},{D.name})
+        slashPos    = getSlashPos(toolboxPath);
+        toolboxPath = toolboxPath(1:slashPos(end-1));
+        D           = dir(toolboxPath);
+    end
+    cd(toolboxPath);
+catch
+    disp([toolbox ' toolbox cannot be found'])
+    version = 'unknown';
+end
+%Check if in main:
+if mainBranchFlag
+    [~,currentBranch] = system('git rev-parse --abbrev-ref HEAD');
+    currentBranch = strtrim(currentBranch);
+    if any([strcmp(currentBranch, "main"), strcmp(currentBranch, "master")])
+        cd(currentPath);
+        error(['ERROR: ' toolbox ' not in main (or master) branch. Check-out this branch of ' toolbox ' before submitting model for Git.'])
+    end
+end
+%Read the version from the toolbox version.txt; report 'unknown' otherwise
+if isempty(version)
+    fid = fopen([toolboxPath 'version.txt'],'r');
+    if fid ~= -1
+        version = fscanf(fid,'%s');
+        fclose(fid);
+    end
+    if isempty(version)
+        version = 'unknown';
+    end
+end
+cd(currentPath);
+end
+
+function slashPos = getSlashPos(path)
+slashPos = strfind(path,'\');       %Windows
+if isempty(slashPos)
+    slashPos = strfind(path,'/');   %MAC/Linux
+end
+end

io/exportForGit.m

@@ -36,9 +36,16 @@ function getMD5HashReturnsHexDigest(testCase)
             testCase.verifyMatches(char(h), '^[0-9a-fA-F]{32}$');
         end
 
-        function getToolboxVersionRuns(testCase)
-            v = getToolboxVersion('RAVEN', 'ravenCobraWrapper.m');
-            testCase.verifyNotEmpty(v);
+        function exportForGitWritesDependencies(testCase)
+            % The toolbox-version lookup is now embedded in exportForGit and
+            % is exercised via the dependencies.txt it writes
+            f = fullfile(testCase.ravenRoot,'tutorial','empty.xml');
+            evalc('model = importModel(f);');
+            outDir = tempname; mkdir(outDir);
+            c = onCleanup(@() rmdir(outDir,'s'));
+            evalc("exportForGit(model,'path',outDir,'formats',{'xml'},'subDirs',false)");
+            dep = fileread(fullfile(outDir,'dependencies.txt'));
+            testCase.verifySubstring(dep, 'RAVEN_toolbox');
         end
 
         function importModelReadsSBML(testCase)