Updated to mainly use the COBRA gitignore information

.gitignore

@@ -134,6 +134,8 @@ mapMitocartaTransportColoured.xml
 mapNodesArea.xml
 mapPPIUnified.xml
 
+#generated MILP problem files
+MILPProblem.mat
 
 # generated tutorial documentation
 docs/source/_static/tutorials/*.html

initCobraToolbox.m

@@ -547,7 +547,7 @@ function initCobraToolbox()
     cd(currentDir);
 
     % cleanup at the end of the successful run
-    removeGitIgnoredNewFiles(CBTDIR, dirContent);
+    removeTempFiles(CBTDIR, dirContent);
 
     % clear all temporary variables
     % Note: global variables are kept in memory - DO NOT clear all the variables!

src/base/install/getFilesInDir.m

@@ -2,7 +2,9 @@
 % List all files in the supplied (git tracked) Directory with their absolute path name
 % based on the git ls-file command. This command will never list git
 % specific files (i.e. files in .git folders or the git specific attribute
-% files e.g. .gitignore)
+% files e.g. .gitignore) if the directory is not git controlled, the
+% gitTypeFlag is assumed to be 'all' and all files (except for .git files
+% will be returned.
 %
 % USAGE:
 %    files = getFilesInDir(varargin)
@@ -21,6 +23,9 @@
 %                                              and not tracked. (new files)
 %                                'all'  - all files except for the git
 %                                         specific files (e.g. .git, .gitignore etc).                               
+%                                'COBRAIgnored' - use the COBRA gitIgnore
+%                                                 file to determine the
+%                                                 ignored files.
 %                                (Default: 'all')   
 %                  restrictToPattern - give a regexp pattern to filter the
 %                                      files, this option is ignored if
@@ -36,7 +41,13 @@
 %    Get only the gitIgnored files in the current folder
 %    files = getFilesInDir('gitTypeFlag', 'ignored');
 
-gitFileTypes = {'tracked','all','untracked','ignored'};
+persistent COBRAIgnored
+
+if isempty(COBRAIgnored)
+    COBRAIgnored = regexptranslate('wildcard',getIgnoredFiles());
+end
+
+gitFileTypes = {'tracked','all','untracked','ignored','COBRAIgnored'};
 parser = inputParser();
 parser.addParamValue('dirToList',pwd,@(x) exist(x,'file') == 7);
 parser.addParamValue('gitTypeFlag','all',@(x) ischar(x) && any(strcmpi(x,gitFileTypes)));
@@ -50,30 +61,64 @@
 absPath = pwd;
 %get all files in the directory.
 gitType = lower(parser.Results.gitTypeFlag);
+
+%test, whether the folder is git controlled
+[gitStatus,~] = system('git status');
+if gitStatus ~= 0 && ~strcmpi(gitType,'cobraignored')
+    gitType = 'all';
+end
+
 switch gitType
     case 'all'
-        [~, trackedfiles] = system('git ls-files');
-        trackedfiles = strsplit(trackedfiles, '\n');
-        [~, untrackedfiles] = system('git ls-files -o');
-        untrackedfiles = strsplit(untrackedfiles, '\n');
-        files = [trackedfiles,untrackedfiles];
+        if gitStatus == 0
+            [status, trackedfiles] = system('git ls-files');             
+            [status, untrackedfiles] = system('git ls-files -o');        
+            trackedfiles = strsplit(trackedfiles, '\n');
+            untrackedfiles = strsplit(untrackedfiles, '\n');
+            files = [trackedfiles,untrackedfiles];
+        else
+           files = rdir(['**' filesep '*']); 
+           files = {files.name}'; %Need to transpose to give consistent results.
+        end
+
     case 'tracked'
-        [~, files] = system('git ls-files');
+        [status, files] = system('git ls-files');
         files = strsplit(files, '\n');
     case 'untracked'
         %Files, which are not tracked but are not ignored.
-        [~, files] = system('git ls-files -o -exclude-standard');
+        [status, files] = system('git ls-files -o -exclude-standard');
         files = strsplit(files, '\n');
     case 'ignored'
         [~, files] = system('git ls-files -o -i --exclude-standard');        
         files = strsplit(files, '\n');
+    case 'cobraignored'
+        if gitStatus == 0
+            [status, trackedfiles] = system('git ls-files');             
+            [status, untrackedfiles] = system('git ls-files -o');        
+            trackedfiles = strsplit(trackedfiles, '\n');
+            untrackedfiles = strsplit(untrackedfiles, '\n');
+            files = [trackedfiles,untrackedfiles];
+        else
+           files = rdir(['**' filesep '*']); 
+           files = {files.name}'; %Need to transpose to give consistent results.
+        end  
+        matching = false(size(files));
+        for i = 1:numel(COBRAIgnored)
+            matching = matching | ~cellfun(@(x) isempty(regexp(x,COBRAIgnored{i},'ONCE')),files);
+        end
+        files = files(matching);
+
 end
 
-files = strcat(absPath, files);
+files = strcat(absPath, filesep, files);
 
 %Filter according to the restriction pattern.
 if ~isempty(parser.Results.restrictToPattern)
     files = files(cellfun(@(x) ~isempty(regexp(x,parser.Results.restrictToPattern)), files));
 end
 
 cd(currentDir);
+end
+
+
+

src/base/install/removeTempFiles.m

@@ -0,0 +1,43 @@
+function removeTempFiles(directory, oldcontent, COBRAGitIgnoredOnly)
+% Removes all files that are in the specified directory but not part of
+% the oldcontent. By default only removes those files which match files
+% mentioned in the COBRA .gitignore file.
+% USAGE:
+%    removeTempFiles(directory, oldcontent, COBRAGitIgnoredOnly)
+%
+% INPUT:
+%    directory: The directory which should be checked for changing files.
+%    content:   Absolute file names of the original conten in a cell array. 
+% 
+% OPTIONAL INPUT:
+%    COBRAGitIgnoredOnly:  Whether to only remove files which are listed by
+%                          the COBRA gitignore file.
+%                          (Default: true)
+%
+
+
+if ~exist('COBRAGitIgnoredOnly','var')
+    COBRAGitIgnoredOnly = true;
+end
+
+currentDir = cd(directory);
+
+if COBRAGitIgnoredOnly
+    gitTypeFlag = 'COBRAIgnored';
+else
+    gitTypeFlag = 'all';
+end
+
+% get the new Content of the folder.
+newContent = getFilesInDir('gitTypeFlag',gitTypeFlag);
+
+% get all .log files that were present only after initCobraToolbox was called.
+newIgnoredFiles = setdiff(newContent, oldcontent);
+
+% by adding the folder, we already have the correct path.
+if ~isempty(newIgnoredFiles)
+    delete(newIgnoredFiles{:});
+end
+
+cd(currentDir);
+end

src/base/solvers/changeCobraSolver.m

@@ -222,7 +222,8 @@
 %actually set i.e. initCobraToolbox is called before). This is only
 %necessary, if the solver is being validated.
 if validationLevel == 1
-    finish = onCleanup(@() removeGitIgnoredNewFiles(pwd, rdir(['**' filesep '*'])));
+    origFiles = getFilesInDir('gitTypeFlag','all');
+    finish = onCleanup(@() removeTempFiles(pwd, origFiles));
 end
     % configure the environment variables
 configEnvVars();

test/testAll.m

@@ -218,15 +218,15 @@
     fprintf(['\n > The exit code is ', num2str(exit_code), '.\n\n']);
 
     %clean up temporary files.
-    removeGitIgnoredNewFiles(testDirPath,testDirContent);
+    removeTempFiles(testDirPath,testDirContent);
 
     % ensure that we ALWAYS call exit
     if ~isempty(strfind(getenv('HOME'), 'jenkins')) || ~isempty(strfind(getenv('USERPROFILE'), 'jenkins'))
         exit(exit_code);
     end
 catch ME
     %Also clean up temporary files in case of an error.
-    removeGitIgnoredNewFiles(testDirPath,testDirContent);
+    removeTempFiles(testDirPath,testDirContent);
     if ~isempty(strfind(getenv('HOME'), 'jenkins')) || ~isempty(strfind(getenv('USERPROFILE'), 'jenkins'))
         % only exit on jenkins.
         exit(1);