Merge pull request #21 from LewisLabUCSD/CobraChange

Update of functions in base
LewisLabUCSD · May 27, 2019 · e9e536b · e9e536b
2 parents 137af58 + 1248546
commit e9e536b
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Showing 9 changed files with 62 additions and 10 deletions.
diff --git a/test/base/clearGlobal.m b/test/base/clearGlobal.m
@@ -6,6 +6,11 @@ function clearGlobal(globalName)
 %
 % INPUTS:
 %    globalName:    The name of the global variable to clear.
+%
+% NOTE:
+%    this function has been uploaded from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/utilities/clearGlobal.m
+%    [e6b4efd]
 
     clearvars('-global',globalName);
 end
diff --git a/test/base/getEnvironment.m b/test/base/getEnvironment.m
@@ -7,6 +7,12 @@
 %    environment:      a struct with two fields
 %                       * .globals - contains all global values
 %                       * .path - contains the current path
+%
+% NOTE:
+%    this function has been uploaded from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/utilities/getEnvironment.m
+%    [cadfa58]
+
 environment = struct();
 globals = struct();
 globalvars = who('global');

diff --git a/test/base/getFilesInDir.m b/test/base/getFilesInDir.m
@@ -43,6 +43,12 @@
 %
 %    % get only the gitIgnored files in the current folder
 %    files = getFilesInDir('type', 'ignored');
+%
+% NOTE:
+%    this function has been uploaded from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/install/getFilesInDir.m
+%    [cdb2478]
+
 
 persistent COBRAIgnored
 

diff --git a/test/base/getGlobalValue.m b/test/base/getGlobalValue.m
@@ -9,6 +9,12 @@
 %
 % OUTPUT:
 %    value:         The value of the requested global variable
+%
+% NOTE:
+%    this function has been uploaded from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/utilities/getGlobalValue.m
+%    [e6b4efd]
+
 
     eval(['global ' globalName]);
     eval(['value = ' globalName ';']);

diff --git a/test/base/getIgnoredFiles.m b/test/base/getIgnoredFiles.m
@@ -14,8 +14,14 @@
 %    ignoredFiles:      All files (and patterns) indicated as ignored in
 %                       the gitignore file.
 %
-% .. Authors: - Original Code: Laurent Heirandt
+% .. Authors: - Original Code: Laurent Heirendt
 %          - Move to function: Thomas Pfau, Jan 2018
+%
+% NOTE:
+%    this function has been adapted from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/install/getIgnoredFiles.m
+%    [f9a9213]
+
 
 
 global CELLFIEDIR

diff --git a/test/base/restoreEnvironment.m b/test/base/restoreEnvironment.m
@@ -12,7 +12,12 @@ function restoreEnvironment(environment, restorePath, printLevel)
 %    printLevel:       Set the verbosity of this method:
 %                       * 0: No outputs (Default)
 %                       * 1: Info what each value is set to
-%                                   
+% 
+% NOTE:
+%    this function has been adapted from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/utilities/restoreEnvironment.m
+%    [005f7d1]
+
     if ~exist('restorePath','var')
         restorePath = true;
     end

diff --git a/test/base/runScriptFile.m b/test/base/runScriptFile.m
@@ -17,23 +17,29 @@
 %                - `.Error`: Error message received from a failed or skipped test
 %
 % .. Author:   - Thomas Pfau Jan 2018.
+%
+% NOTE:
+%    this function has been adapted from
+%    https://github.com/opencobra/cobratoolbox/blob/master/test/runScriptFile.m
+%    [b58da0c]
+
 
 global CBT_MISSING_REQUIREMENTS_ERROR_ID
 
-COBRA_TESTSUITE_TESTFILE = fileName;
+CELLFIE_TESTSUITE_TESTFILE = fileName;
 
 % get the timinig (and hope these values are not overwritten.
-COBRA_TESTSUITE_STARTTIME = clock();
+CELLFIE_TESTSUITE_STARTTIME = clock();
 
 try
     % run the file
     executefile(fileName);
 catch ME
     % vatch errors and interpret them
-    clearvars -except ME COBRA_TESTSUITE_STARTTIME COBRA_TESTSUITE_TESTFILE CBT_MISSING_REQUIREMENTS_ERROR_ID
-    scriptTime = etime(clock(), COBRA_TESTSUITE_STARTTIME);
+    clearvars -except ME CELLFIE_TESTSUITE_STARTTIME CELLFIE_TESTSUITE_TESTFILE CBT_MISSING_REQUIREMENTS_ERROR_ID
+    scriptTime = etime(clock(), CELLFIE_TESTSUITE_STARTTIME);
     result = struct('status', 'failed', 'failed', true, 'passed', false, 'skipped', false, 'fileName', ...
-                    COBRA_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'fail', 'Error', ME);
+                    CELLFIE_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'fail', 'Error', ME);
     if strcmp(ME.identifier, CBT_MISSING_REQUIREMENTS_ERROR_ID)
         % requirement missing, so the test was skipped.
         result.status = 'skipped';
@@ -50,10 +56,10 @@
 end
 
 % get the timinig.
-scriptTime = etime(clock(), COBRA_TESTSUITE_STARTTIME);
+scriptTime = etime(clock(), CELLFIE_TESTSUITE_STARTTIME);
 
 result = struct('status', 'passed', 'failed', false, 'passed', true, 'skipped', false, 'fileName', ...
-                COBRA_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'success', 'Error', MException('', ''));
+                CELLFIE_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'success', 'Error', MException('', ''));
 
 end
 

diff --git a/test/base/runTestSuite.m b/test/base/runTestSuite.m
@@ -24,6 +24,12 @@
 %
 % Author:
 %    - Thomas Pfau Jan 2018.
+%
+% NOTE:
+%    this function has been adapted from
+%    https://github.com/opencobra/cobratoolbox/blob/master/test/runTestSuite.m
+%    [5395578]
+
 
 global CELLFIEDIR
 

diff --git a/test/base/setGlobal.m b/test/base/setGlobal.m
@@ -6,7 +6,13 @@ function setGlobal(globalName,globalValue)
 %
 % INPUTS:
 %    globalName:    A string representing the name of the global variable
-%    globalValue:   The value to set the global variable to
+%    globalValue:   The value to set the global variable 
+%
+% NOTE:
+%    this function has been adapted from
+%    https://github.com/opencobra/cobratoolbox/blob/master/src/base/utilities/setGlobal.m
+%    [e6b4efd]
+
 
     eval([ globalName '_val = globalValue;']);
     eval(['global ' globalName]);