From 1248546684bb6a6de3329d5a92f9d117a622b255 Mon Sep 17 00:00:00 2001
From: Loic Marx <loic.marx@gmail.com>
Date: Mon, 27 May 2019 10:43:58 +0200
Subject: [PATCH] add provenance note to function in base

---
 test/base/clearGlobal.m        | 5 +++++
 test/base/getEnvironment.m     | 6 ++++++
 test/base/getFilesInDir.m      | 6 ++++++
 test/base/getGlobalValue.m     | 6 ++++++
 test/base/getIgnoredFiles.m    | 8 +++++++-
 test/base/restoreEnvironment.m | 7 ++++++-
 test/base/runScriptFile.m      | 6 ++++++
 test/base/runTestSuite.m       | 6 ++++++
 test/base/setGlobal.m          | 8 +++++++-
 9 files changed, 55 insertions(+), 3 deletions(-)

diff --git a/test/base/clearGlobal.m b/test/base/clearGlobal.m
index 5240fce..75a273d 100644
--- 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
\ No newline at end of file
diff --git a/test/base/getEnvironment.m b/test/base/getEnvironment.m
index 1ee5fe0..525dab0 100644
--- 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
index 220940e..3b5e399 100644
--- 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
index 9c8c879..cabc519 100644
--- 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
index 412fa40..18c9345 100644
--- 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
index 95db5e4..a9184b4 100644
--- 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
index 93d6fff..b817502 100644
--- a/test/base/runScriptFile.m
+++ b/test/base/runScriptFile.m
@@ -17,6 +17,12 @@
 %                - `.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
 
diff --git a/test/base/runTestSuite.m b/test/base/runTestSuite.m
index 9e9d420..c8cc325 100644
--- 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
index d2d1493..2bd7dae 100644
--- 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]);