Merge pull request #22 from LewisLabUCSD/develop

Regular merge of develop

Author: laurentheirendt

.artenolis.yml

@@ -16,6 +16,6 @@ script:
 after_success:
 
     # submit coverage report
-    #- if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" ]]; then
-    #  bash <(curl -s https://codecov.io/bash) -f "!*.lst";
-    #  fi
+    - if [[ "$MATLAB_VER" == "R2018b" && "$ARCH" == "Linux" ]]; then
+      bash <(curl -s https://codecov.io/bash) -f "!*.lst";
+      fi

.artenolis/runtests.sh

@@ -2,7 +2,20 @@
 
 # launch MATLAB
 if [ "$ARCH" == "Linux" ]; then
-    $ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash -r "fprintf('Hello ARTENOLIS.\n'); quit();"
+
+    CURRENTDIR=$(pwd)
+
+    # update the COBRA Toolbox
+    cd $ARTENOLIS_DATA_PATH/repos/cobratoolbox
+    git pull origin master
+
+    # change to the current directory
+    echo $CURRENTDIR
+    cd $CURRENTDIR
+
+    # launch the test suite
+    $ARTENOLIS_SOFT_PATH/MATLAB/$MATLAB_VER/bin/./matlab -nodesktop -nosplash < test/testAll.m
+
 fi
 
 CODE=$?

.gitignore

@@ -1,3 +1,5 @@
+coverage.json
+coverage_html
 *.asv
 *.m~
 *.mex*

external/rdir/LICENSE.md

@@ -0,0 +1,25 @@
+Copyright (c) 2014, Thomas Vanaret
+Copyright (c) 2009, Gus Brown
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

external/rdir/README.md

@@ -0,0 +1,8 @@
+# Recursive directory listing
+
+Original version is
+[here](https://nl.mathworks.com/matlabcentral/fileexchange/19550-recursive-directory-listing?requestedDomain=true).
+
+The script has been adapted for `opencobra` repositories, such as [the COBRA
+Toolbox](https://github.com/opencobra/cobratoolbox) and [the
+MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools).

external/rdir/enhanced_rdir.m

@@ -0,0 +1,65 @@
+%% RDIR Enhanced - Examples of use
+%
+% This script demonstrates how to use the different abilities of the
+% enhanced |rdir| function.
+%
+% Examples are based on |matlabroot| directory content. Results may vary
+% depending on your version of Matlab.
+%
+
+%% Standard use
+rdir([matlabroot, '\*.txt'])
+
+%% Using double wildcard **
+% List |".m"| files whose name contains |"tmpl"| in all subdirectories of
+% |matlabroot|
+rdir([matlabroot, '\**\*tmpl*.m'])
+
+%% RDIR output
+d = rdir([matlabroot, '\**\*tmpl*.m'])
+
+%%
+disp(d(1))
+
+
+%% Using 3rd argument to shorten output names
+% Remove |"C:\Program Files\"| in returned names
+rdir([matlabroot, '\*.txt'], '', 'C:\Program Files\')
+
+%%
+% Remove |matlabroot| in returned names
+rdir([matlabroot, '\*.txt'], '', true)
+
+%%
+% Optional 2nd |rdir| output indicates common path removed from each output
+% name
+[d, p] = rdir([matlabroot, '\*.txt'], '', true);
+
+fprintf('Common path : \n%s\n\n', p)
+
+disp( d(1) )
+
+%% Using a filter with "regexp"
+% List |".mat"| files, then select those whose name match regular expression
+% |'data\d'| (ie |"data"| followed by a numeric digit)
+rdir([matlabroot '\toolbox\**\*.mat'], 'regexp(name, ''data\d'')', true)
+
+%% Using a function handle as filter
+
+fun = @(d) ~isempty(regexp(d.name, 'data\d')) && (d.bytes < 10*1024)
+
+rdir([matlabroot '\toolbox\**\*.mat'], fun, true)
+
+%% Specific display - No item matching filter
+% When some items match input path, but none match filter, a specific
+% message is displayed.
+rdir(matlabroot, 'strcmp(name, ''unknowtoolbox'')', 1)
+
+
+%% Specific display - Wrong filter
+% A warning is displayed after the non-filtered result list if entered
+% filter is wrong.
+rdir(matlabroot, 'wrong filter', 1)
+
+
+% EOF