From af3d647e146ca025bb220db9cdecd984df7baf1e Mon Sep 17 00:00:00 2001
From: laurentheirendt <laurent.heirendt@uni.lu>
Date: Tue, 25 Apr 2017 10:53:50 +0200
Subject: [PATCH] Fix for update and init scripts

---
 .github/SOLVERS.md   |  1 +
 initCobraToolbox.m   | 13 ++++++++-----
 updateCobraToolbox.m |  4 ++--
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/.github/SOLVERS.md b/.github/SOLVERS.md
index 4bc3e79380..a4142b0bcc 100644
--- a/.github/SOLVERS.md
+++ b/.github/SOLVERS.md
@@ -157,6 +157,7 @@ Platform-specific instructions are marked with
     ````
     <img src="https://prince.lcsb.uni.lu/jenkins/userContent/windows.png" height="20px" alt="Windows"> Run `moseksetupwin64x86.msi` and select `Typical` installation. This will install `mosek` in `C:\Program Files\Mosek`.
     <img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" alt="Linux"> Browse to `/Applications` and double-click the archive to uncompress.
+    :warning: It is important to run the script `python /Applications/mosek/<ver>/tools/platform/osx64x86/bin/install.py`, which makes important updates to the installation. 
 
 5) <img src="https://prince.lcsb.uni.lu/jenkins/userContent/apple.png" height="20px" alt="macOS"> <img src="https://prince.lcsb.uni.lu/jenkins/userContent/linux.png" height="20px" alt="Linux"> Configure the `PATH` and `MOSEKLM_LICENSE_FILE` environment variables in `~/.bashrc` by editing your `bashrc` file
     ````bash
diff --git a/initCobraToolbox.m b/initCobraToolbox.m
index e9e4323226..23e1e34b9f 100644
--- a/initCobraToolbox.m
+++ b/initCobraToolbox.m
@@ -157,7 +157,7 @@ function initCobraToolbox()
     % add the folders of The COBRA Toolbox
     onPath = ~isempty(strfind(lower(path), lower(CBTDIR)));
 
-    folders = {'external', 'tutorials', 'papers', 'binary', 'deprecated', 'src', 'test'};
+    folders = {'tutorials', 'papers', 'binary', 'deprecated', 'src', 'test'};
 
     if ~onPath
         if ENV_VARS.printLevel
@@ -167,14 +167,17 @@ function initCobraToolbox()
         % add the root folder
         addpath(CBTDIR);
 
+        % add the external folder first
+        addpath(genpath([CBTDIR, filesep, 'external']));
+
+        % remove the SBML Toolbox
+        rmpath(genpath([CBTDIR, filesep, 'external', filesep, 'SBMLToolbox']));
+
         % add specific subfolders
         for k = 1:length(folders)
             addpath(genpath([CBTDIR, filesep, folders{k}]));
         end
 
-        % remove the SBML Toolbox
-        rmpath(genpath([CBTDIR, filesep, 'external', filesep, 'SBMLToolbox']));
-
         % print a success message
         if ENV_VARS.printLevel
             fprintf(' Done.\n');
@@ -251,7 +254,7 @@ function initCobraToolbox()
     SOLVERS.glpk.type = {'LP', 'MILP'};
     SOLVERS.gurobi.type = {'LP', 'MILP', 'QP', 'MIQP'};
     SOLVERS.ibm_cplex.type = {'LP', 'MILP', 'QP', 'MIQP'};
-    SOLVERS.matlab.type = {'NLP'};
+    SOLVERS.matlab.type = {'LP', 'NLP'};
     SOLVERS.mosek.type = {'LP', 'QP', 'MILP'};
     SOLVERS.pdco.type = {'LP', 'QP', 'NLP'};
     SOLVERS.quadMinos.type = {'LP', 'NLP'};
diff --git a/updateCobraToolbox.m b/updateCobraToolbox.m
index c332bd3f27..b5f441e193 100644
--- a/updateCobraToolbox.m
+++ b/updateCobraToolbox.m
@@ -25,11 +25,11 @@ function updateCobraToolbox(fetchAndCheckOnly)
         end
 
         % determine the number of commits that the local master branch is behind
-        [status_gitCountMaster, result_gitCountMaster] = system('git rev-list --count origin/master...HEAD');
+        [status_gitCountMaster, result_gitCountMaster] = system('git rev-list --no-merges --count origin/master...HEAD');
         result_gitCountMaster = char(result_gitCountMaster);
         result_gitCountMaster = result_gitCountMaster(1:end-1);
 
-        [status_gitCountDevelop, result_gitCountDevelop] = system('git rev-list --count origin/develop...HEAD');
+        [status_gitCountDevelop, result_gitCountDevelop] = system('git rev-list --no-merges --count origin/develop...HEAD');
         result_gitCountDevelop = char(result_gitCountDevelop);
         result_gitCountDevelop = result_gitCountDevelop(1:end-1);