Merge pull request #314 from schorschinho/develop

Bring CI changes into master [skip ci]

ci/FullMEGA.m

@@ -1,14 +1,4 @@
-% assume it always fails
-exit_code = 1;
-
 % MATLAB runs the test
 [result,rt] = UnitTest('MEGA',1,1);
 
-% check the result
-if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0
-    exit_code = 0;
-end
-
-
-% Ensure that we ALWAYS call exit that is always a success so that CI doesn't stop
-exit
+assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)

ci/FullPRESS.m

@@ -1,13 +1,4 @@
-% assume it always fails
-exit_code = 1;
-
 % MATLAB runs the test
 [result,rt] = UnitTest('PRESS',1,1);
 
-% check the result
-if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0
-    exit_code = 0;
-end
-
-% Ensure that we ALWAYS call exit that is always a success so that CI doesn't stop
-exit
+assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)

ci/SinglePRESS.m

@@ -1,14 +1,4 @@
-% assume it always fails
-exit_code = 1;
 
-% MATLAB runs the test
-[result,rt] = UnitTest('SinglePRESS',0,0);
+    [result,rt] = UnitTest('SinglePRESS',0,0);
 
-% check the result
-if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0
-    exit_code = 0;
-end
-
-
-% Ensure that we ALWAYS call exit that is always a success so that CI doesn't stop
-exit
+    assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0)

ci/SinglePRESSdownstream.m

@@ -1,13 +1,5 @@
-% assume it always fails
-exit_code = 1;
 
-% MATLAB runs the test
-[result,rt] = UnitTest('SinglePRESS',2,1);
+    % MATLAB runs the test
+    [result,rt] = UnitTest('SinglePRESS',2,1);
 
-% check the result
-if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0
-    exit_code = 0;
-end
-
-% Ensure that we ALWAYS call exit that is always a success so that CI doesn't stop
-exit
+    assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)

ci/azure-pipelines-develop-pull.yml

@@ -4,22 +4,27 @@
 # If the first stage is successful a Full PRESS job is triggered
 
 trigger:
-- develop
+  branches:
+    include:
+      - develop
+    exclude:
+      - master
+
 
 pool: 'Default'
 
 stages:
-- stage: PRESS
+- stage: Stage_1
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r " SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESS; quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
-- stage: PRESSdownstream
-  dependsOn: PRESS
+- stage: Stage_2
+  dependsOn: Stage_1
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r " SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'

job/OspreyJob.m

@@ -45,7 +45,6 @@
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
 
-
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

plot/osp_plotProcess.m

@@ -45,7 +45,7 @@
 if nargin<6
     switch which_spec
         case {'A', 'B', 'C', 'D', 'diff1', 'diff2','diff3', 'sum','mm'}
-            ppmmax = 8;
+            ppmmax = 4.2;
         case {'ref', 'w'}
             ppmmax = 2*4.68;
         otherwise