From f22e0136817b055ffd98b95d40cf4f8af7efed81 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 15:33:14 -0400
Subject: [PATCH 01/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines

---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 7db15ce8..b081bbfc 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -3,8 +3,8 @@
 # Starts with a quick Single Subject PRESS test
 # If the first stage is successful a Full PRESS job is triggered
 
-trigger:
-- develop
+trigger: [ develop ]
+pr: [ develop ]
 
 pool: 'Default'
 

From c2ae757c8607c128bd5f587e024560a373e1caff Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 15:44:56 -0400
Subject: [PATCH 02/27] Delete azure-pipelines-master-pull.yml

---
 ci/azure-pipelines-master-pull.yml | 24 ------------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 ci/azure-pipelines-master-pull.yml

diff --git a/ci/azure-pipelines-master-pull.yml b/ci/azure-pipelines-master-pull.yml
deleted file mode 100644
index b2af7500..00000000
--- a/ci/azure-pipelines-master-pull.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-# Pull request CI pipeline for Osprey
-# Triggers for each pull request into the master branch
-# Starts with a quick Full PRESS job
-# If the first stage is successful a Full MEGA job is triggered
-
-trigger:
-- master
-
-pool: 'Default'
-
-stages:
-- stage: FullPRESS
-  jobs:
-  - job: FullPRESS
-    steps:
-    - script: matlab -nodisplay -wait -nosplash -r " FullPRESS; quit"
-      displayName: 'Full PRESS with Segmentation & GUI'
-
-- stage: FullMEGA
-  jobs:
-  - job: FullMEGA
-    steps:
-    - script: matlab -nodisplay -wait -nosplash -r " FullMEGA; quit"
-      displayName: 'Full MEGA add Segmentation & GUI'
\ No newline at end of file

From 7578cf24fc833e0047208ae3cd732fa68f54c22c Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 16:31:48 -0400
Subject: [PATCH 03/27] Continuous Integration #11

Test whether the develop branch triggers a pull request and test
---
 plot/osp_plotProcess.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plot/osp_plotProcess.m b/plot/osp_plotProcess.m
index 30c53308..aa6e8911 100755
--- a/plot/osp_plotProcess.m
+++ b/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 = 10;
         case {'ref', 'w'}
             ppmmax = 2*4.68;
         otherwise

From 8a3b1e326546f8a7d49baa7ce88c9c21ebfaff54 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 16:55:16 -0400
Subject: [PATCH 04/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines

---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index b081bbfc..8181f62c 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -13,7 +13,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r " SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath('C:\CI-agent\_work\1\s'); SinglePRESS; quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: PRESSdownstream
@@ -21,5 +21,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r " SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath('C:\CI-agent\_work\1\s'); SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From 4f3a6b48a6654d2ed687b9180b3b7ece82d77d50 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 16:59:39 -0400
Subject: [PATCH 05/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines

---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 8181f62c..83bb8b0b 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -13,7 +13,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath('C:\CI-agent\_work\1\s'); SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESS; quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: PRESSdownstream
@@ -21,5 +21,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath('C:\CI-agent\_work\1\s'); SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From 06dc9dfbef60cddf1854d257e242a5aee836014b Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 17:10:51 -0400
Subject: [PATCH 06/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines

---
 ci/azure-pipelines-develop-pull.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 83bb8b0b..138b1ddc 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -9,15 +9,15 @@ pr: [ develop ]
 pool: 'Default'
 
 stages:
-- stage: PRESS
+- stage: Stage_1
   jobs:
   - job: PRESS
     steps:
     - script: matlab -nodisplay -wait -nosplash -r "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:

From b6e7116b15610ab74452c97e6830fb6abd91333b Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 17:16:37 -0400
Subject: [PATCH 07/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

---
 ci/azure-pipelines-develop-pull.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 138b1ddc..05520d14 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -3,8 +3,13 @@
 # Starts with a quick Single Subject PRESS test
 # If the first stage is successful a Full PRESS job is triggered
 
-trigger: [ develop ]
-pr: [ develop ]
+trigger:
+  branches:
+    include:
+      - develop
+    exclude:
+      - master
+
 
 pool: 'Default'
 

From b88f42fc09503b09da4b6cf5c409e0c829c39c70 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Tue, 20 Jul 2021 17:19:17 -0400
Subject: [PATCH 08/27] Continuous Integration #12

Try again. Updated the branch checkout on the server
---
 plot/osp_plotProcess.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plot/osp_plotProcess.m b/plot/osp_plotProcess.m
index aa6e8911..80be6bd8 100755
--- a/plot/osp_plotProcess.m
+++ b/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 = 10;
+            ppmmax = 4.2;
         case {'ref', 'w'}
             ppmmax = 2*4.68;
         otherwise

From d267fe50d8ab04ecdd79bf396e77d40efe961199 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 09:47:14 -0400
Subject: [PATCH 09/27] Continuous Integration #13

Added a deliberate bug to test the CI
---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index 19713940..f00219fb 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -45,7 +45,7 @@
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
 
-
+HorribleBug
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From d4b23a633fad723b1d1b0a3bbefc72cdd48b177b Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 09:52:11 -0400
Subject: [PATCH 10/27] Revert "Continuous Integration #13"

---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index f00219fb..19713940 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -45,7 +45,7 @@
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
 
-HorribleBug
+
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From 21e327923d28de7c600ed9d677ede7d31e3d3497 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 10:11:16 -0400
Subject: [PATCH 11/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]]

---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 05520d14..41128722 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESS; assert(exit_code > 0); quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; assert(exit_code > 0); quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From d4893e3ce2684e4f1d51bd640c69547ab1e08050 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 10:13:25 -0400
Subject: [PATCH 12/27] Continuous Integration #14 [ci skip]

- Add assert statement to verify successful test
---
 ci/FullMEGA.m              | 6 +-----
 ci/FullPRESS.m             | 5 +----
 ci/SinglePRESS.m           | 4 ----
 ci/SinglePRESSdownstream.m | 3 ---
 job/OspreyJob.m            | 1 -
 5 files changed, 2 insertions(+), 17 deletions(-)

diff --git a/ci/FullMEGA.m b/ci/FullMEGA.m
index b35b22f8..98e8660d 100644
--- a/ci/FullMEGA.m
+++ b/ci/FullMEGA.m
@@ -7,8 +7,4 @@
 % 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
\ No newline at end of file
+end
\ No newline at end of file
diff --git a/ci/FullPRESS.m b/ci/FullPRESS.m
index 9a14f514..34bbd954 100644
--- a/ci/FullPRESS.m
+++ b/ci/FullPRESS.m
@@ -7,7 +7,4 @@
 % 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
\ No newline at end of file
+end
\ No newline at end of file
diff --git a/ci/SinglePRESS.m b/ci/SinglePRESS.m
index 7a916574..ed0bc159 100644
--- a/ci/SinglePRESS.m
+++ b/ci/SinglePRESS.m
@@ -8,7 +8,3 @@
 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
\ No newline at end of file
diff --git a/ci/SinglePRESSdownstream.m b/ci/SinglePRESSdownstream.m
index 20ef3c53..d8033fa3 100644
--- a/ci/SinglePRESSdownstream.m
+++ b/ci/SinglePRESSdownstream.m
@@ -8,6 +8,3 @@
 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
\ No newline at end of file
diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index f00219fb..d6323f94 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -45,7 +45,6 @@
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
 
-HorribleBug
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From b3c49606d5515d33d5b91fb9785336cb50de2544 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 10:28:15 -0400
Subject: [PATCH 13/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 41128722..d2fea0b8 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESS; assert(exit_code > 0); quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; assert(exit_code > 0); quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; assert(exit_code > 0); quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; assert(exit_code > 0); quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From 3fb861335c6ca8d53bdd6638fecccce3d7d18675 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 10:29:41 -0400
Subject: [PATCH 14/27] Continuous Integration #15 [ci skip]

- add assertion code to function [ci skip]
---
 ci/SinglePRESS.m           | 18 ++++++++++--------
 ci/SinglePRESSdownstream.m | 18 ++++++++++--------
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/ci/SinglePRESS.m b/ci/SinglePRESS.m
index ed0bc159..0e7fd09c 100644
--- a/ci/SinglePRESS.m
+++ b/ci/SinglePRESS.m
@@ -1,10 +1,12 @@
-% assume it always fails
-exit_code = 1;
+function [exit_code] = SinglePRESS
+    % assume it always fails
+    exit_code = 1;
 
-% MATLAB runs the test
-[result,rt] = UnitTest('SinglePRESS',0,0);
+    % MATLAB runs the test
+    [result,rt] = UnitTest('SinglePRESS',0,0);
 
-% check the result
-if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0
-    exit_code = 0;
-end
+    % check the result
+    if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0
+        exit_code = 0;
+    end
+end
\ No newline at end of file
diff --git a/ci/SinglePRESSdownstream.m b/ci/SinglePRESSdownstream.m
index d8033fa3..87087b9e 100644
--- a/ci/SinglePRESSdownstream.m
+++ b/ci/SinglePRESSdownstream.m
@@ -1,10 +1,12 @@
-% assume it always fails
-exit_code = 1;
+function [exit_code] = SinglePRESSdownstream
+    % 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
+    % 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
+end
\ No newline at end of file

From edfab605b8049907e653285ecb634039be000ddc Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:06:54 -0400
Subject: [PATCH 15/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

[ci skip]
---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index d2fea0b8..8b452b5c 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; assert(exit_code > 0); quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; assert(exit_code > 0); quit"
+    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From dce75aeaa23a23bd06456a1acce8218665e01ceb Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:09:13 -0400
Subject: [PATCH 16/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

[ci skip]
---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 8b452b5c..d20cba3f 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -r "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From c0b970f4f689f14b6ff29f5aa9c0b3d547243f91 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:25:30 -0400
Subject: [PATCH 17/27] CI #16

Added a new bug for testing
---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index d6323f94..af3558d4 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -44,7 +44,7 @@
 
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
-
+HugeBug
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From 2a2a5eaefa3806a8184df1a4430cda922bac98b8 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:37:13 -0400
Subject: [PATCH 18/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

[ci skip]
---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index d20cba3f..4a32b524 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; assert(exit_code > 1); quit"
       displayName: 'Single Subject PRESS without Segmentation & GUI'
 
 - stage: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; assert(exit_code > 1); quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From 98de0d0267a3e51108a82081beb5bcf76a262fdc Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:43:22 -0400
Subject: [PATCH 19/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [skip ci]

[skip ci]
---
 ci/azure-pipelines-develop-pull.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 4a32b524..8c700261 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -3,7 +3,7 @@
 # Starts with a quick Single Subject PRESS test
 # If the first stage is successful a Full PRESS job is triggered
 
-trigger:
+pr:
   branches:
     include:
       - develop

From 13bdc7dfe7b76d540286b12bf6bf7aebefd33a2c Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:44:07 -0400
Subject: [PATCH 20/27] CI #17

Remove the deliberate bug
---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index af3558d4..d6323f94 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -44,7 +44,7 @@
 
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
-HugeBug
+
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From 76c353b1180229c0b752c14f2581ceb97128fffe Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 11:58:19 -0400
Subject: [PATCH 21/27] CI #19

- Move assertion into the test
---
 ci/SinglePRESS.m           | 10 +---------
 ci/SinglePRESSdownstream.m |  9 +--------
 extdata/ABfit.BASIS        |  1 +
 3 files changed, 3 insertions(+), 17 deletions(-)
 create mode 100644 extdata/ABfit.BASIS

diff --git a/ci/SinglePRESS.m b/ci/SinglePRESS.m
index 0e7fd09c..a62092c4 100644
--- a/ci/SinglePRESS.m
+++ b/ci/SinglePRESS.m
@@ -1,12 +1,4 @@
-function [exit_code] = SinglePRESS
-    % assume it always fails
-    exit_code = 1;
 
-    % MATLAB runs the test
     [result,rt] = UnitTest('SinglePRESS',0,0);
 
-    % check the result
-    if sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0
-        exit_code = 0;
-    end
-end
\ No newline at end of file
+    assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0)
diff --git a/ci/SinglePRESSdownstream.m b/ci/SinglePRESSdownstream.m
index 87087b9e..12007309 100644
--- a/ci/SinglePRESSdownstream.m
+++ b/ci/SinglePRESSdownstream.m
@@ -1,12 +1,5 @@
-function [exit_code] = SinglePRESSdownstream
-    % assume it always fails
-    exit_code = 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
-end
\ No newline at end of file
+    assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)
\ No newline at end of file
diff --git a/extdata/ABfit.BASIS b/extdata/ABfit.BASIS
new file mode 100644
index 00000000..9c8296ff
--- /dev/null
+++ b/extdata/ABfit.BASIS
@@ -0,0 +1 @@
+ BADELT =  5e-04,

From 8cbf30dca16d1db197d3b15eee5a2737a2387396 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 12:00:03 -0400
Subject: [PATCH 22/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [ci skip]

[ci skip]
---
 ci/azure-pipelines-develop-pull.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 8c700261..406b7a5a 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -18,7 +18,7 @@ stages:
   jobs:
   - job: PRESS
     steps:
-    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESS; assert(exit_code > 1); 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: Stage_2
@@ -26,5 +26,5 @@ stages:
   jobs:
   - job: PRESSdownstream
     steps:
-    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); exit_code = SinglePRESSdownstream; assert(exit_code > 1); quit"
+    - script: matlab -nodisplay -wait -nosplash -batch "addpath(genpath('C:\CI-agent\_work\1\s')); SinglePRESSdownstream; quit"
       displayName: 'Single Subject PRESS add Segmentation & GUI'
\ No newline at end of file

From 96073422a820876d05b39688e97f0eb26362cd3a Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 13:55:55 -0400
Subject: [PATCH 23/27] Update azure-pipelines-develop-pull.yml for Azure
 Pipelines [skip ci]

[skip ci]
---
 ci/azure-pipelines-develop-pull.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci/azure-pipelines-develop-pull.yml b/ci/azure-pipelines-develop-pull.yml
index 406b7a5a..91a9d6c6 100644
--- a/ci/azure-pipelines-develop-pull.yml
+++ b/ci/azure-pipelines-develop-pull.yml
@@ -3,7 +3,7 @@
 # Starts with a quick Single Subject PRESS test
 # If the first stage is successful a Full PRESS job is triggered
 
-pr:
+trigger:
   branches:
     include:
       - develop

From 3a5d74c82ff35352d752b3275bccf6155afa1609 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 13:56:57 -0400
Subject: [PATCH 24/27] CI #20

Test new setup
---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index d6323f94..520fa386 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -44,7 +44,7 @@
 
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
-
+HorribleBug
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From 2b8e4da4d0e3a626f5e5ac5212135b96c419b8e9 Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 13:58:55 -0400
Subject: [PATCH 25/27] Revert "CI #20"

---
 job/OspreyJob.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
index 520fa386..d6323f94 100755
--- a/job/OspreyJob.m
+++ b/job/OspreyJob.m
@@ -44,7 +44,7 @@
 
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
-HorribleBug
+
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
 switch ext

From f640ff698ad5dfb85772bb5fd06c831e922b5cec Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 14:07:50 -0400
Subject: [PATCH 26/27] CI #21 [ci skip]

- update the master-pull jobs to have the same structure as the develop-pull jobs

[ci skip]
---
 ci/FullMEGA.m  | 8 +-------
 ci/FullPRESS.m | 8 +-------
 2 files changed, 2 insertions(+), 14 deletions(-)

diff --git a/ci/FullMEGA.m b/ci/FullMEGA.m
index 98e8660d..45fdab8c 100644
--- a/ci/FullMEGA.m
+++ b/ci/FullMEGA.m
@@ -1,10 +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
\ No newline at end of file
+assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)
diff --git a/ci/FullPRESS.m b/ci/FullPRESS.m
index 34bbd954..350096d5 100644
--- a/ci/FullPRESS.m
+++ b/ci/FullPRESS.m
@@ -1,10 +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
\ No newline at end of file
+assert(sum(rt{1}.Failed) == 0 && sum(rt{1}.Incomplete) == 0 &&sum(rt{2}.Failed) == 0 && sum(rt{2}.Incomplete) == 0)

From f08fb58f0cd6e3253888db66d1e886888bdaf40d Mon Sep 17 00:00:00 2001
From: Helge <47348963+HJZollner@users.noreply.github.com>
Date: Wed, 21 Jul 2021 14:10:38 -0400
Subject: [PATCH 27/27] Remove unwanted directory [skip ci]

[skip ci]
---
 extdata/ABfit.BASIS | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 extdata/ABfit.BASIS

diff --git a/extdata/ABfit.BASIS b/extdata/ABfit.BASIS
deleted file mode 100644
index 9c8296ff..00000000
--- a/extdata/ABfit.BASIS
+++ /dev/null
@@ -1 +0,0 @@
- BADELT =  5e-04,