From f9161f23425d592d7d5e39fc59c5a0bced9e9898 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 28 May 2025 08:53:43 +0200
Subject: [PATCH 01/18] Matlab installation + adding Amita's code to wrapper

Unit test will fail. Mainly checking whether matlab is called
---
 .github/workflows/unit_test.yml               |  6 ++
 .../MRI-QAMPER_IVIM/IVIM_standard_bcin.m      |  1 +
 .../ASD_MemorialSloanKettering_QAMPER_IVIM.py | 97 +++++++++++++++++++
 tests/IVIMmodels/unit_tests/algorithms.json   |  1 +
 4 files changed, 105 insertions(+)
 create mode 100644 src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index c5475ed2..946a340b 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -30,6 +30,12 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up MATLAB
+        uses: matlab-actions/setup-matlab@v2
+      - name: Run build
+        uses: matlab-actions/run-build@v2
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
diff --git a/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m b/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
index 09828228..220980fc 100755
--- a/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
+++ b/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
@@ -7,6 +7,7 @@
 end
 
 numVoxels = size(dwi_arr,2);
+print(numVoxels)
 numBvals = length(bval_arr);
 
 f_lb = 0;
diff --git a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
new file mode 100644
index 00000000..a5a92d49
--- /dev/null
+++ b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
@@ -0,0 +1,97 @@
+from src.wrappers.OsipiBase import OsipiBase
+import numpy as np
+import matlab.engine
+
+class ASD_MemorialSloanKettering_QAMPER_IVIM(OsipiBase):
+    """
+    Bi-exponential fitting algorithm by Oliver Gurney-Champion, Amsterdam UMC
+    """
+
+    # I'm thinking that we define default attributes for each submission like this
+    # And in __init__, we can call the OsipiBase control functions to check whether
+    # the user inputs fulfil the requirements
+
+    # Some basic stuff that identifies the algorithm
+    id_author = "LoCastro, Dr. Ramesh Paudyal, Dr. Amita Shukla-Dave"
+    id_algorithm_type = "Bi-exponential fit"
+    id_return_parameters = "f, D*, D, S0"
+    id_units = "seconds per milli metre squared or milliseconds per micro metre squared"
+
+    # Algorithm requirements
+    required_bvalues = 4
+    required_thresholds = [0,
+                           0]  # Interval from "at least" to "at most", in case submissions allow a custom number of thresholds
+    required_bounds = False
+    required_bounds_optional = True  # Bounds may not be required but are optional
+    required_initial_guess = False
+    required_initial_guess_optional = True
+    accepted_dimensions = 1  # Not sure how to define this for the number of accepted dimensions. Perhaps like the thresholds, at least and at most?
+
+
+    # Supported inputs in the standardized class
+    supported_bounds = True
+    supported_initial_guess = True
+    supported_thresholds = False
+
+    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None):
+        """
+            Everything this algorithm requires should be implemented here.
+            Number of segmentation thresholds, bounds, etc.
+
+            Our OsipiBase object could contain functions that compare the inputs with
+            the requirements.
+        """
+        #super(OGC_AmsterdamUMC_biexp, self).__init__(bvalues, bounds, initial_guess, fitS0)
+        super(ASD_MemorialSloanKettering_QAMPER_IVIM, self).__init__(bvalues=bvalues, bounds=bounds, initial_guess=initial_guess)
+        self.initialize(bounds, initial_guess)
+
+    def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
+        eng = matlab.engine.start_matlab()
+        dwi_arr = matlab.double(dwi_arr.tolist())
+        bval_arr = matlab.double(bval_arr.tolist())
+        LB0 = matlab.double(LB0.tolist())
+        UB0 = matlab.double(UB0.tolist())
+        x0in = matlab.double(x0in.tolist())
+        f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq = eng.IVIM_standard_bcin(
+            dwi_arr, bval_arr, 0.0, LB0, UB0, x0in, False, 0, 0)
+        eng.quit()
+        return D_arr, f_arr, Dx_arr, s0_arr
+
+    def initialize(self, bounds, initial_guess):
+        if bounds is None:
+            print('warning, no bounds were defined, so algorithm-specific default bounds are used')
+            self.bounds=([1e-6, 0, 1e-6, 0],[0.003, 1.0, 5e-2, 5])
+        else:
+            self.bounds=bounds
+        if initial_guess is None:
+            print('warning, no initial guesses were defined, so algorithm-specific default initial guess is used')
+            self.initial_guess = [0.001, 0.001, 0.2, 1]
+        else:
+            self.initial_guess = initial_guess
+            self.use_initial_guess = True
+        self.use_initial_guess = True
+        self.use_bounds = True
+
+    def ivim_fit(self, signals, bvalues, **kwargs):
+        """Perform the IVIM fit
+
+        Args:
+            signals (array-like)
+            bvalues (array-like, optional): b-values for the signals. If None, self.bvalues will be used. Default is None.
+
+        Returns:
+            _type_: _description_
+        """
+
+        bvalues=np.array(bvalues)
+        LB = np.array(self.bounds[0])
+        UB = np.array(self.bounds[1])
+
+        fit_results = self.algorithm(np.array(signals), bvalues, LB, UB, np.array(self.initial_guess))
+
+        results = {}
+        results["D"] = fit_results[0]
+        results["f"] = fit_results[1]
+        results["Dp"] = fit_results[2]
+
+        return results
\ No newline at end of file
diff --git a/tests/IVIMmodels/unit_tests/algorithms.json b/tests/IVIMmodels/unit_tests/algorithms.json
index 51a56500..c6ca198e 100644
--- a/tests/IVIMmodels/unit_tests/algorithms.json
+++ b/tests/IVIMmodels/unit_tests/algorithms.json
@@ -1,5 +1,6 @@
 {
     "algorithms": [
+        "ASD_MemorialSloanKettering_QAMPER_IVIM",
         "ETP_SRI_LinearFitting",
         "IAR_LU_biexp",
         "IAR_LU_modified_mix",

From 3a5095ffec34757fc9da983bc134d653467cf0cb Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 28 May 2025 09:34:03 +0200
Subject: [PATCH 02/18] Handle Matlab engine to remain open

---
 .../ASD_MemorialSloanKettering_QAMPER_IVIM.py | 28 ++++++++++++++++---
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
index a5a92d49..3b98fc74 100644
--- a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
+++ b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
@@ -44,17 +44,17 @@ def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=Non
         #super(OGC_AmsterdamUMC_biexp, self).__init__(bvalues, bounds, initial_guess, fitS0)
         super(ASD_MemorialSloanKettering_QAMPER_IVIM, self).__init__(bvalues=bvalues, bounds=bounds, initial_guess=initial_guess)
         self.initialize(bounds, initial_guess)
+        self.eng=matlab.engine.start_matlab()
+
 
     def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
-        eng = matlab.engine.start_matlab()
         dwi_arr = matlab.double(dwi_arr.tolist())
         bval_arr = matlab.double(bval_arr.tolist())
         LB0 = matlab.double(LB0.tolist())
         UB0 = matlab.double(UB0.tolist())
         x0in = matlab.double(x0in.tolist())
-        f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq = eng.IVIM_standard_bcin(
+        f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq = self.eng.IVIM_standard_bcin(
             dwi_arr, bval_arr, 0.0, LB0, UB0, x0in, False, 0, 0)
-        eng.quit()
         return D_arr, f_arr, Dx_arr, s0_arr
 
     def initialize(self, bounds, initial_guess):
@@ -94,4 +94,24 @@ def ivim_fit(self, signals, bvalues, **kwargs):
         results["f"] = fit_results[1]
         results["Dp"] = fit_results[2]
 
-        return results
\ No newline at end of file
+        return results
+
+
+    def __del__(self):
+        if hasattr(self, "eng") and self.eng:
+            try:
+                self.eng.quit()
+            except Exception as e:
+                print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
+
+
+    def __enter__(self):
+        return self
+
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if hasattr(self, "eng") and self.eng:
+            try:
+                self.eng.quit()
+            except Exception as e:
+                print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")

From 9d407fd6c4076875000c2790ac117e2f66b3a5b0 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Fri, 30 May 2025 11:01:34 +0200
Subject: [PATCH 03/18] Wrapper now runs for ASD Memorial Sloan Kettering. But
 unit tests fail

---
 .../MRI-QAMPER_IVIM/IVIM_standard_bcin.m                 | 1 -
 .../ASD_MemorialSloanKettering_QAMPER_IVIM.py            | 9 +++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m b/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
index 220980fc..09828228 100755
--- a/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
+++ b/src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/IVIM_standard_bcin.m
@@ -7,7 +7,6 @@
 end
 
 numVoxels = size(dwi_arr,2);
-print(numVoxels)
 numBvals = length(bval_arr);
 
 f_lb = 0;
diff --git a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
index 3b98fc74..0c651922 100644
--- a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
+++ b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
@@ -53,9 +53,10 @@ def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
         LB0 = matlab.double(LB0.tolist())
         UB0 = matlab.double(UB0.tolist())
         x0in = matlab.double(x0in.tolist())
-        f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq = self.eng.IVIM_standard_bcin(
-            dwi_arr, bval_arr, 0.0, LB0, UB0, x0in, False, 0, 0)
-        return D_arr, f_arr, Dx_arr, s0_arr
+        results = self.eng.IVIM_standard_bcin(
+            dwi_arr, bval_arr, 0.0, LB0, UB0, x0in, False, 0, 0,nargout=11)
+        (f_arr, D_arr, Dx_arr, s0_arr, fitted_dwi_arr, RSS, rms_val, chi, AIC, BIC, R_sq) = results
+        return D_arr/1000, f_arr, Dx_arr/1000, s0_arr
 
     def initialize(self, bounds, initial_guess):
         if bounds is None:
@@ -87,7 +88,7 @@ def ivim_fit(self, signals, bvalues, **kwargs):
         LB = np.array(self.bounds[0])
         UB = np.array(self.bounds[1])
 
-        fit_results = self.algorithm(np.array(signals), bvalues, LB, UB, np.array(self.initial_guess))
+        fit_results = self.algorithm(np.array(signals)[:,np.newaxis], bvalues, LB, UB, np.array(self.initial_guess))
 
         results = {}
         results["D"] = fit_results[0]

From d471105a6ac8869ad79b4c7bb8715fa8f8376396 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Mon, 2 Jun 2025 14:34:42 +0200
Subject: [PATCH 04/18] fixed bugs

- fixed initial guesses and bounds such that it passes tests
- changed matlab huild for github, hopefully overcoming errors.
---
 .github/workflows/unit_test.yml               |  7 ++-
 .gitignore                                    |  2 +-
 .../ASD_MemorialSloanKettering_QAMPER_IVIM.py | 43 +++++++++++--------
 src/standardized/OGC_AmsterdamUMC_biexp.py    |  2 +-
 tests/IVIMmodels/unit_tests/algorithms.json   |  4 ++
 tests/IVIMmodels/unit_tests/test_ivim_fit.py  | 13 ++++--
 6 files changed, 46 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index 946a340b..a9dce575 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -34,8 +34,11 @@ jobs:
         uses: actions/checkout@v4
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
-      - name: Run build
-        uses: matlab-actions/run-build@v2
+        with:
+          release: R2025a 
+      - name: Install MATLAB Engine for Python
+        run: |
+          python -m pip install matlabengine==25.1.2
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
diff --git a/.gitignore b/.gitignore
index faf3523d..a4125b0c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -19,7 +19,7 @@ md5sums.txt
 *.asv
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/test_data
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/output_files
-
+tests/IVIMmodels/unit_tests/*.log
 
 
 # Unit test / coverage reports
diff --git a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
index 0c651922..887dbbd2 100644
--- a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
+++ b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
@@ -33,7 +33,7 @@ class ASD_MemorialSloanKettering_QAMPER_IVIM(OsipiBase):
     supported_initial_guess = True
     supported_thresholds = False
 
-    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None):
+    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None,eng=None):
         """
             Everything this algorithm requires should be implemented here.
             Number of segmentation thresholds, bounds, etc.
@@ -44,7 +44,14 @@ def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=Non
         #super(OGC_AmsterdamUMC_biexp, self).__init__(bvalues, bounds, initial_guess, fitS0)
         super(ASD_MemorialSloanKettering_QAMPER_IVIM, self).__init__(bvalues=bvalues, bounds=bounds, initial_guess=initial_guess)
         self.initialize(bounds, initial_guess)
-        self.eng=matlab.engine.start_matlab()
+        if eng is None:
+            print('initiating matlab; this may take some time. For repeated testing one could use the optional input eng as an already initiated matlab engine')
+            self.eng=matlab.engine.start_matlab()
+            self.keep_alive=False
+        else:
+            self.eng = eng
+            self.keep_alive=True
+
 
 
     def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
@@ -61,12 +68,12 @@ def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
     def initialize(self, bounds, initial_guess):
         if bounds is None:
             print('warning, no bounds were defined, so algorithm-specific default bounds are used')
-            self.bounds=([1e-6, 0, 1e-6, 0],[0.003, 1.0, 5e-2, 5])
+            self.bounds=([1e-6, 0, 0.004, 0],[0.003, 1.0, 0.2, 5])
         else:
             self.bounds=bounds
         if initial_guess is None:
             print('warning, no initial guesses were defined, so algorithm-specific default initial guess is used')
-            self.initial_guess = [0.001, 0.001, 0.2, 1]
+            self.initial_guess = [0.001, 0.2, 0.01, 1]
         else:
             self.initial_guess = initial_guess
             self.use_initial_guess = True
@@ -85,10 +92,10 @@ def ivim_fit(self, signals, bvalues, **kwargs):
         """
 
         bvalues=np.array(bvalues)
-        LB = np.array(self.bounds[0])
-        UB = np.array(self.bounds[1])
+        LB = np.array(self.bounds[0])[[1,0,2,3]]
+        UB = np.array(self.bounds[1])[[1,0,2,3]]
 
-        fit_results = self.algorithm(np.array(signals)[:,np.newaxis], bvalues, LB, UB, np.array(self.initial_guess))
+        fit_results = self.algorithm(np.array(signals)[:,np.newaxis], bvalues, LB, UB, np.array(self.initial_guess)[[1,0,2,3]])
 
         results = {}
         results["D"] = fit_results[0]
@@ -99,11 +106,12 @@ def ivim_fit(self, signals, bvalues, **kwargs):
 
 
     def __del__(self):
-        if hasattr(self, "eng") and self.eng:
-            try:
-                self.eng.quit()
-            except Exception as e:
-                print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
+        if not self.keep_alive:
+            if hasattr(self, "eng") and self.eng:
+                try:
+                    self.eng.quit()
+                except Exception as e:
+                    print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
 
 
     def __enter__(self):
@@ -111,8 +119,9 @@ def __enter__(self):
 
 
     def __exit__(self, exc_type, exc_val, exc_tb):
-        if hasattr(self, "eng") and self.eng:
-            try:
-                self.eng.quit()
-            except Exception as e:
-                print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
+        if not self.keep_alive:
+            if hasattr(self, "eng") and self.eng:
+                try:
+                    self.eng.quit()
+                except Exception as e:
+                    print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
diff --git a/src/standardized/OGC_AmsterdamUMC_biexp.py b/src/standardized/OGC_AmsterdamUMC_biexp.py
index 49a16b27..5afd0cb8 100644
--- a/src/standardized/OGC_AmsterdamUMC_biexp.py
+++ b/src/standardized/OGC_AmsterdamUMC_biexp.py
@@ -55,7 +55,7 @@ def initialize(self, bounds, initial_guess, fitS0):
             self.bounds=bounds
         if initial_guess is None:
             print('warning, no initial guesses were defined, so default bounds are used of  [0.001, 0.001, 0.01, 1]')
-            self.initial_guess = [0.001, 0.001, 0.01, 1]
+            self.initial_guess = [0.001, 0.1, 0.01, 1]
         else:
             self.initial_guess = initial_guess
             self.use_initial_guess = True
diff --git a/tests/IVIMmodels/unit_tests/algorithms.json b/tests/IVIMmodels/unit_tests/algorithms.json
index c6ca198e..3e289721 100644
--- a/tests/IVIMmodels/unit_tests/algorithms.json
+++ b/tests/IVIMmodels/unit_tests/algorithms.json
@@ -15,6 +15,10 @@
         "PvH_KB_NKI_IVIMfit",
         "OJ_GU_seg"
     ],
+    "ASD_MemorialSloanKettering_QAMPER_IVIM": {
+        "requieres_matlab": true,
+        "fail_first_time": true
+    },
     "IAR_LU_biexp": {
         "fail_first_time": true
     },
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index fb58d13b..5711d879 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -6,6 +6,9 @@
 import time
 from src.wrappers.OsipiBase import OsipiBase
 #run using python -m pytest from the root folder
+import matlab.engine
+
+eng=matlab.engine.start_matlab()
 
 def signal_helper(signal):
     signal = np.asarray(signal)
@@ -44,9 +47,9 @@ def data_ivim_fit_saved():
     algorithms = algorithm_information["algorithms"]
     bvals = all_data.pop('config')
     bvals = bvals['bvalues']
-    first=True
-    for name, data in all_data.items():
-        for algorithm in algorithms:
+    for algorithm in algorithms:
+        first = True
+        for name, data in all_data.items():
             algorithm_dict = algorithm_information.get(algorithm, {})
             xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
                 "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
@@ -56,7 +59,9 @@ def data_ivim_fit_saved():
             if first == True:
                 if algorithm_dict.get("fail_first_time", {}) == True:
                     skiptime = True
-                    first = False
+                    first = False # this will only work for 1 algorithm... If two algorithms use fail_first_time, the second will not see it is the first time.
+            if algorithm_dict.get("requieres_matlab", {}) == True:
+                kwargs={**kwargs,'eng': eng}
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime
 
 @pytest.mark.parametrize("name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime", data_ivim_fit_saved())

From 648a7a6ab93dd863b8c51618ad986aafc57dd3b2 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Mon, 2 Jun 2025 15:07:31 +0200
Subject: [PATCH 05/18] fix bug for linux and mac

---
 .github/workflows/unit_test.yml              | 10 ++++++++++
 tests/IVIMmodels/unit_tests/test_ivim_fit.py | 16 +++++++++++-----
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index a9dce575..fef5dab1 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -32,6 +32,15 @@ jobs:
           pip install -r requirements.txt
       - name: Check out repository
         uses: actions/checkout@v4
+      - name: Set environment variables for MATLAB Engine
+        run: |
+          if [[ "${{ runner.os }}" == "macOS" ]]; then
+            echo "DYLD_LIBRARY_PATH=/Applications/MATLAB_R2025a.app/bin/maci64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+          elif [[ "${{ runner.os }}" == "Linux" ]]; then
+            echo "LD_LIBRARY_PATH=/usr/local/MATLAB/R2025a/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          elif [[ "${{ runner.os }}" == "Windows" ]]; then
+            echo "C:\Program Files\MATLAB\R2025a\bin\win64" >> $GITHUB_PATH
+          fi
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:
@@ -39,6 +48,7 @@ jobs:
       - name: Install MATLAB Engine for Python
         run: |
           python -m pip install matlabengine==25.1.2
+
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index 5711d879..f00e68af 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -108,11 +108,15 @@ def algorithms():
         algorithm_information = json.load(f)
     algorithms = algorithm_information["algorithms"]
     for algorithm in algorithms:
-        yield algorithm
-
-@pytest.mark.parametrize("algorithm", algorithms())
-def test_default_bounds_and_initial_guesses(algorithm):
-    fit = OsipiBase(algorithm=algorithm)
+        algorithm_dict = algorithm_information.get(algorithm, {})
+        args={}
+        if algorithm_dict.get("requieres_matlab", {}) == True:
+            args['eng'] = eng
+        yield algorithm, args
+
+@pytest.mark.parametrize("algorithm, args", algorithms())
+def test_default_bounds_and_initial_guesses(algorithm, args):
+    fit = OsipiBase(algorithm=algorithm,**args)
     #assert fit.bounds is not None, f"For {algorithm}, there is no default fit boundary"
     #assert fit.initial_guess is not None, f"For {algorithm}, there is no default fit initial guess"
     if fit.use_bounds:
@@ -154,6 +158,8 @@ def bound_input():
                 "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
             kwargs = algorithm_dict.get("options", {})
             tolerances = algorithm_dict.get("tolerances", {})
+            if algorithm_dict.get("requieres_matlab", {}) == True:
+                kwargs={**kwargs,'eng': eng}
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances
 
 

From 8ffbeb4a14ffe58fc13d6e15a0c1fe1a4f65498e Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Mon, 2 Jun 2025 15:23:52 +0200
Subject: [PATCH 06/18] update workflow...

---
 .github/workflows/unit_test.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index fef5dab1..06aa4c90 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -35,11 +35,9 @@ jobs:
       - name: Set environment variables for MATLAB Engine
         run: |
           if [[ "${{ runner.os }}" == "macOS" ]]; then
-            echo "DYLD_LIBRARY_PATH=/Applications/MATLAB_R2025a.app/bin/maci64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+            echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
           elif [[ "${{ runner.os }}" == "Linux" ]]; then
-            echo "LD_LIBRARY_PATH=/usr/local/MATLAB/R2025a/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-          elif [[ "${{ runner.os }}" == "Windows" ]]; then
-            echo "C:\Program Files\MATLAB\R2025a\bin\win64" >> $GITHUB_PATH
+            echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
           fi
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2

From 1159bc2cfaca8aa5a81ffc0029b91070a3de2eec Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Mon, 2 Jun 2025 17:11:01 +0200
Subject: [PATCH 07/18] Update unit_test.yml

---
 .github/workflows/unit_test.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index 06aa4c90..3517c2ba 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -33,6 +33,7 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
       - name: Set environment variables for MATLAB Engine
+	if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
         run: |
           if [[ "${{ runner.os }}" == "macOS" ]]; then
             echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV

From c2e9bd2108a727bbb46f7de2de35d8a82a228184 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Tue, 3 Jun 2025 12:01:28 +0200
Subject: [PATCH 08/18] update unit test

---
 .github/workflows/unit_test.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index 3517c2ba..bb407502 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -30,16 +30,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-      - name: Check out repository
-        uses: actions/checkout@v4
       - name: Set environment variables for MATLAB Engine
-	if: ${{ runner.os == 'Linux' || runner.os == 'macOS' }}
+	if: ${{ runner.os == 'macOS'}}
+        run: |
+          echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+	if: ${{ runner.os == 'Linux'}}
         run: |
-          if [[ "${{ runner.os }}" == "macOS" ]]; then
-            echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
-          elif [[ "${{ runner.os }}" == "Linux" ]]; then
             echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-          fi
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:

From aa3c5b09b9b217aee5df3b5acb1a544a941e009b Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Tue, 3 Jun 2025 12:09:09 +0200
Subject: [PATCH 09/18] fix?

---
 .github/workflows/unit_test.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index bb407502..c2766a09 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -1,7 +1,5 @@
 name: Unit tests
-
 on: [push, pull_request]
-
 jobs:
   build:
 
@@ -36,7 +34,7 @@ jobs:
           echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
 	if: ${{ runner.os == 'Linux'}}
         run: |
-            echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:
@@ -44,7 +42,6 @@ jobs:
       - name: Install MATLAB Engine for Python
         run: |
           python -m pip install matlabengine==25.1.2
-
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov

From 4e2fd54f4bb2147a1fc01eeda25817497eaa690e Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Tue, 3 Jun 2025 12:16:02 +0200
Subject: [PATCH 10/18] Update unit_test.yml

---
 .github/workflows/unit_test.yml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index c2766a09..ca2f15b4 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -28,13 +28,12 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-      - name: Set environment variables for MATLAB Engine
-	if: ${{ runner.os == 'macOS'}}
-        run: |
-          echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
-	if: ${{ runner.os == 'Linux'}}
-        run: |
-          echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+       - name: Set env var for MATLAB on macOS
+         if: runner.os == 'macOS'
+         run: echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+       - name: Set env var for MATLAB on Linux
+         if: runner.os == 'Linux'
+         run: echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:

From 799920b9e39bb9db3a91fe3bed4eaee21ef0ec0c Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Tue, 3 Jun 2025 12:22:32 +0200
Subject: [PATCH 11/18] Update unit_test.yml

---
 .github/workflows/unit_test.yml | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index ca2f15b4..03a2998c 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -1,8 +1,8 @@
 name: Unit tests
 on: [push, pull_request]
+
 jobs:
   build:
-
     runs-on: ${{ matrix.os }}
     continue-on-error: false
     strategy:
@@ -13,34 +13,40 @@ jobs:
         exclude:
           - os: windows-latest
             python-version: "3.13"
-        # Windows chokes on py3.13: https://github.com/numpy/numpy/issues/27894
+
     steps:
       - uses: actions/checkout@v4
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-      # You can test your matrix by printing the current Python version
+
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-       - name: Set env var for MATLAB on macOS
-         if: runner.os == 'macOS'
-         run: echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
-       - name: Set env var for MATLAB on Linux
-         if: runner.os == 'Linux'
-         run: echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Set env var for MATLAB on macOS
+        if: runner.os == 'macOS'
+        run: echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Set env var for MATLAB on Linux
+        if: runner.os == 'Linux'
+        run: echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
       - name: Set up MATLAB
         uses: matlab-actions/setup-matlab@v2
         with:
           release: R2025a 
+
       - name: Install MATLAB Engine for Python
-        run: |
-          python -m pip install matlabengine==25.1.2
+        run: python -m pip install matlabengine==25.1.2
+
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov

From e75897428fca3415fd645017f768accd457ee1f0 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 4 Jun 2025 14:36:56 +0200
Subject: [PATCH 12/18] add flag for running matlab tests

---
 tests/IVIMmodels/unit_tests/algorithms.json  |  1 -
 tests/IVIMmodels/unit_tests/test_ivim_fit.py | 36 ++++++++++++++++----
 2 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/tests/IVIMmodels/unit_tests/algorithms.json b/tests/IVIMmodels/unit_tests/algorithms.json
index 3e289721..1f64576f 100644
--- a/tests/IVIMmodels/unit_tests/algorithms.json
+++ b/tests/IVIMmodels/unit_tests/algorithms.json
@@ -17,7 +17,6 @@
     ],
     "ASD_MemorialSloanKettering_QAMPER_IVIM": {
         "requieres_matlab": true,
-        "fail_first_time": true
     },
     "IAR_LU_biexp": {
         "fail_first_time": true
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index f00e68af..d2b3a147 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -6,9 +6,22 @@
 import time
 from src.wrappers.OsipiBase import OsipiBase
 #run using python -m pytest from the root folder
-import matlab.engine
 
-eng=matlab.engine.start_matlab()
+
+eng = None
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--with-matlab", action="store_true", default=False, help="Run MATLAB-dependent tests"
+    )
+
+@pytest.hookimpl
+def pytest_configure(config):
+    global eng
+    if config.getoption("--with-matlab"):
+        import matlab.engine
+        eng = matlab.engine.start_matlab()
+
 
 def signal_helper(signal):
     signal = np.asarray(signal)
@@ -61,7 +74,10 @@ def data_ivim_fit_saved():
                     skiptime = True
                     first = False # this will only work for 1 algorithm... If two algorithms use fail_first_time, the second will not see it is the first time.
             if algorithm_dict.get("requieres_matlab", {}) == True:
-                kwargs={**kwargs,'eng': eng}
+                if eng is None:
+                    continue
+                else:
+                    kwargs={**kwargs,'eng': eng}
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime
 
 @pytest.mark.parametrize("name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime", data_ivim_fit_saved())
@@ -100,7 +116,7 @@ def to_list_if_needed(value):
         assert elapsed_time < 0.5, f"Algorithm {name} took {elapsed_time} seconds, which is longer than 2 second to fit per voxel" #less than 0.5 seconds per voxel
 
 
-def algorithms():
+def algorithmlist():
     # Find the algorithms from algorithms.json
     file = pathlib.Path(__file__)
     algorithm_path = file.with_name('algorithms.json')
@@ -111,10 +127,13 @@ def algorithms():
         algorithm_dict = algorithm_information.get(algorithm, {})
         args={}
         if algorithm_dict.get("requieres_matlab", {}) == True:
-            args['eng'] = eng
+            if eng is None:
+                continue
+            else:
+                kwargs = {**kwargs, 'eng': eng}
         yield algorithm, args
 
-@pytest.mark.parametrize("algorithm, args", algorithms())
+@pytest.mark.parametrize("algorithm, args", algorithmlist())
 def test_default_bounds_and_initial_guesses(algorithm, args):
     fit = OsipiBase(algorithm=algorithm,**args)
     #assert fit.bounds is not None, f"For {algorithm}, there is no default fit boundary"
@@ -159,7 +178,10 @@ def bound_input():
             kwargs = algorithm_dict.get("options", {})
             tolerances = algorithm_dict.get("tolerances", {})
             if algorithm_dict.get("requieres_matlab", {}) == True:
-                kwargs={**kwargs,'eng': eng}
+                if eng is None:
+                    continue
+                else:
+                    kwargs = {**kwargs, 'eng': eng}
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances
 
 

From fc31bc6d0a4bc91d69c0cffb532b7d56bffdff89 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 4 Jun 2025 14:43:30 +0200
Subject: [PATCH 13/18] remove matlab install from workflow

---
 .github/workflows/unit_test.yml | 25 ++++---------------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml
index 03a2998c..c5475ed2 100644
--- a/.github/workflows/unit_test.yml
+++ b/.github/workflows/unit_test.yml
@@ -1,8 +1,10 @@
 name: Unit tests
+
 on: [push, pull_request]
 
 jobs:
   build:
+
     runs-on: ${{ matrix.os }}
     continue-on-error: false
     strategy:
@@ -13,40 +15,21 @@ jobs:
         exclude:
           - os: windows-latest
             python-version: "3.13"
-
+        # Windows chokes on py3.13: https://github.com/numpy/numpy/issues/27894
     steps:
       - uses: actions/checkout@v4
-
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-
+      # You can test your matrix by printing the current Python version
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
-
-      - name: Set env var for MATLAB on macOS
-        if: runner.os == 'macOS'
-        run: echo "DYLD_LIBRARY_PATH=/Users/runner/hostedtoolcache/MATLAB/2025.1.999/arm64/MATLAB.app/bin/maca64:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
-
-      - name: Set env var for MATLAB on Linux
-        if: runner.os == 'Linux'
-        run: echo "LD_LIBRARY_PATH=/opt/hostedtoolcache/MATLAB/2025.1.999/x64/bin/glnxa64:$LD_LIBRARY_PATH" >> $GITHUB_ENV
-
-      - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v2
-        with:
-          release: R2025a 
-
-      - name: Install MATLAB Engine for Python
-        run: python -m pip install matlabengine==25.1.2
-
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov

From 4e4a6dc05e59f55bf1d8a3ad801a849e5d61258e Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 4 Jun 2025 15:24:00 +0200
Subject: [PATCH 14/18] fix right location for matlab avail

---
 conftest.py                                  | 17 ++++++++++++++++-
 tests/IVIMmodels/unit_tests/algorithms.json  |  2 +-
 tests/IVIMmodels/unit_tests/test_ivim_fit.py | 20 +++-----------------
 3 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/conftest.py b/conftest.py
index 086585c2..bd24d7ef 100644
--- a/conftest.py
+++ b/conftest.py
@@ -4,7 +4,6 @@
 import csv
 # import datetime
 
-
 def pytest_addoption(parser):
     parser.addoption(
         "--SNR",
@@ -81,6 +80,22 @@ def pytest_addoption(parser):
         type=str,
         help="Drop this algorithm from the list"
     )
+    parser.addoption(
+        "--with-matlab",
+        action="store_true",
+        default=False,
+        help="Run MATLAB-dependent tests"
+    )
+
+eng = None
+
+def pytest_configure(config):
+    global eng
+    if config.getoption("--with-matlab"):
+        import matlab.engine
+        print("Starting MATLAB engine...")
+        eng = matlab.engine.start_matlab()
+        print("MATLAB engine started.")
 
 
 @pytest.fixture(scope="session")
diff --git a/tests/IVIMmodels/unit_tests/algorithms.json b/tests/IVIMmodels/unit_tests/algorithms.json
index 1f64576f..584d55c4 100644
--- a/tests/IVIMmodels/unit_tests/algorithms.json
+++ b/tests/IVIMmodels/unit_tests/algorithms.json
@@ -16,7 +16,7 @@
         "OJ_GU_seg"
     ],
     "ASD_MemorialSloanKettering_QAMPER_IVIM": {
-        "requieres_matlab": true,
+        "requieres_matlab": true
     },
     "IAR_LU_biexp": {
         "fail_first_time": true
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index d2b3a147..898d51b8 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -5,24 +5,10 @@
 import pathlib
 import time
 from src.wrappers.OsipiBase import OsipiBase
+from conftest import eng
 #run using python -m pytest from the root folder
 
 
-eng = None
-
-def pytest_addoption(parser):
-    parser.addoption(
-        "--with-matlab", action="store_true", default=False, help="Run MATLAB-dependent tests"
-    )
-
-@pytest.hookimpl
-def pytest_configure(config):
-    global eng
-    if config.getoption("--with-matlab"):
-        import matlab.engine
-        eng = matlab.engine.start_matlab()
-
-
 def signal_helper(signal):
     signal = np.asarray(signal)
     #signal[signal < 0] = 0.00001
@@ -72,7 +58,7 @@ def data_ivim_fit_saved():
             if first == True:
                 if algorithm_dict.get("fail_first_time", {}) == True:
                     skiptime = True
-                    first = False # this will only work for 1 algorithm... If two algorithms use fail_first_time, the second will not see it is the first time.
+                    first = False
             if algorithm_dict.get("requieres_matlab", {}) == True:
                 if eng is None:
                     continue
@@ -130,7 +116,7 @@ def algorithmlist():
             if eng is None:
                 continue
             else:
-                kwargs = {**kwargs, 'eng': eng}
+                args = {**args, 'eng': eng}
         yield algorithm, args
 
 @pytest.mark.parametrize("algorithm, args", algorithmlist())

From 52d7debc20b6ce475ec3830d2a1f2425fa27918d Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 4 Jun 2025 15:57:21 +0200
Subject: [PATCH 15/18] exclude matlab algorithms from testing algorithm list
 if matlab is not isntalled

---
 conftest.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/conftest.py b/conftest.py
index bd24d7ef..9d052624 100644
--- a/conftest.py
+++ b/conftest.py
@@ -81,7 +81,7 @@ def pytest_addoption(parser):
         help="Drop this algorithm from the list"
     )
     parser.addoption(
-        "--with-matlab",
+        "--withmatlab",
         action="store_true",
         default=False,
         help="Run MATLAB-dependent tests"
@@ -91,7 +91,7 @@ def pytest_addoption(parser):
 
 def pytest_configure(config):
     global eng
-    if config.getoption("--with-matlab"):
+    if config.getoption("--withmatlab"):
         import matlab.engine
         print("Starting MATLAB engine...")
         eng = matlab.engine.start_matlab()
@@ -178,6 +178,11 @@ def algorithm_list(filename, selected, dropped):
     with algorithm_path.open() as f:
         algorithm_information = json.load(f)
     algorithms = set(algorithm_information["algorithms"])
+    for algorithm in algorithms:
+        algorithm_dict = algorithm_information.get(algorithm, {})
+        if algorithm_dict.get("requieres_matlab", {}) == True:
+            if eng is None:
+                algorithms = algorithms - set(algorithm)
     algorithms = algorithms - set(dropped)
     if len(selected) > 0 and selected[0]:
         algorithms = algorithms & set(selected)

From b7f2f8ea7d8611a5df67605531c0f4de34699542 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 4 Jun 2025 16:29:42 +0200
Subject: [PATCH 16/18] ensure testing is only done in the test folder

when testing in all folders, all code is initiated. When matlab is not available, it gives an error.
---
 .gitignore | 4 +++-
 pytest.ini | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index a4125b0c..977ba281 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,7 +20,9 @@ md5sums.txt
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/test_data
 src/original/ASD_MemorialSloanKettering/MRI-QAMPER_IVIM/output_files
 tests/IVIMmodels/unit_tests/*.log
-
+junit/*
+ivim_simulation.bval
+ivim_simulation.bvec
 
 # Unit test / coverage reports
 .tox/
diff --git a/pytest.ini b/pytest.ini
index e61feaf8..ed02be7a 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -2,4 +2,5 @@
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
 addopts =  
-    -m 'not slow'
\ No newline at end of file
+    -m 'not slow'
+testpaths = tests
\ No newline at end of file

From c32bfbdceb6972d3639b96da58302e904e313838 Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Tue, 10 Jun 2025 21:20:01 +0200
Subject: [PATCH 17/18] Fixed comments

- Moved all the initiation functions from the unit_test folder to conftest.py
- Added a skip option for all matlab tests (instead of removing them)
- Removed some typos
- Removed "redundant" code
---
 conftest.py                                   | 120 +++++++++++++----
 .../ASD_MemorialSloanKettering_QAMPER_IVIM.py |  19 +--
 tests/IVIMmodels/unit_tests/algorithms.json   |   2 +-
 tests/IVIMmodels/unit_tests/test_ivim_fit.py  | 125 +++++-------------
 .../unit_tests/test_ivim_synthetic.py         |   6 +-
 5 files changed, 137 insertions(+), 135 deletions(-)

diff --git a/conftest.py b/conftest.py
index 9d052624..598820e2 100644
--- a/conftest.py
+++ b/conftest.py
@@ -4,6 +4,7 @@
 import csv
 # import datetime
 
+
 def pytest_addoption(parser):
     parser.addoption(
         "--SNR",
@@ -87,15 +88,17 @@ def pytest_addoption(parser):
         help="Run MATLAB-dependent tests"
     )
 
-eng = None
 
-def pytest_configure(config):
-    global eng
-    if config.getoption("--withmatlab"):
-        import matlab.engine
-        print("Starting MATLAB engine...")
-        eng = matlab.engine.start_matlab()
-        print("MATLAB engine started.")
+@pytest.fixture(scope="session")
+def eng(request):
+    """Start and return a MATLAB engine session if --withmatlab is set."""
+    if not request.config.getoption("--withmatlab"):
+        return None
+    import matlab.engine
+    print("Starting MATLAB engine...")
+    eng = matlab.engine.start_matlab()
+    print("MATLAB engine started.")
+    return eng
 
 
 @pytest.fixture(scope="session")
@@ -164,37 +167,102 @@ def use_prior(request):
 def pytest_generate_tests(metafunc):
     if "SNR" in metafunc.fixturenames:
         metafunc.parametrize("SNR", metafunc.config.getoption("SNR"))
-    if "ivim_algorithm" in metafunc.fixturenames:
-        algorithms = algorithm_list(metafunc.config.getoption("algorithmFile"), metafunc.config.getoption("selectAlgorithm"), metafunc.config.getoption("dropAlgorithm"))
-        metafunc.parametrize("ivim_algorithm", algorithms)
     if "ivim_data" in metafunc.fixturenames:
         data = data_list(metafunc.config.getoption("dataFile"))
         metafunc.parametrize("ivim_data", data)
+    if "data_ivim_fit_saved" in  metafunc.fixturenames:
+        args = data_ivim_fit_saved(metafunc.config.getoption("dataFile"),metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("data_ivim_fit_saved", args)
+    if "algorithmlist" in metafunc.fixturenames:
+        args = algorithmlist(metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("algorithmlist", args)
+    if "bound_input" in metafunc.fixturenames:
+        args = bound_input(metafunc.config.getoption("dataFile"),metafunc.config.getoption("algorithmFile"))
+        metafunc.parametrize("bound_input", args)
+
+
+def data_list(filename):
+    current_folder = pathlib.Path.cwd()
+    data_path = current_folder / filename
+    with data_path.open() as f:
+        all_data = json.load(f)
+
+    bvals = all_data.pop('config')
+    bvals = bvals['bvalues']
+    for name, data in all_data.items():
+        yield name, bvals, data
+
 
+def data_ivim_fit_saved(datafile, algorithmFile):
+    # Find the algorithms from algorithms.json
+    current_folder = pathlib.Path.cwd()
+    algorithm_path = current_folder / algorithmFile
+    with algorithm_path.open() as f:
+        algorithm_information = json.load(f)
+    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
+    generic = current_folder / datafile
+    with generic.open() as f:
+        all_data = json.load(f)
+    algorithms = algorithm_information["algorithms"]
+    bvals = all_data.pop('config')
+    bvals = bvals['bvalues']
+    for algorithm in algorithms:
+        first = True
+        for name, data in all_data.items():
+            algorithm_dict = algorithm_information.get(algorithm, {})
+            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
+                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
+            kwargs = algorithm_dict.get("options", {})
+            tolerances = algorithm_dict.get("tolerances", {})
+            skiptime=False
+            if first == True:
+                if algorithm_dict.get("fail_first_time", {}) == True:
+                    skiptime = True
+                    first = False
+            if algorithm_dict.get("requires_matlab", False) == True:
+                requires_matlab = True
+            else:
+                requires_matlab = False
+            yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime, requires_matlab
 
-def algorithm_list(filename, selected, dropped):
+def algorithmlist(algorithmFile):
+    # Find the algorithms from algorithms.json
     current_folder = pathlib.Path.cwd()
-    algorithm_path = current_folder / filename
+    algorithm_path = current_folder / algorithmFile
     with algorithm_path.open() as f:
         algorithm_information = json.load(f)
-    algorithms = set(algorithm_information["algorithms"])
+
+    algorithms = algorithm_information["algorithms"]
     for algorithm in algorithms:
         algorithm_dict = algorithm_information.get(algorithm, {})
-        if algorithm_dict.get("requieres_matlab", {}) == True:
-            if eng is None:
-                algorithms = algorithms - set(algorithm)
-    algorithms = algorithms - set(dropped)
-    if len(selected) > 0 and selected[0]:
-        algorithms = algorithms & set(selected)
-    return list(algorithms)
+        if algorithm_dict.get("requires_matlab", False) == True:
+            requires_matlab = True
+        else:
+            requires_matlab = False
+        yield algorithm, requires_matlab
 
-def data_list(filename):
+def bound_input(datafile,algorithmFile):
+    # Find the algorithms from algorithms.json
     current_folder = pathlib.Path.cwd()
-    data_path = current_folder / filename
-    with data_path.open() as f:
+    algorithm_path = current_folder / algorithmFile
+    with algorithm_path.open() as f:
+        algorithm_information = json.load(f)
+    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
+    generic = current_folder / datafile
+    with generic.open() as f:
         all_data = json.load(f)
-
+    algorithms = algorithm_information["algorithms"]
     bvals = all_data.pop('config')
     bvals = bvals['bvalues']
     for name, data in all_data.items():
-        yield name, bvals, data
+        for algorithm in algorithms:
+            algorithm_dict = algorithm_information.get(algorithm, {})
+            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
+                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
+            kwargs = algorithm_dict.get("options", {})
+            tolerances = algorithm_dict.get("tolerances", {})
+            if algorithm_dict.get("requires_matlab", False) == True:
+                requires_matlab = True
+            else:
+                requires_matlab = False
+            yield name, bvals, data, algorithm, xfail, kwargs, tolerances, requires_matlab
\ No newline at end of file
diff --git a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
index 887dbbd2..455e6397 100644
--- a/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
+++ b/src/standardized/ASD_MemorialSloanKettering_QAMPER_IVIM.py
@@ -2,6 +2,7 @@
 import numpy as np
 import matlab.engine
 
+
 class ASD_MemorialSloanKettering_QAMPER_IVIM(OsipiBase):
     """
     Bi-exponential fitting algorithm by Oliver Gurney-Champion, Amsterdam UMC
@@ -27,13 +28,12 @@ class ASD_MemorialSloanKettering_QAMPER_IVIM(OsipiBase):
     required_initial_guess_optional = True
     accepted_dimensions = 1  # Not sure how to define this for the number of accepted dimensions. Perhaps like the thresholds, at least and at most?
 
-
     # Supported inputs in the standardized class
     supported_bounds = True
     supported_initial_guess = True
     supported_thresholds = False
 
-    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None,eng=None):
+    def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=None, eng=None):
         """
             Everything this algorithm requires should be implemented here.
             Number of segmentation thresholds, bounds, etc.
@@ -52,8 +52,6 @@ def __init__(self, bvalues=None, thresholds=None, bounds=None, initial_guess=Non
             self.eng = eng
             self.keep_alive=True
 
-
-
     def algorithm(self,dwi_arr, bval_arr, LB0, UB0, x0in):
         dwi_arr = matlab.double(dwi_arr.tolist())
         bval_arr = matlab.double(bval_arr.tolist())
@@ -104,8 +102,7 @@ def ivim_fit(self, signals, bvalues, **kwargs):
 
         return results
 
-
-    def __del__(self):
+    def clean(self):
         if not self.keep_alive:
             if hasattr(self, "eng") and self.eng:
                 try:
@@ -113,15 +110,11 @@ def __del__(self):
                 except Exception as e:
                     print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
 
+    def __del__(self):
+        self.clean()
 
     def __enter__(self):
         return self
 
-
     def __exit__(self, exc_type, exc_val, exc_tb):
-        if not self.keep_alive:
-            if hasattr(self, "eng") and self.eng:
-                try:
-                    self.eng.quit()
-                except Exception as e:
-                    print(f"Warning: Failed to quit MATLAB engine cleanly: {e}")
+        self.clean()
diff --git a/tests/IVIMmodels/unit_tests/algorithms.json b/tests/IVIMmodels/unit_tests/algorithms.json
index 584d55c4..fa90ce5a 100644
--- a/tests/IVIMmodels/unit_tests/algorithms.json
+++ b/tests/IVIMmodels/unit_tests/algorithms.json
@@ -16,7 +16,7 @@
         "OJ_GU_seg"
     ],
     "ASD_MemorialSloanKettering_QAMPER_IVIM": {
-        "requieres_matlab": true
+        "requires_matlab": true
     },
     "IAR_LU_biexp": {
         "fail_first_time": true
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index 898d51b8..350d85af 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -5,7 +5,6 @@
 import pathlib
 import time
 from src.wrappers.OsipiBase import OsipiBase
-from conftest import eng
 #run using python -m pytest from the root folder
 
 
@@ -31,50 +30,24 @@ def tolerances_helper(tolerances, data):
         tolerances["atol"] = tolerances.get("atol", {"f": 2e-1, "D": 5e-4, "Dp": 4e-2})
     return tolerances
 
-def data_ivim_fit_saved():
-    # Find the algorithms from algorithms.json
-    file = pathlib.Path(__file__)
-    algorithm_path = file.with_name('algorithms.json')
-    with algorithm_path.open() as f:
-        algorithm_information = json.load(f)
-
-    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
-    generic = file.with_name('generic.json')
-    with generic.open() as f:
-        all_data = json.load(f)
-
-    algorithms = algorithm_information["algorithms"]
-    bvals = all_data.pop('config')
-    bvals = bvals['bvalues']
-    for algorithm in algorithms:
-        first = True
-        for name, data in all_data.items():
-            algorithm_dict = algorithm_information.get(algorithm, {})
-            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
-                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
-            kwargs = algorithm_dict.get("options", {})
-            tolerances = algorithm_dict.get("tolerances", {})
-            skiptime=False
-            if first == True:
-                if algorithm_dict.get("fail_first_time", {}) == True:
-                    skiptime = True
-                    first = False
-            if algorithm_dict.get("requieres_matlab", {}) == True:
-                if eng is None:
-                    continue
-                else:
-                    kwargs={**kwargs,'eng': eng}
-            yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime
-
-@pytest.mark.parametrize("name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime", data_ivim_fit_saved())
-def test_ivim_fit_saved(name, bvals, data, algorithm, xfail, kwargs, tolerances,skiptime, request, record_property):
+def test_ivim_fit_saved(data_ivim_fit_saved, eng, request, record_property):
+    name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime, requires_matlab = data_ivim_fit_saved
+    max_time = 0.5
+    if requires_matlab:
+        max_time = 2
+        if eng is None:
+            print('test is here')
+            pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
+        else:
+            print('test is not here')
+            kwargs = {**kwargs, 'eng': eng}
     if xfail["xfail"]:
         mark = pytest.mark.xfail(reason="xfail", strict=xfail["strict"])
         request.node.add_marker(mark)
     signal = signal_helper(data["data"])
     tolerances = tolerances_helper(tolerances, data)
-    start_time = time.time()  # Record the start time
     fit = OsipiBase(algorithm=algorithm,  **kwargs)
+    start_time = time.time()  # Record the start time
     fit_result = fit.osipi_fit(signal, bvals)
     elapsed_time = time.time() - start_time  # Calculate elapsed time
     def to_list_if_needed(value):
@@ -99,29 +72,18 @@ def to_list_if_needed(value):
         npt.assert_allclose(fit_result['Dp'],data['Dp'], rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"])
     #assert fit_result['D'] < fit_result['Dp'], f"D {fit_result['D']} is larger than D* {fit_result['Dp']} for {name}"
     if not skiptime:
-        assert elapsed_time < 0.5, f"Algorithm {name} took {elapsed_time} seconds, which is longer than 2 second to fit per voxel" #less than 0.5 seconds per voxel
-
-
-def algorithmlist():
-    # Find the algorithms from algorithms.json
-    file = pathlib.Path(__file__)
-    algorithm_path = file.with_name('algorithms.json')
-    with algorithm_path.open() as f:
-        algorithm_information = json.load(f)
-    algorithms = algorithm_information["algorithms"]
-    for algorithm in algorithms:
-        algorithm_dict = algorithm_information.get(algorithm, {})
-        args={}
-        if algorithm_dict.get("requieres_matlab", {}) == True:
-            if eng is None:
-                continue
-            else:
-                args = {**args, 'eng': eng}
-        yield algorithm, args
-
-@pytest.mark.parametrize("algorithm, args", algorithmlist())
-def test_default_bounds_and_initial_guesses(algorithm, args):
-    fit = OsipiBase(algorithm=algorithm,**args)
+        assert elapsed_time < max_time, f"Algorithm {name} took {elapsed_time} seconds, which is longer than 2 second to fit per voxel" #less than 0.5 seconds per voxel
+
+def test_default_bounds_and_initial_guesses(algorithmlist,eng):
+    algorithm, requires_matlab = algorithmlist
+    if requires_matlab:
+        if eng is None:
+            pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
+        else:
+            kwargs = {'eng': eng}
+    else:
+        kwargs={}
+    fit = OsipiBase(algorithm=algorithm,**kwargs)
     #assert fit.bounds is not None, f"For {algorithm}, there is no default fit boundary"
     #assert fit.initial_guess is not None, f"For {algorithm}, there is no default fit initial guess"
     if fit.use_bounds:
@@ -141,38 +103,13 @@ def test_default_bounds_and_initial_guesses(algorithm, args):
         assert 0.9 <= fit.initial_guess[3] <= 1.1, f"For {algorithm}, the default initial guess for S {fit.initial_guess[3]} is unrealistic; note signal is normalized"
 
 
-def bound_input():
-    # Find the algorithms from algorithms.json
-    file = pathlib.Path(__file__)
-    algorithm_path = file.with_name('algorithms.json')
-    with algorithm_path.open() as f:
-        algorithm_information = json.load(f)
-
-    # Load generic test data generated from the included phantom: phantoms/MR_XCAT_qMRI
-    generic = file.with_name('generic.json')
-    with generic.open() as f:
-        all_data = json.load(f)
-
-    algorithms = algorithm_information["algorithms"]
-    bvals = all_data.pop('config')
-    bvals = bvals['bvalues']
-    for name, data in all_data.items():
-        for algorithm in algorithms:
-            algorithm_dict = algorithm_information.get(algorithm, {})
-            xfail = {"xfail": name in algorithm_dict.get("xfail_names", {}),
-                "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
-            kwargs = algorithm_dict.get("options", {})
-            tolerances = algorithm_dict.get("tolerances", {})
-            if algorithm_dict.get("requieres_matlab", {}) == True:
-                if eng is None:
-                    continue
-                else:
-                    kwargs = {**kwargs, 'eng': eng}
-            yield name, bvals, data, algorithm, xfail, kwargs, tolerances
-
-
-@pytest.mark.parametrize("name, bvals, data, algorithm, xfail, kwargs, tolerances", bound_input())
-def test_bounds(name, bvals, data, algorithm, xfail, kwargs, tolerances, request):
+def test_bounds(bound_input, eng):
+    name, bvals, data, algorithm, xfail, kwargs, tolerances, requires_matlab = bound_input
+    if requires_matlab:
+        if eng is None:
+            pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
+        else:
+            kwargs = {**kwargs, 'eng': eng}
     bounds = ([0.0008, 0.2, 0.01, 1.1], [0.0012, 0.3, 0.02, 1.3])
     # deliberately have silly bounds to see whether they are used
     fit = OsipiBase(algorithm=algorithm, bounds=bounds, initial_guess = [0.001, 0.25, 0.015, 1.2], **kwargs)
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py b/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
index 20741327..0534f82e 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
@@ -14,8 +14,12 @@
 #run using pytest <path_to_this_file> --saveFileName test_output.txt --SNR 50 100 200
 #e.g. pytest -m slow tests/IVIMmodels/unit_tests/test_ivim_synthetic.py  --saveFileName test_output.csv --SNR 10 50 100 200 --fitCount 20
 @pytest.mark.slow
-def test_generated(ivim_algorithm, ivim_data, SNR, rtol, atol, fit_count, rician_noise, save_file, save_duration_file, use_prior):
+def test_generated(algorithmlist, skip_list, ivim_data, SNR, rtol, atol, fit_count, rician_noise, save_file, save_duration_file, use_prior):
     # assert save_file == "test"
+    ivim_algorithm, requires_matlab = algorithmlist
+    if requires_matlab:
+        if eng is None:
+            pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
     rng = np.random.RandomState(42)
     # random.seed(42)
     S0 = 1

From 1d48e6cd7b976203eac57a6f3bec0d589597746a Mon Sep 17 00:00:00 2001
From: Oliver Gurney-Champion <oliverchampion@gmail.com>
Date: Wed, 11 Jun 2025 14:55:20 +0200
Subject: [PATCH 18/18] fixed stuff

---
 conftest.py                                   | 19 +++++--------------
 tests/IVIMmodels/unit_tests/test_ivim_fit.py  |  2 --
 .../unit_tests/test_ivim_synthetic.py         |  5 ++---
 3 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/conftest.py b/conftest.py
index 598820e2..3c33bda6 100644
--- a/conftest.py
+++ b/conftest.py
@@ -215,14 +215,11 @@ def data_ivim_fit_saved(datafile, algorithmFile):
             kwargs = algorithm_dict.get("options", {})
             tolerances = algorithm_dict.get("tolerances", {})
             skiptime=False
-            if first == True:
-                if algorithm_dict.get("fail_first_time", {}) == True:
+            if first:
+                if algorithm_dict.get("fail_first_time", False):
                     skiptime = True
                     first = False
-            if algorithm_dict.get("requires_matlab", False) == True:
-                requires_matlab = True
-            else:
-                requires_matlab = False
+            requires_matlab = algorithm_dict.get("requires_matlab", False)
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances, skiptime, requires_matlab
 
 def algorithmlist(algorithmFile):
@@ -235,10 +232,7 @@ def algorithmlist(algorithmFile):
     algorithms = algorithm_information["algorithms"]
     for algorithm in algorithms:
         algorithm_dict = algorithm_information.get(algorithm, {})
-        if algorithm_dict.get("requires_matlab", False) == True:
-            requires_matlab = True
-        else:
-            requires_matlab = False
+        requires_matlab = algorithm_dict.get("requires_matlab", False)
         yield algorithm, requires_matlab
 
 def bound_input(datafile,algorithmFile):
@@ -261,8 +255,5 @@ def bound_input(datafile,algorithmFile):
                 "strict": algorithm_dict.get("xfail_names", {}).get(name, True)}
             kwargs = algorithm_dict.get("options", {})
             tolerances = algorithm_dict.get("tolerances", {})
-            if algorithm_dict.get("requires_matlab", False) == True:
-                requires_matlab = True
-            else:
-                requires_matlab = False
+            requires_matlab = algorithm_dict.get("requires_matlab", False)
             yield name, bvals, data, algorithm, xfail, kwargs, tolerances, requires_matlab
\ No newline at end of file
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
index 350d85af..ea9b336b 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -36,10 +36,8 @@ def test_ivim_fit_saved(data_ivim_fit_saved, eng, request, record_property):
     if requires_matlab:
         max_time = 2
         if eng is None:
-            print('test is here')
             pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
         else:
-            print('test is not here')
             kwargs = {**kwargs, 'eng': eng}
     if xfail["xfail"]:
         mark = pytest.mark.xfail(reason="xfail", strict=xfail["strict"])
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py b/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
index 0534f82e..6f2cb7c1 100644
--- a/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
+++ b/tests/IVIMmodels/unit_tests/test_ivim_synthetic.py
@@ -17,9 +17,8 @@
 def test_generated(algorithmlist, skip_list, ivim_data, SNR, rtol, atol, fit_count, rician_noise, save_file, save_duration_file, use_prior):
     # assert save_file == "test"
     ivim_algorithm, requires_matlab = algorithmlist
-    if requires_matlab:
-        if eng is None:
-            pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
+    if requires_matlab and eng is None:
+        pytest.skip(reason="Running without matlab; if Matlab is available please run pytest --withmatlab")
     rng = np.random.RandomState(42)
     # random.seed(42)
     S0 = 1