From a04a6262056d5d5b8ad7f39f6c783b31c5f5a2a2 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Mon, 11 Mar 2024 17:36:39 +0100
Subject: [PATCH 01/17] make pyopenms compile again

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 54 ++++++++++++++++------------
 1 file changed, 31 insertions(+), 23 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 7dde4217fc8..6a43cc3ac4d 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -3,7 +3,7 @@ from Matrix cimport *
 
 # continue with extra code if needed
 
-    def get_matrix(self):
+    def get_matrix_as_view(self):
         """Cython signature: numpy_matrix get_matrix()
         """
 
@@ -11,15 +11,23 @@ from Matrix cimport *
 
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
+        cdef unsigned int n = rows * cols
+        cdef np.ndarray[double, ndim=2] data
+        data = np.zeros( (rows,cols), dtype=np.float64)
 
-        cdef libcpp_vector[double] tmp_vec;
-        tmp_vec = mat_.asVector();
+        cdef libcpp_vector[double] * vec_ptr = <libcpp_vector[double]*> mat_
+        cdef double * raw_ptr =  address(deref(vec_ptr)[0]) 
 
-        xarr = np.asarray(tmp_vec)
+        ## # We use a memory view to get the data from the raw data
+        ## # See https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html 
+        ## # See https://stackoverflow.com/questions/43021574/cast-c-array-into-numpy-array-cython-typed-memoryview-in-cython-code
+        cdef double[:] vec_view = <double[:n]>raw_ptr # cast to memoryview, refer to the underlying buffer without copy
+        xarr = np.asarray(vec_view) # numpy array refer to the underlying buffer without copy
         xarr = xarr.reshape(rows, cols)
-        return xarr
+        return xarr.transpose()
 
-    def get_matrix_as_view(self):
+
+    def get_matrix(self):
         """Cython signature: numpy_matrix get_matrix()
         """
 
@@ -40,23 +48,23 @@ from Matrix cimport *
         cdef double[:] vec_view = <double[:n]>raw_ptr # cast to memoryview, refer to the underlying buffer without copy
         xarr = np.asarray(vec_view) # numpy array refer to the underlying buffer without copy
         xarr = xarr.reshape(rows, cols)
-        return xarr
-
-    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
-        """Cython signature: numpy_matrix set_matrix()
-        """
-
-        cdef _Matrix[double] * mat_ = self.inst.get()
-
-        cdef unsigned int rows = data.shape[0]
-        cdef unsigned int cols = data.shape[1]
-        mat_.resize(rows, cols, 0)
-
-        cdef int i = 0
-        cdef int j = 0
-        for i in range(int(rows)):
-            for j in range(int(cols)):
-                mat_.setValue(i,j,data[i][j])
+        return xarr.transpose().copy()
+
+#    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
+#        """Cython signature: numpy_matrix set_matrix()
+#        """
+#
+#        cdef _Matrix[double] * mat_ = self.inst.get()
+#
+#        cdef unsigned int rows = data.shape[0]
+#        cdef unsigned int cols = data.shape[1]
+#        mat_.resize(rows, cols, 0)
+#
+#        cdef int i = 0
+#        cdef int j = 0
+#        for i in range(int(rows)):
+#            for j in range(int(cols)):
+#                mat_.setValue(i,j,data[i][j])
 
 
 

From 4276c98bd2b12c113526237d75ae6a7a10307653 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Mon, 11 Mar 2024 19:15:40 +0100
Subject: [PATCH 02/17] fix more tests

---
 src/pyOpenMS/tests/unittests/test000.py       |  5 +-
 .../unittests/test_BilinearInterpolation.py   | 54 +++++++------------
 2 files changed, 22 insertions(+), 37 deletions(-)

diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index a18e506a2cc..7f6f1d4e44c 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -3631,9 +3631,8 @@ def testMatrixDouble():
      MapAlignmentAlgorithmIdentification.__init__
      """
 
-    m = pyopenms.MatrixDouble()
     N = 90
-    m.resize(N-1, N+2, 5.0)
+    m = pyopenms.MatrixDouble(N-1, N+2, 5.0)
 
     assert m.rows() == 89
     assert m.cols() == 92
@@ -3680,7 +3679,7 @@ def testMatrixDouble():
     assert m.getValue(1, 6) == 11.0
     assert matrix_view[1, 6] == 11.0
 
-    m.clear()
+    m = pyopenms.MatrixDouble()
     assert m.rows() == 0
     assert m.cols() == 0
 
diff --git a/src/pyOpenMS/tests/unittests/test_BilinearInterpolation.py b/src/pyOpenMS/tests/unittests/test_BilinearInterpolation.py
index fa8877b20f5..43fd759a0cb 100644
--- a/src/pyOpenMS/tests/unittests/test_BilinearInterpolation.py
+++ b/src/pyOpenMS/tests/unittests/test_BilinearInterpolation.py
@@ -8,8 +8,7 @@
 class TestBilinearInterpolation(unittest.TestCase):
 
     def test_BilinearInterpolation(self):
-        mat = pyopenms.MatrixDouble()
-        mat.resize(2, 3, float())
+        mat = pyopenms.MatrixDouble(2, 3, 0.0)
         mat.setValue(0, 0, 17)
         mat.setValue(0, 1, 18.9)
         mat.setValue(0, 2, 20.333)
@@ -43,8 +42,8 @@ def test_BilinearInterpolation(self):
     def test_getData_setData(self):
         bilip = pyopenms.BilinearInterpolation()
 
-        tmp = bilip.getData()
-        tmp.resize(2, 3, float())
+        tmp = pyopenms.MatrixDouble(2, 3, 0.0)
+
         tmp.setValue(1, 2, 10012)
         tmp.setValue(0, 0, 10000)
         tmp.setValue(1, 0, 10010)
@@ -108,8 +107,8 @@ def test_supportMax_0(self):
         bilip.setMapping_0(3.0, 1.0, 2.0)
         bilip.setMapping_1(5.0, 3.0, 4.0)
 
-        tmp = bilip.getData()
-        tmp.resize(2, 3, float())
+        tmp = pyopenms.MatrixDouble(2, 3, 0.0)
+
         bilip.setData(tmp)
         self.assertAlmostEqual(bilip.index2key_0(0), -1)
         self.assertAlmostEqual(bilip.index2key_0(1), 2)
@@ -174,8 +173,7 @@ def test_supportMax_1(self):
         bilip.setMapping_1(3.0, 1.0, 2.0)
         bilip.setMapping_0(5.0, 3.0, 4.0)
 
-        tmp = bilip.getData()
-        tmp.resize(3, 2, float())
+        tmp = pyopenms.MatrixDouble(3, 2, 0.0)
         bilip.setData(tmp)
         self.assertAlmostEqual(bilip.index2key_1(0), -1)
         self.assertAlmostEqual(bilip.index2key_1(1), 2)
@@ -191,43 +189,36 @@ def test_empty(self):
         bilip = pyopenms.BilinearInterpolation()
         self.assertTrue(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(1, 2, float())
+        tmp = pyopenms.MatrixDouble(1, 2, 0.0)
         bilip.setData(tmp)
         self.assertFalse(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(0, 0, float())
+        tmp = pyopenms.MatrixDouble(0, 0, 0.0)
         bilip.setData(tmp)
         self.assertTrue(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(1, 2, float())
+        tmp = pyopenms.MatrixDouble(1, 2, 0.0)
         bilip.setData(tmp)
         self.assertFalse(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(1, 0, float())
+        tmp = pyopenms.MatrixDouble(1, 0, 0.0)
         bilip.setData(tmp)
         self.assertTrue(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(1, 2, float())
+        tmp = pyopenms.MatrixDouble(1, 2, 0.0)
         bilip.setData(tmp)
         self.assertFalse(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(0, 0, float())
+        tmp = pyopenms.MatrixDouble(0, 0, 0.0)
         bilip.setData(tmp)
         self.assertTrue(bilip.empty())
 
-        tmp = bilip.getData()
-        tmp.resize(2, 2, float())
+        tmp = pyopenms.MatrixDouble(2, 2, 0.0)
         bilip.setData(tmp)
         self.assertFalse(bilip.empty())
 
         tmp = bilip.getData()
-        tmp.clear()
+        tmp = pyopenms.MatrixDouble(0, 0, 0.0)
         bilip.setData(tmp)
         self.assertTrue(bilip.empty())
 
@@ -239,23 +230,21 @@ def test_addValue(self):
                 q = j / 10.0
 
                 bilip_small = pyopenms.BilinearInterpolation()
-                tmp = bilip_small.getData()
-                tmp.resize(5, 5, float())
+                tmp = pyopenms.MatrixDouble(5, 5, 0.0)
                 bilip_small.setData(tmp)
                 bilip_small.setMapping_0(0.0, 0.0, 5.0, 5.0)
                 bilip_small.setMapping_1(0.0, 0.0, 5.0, 5.0)
                 bilip_small.addValue(p, q, 100)
 
                 bilip_big = pyopenms.BilinearInterpolation()
-                tmp = bilip_big.getData()
-                tmp.resize(15, 15, float())
+                tmp = pyopenms.MatrixDouble(15, 15, 0.0)
                 bilip_big.setData(tmp)
                 bilip_big.setMapping_0(5.0, 0.0, 10.0, 5.0)
                 bilip_big.setMapping_1(5.0, 0.0, 10.0, 5.0)
                 bilip_big.addValue(p, q, 100)
 
-                big_submatrix = pyopenms.MatrixDouble()
-                big_submatrix.resize(5, 5, float())
+                big_submatrix = pyopenms.MatrixDouble(5, 5, 0.0)
+
                 for m in range(5):
                     for n in range(5):
                         big_submatrix.setValue(m, n,
@@ -271,11 +260,8 @@ def test_value(self):
         bilip_small = pyopenms.BilinearInterpolation()
         bilip_big = pyopenms.BilinearInterpolation()
 
-        tmp_small = bilip_small.getData()
-        tmp_big = bilip_big.getData()
-
-        tmp_small.resize(5, 5, float())
-        tmp_big.resize(15, 15, float())
+        tmp_small = pyopenms.MatrixDouble(5, 5, 0.0)
+        tmp_big = pyopenms.MatrixDouble(15, 15, 0.0)
 
         for i in range(5):
             for j in range(5):

From 0fe3c90904d932dd5f63e3b96cb9cf87f1ca8c5c Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Tue, 12 Mar 2024 10:01:49 +0100
Subject: [PATCH 03/17] new attempt with inheritance

---
 .../include/OpenMS/DATASTRUCTURES/Matrix.h    | 86 ++++---------------
 .../source/ANALYSIS/OPENSWATH/MRMScoring.cpp  | 48 +++++------
 .../QUANTITATION/IsotopeLabelingMDVs.cpp      |  4 +-
 .../ANALYSIS/QUANTITATION/ItraqConstants.cpp  |  2 +-
 .../COMPARISON/SPECTRA/PeakAlignment.cpp      | 16 ++--
 .../MISC/NonNegativeLeastSquaresSolver.cpp    |  6 +-
 src/pyOpenMS/pxds/Matrix.pxd                  |  1 +
 7 files changed, 56 insertions(+), 107 deletions(-)

diff --git a/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h b/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
index 3f6eb7820f2..3c95fdd5fb0 100644
--- a/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
+++ b/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
@@ -28,13 +28,15 @@ namespace OpenMS
    * @ingroup Datastructures
    */
   template <typename Value>
-  class Matrix
+  class Matrix : public Eigen::Matrix<Value, Eigen::Dynamic, Eigen::Dynamic>
   {
   public:
     /**
      * @brief Eigen matrix type.
      */
     using EigenMatrixType = Eigen::Matrix<Value, Eigen::Dynamic, Eigen::Dynamic>;
+    using EigenMatrixType::resize;
+    using EigenMatrixType::fill;
 
     // Default constructor. Creates the "null" matrix.
     Matrix() = default;
@@ -61,33 +63,9 @@ namespace OpenMS
      * @param cols Number of columns in the matrix.
      * @param value Initial value to fill the matrix.
      */
-    Matrix(Size rows, Size cols, Value value = Value()) : data_(rows, cols)
+    Matrix(Size rows, Size cols, Value value = Value()) : EigenMatrixType(rows, cols)
     {
-      data_.fill(value);
-    }
-    
-    /**
-     * @brief Accessor to get the value at the specified position in the matrix.
-     * 
-     * @param i Row index.
-     * @param j Column index.
-     * @return reference to the value at the specified position.
-     */
-    const Value& operator()(int i, int j) const
-    {
-      return data_(i, j);
-    }
-
-    /**
-     * @brief Accessor to get the value at the specified position in the matrix.
-     * 
-     * @param i Row index.
-     * @param j Column index.
-     * @return const reference to the value at the specified position.
-     */
-    Value& operator()(int i, int j)
-    {
-      return data_(i, j);
+      fill(value);
     }
 
     /*
@@ -96,7 +74,7 @@ namespace OpenMS
     */
     const Value& getValue(size_t const i, size_t const j) const
     {
-      return data_(i, j);
+      return *this(i, j);
     }
 
     /*
@@ -105,7 +83,7 @@ namespace OpenMS
     */
     Value& getValue(size_t const i, size_t const j)
     {
-      return data_(i, j);
+      return this->operator()(i, j);
     }    
 
     /*
@@ -114,23 +92,7 @@ namespace OpenMS
     */
     void setValue(size_t const i, size_t const j, const Value& value)
     {
-      data_(i, j) = value;
-    }
-
-    /**
-     * @brief Number of rows
-     */
-    size_t rows() const 
-    { 
-      return data_.rows(); 
-    }
-
-    /**
-     * @brief Number of columns
-     */
-    size_t cols() const 
-    { 
-      return data_.cols(); 
+      this->operator()(i, j) = value;
     }
 
     /**
@@ -145,15 +107,15 @@ namespace OpenMS
      * @tparam COLS The number of columns in the matrix.
      * @param array The 2D array containing the values to be assigned to the matrix.
      */
-    template <typename T, int ROWS, int COLS>
+    template <typename T, long int ROWS, long int COLS>
     void setMatrix(T const (&array)[ROWS][COLS]) 
     {
-      data_.resize(ROWS, COLS);
+      resize(ROWS, COLS);
       for (int i = 0; i < ROWS; ++i) 
       {
         for (int j = 0; j < COLS; ++j) 
         {
-          data_(i, j) = array[i][j];
+          this->operator()(i, j) = array[i][j];
         }
       }
     }
@@ -164,20 +126,8 @@ namespace OpenMS
      * @param rhs The matrix to be compared.
      * @return True if matrices are equal, false otherwise.
      */
-    bool operator==(const Matrix& rhs) const
-    {
-      return data_ == rhs.data_;
-    }
-
-    /**
-     * @brief Get the total number of elements in the matrix. Useful for checking if the matrix is empty
-     * or iterating over raw data.
-     * 
-     * @return The total number of elements.
-     */
-    size_t size() const
-    {
-      return data_.size();
+    bool operator==(const Matrix& rhs) const { 
+      return EigenMatrixType::operator==(rhs);
     }
 
     /**
@@ -189,9 +139,9 @@ namespace OpenMS
      */
     friend std::ostream& operator<<(std::ostream& os, const Matrix<Value>& matrix)
     {
-      for (size_t i = 0; i < matrix.rows(); ++i)
+      for (long int i = 0; i < matrix.rows(); ++i)
       {
-        for (size_t j = 0; j < matrix.cols(); ++j)
+        for (long int j = 0; j < matrix.cols(); ++j)
         {
           os << std::setprecision(6) << std::setw(6) << matrix(i, j) << ' ';
         }
@@ -207,7 +157,7 @@ namespace OpenMS
      */
     const EigenMatrixType& getEigenMatrix() const
     {
-      return data_;
+      return *this;
     }
 
     /**
@@ -217,9 +167,7 @@ namespace OpenMS
      */
     EigenMatrixType& getEigenMatrix()
     {
-      return data_;
+      return *this;
     }
-  private:
-    EigenMatrixType data_; ///< Eigen matrix storing the actual data.
   };
 } // namespace OpenMS
diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMScoring.cpp
index a64e19b7525..2bea1a59c77 100644
--- a/src/openms/source/ANALYSIS/OPENSWATH/MRMScoring.cpp
+++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMScoring.cpp
@@ -252,9 +252,9 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_matrix_max_peak_.rows() > 1, "Expect cross-correlation matrix of at least 2x2");
     
       OpenSwath::mean_and_stddev msc;
-      for (std::size_t i = 0; i < xcorr_matrix_max_peak_.rows(); i++)
+      for (long int i = 0; i < xcorr_matrix_max_peak_.rows(); i++)
       {
-        for (std::size_t  j = i; j < xcorr_matrix_max_peak_.rows(); j++)
+        for (long int  j = i; j < xcorr_matrix_max_peak_.rows(); j++)
         {
           // first is the X value (RT), should be an int
           //deltas.push_back(std::abs(Scoring::xcorrArrayGetMaxPeak(xcorr_matrix_.getValue(i, j))->first));
@@ -281,7 +281,7 @@ namespace OpenSwath
       double weights = 0;
 #endif
       double deltas{0};
-      for (std::size_t i = 0; i < xcorr_matrix_max_peak_.rows(); i++)
+      for (long int i = 0; i < xcorr_matrix_max_peak_.rows(); i++)
       {
         deltas += (xcorr_matrix_max_peak_(i, i)//std::abs(Scoring::xcorrArrayGetMaxPeak(xcorr_matrix_.getValue(i, i))->first)
                    * normalized_library_intensity[i]
@@ -291,7 +291,7 @@ namespace OpenSwath
         normalized_library_intensity[i] * normalized_library_intensity[i] << std::endl;
       weights += normalized_library_intensity[i] * normalized_library_intensity[i];
 #endif
-        for (std::size_t j = i + 1; j < xcorr_matrix_max_peak_.rows(); j++)
+        for (long int j = i + 1; j < xcorr_matrix_max_peak_.rows(); j++)
         {
           // first is the X value (RT), should be an int
           deltas += (xcorr_matrix_max_peak_(i, j)//std::abs(Scoring::xcorrArrayGetMaxPeak(xcorr_matrix_.getValue(i, j))->first)
@@ -318,10 +318,10 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_contrast_matrix_.rows() > 0 && xcorr_contrast_matrix_.cols() > 1, "Expect cross-correlation matrix of at least 1x2");
 
       std::vector<double > deltas;
-      for (std::size_t i = 0; i < xcorr_contrast_matrix_.rows(); i++)
+      for (long int i = 0; i < xcorr_contrast_matrix_.rows(); i++)
       {
         double deltas_id = 0;
-        for (std::size_t  j = 0; j < xcorr_contrast_matrix_.cols(); j++)
+        for (long int  j = 0; j < xcorr_contrast_matrix_.cols(); j++)
         {
           // first is the X value (RT), should be an int
           auto x = Scoring::xcorrArrayGetMaxPeak(xcorr_contrast_matrix_(i, j));
@@ -341,9 +341,9 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_precursor_matrix_.rows() > 1, "Expect cross-correlation matrix of at least 2x2");
 
       OpenSwath::mean_and_stddev msc;
-      for (std::size_t i = 0; i < xcorr_precursor_matrix_.rows(); i++)
+      for (long int i = 0; i < xcorr_precursor_matrix_.rows(); i++)
       {
-        for (std::size_t  j = i; j < xcorr_precursor_matrix_.rows(); j++)
+        for (long int  j = i; j < xcorr_precursor_matrix_.rows(); j++)
         {
           // first is the X value (RT), should be an int
           auto x = Scoring::xcorrArrayGetMaxPeak(xcorr_precursor_matrix_(i, j));
@@ -416,9 +416,9 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_precursor_combined_matrix_.rows() > 1, "Expect cross-correlation matrix of at least 2x2");
 
       OpenSwath::mean_and_stddev msc;
-      for (std::size_t i = 0; i < xcorr_precursor_combined_matrix_.rows(); i++)
+      for (long int i = 0; i < xcorr_precursor_combined_matrix_.rows(); i++)
       {
-        for (std::size_t  j = i; j < xcorr_precursor_combined_matrix_.rows(); j++)
+        for (long int  j = i; j < xcorr_precursor_combined_matrix_.rows(); j++)
         {
           // first is the X value (RT), should be an int
           auto x = Scoring::xcorrArrayGetMaxPeak(xcorr_precursor_combined_matrix_(i, j));
@@ -448,9 +448,9 @@ namespace OpenSwath
 
       size_t element_number{0};
       double intensities{0};
-      for (std::size_t i = 0; i < xcorr_matrix_max_peak_sec_.rows(); i++)
+      for (long int i = 0; i < xcorr_matrix_max_peak_sec_.rows(); i++)
       {
-        for (std::size_t j = i; j < xcorr_matrix_max_peak_sec_.rows(); j++)
+        for (long int j = i; j < xcorr_matrix_max_peak_sec_.rows(); j++)
         {
           // second is the Y value (intensity)
           intensities += xcorr_matrix_max_peak_sec_(i, j);
@@ -469,7 +469,7 @@ namespace OpenSwath
       //         see _calc_weighted_xcorr_shape_score in MRM_pgroup.pm
       //         -- they only multiply up the intensity once
       double intensities{0};
-      for (std::size_t i = 0; i < xcorr_matrix_max_peak_sec_.rows(); i++)
+      for (long int i = 0; i < xcorr_matrix_max_peak_sec_.rows(); i++)
       {
         intensities += (xcorr_matrix_max_peak_sec_(i, i)
                         * normalized_library_intensity[i]
@@ -478,7 +478,7 @@ namespace OpenSwath
         std::cout << "_xcorr_weighted " << i << " " << i << " " << Scoring::xcorrArrayGetMaxPeak(xcorr_matrix_[i][i])->second << " weight " <<
         normalized_library_intensity[i] * normalized_library_intensity[i] << std::endl;
 #endif
-        for (std::size_t j = i + 1; j < xcorr_matrix_max_peak_sec_.rows(); j++)
+        for (long int j = i + 1; j < xcorr_matrix_max_peak_sec_.rows(); j++)
         {
           intensities += (xcorr_matrix_max_peak_sec_(i, j)
                           * normalized_library_intensity[i]
@@ -504,10 +504,10 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_contrast_matrix_max_peak_sec_.rows() > 0 && xcorr_contrast_matrix_max_peak_sec_.cols() > 1, "Expect cross-correlation matrix of at least 1x2");
 
       std::vector<double> intensities;
-      for (std::size_t i = 0; i < xcorr_contrast_matrix_max_peak_sec_.rows(); i++)
+      for (long int i = 0; i < xcorr_contrast_matrix_max_peak_sec_.rows(); i++)
       {
         double intensities_id = 0;
-        for (std::size_t j = 0; j < xcorr_contrast_matrix_max_peak_sec_.cols(); j++)
+        for (long int j = 0; j < xcorr_contrast_matrix_max_peak_sec_.cols(); j++)
         {
           // second is the Y value (intensity)
           intensities_id += xcorr_contrast_matrix_max_peak_sec_(i,j);
@@ -523,9 +523,9 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_precursor_matrix_.rows() > 1, "Expect cross-correlation matrix of at least 2x2");
 
       double intensities{0};
-      for(size_t i = 0; i < xcorr_precursor_matrix_.rows(); i++)
+      for(long int i = 0; i < xcorr_precursor_matrix_.rows(); i++)
       {
-        for(size_t j = i; j < xcorr_precursor_matrix_.cols(); j++)
+        for(long int j = i; j < xcorr_precursor_matrix_.cols(); j++)
         {
           auto x = Scoring::xcorrArrayGetMaxPeak(xcorr_precursor_matrix_(i, j));
           intensities += x->second;
@@ -573,9 +573,9 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(xcorr_precursor_combined_matrix_.rows() > 1, "Expect cross-correlation matrix of at least 2x2");
 
       double intensities{0};
-      for(size_t i = 0; i < xcorr_precursor_combined_matrix_.rows(); i++)
+      for(long int i = 0; i < xcorr_precursor_combined_matrix_.rows(); i++)
       {
-        for(size_t j = i; j < xcorr_precursor_combined_matrix_.cols(); j++)
+        for(long int j = i; j < xcorr_precursor_combined_matrix_.cols(); j++)
         {
           auto x = Scoring::xcorrArrayGetMaxPeak(xcorr_precursor_combined_matrix_(i, j));
           intensities += x->second;
@@ -837,7 +837,7 @@ namespace OpenSwath
       OPENSWATH_PRECONDITION(mi_matrix_.rows() > 1, "Expect mutual information matrix of at least 2x2");
 
       double mi_scores{0};
-      for (std::size_t i = 0; i < mi_matrix_.rows(); i++)
+      for (long int i = 0; i < mi_matrix_.rows(); i++)
       {
         mi_scores += mi_matrix_(i, i)
                      * normalized_library_intensity[i]
@@ -846,7 +846,7 @@ namespace OpenSwath
         std::cout << "_mi_weighted " << i << " " << i << " " << mi_matrix_[i][i] << " weight " <<
         normalized_library_intensity[i] * normalized_library_intensity[i] << std::endl;
 #endif
-        for (std::size_t j = i + 1; j < mi_matrix_.rows(); j++)
+        for (long int j = i + 1; j < mi_matrix_.rows(); j++)
         {
           mi_scores += mi_matrix_(i, j)
                        * normalized_library_intensity[i]
@@ -900,10 +900,10 @@ namespace OpenSwath
 
       std::vector<double> mi_scores;
       mi_scores.resize(mi_contrast_matrix_.rows());      
-      for (std::size_t i = 0; i < mi_contrast_matrix_.rows(); i++)
+      for (long int i = 0; i < mi_contrast_matrix_.rows(); i++)
       {
         double mi_scores_id = 0;
-        for (std::size_t j = 0; j < mi_contrast_matrix_.cols(); j++)
+        for (long int j = 0; j < mi_contrast_matrix_.cols(); j++)
         {
           mi_scores_id += mi_contrast_matrix_(i, j);
         }
diff --git a/src/openms/source/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.cpp b/src/openms/source/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.cpp
index 08dce160b27..2dfc52ad344 100644
--- a/src/openms/source/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.cpp
+++ b/src/openms/source/ANALYSIS/QUANTITATION/IsotopeLabelingMDVs.cpp
@@ -84,9 +84,9 @@ namespace OpenMS
     else
     {
       correction_matrix_eigen.resize(correction_matrix.rows(), correction_matrix.cols());
-      for (size_t i = 0; i < correction_matrix.rows(); ++i)
+      for (long int i = 0; i < correction_matrix.rows(); ++i)
       {
-        for (size_t j = 0; j < correction_matrix.cols(); ++j)
+        for (long int j = 0; j < correction_matrix.cols(); ++j)
         {
           correction_matrix_eigen(i,j) = correction_matrix(i,j);
         }
diff --git a/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp b/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp
index e5d3cdb99b4..af586478933 100644
--- a/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp
+++ b/src/openms/source/ANALYSIS/QUANTITATION/ItraqConstants.cpp
@@ -177,7 +177,7 @@ namespace OpenMS
     channel_names[2].setMatrix<Int, 6, 1>(CHANNELS_TMT_SIXPLEX);
 
     map.clear();
-    for (Size i = 0; i < channel_names[itraq_type].rows(); ++i)
+    for (long int i = 0; i < channel_names[itraq_type].rows(); ++i)
     {
       ChannelInfo info;
       info.description = "";
diff --git a/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp b/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
index 3601171a0f9..7c15e2978d4 100644
--- a/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
+++ b/src/openms/source/COMPARISON/SPECTRA/PeakAlignment.cpp
@@ -100,11 +100,11 @@ namespace OpenMS
 
     //initialize alignment matrix with 0 in (0,0) and a multiple of gapcost in the first row/col matrix(row,col,values)
     Matrix<double> matrix(spec1.size() + 1, spec2.size() + 1, 0);
-    for (Size i = 1; i < matrix.rows(); i++)
+    for (long int i = 1; i < matrix.rows(); i++)
     {
       matrix(i, 0) = -gap * i;
     }
-    for (Size i = 1; i < matrix.cols(); i++)
+    for (long int i = 1; i < matrix.cols(); i++)
     {
       matrix(0, i) = -gap * i;
     }
@@ -184,11 +184,11 @@ namespace OpenMS
 
     //get best overall score and return
     double best_score(numeric_limits<double>::min());
-    for (Size i = 0; i < matrix.cols(); i++)
+    for (long int i = 0; i < matrix.cols(); i++)
     {
       best_score = max(best_score, matrix(matrix.rows() - 1, i));
     }
-    for (Size i = 0; i < matrix.rows(); i++)
+    for (long int i = 0; i < matrix.rows(); i++)
     {
       best_score = max(best_score, matrix(i, matrix.cols() - 1));
     }
@@ -235,11 +235,11 @@ namespace OpenMS
 
     //initialize alignment matrix with 0 in (0,0) and a multiple of gapcost in the first row/col matrix(row,col,values)
     Matrix<double> matrix(spec1.size() + 1, spec2.size() + 1, 0);
-    for (Size i = 1; i < matrix.rows(); i++)
+    for (long int i = 1; i < matrix.rows(); i++)
     {
       matrix(i, 0) = -gap * i;
     }
-    for (Size i = 1; i < matrix.cols(); i++)
+    for (long int i = 1; i < matrix.cols(); i++)
     {
       matrix(0, i) = -gap * i;
     }
@@ -346,7 +346,7 @@ namespace OpenMS
     //get matrix coordinates from best alloverscore
     Size row_index(0), col_index(0);
     double best_score(numeric_limits<double>::min());
-    for (Size i = 0; i < matrix.cols(); i++)
+    for (long int i = 0; i < matrix.cols(); i++)
     {
       if (best_score < matrix(matrix.rows() - 1, i))
       {
@@ -355,7 +355,7 @@ namespace OpenMS
         col_index = i;
       }
     }
-    for (Size i = 0; i < matrix.rows(); i++)
+    for (long int i = 0; i < matrix.rows(); i++)
     {
       if (best_score < matrix(i, matrix.cols() - 1))
       {
diff --git a/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp b/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp
index af72bf38877..b5fe54df4ac 100644
--- a/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp
+++ b/src/openms/source/MATH/MISC/NonNegativeLeastSquaresSolver.cpp
@@ -22,9 +22,9 @@ namespace OpenMS
     // translate A to array a (column major order)
     double * a_vec = new double[A.rows() * A.cols()];
     size_t idx = 0;
-    for (size_t col = 0; col < A.cols(); ++col)
+    for (long int col = 0; col < A.cols(); ++col)
     {
-      for (size_t row = 0; row < A.rows(); ++row)
+      for (long int row = 0; row < A.rows(); ++row)
       {
         a_vec[idx] = A(row, col);
         idx++;
@@ -41,7 +41,7 @@ namespace OpenMS
 
     // translate b
     double * b_vec = new double[a_rows];
-    for (size_t row = 0; row < b.rows(); ++row)
+    for (long int row = 0; row < b.rows(); ++row)
     {
       b_vec[row] = b(row, 0);
     }
diff --git a/src/pyOpenMS/pxds/Matrix.pxd b/src/pyOpenMS/pxds/Matrix.pxd
index 102c0cdce9b..5180d558ddf 100644
--- a/src/pyOpenMS/pxds/Matrix.pxd
+++ b/src/pyOpenMS/pxds/Matrix.pxd
@@ -17,6 +17,7 @@ cdef extern from "<OpenMS/DATASTRUCTURES/Matrix.h>" namespace "OpenMS":
         size_t rows() nogil
         size_t cols() nogil
         size_t size() nogil
+        ValueT* data() nogil
         ## bool operator==(Matrix & rhs) except + nogil 
         ## bool operator<(Matrix & rhs) except + nogil 
         # TEMPLATE # void setMatrix(ValueType matrix) except + nogil 

From adb5e6b608ce7f49f420aa4f0a0741fb0609e31e Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Wed, 13 Mar 2024 22:37:05 +0100
Subject: [PATCH 04/17] fix normal test

---
 src/pyOpenMS/addons/MatrixDouble.pyx    | 38 ++++++-------------------
 src/pyOpenMS/tests/unittests/test000.py |  2 ++
 2 files changed, 10 insertions(+), 30 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 6a43cc3ac4d..b07de66fbd2 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -1,30 +1,19 @@
 from Matrix cimport *
-
+cimport numpy as np
 
 # continue with extra code if needed
 
     def get_matrix_as_view(self):
-        """Cython signature: numpy_matrix get_matrix()
+        """Cython signature: numpy_matrix get_matrix_as_view()
         """
 
         cdef _Matrix[double] * mat_ = self.inst.get()
 
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
-        cdef unsigned int n = rows * cols
-        cdef np.ndarray[double, ndim=2] data
-        data = np.zeros( (rows,cols), dtype=np.float64)
-
-        cdef libcpp_vector[double] * vec_ptr = <libcpp_vector[double]*> mat_
-        cdef double * raw_ptr =  address(deref(vec_ptr)[0]) 
-
-        ## # We use a memory view to get the data from the raw data
-        ## # See https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html 
-        ## # See https://stackoverflow.com/questions/43021574/cast-c-array-into-numpy-array-cython-typed-memoryview-in-cython-code
-        cdef double[:] vec_view = <double[:n]>raw_ptr # cast to memoryview, refer to the underlying buffer without copy
-        xarr = np.asarray(vec_view) # numpy array refer to the underlying buffer without copy
-        xarr = xarr.reshape(rows, cols)
-        return xarr.transpose()
+        cdef double* data = mat_.data()
+        # Create a NumPy array from the buffer, specifying not to copy the data.
+        return np.array(<double[:rows * cols:1]> data, copy=False).reshape(rows, cols)
 
 
     def get_matrix(self):
@@ -32,23 +21,12 @@ from Matrix cimport *
         """
 
         cdef _Matrix[double] * mat_ = self.inst.get()
-
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
-        cdef unsigned int n = rows * cols
-        cdef np.ndarray[double, ndim=2] data
-        data = np.zeros( (rows,cols), dtype=np.float64)
-
-        cdef libcpp_vector[double] * vec_ptr = <libcpp_vector[double]*> mat_
-        cdef double * raw_ptr =  address(deref(vec_ptr)[0]) 
+        cdef double* data = mat_.data()
+        # Create a NumPy array from the buffer, specifying not to copy the data.
+        return np.array(<double[:rows * cols:1]> data, copy=True).reshape(rows, cols)
 
-        ## # We use a memory view to get the data from the raw data
-        ## # See https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html 
-        ## # See https://stackoverflow.com/questions/43021574/cast-c-array-into-numpy-array-cython-typed-memoryview-in-cython-code
-        cdef double[:] vec_view = <double[:n]>raw_ptr # cast to memoryview, refer to the underlying buffer without copy
-        xarr = np.asarray(vec_view) # numpy array refer to the underlying buffer without copy
-        xarr = xarr.reshape(rows, cols)
-        return xarr.transpose().copy()
 
 #    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
 #        """Cython signature: numpy_matrix set_matrix()
diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index 7f6f1d4e44c..199f998f554 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -3666,7 +3666,9 @@ def testMatrixDouble():
     m.setValue(3, 5, 8.0)
     assert m.getValue(3, 5) == 8.0
 
+    print(m)
     mat = m.get_matrix_as_view()
+    print(mat)
     assert mat[3, 5] == 8.0
 
     mat = m.get_matrix()

From 8e06fab1ca8cf289c306e5783a5955d433a65874 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Thu, 14 Mar 2024 09:24:23 +0100
Subject: [PATCH 05/17] why?

---
 src/pyOpenMS/pxds/Matrix.pxd            |  2 +-
 src/pyOpenMS/tests/unittests/test000.py | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/pyOpenMS/pxds/Matrix.pxd b/src/pyOpenMS/pxds/Matrix.pxd
index 5180d558ddf..ee4afc73629 100644
--- a/src/pyOpenMS/pxds/Matrix.pxd
+++ b/src/pyOpenMS/pxds/Matrix.pxd
@@ -17,7 +17,7 @@ cdef extern from "<OpenMS/DATASTRUCTURES/Matrix.h>" namespace "OpenMS":
         size_t rows() nogil
         size_t cols() nogil
         size_t size() nogil
-        ValueT* data() nogil
+        ValueT* data() nogil # wrap-ignore
         ## bool operator==(Matrix & rhs) except + nogil 
         ## bool operator<(Matrix & rhs) except + nogil 
         # TEMPLATE # void setMatrix(ValueType matrix) except + nogil 
diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index 199f998f554..037e711c238 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -3659,21 +3659,21 @@ def testMatrixDouble():
     assert sum(sum(matrix_view)) == (N-1)*(N+2)*5
 
 
-    # Column = 3 / Row = 5
+    # Column = 2 / Row = 3
     ## Now change a value:
 
-    assert m.getValue(3, 5) == 5.0
-    m.setValue(3, 5, 8.0)
-    assert m.getValue(3, 5) == 8.0
+    assert m.getValue(2, 3) == 5.0
+    m.setValue(2, 3, 8.0)
+    assert m.getValue(2, 3) == 8.0
 
     print(m)
     mat = m.get_matrix_as_view()
     print(mat)
-    assert mat[3, 5] == 8.0
+    assert mat[2, 3] == 8.0
 
     mat = m.get_matrix()
-    assert m.getValue(3, 5) == 8.0
-    assert mat[3, 5] == 8.0
+    assert m.getValue(2, 3) == 8.0
+    assert mat[2, 3] == 8.0
 
     # Whatever we change here gets changed in the raw data as well
     matrix_view = m.get_matrix_as_view()
@@ -3687,7 +3687,7 @@ def testMatrixDouble():
 
     mat[3, 6] = 9.0
     m.set_matrix(mat)
-    assert m.getValue(3, 5) == 8.0
+    assert m.getValue(2, 3) == 8.0
     assert m.getValue(3, 6) == 9.0
 
 

From f6aafe958d42ab23cd0775e95fb6f61d75d9c29a Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Thu, 14 Mar 2024 09:56:15 +0100
Subject: [PATCH 06/17] 1,2

---
 src/pyOpenMS/tests/unittests/test000.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index 037e711c238..8fb92c67f6c 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -3659,21 +3659,21 @@ def testMatrixDouble():
     assert sum(sum(matrix_view)) == (N-1)*(N+2)*5
 
 
-    # Column = 2 / Row = 3
+    # Column = 1 / Row = 2
     ## Now change a value:
 
-    assert m.getValue(2, 3) == 5.0
-    m.setValue(2, 3, 8.0)
-    assert m.getValue(2, 3) == 8.0
+    assert m.getValue(1, 2) == 5.0
+    m.setValue(1, 2, 8.0)
+    assert m.getValue(1, 2) == 8.0
 
     print(m)
     mat = m.get_matrix_as_view()
     print(mat)
-    assert mat[2, 3] == 8.0
+    assert mat[1, 2] == 8.0
 
     mat = m.get_matrix()
-    assert m.getValue(2, 3) == 8.0
-    assert mat[2, 3] == 8.0
+    assert m.getValue(1, 2) == 8.0
+    assert mat[1, 2] == 8.0
 
     # Whatever we change here gets changed in the raw data as well
     matrix_view = m.get_matrix_as_view()
@@ -3687,7 +3687,7 @@ def testMatrixDouble():
 
     mat[3, 6] = 9.0
     m.set_matrix(mat)
-    assert m.getValue(2, 3) == 8.0
+    assert m.getValue(1, 2) == 8.0
     assert m.getValue(3, 6) == 9.0
 
 

From 146953c367184d50c1dc1f40b355ea95ca87119c Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 00:57:37 +0100
Subject: [PATCH 07/17] test

---
 src/pyOpenMS/addons/MatrixDouble.pyx    | 41 ++++++++++++++++++++++---
 src/pyOpenMS/tests/unittests/test000.py | 14 +++++++++
 2 files changed, 51 insertions(+), 4 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index b07de66fbd2..47bc287fb67 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -1,11 +1,44 @@
 from Matrix cimport *
 cimport numpy as np
+from numpy.lib.stride_tricks import as_strided
 
 # continue with extra code if needed
-
     def get_matrix_as_view(self):
         """Cython signature: numpy_matrix get_matrix_as_view()
         """
+        cdef _Matrix[double] * mat_ = self.inst.get()
+ 
+        cdef unsigned int rows = mat_.rows()
+        cdef unsigned int cols = mat_.cols()
+        cdef double* data = mat_.data()
+        cdef double[:,:] mem_view = <double[:rows,:cols]>data
+        dtype = 'double'
+        cdef int itemsize = np.dtype(dtype).itemsize
+        cdef int row_stride = 1
+        cdef int col_stride = 1
+                
+        return as_strided(np.asarray(mem_view, dtype=dtype, order="C"), strides=[row_stride*itemsize, col_stride*itemsize])            
+    
+    def get_matrix(self):
+        """Cython signature: numpy_matrix get_matrix()
+        """
+        cdef _Matrix[double] * mat_ = self.inst.get()
+ 
+        cdef unsigned int rows = mat_.rows()
+        cdef unsigned int cols = mat_.cols()
+        cdef double* data = mat_.data()
+        cdef double[:,:] mem_view = <double[:rows,:cols]>data
+        dtype = 'double'
+        cdef int itemsize = np.dtype(dtype).itemsize
+        cdef int row_stride = 1
+        cdef int col_stride = 1
+                
+        return np.copy(as_strided(np.asarray(mem_view, dtype=dtype, order="C"), strides=[row_stride*itemsize, col_stride*itemsize]))           
+            
+
+    def get_matrix_as_view2(self):
+        """Cython signature: numpy_matrix get_matrix_as_view()
+        """
 
         cdef _Matrix[double] * mat_ = self.inst.get()
 
@@ -13,10 +46,10 @@ cimport numpy as np
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
         # Create a NumPy array from the buffer, specifying not to copy the data.
-        return np.array(<double[:rows * cols:1]> data, copy=False).reshape(rows, cols)
+        return np.array(<double[:rows * cols:1]> data, order='C', copy=False).reshape(rows, cols)
 
 
-    def get_matrix(self):
+    def get_matrix2(self):
         """Cython signature: numpy_matrix get_matrix()
         """
 
@@ -25,7 +58,7 @@ cimport numpy as np
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
         # Create a NumPy array from the buffer, specifying not to copy the data.
-        return np.array(<double[:rows * cols:1]> data, copy=True).reshape(rows, cols)
+        return np.array(<double[:rows * cols:1]> data, order='C', copy=True).reshape(rows, cols)
 
 
 #    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
diff --git a/src/pyOpenMS/tests/unittests/test000.py b/src/pyOpenMS/tests/unittests/test000.py
index 8fb92c67f6c..9f03d134fba 100644
--- a/src/pyOpenMS/tests/unittests/test000.py
+++ b/src/pyOpenMS/tests/unittests/test000.py
@@ -3631,6 +3631,20 @@ def testMatrixDouble():
      MapAlignmentAlgorithmIdentification.__init__
      """
 
+    m = pyopenms.MatrixDouble(3, 2, 0.0)
+    for i in range(3):
+        for j in range(2):
+            m.setValue(i, j, i * 10.0 + j) 
+    print(m)
+
+    mv = m.get_matrix_as_view()
+    print(mv)
+
+    mc = m.get_matrix()
+    print(mc)
+
+    mat = m.get_matrix_as_view()
+
     N = 90
     m = pyopenms.MatrixDouble(N-1, N+2, 5.0)
 

From 47d9374a9afe66433f45ad965480fdab54ea60a6 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 08:28:03 +0100
Subject: [PATCH 08/17] set order in reshape

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 69 +++++++---------------------
 1 file changed, 17 insertions(+), 52 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 47bc287fb67..11095845f29 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -1,42 +1,11 @@
 from Matrix cimport *
 cimport numpy as np
-from numpy.lib.stride_tricks import as_strided
+
 
 # continue with extra code if needed
-    def get_matrix_as_view(self):
-        """Cython signature: numpy_matrix get_matrix_as_view()
-        """
-        cdef _Matrix[double] * mat_ = self.inst.get()
- 
-        cdef unsigned int rows = mat_.rows()
-        cdef unsigned int cols = mat_.cols()
-        cdef double* data = mat_.data()
-        cdef double[:,:] mem_view = <double[:rows,:cols]>data
-        dtype = 'double'
-        cdef int itemsize = np.dtype(dtype).itemsize
-        cdef int row_stride = 1
-        cdef int col_stride = 1
-                
-        return as_strided(np.asarray(mem_view, dtype=dtype, order="C"), strides=[row_stride*itemsize, col_stride*itemsize])            
-    
-    def get_matrix(self):
-        """Cython signature: numpy_matrix get_matrix()
-        """
-        cdef _Matrix[double] * mat_ = self.inst.get()
- 
-        cdef unsigned int rows = mat_.rows()
-        cdef unsigned int cols = mat_.cols()
-        cdef double* data = mat_.data()
-        cdef double[:,:] mem_view = <double[:rows,:cols]>data
-        dtype = 'double'
-        cdef int itemsize = np.dtype(dtype).itemsize
-        cdef int row_stride = 1
-        cdef int col_stride = 1
-                
-        return np.copy(as_strided(np.asarray(mem_view, dtype=dtype, order="C"), strides=[row_stride*itemsize, col_stride*itemsize]))           
             
 
-    def get_matrix_as_view2(self):
+    def get_matrix_as_view(self):
         """Cython signature: numpy_matrix get_matrix_as_view()
         """
 
@@ -46,10 +15,10 @@ from numpy.lib.stride_tricks import as_strided
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
         # Create a NumPy array from the buffer, specifying not to copy the data.
-        return np.array(<double[:rows * cols:1]> data, order='C', copy=False).reshape(rows, cols)
+        return np.array(<double[:rows * cols:1]> data, order='F', copy=False).reshape(rows, cols, order='F')
 
 
-    def get_matrix2(self):
+    def get_matrix(self):
         """Cython signature: numpy_matrix get_matrix()
         """
 
@@ -57,25 +26,21 @@ from numpy.lib.stride_tricks import as_strided
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
-        # Create a NumPy array from the buffer, specifying not to copy the data.
-        return np.array(<double[:rows * cols:1]> data, order='C', copy=True).reshape(rows, cols)
+        return np.array(<double[:rows * cols:1]> data, order='F', copy=True).reshape(rows, cols, order='F')
 
+    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
+        """Cython signature: numpy_matrix set_matrix()
+        """
 
-#    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
-#        """Cython signature: numpy_matrix set_matrix()
-#        """
-#
-#        cdef _Matrix[double] * mat_ = self.inst.get()
-#
-#        cdef unsigned int rows = data.shape[0]
-#        cdef unsigned int cols = data.shape[1]
-#        mat_.resize(rows, cols, 0)
-#
-#        cdef int i = 0
-#        cdef int j = 0
-#        for i in range(int(rows)):
-#            for j in range(int(cols)):
-#                mat_.setValue(i,j,data[i][j])
+        cdef _Matrix[double] * mat_ = self.inst.get()
 
+        cdef unsigned int rows = data.shape[0]
+        cdef unsigned int cols = data.shape[1]
+        mat_.resize(rows, cols, 0)
 
+        cdef int i = 0
+        cdef int j = 0
+        for i in range(int(rows)):
+            for j in range(int(cols)):
+                mat_.setValue(i,j,data[i][j])
 

From 02d7a93e4ef07a50a23148cd8820b899eb6c08f4 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 08:32:25 +0100
Subject: [PATCH 09/17] fix compile errors

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 11095845f29..a6314a7343d 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -36,7 +36,7 @@ cimport numpy as np
 
         cdef unsigned int rows = data.shape[0]
         cdef unsigned int cols = data.shape[1]
-        mat_.resize(rows, cols, 0)
+        mat_.resize(rows, cols)
 
         cdef int i = 0
         cdef int j = 0

From 48f55af186142ac3a38cfc251b29b96662b4c515 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 09:37:53 +0100
Subject: [PATCH 10/17] fix

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 24 ++++++++++++------------
 src/pyOpenMS/pxds/Matrix.pxd         |  1 +
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index a6314a7343d..9970f3eeb40 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -28,19 +28,19 @@ cimport numpy as np
         cdef double* data = mat_.data()
         return np.array(<double[:rows * cols:1]> data, order='F', copy=True).reshape(rows, cols, order='F')
 
-    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
-        """Cython signature: numpy_matrix set_matrix()
-        """
+#    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
+#        """Cython signature: numpy_matrix set_matrix()
+#        """
 
-        cdef _Matrix[double] * mat_ = self.inst.get()
+#        cdef _Matrix[double] * mat_ = self.inst.get()
 
-        cdef unsigned int rows = data.shape[0]
-        cdef unsigned int cols = data.shape[1]
-        mat_.resize(rows, cols)
+#        cdef unsigned int rows = data.shape[0]
+#        cdef unsigned int cols = data.shape[1]
+#        mat_.resize(rows, cols)
 
-        cdef int i = 0
-        cdef int j = 0
-        for i in range(int(rows)):
-            for j in range(int(cols)):
-                mat_.setValue(i,j,data[i][j])
+#        cdef int i = 0
+#        cdef int j = 0
+#        for i in range(int(rows)):
+#            for j in range(int(cols)):
+#                mat_.setValue(i,j,data[i][j])
 
diff --git a/src/pyOpenMS/pxds/Matrix.pxd b/src/pyOpenMS/pxds/Matrix.pxd
index ee4afc73629..d0057a73c56 100644
--- a/src/pyOpenMS/pxds/Matrix.pxd
+++ b/src/pyOpenMS/pxds/Matrix.pxd
@@ -17,6 +17,7 @@ cdef extern from "<OpenMS/DATASTRUCTURES/Matrix.h>" namespace "OpenMS":
         size_t rows() nogil
         size_t cols() nogil
         size_t size() nogil
+        #resize(size_t rows, size_t cols) nogil
         ValueT* data() nogil # wrap-ignore
         ## bool operator==(Matrix & rhs) except + nogil 
         ## bool operator<(Matrix & rhs) except + nogil 

From 0c19ad3bb4145e480511c013dbe4bd3b1202ec02 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 16:31:05 +0100
Subject: [PATCH 11/17] why

---
 .../include/OpenMS/DATASTRUCTURES/Matrix.h    | 24 ++++++++++++++-
 src/pyOpenMS/addons/MatrixDouble.pyx          | 29 ++++++++++++++++---
 src/pyOpenMS/pxds/Matrix.pxd                  |  3 ++
 3 files changed, 51 insertions(+), 5 deletions(-)

diff --git a/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h b/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
index 3c95fdd5fb0..81d034c0ec7 100644
--- a/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
+++ b/src/openms/include/OpenMS/DATASTRUCTURES/Matrix.h
@@ -35,8 +35,9 @@ namespace OpenMS
      * @brief Eigen matrix type.
      */
     using EigenMatrixType = Eigen::Matrix<Value, Eigen::Dynamic, Eigen::Dynamic>;
-    using EigenMatrixType::resize;
     using EigenMatrixType::fill;
+    using EigenMatrixType::innerStride;
+    using EigenMatrixType::outerStride;
 
     // Default constructor. Creates the "null" matrix.
     Matrix() = default;
@@ -95,6 +96,27 @@ namespace OpenMS
       this->operator()(i, j) = value;
     }
 
+    // apparently needed for cython
+    void resize(size_t rows, size_t cols)
+    {
+      EigenMatrixType::resize(rows, cols);
+    }
+
+    int innerStride() const
+    {
+      return EigenMatrixType::innerStride();
+    }
+
+    int outerStride() const
+    {
+      return EigenMatrixType::outerStride();
+    }
+
+    bool rowMajor() const
+    {
+      return EigenMatrixType::IsRowMajor;
+    }
+
     /**
      * @brief Sets the matrix values using a 2D array.
      * 
diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 9970f3eeb40..478aa7c3e0e 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -1,5 +1,6 @@
 from Matrix cimport *
 cimport numpy as np
+from numpy.lib.stride_tricks import as_strided
 
 
 # continue with extra code if needed
@@ -10,12 +11,21 @@ cimport numpy as np
         """
 
         cdef _Matrix[double] * mat_ = self.inst.get()
-
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
-        # Create a NumPy array from the buffer, specifying not to copy the data.
-        return np.array(<double[:rows * cols:1]> data, order='F', copy=False).reshape(rows, cols, order='F')
+        cdef double[:,:] mem_view = <double[:rows,:cols]>data
+        dtype = 'double'
+        cdef int itemsize = np.dtype(dtype).itemsize
+        cdef unsigned int row_stride, col_stride
+        if mat_.rowMajor():
+            row_stride = mat_.outerStride() if mat_.outerStride() > 0 else cols
+            col_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+        else:
+            row_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+            col_stride = mat_.outerStride() if mat_.outerStride() > 0 else rows
+
+        return np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order="F"), strides=[row_stride*itemsize, col_stride*itemsize])
 
 
     def get_matrix(self):
@@ -26,7 +36,18 @@ cimport numpy as np
         cdef unsigned int rows = mat_.rows()
         cdef unsigned int cols = mat_.cols()
         cdef double* data = mat_.data()
-        return np.array(<double[:rows * cols:1]> data, order='F', copy=True).reshape(rows, cols, order='F')
+        cdef double[:,:] mem_view = <double[:rows,:cols]>data
+        dtype = 'double'
+        cdef int itemsize = np.dtype(dtype).itemsize
+        cdef unsigned int row_stride, col_stride
+        if mat_.rowMajor():
+            row_stride = mat_.outerStride() if mat_.outerStride() > 0 else cols
+            col_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+        else:
+            row_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+            col_stride = mat_.outerStride() if mat_.outerStride() > 0 else rows
+
+        return np.copy(np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order="F"), strides=[row_stride*itemsize, col_stride*itemsize]))
 
 #    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
 #        """Cython signature: numpy_matrix set_matrix()
diff --git a/src/pyOpenMS/pxds/Matrix.pxd b/src/pyOpenMS/pxds/Matrix.pxd
index d0057a73c56..eaa188a2eb1 100644
--- a/src/pyOpenMS/pxds/Matrix.pxd
+++ b/src/pyOpenMS/pxds/Matrix.pxd
@@ -17,6 +17,9 @@ cdef extern from "<OpenMS/DATASTRUCTURES/Matrix.h>" namespace "OpenMS":
         size_t rows() nogil
         size_t cols() nogil
         size_t size() nogil
+        int innerStride() nogil # wrap-ignore
+        int outerStride() nogil # wrap-ignore
+        bool rowMajor() nogil # wrap-ignore
         #resize(size_t rows, size_t cols) nogil
         ValueT* data() nogil # wrap-ignore
         ## bool operator==(Matrix & rhs) except + nogil 

From f8da39233b63fa89cc76803ac14627533c97bfc0 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 16:41:34 +0100
Subject: [PATCH 12/17] yeeeeeeeeeees

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index 478aa7c3e0e..f9c5fe922e0 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -18,14 +18,17 @@ from numpy.lib.stride_tricks import as_strided
         dtype = 'double'
         cdef int itemsize = np.dtype(dtype).itemsize
         cdef unsigned int row_stride, col_stride
+        o = 'F'
         if mat_.rowMajor():
             row_stride = mat_.outerStride() if mat_.outerStride() > 0 else cols
             col_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+            o = 'F'
         else:
             row_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
             col_stride = mat_.outerStride() if mat_.outerStride() > 0 else rows
+            o = 'C'
 
-        return np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order="F"), strides=[row_stride*itemsize, col_stride*itemsize])
+        return np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order=o), strides=[row_stride*itemsize, col_stride*itemsize])
 
 
     def get_matrix(self):
@@ -40,14 +43,18 @@ from numpy.lib.stride_tricks import as_strided
         dtype = 'double'
         cdef int itemsize = np.dtype(dtype).itemsize
         cdef unsigned int row_stride, col_stride
+        o = 'F'
+        
         if mat_.rowMajor():
             row_stride = mat_.outerStride() if mat_.outerStride() > 0 else cols
             col_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
+            o = 'F'
         else:
             row_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
             col_stride = mat_.outerStride() if mat_.outerStride() > 0 else rows
+            o = 'C'
 
-        return np.copy(np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order="F"), strides=[row_stride*itemsize, col_stride*itemsize]))
+        return np.copy(np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order=o), strides=[row_stride*itemsize, col_stride*itemsize]))
 
 #    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
 #        """Cython signature: numpy_matrix set_matrix()

From aa31df00305394ae19c4c98f32086201464a5889 Mon Sep 17 00:00:00 2001
From: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>
Date: Fri, 15 Mar 2024 17:05:00 +0100
Subject: [PATCH 13/17] added back set_matrix

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 24 ++++++++++++------------
 src/pyOpenMS/pxds/Matrix.pxd         |  2 +-
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index f9c5fe922e0..abddf6d7eec 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -56,19 +56,19 @@ from numpy.lib.stride_tricks import as_strided
 
         return np.copy(np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order=o), strides=[row_stride*itemsize, col_stride*itemsize]))
 
-#    def set_matrix(self, np.ndarray[double, ndim=2, mode="c"] data not None):
-#        """Cython signature: numpy_matrix set_matrix()
-#        """
+    def set_matrix(self, np.ndarray[double, ndim=2] data not None):
+        """Cython signature: numpy_matrix set_matrix()
+        """
 
-#        cdef _Matrix[double] * mat_ = self.inst.get()
+        cdef _Matrix[double] * mat_ = self.inst.get()
 
-#        cdef unsigned int rows = data.shape[0]
-#        cdef unsigned int cols = data.shape[1]
-#        mat_.resize(rows, cols)
+        cdef unsigned int rows = data.shape[0]
+        cdef unsigned int cols = data.shape[1]
+        mat_.resize(rows, cols)
 
-#        cdef int i = 0
-#        cdef int j = 0
-#        for i in range(int(rows)):
-#            for j in range(int(cols)):
-#                mat_.setValue(i,j,data[i][j])
+        cdef int i = 0
+        cdef int j = 0
+        for i in range(int(rows)):
+            for j in range(int(cols)):
+                mat_.setValue(i, j, data[i][j])
 
diff --git a/src/pyOpenMS/pxds/Matrix.pxd b/src/pyOpenMS/pxds/Matrix.pxd
index eaa188a2eb1..b289b87eff5 100644
--- a/src/pyOpenMS/pxds/Matrix.pxd
+++ b/src/pyOpenMS/pxds/Matrix.pxd
@@ -20,7 +20,7 @@ cdef extern from "<OpenMS/DATASTRUCTURES/Matrix.h>" namespace "OpenMS":
         int innerStride() nogil # wrap-ignore
         int outerStride() nogil # wrap-ignore
         bool rowMajor() nogil # wrap-ignore
-        #resize(size_t rows, size_t cols) nogil
+        void resize(size_t rows, size_t cols) nogil
         ValueT* data() nogil # wrap-ignore
         ## bool operator==(Matrix & rhs) except + nogil 
         ## bool operator<(Matrix & rhs) except + nogil 

From a905b2e4cce600176649abf4018a4c6c4b11fcd3 Mon Sep 17 00:00:00 2001
From: julianuspfeuffer <julianus.pfeuffer@pfizer.com>
Date: Sat, 16 Mar 2024 10:41:32 +0100
Subject: [PATCH 14/17] docs and refactor

---
 src/pyOpenMS/addons/MatrixDouble.pyx | 36 +++++++++++-----------------
 1 file changed, 14 insertions(+), 22 deletions(-)

diff --git a/src/pyOpenMS/addons/MatrixDouble.pyx b/src/pyOpenMS/addons/MatrixDouble.pyx
index abddf6d7eec..534160b8b9b 100644
--- a/src/pyOpenMS/addons/MatrixDouble.pyx
+++ b/src/pyOpenMS/addons/MatrixDouble.pyx
@@ -7,7 +7,13 @@ from numpy.lib.stride_tricks import as_strided
             
 
     def get_matrix_as_view(self):
-        """Cython signature: numpy_matrix get_matrix_as_view()
+        """get_matrix(self) -> np.ndarray[double, ndim=2]
+
+        Returns a view on the underlying Matrix as a 2D numpy ndarray.
+        .. caution::
+           Future changes to the Matrix will affect the ndarray and vice versa.
+           Make sure that the Matrix does not go out of scope before the last use
+           of your ndarray.
         """
 
         cdef _Matrix[double] * mat_ = self.inst.get()
@@ -32,32 +38,18 @@ from numpy.lib.stride_tricks import as_strided
 
 
     def get_matrix(self):
-        """Cython signature: numpy_matrix get_matrix()
+        """get_matrix(self) -> np.ndarray[double, ndim=2]
+
+        Returns a copy of the underlying Matrix as a 2D numpy ndarray.
         """
 
-        cdef _Matrix[double] * mat_ = self.inst.get()
-        cdef unsigned int rows = mat_.rows()
-        cdef unsigned int cols = mat_.cols()
-        cdef double* data = mat_.data()
-        cdef double[:,:] mem_view = <double[:rows,:cols]>data
-        dtype = 'double'
-        cdef int itemsize = np.dtype(dtype).itemsize
-        cdef unsigned int row_stride, col_stride
-        o = 'F'
-        
-        if mat_.rowMajor():
-            row_stride = mat_.outerStride() if mat_.outerStride() > 0 else cols
-            col_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
-            o = 'F'
-        else:
-            row_stride = mat_.innerStride() if mat_.innerStride() > 0 else 1
-            col_stride = mat_.outerStride() if mat_.outerStride() > 0 else rows
-            o = 'C'
+        return np.copy(self.get_matrix_as_view())
 
-        return np.copy(np.lib.stride_tricks.as_strided(np.asarray(mem_view, dtype=dtype, order=o), strides=[row_stride*itemsize, col_stride*itemsize]))
 
     def set_matrix(self, np.ndarray[double, ndim=2] data not None):
-        """Cython signature: numpy_matrix set_matrix()
+        """set_matrix(self, data: np.ndarray[double, ndim=2]) -> None
+
+        Copies the values from the numpy ndarray into the Matrix.
         """
 
         cdef _Matrix[double] * mat_ = self.inst.get()

From 65f728755083b7d7a1039fb0e374dded64cdb16d Mon Sep 17 00:00:00 2001
From: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>
Date: Sat, 16 Mar 2024 14:41:34 +0100
Subject: [PATCH 15/17] [Fix] GHA MacOS python brew problem

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

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 7142c6f28ab..286c90ed1e1 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -266,12 +266,12 @@ jobs:
         fi
 
         if [[ "${{ matrix.os }}" == macos-* ]]; then
-          brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
+## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
+brew install python3 --force --overwrite          brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
           brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@5
           echo "cmake_prefix=$(brew --prefix qt@5)/lib/cmake;$(brew --prefix qt@5)" >> $GITHUB_OUTPUT
           echo "Qt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5" >> $GITHUB_ENV
           if [[ "${{ steps.set-vars.outputs.pkg_type }}" != "none" ]]; then
-            brew install python3 --force --overwrite
             brew install --quiet doxygen ghostscript graphviz
           fi
         fi

From cc1e042190feebd1c94e22781d76c1487455930a Mon Sep 17 00:00:00 2001
From: Julianus Pfeuffer <julianus.pfeuffer@pfizer.com>
Date: Sat, 16 Mar 2024 15:01:52 +0100
Subject: [PATCH 16/17] indent

---
 .github/workflows/openms_ci_matrix_full.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/openms_ci_matrix_full.yml b/.github/workflows/openms_ci_matrix_full.yml
index 286c90ed1e1..9da9679bf0c 100644
--- a/.github/workflows/openms_ci_matrix_full.yml
+++ b/.github/workflows/openms_ci_matrix_full.yml
@@ -265,9 +265,10 @@ jobs:
           fi
         fi
 
-        if [[ "${{ matrix.os }}" == macos-* ]]; then
-## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
-brew install python3 --force --overwrite          brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
+        if [[ "${{ matrix.os }}" == macos-* ]];      then
+          ## Needed for Qt. Install before to overwrite the default softlinks on the GH runners
+          brew install python3 --force --overwrite
+          brew install --quiet ccache autoconf automake libtool ninja && brew link --overwrite ccache
           brew install libsvm xerces-c boost eigen sqlite coinutils cbc cgl clp qt@5
           echo "cmake_prefix=$(brew --prefix qt@5)/lib/cmake;$(brew --prefix qt@5)" >> $GITHUB_OUTPUT
           echo "Qt5_DIR=$(brew --prefix qt@5)/lib/cmake/Qt5" >> $GITHUB_ENV

From 9643475fbf3023376f34e2b9b46b0733ec3c6bc5 Mon Sep 17 00:00:00 2001
From: Samuel Wein <sam@samwein.com>
Date: Mon, 18 Mar 2024 01:26:24 +0100
Subject: [PATCH 17/17] Update CMakeLists.txt

Fix typos
---
 doc/CMakeLists.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index f652e12dd9f..ca645b28a67 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -323,7 +323,7 @@ if(ENABLE_DOCS)
     #------------------------------------------------------------------------------
     # add virtual dependency of doc_minimal on TOPP
     # this is not necessary but defers the generation of doc_minimal to a later
-    # stage to avoid confusion if doc_minimal is build first
+    # stage to avoid confusion if doc_minimal is built first
     add_dependencies(doc_minimal TOPP)
 
     if (DOXYGEN_DOT_FOUND OR DOXYGEN_DOT_EXECUTABLE)
@@ -381,9 +381,9 @@ if(ENABLE_DOCS)
   message(STATUS "Build C++ tutorials: ${BUILD_EXAMPLES} (-DBUILD_EXAMPLES=ON/OFF);")
   if(BUILD_EXAMPLES AND "${PACKAGE_TYPE}" STREQUAL "none")
     add_subdirectory(code_examples)
-    message(STATUS " --> Tutorials in '${PROJECT_SOURCE_DIR}/code_examples' will be build!")
+    message(STATUS " --> Tutorials in '${PROJECT_SOURCE_DIR}/code_examples' will be built!")
   else()
-    message(STATUS " --> Tutorials in '${PROJECT_SOURCE_DIR}/code_examples' will NOT be build! (since PACKAGE_TYPE=${PACKAGE_TYPE}, but must be 'none')")
+    message(STATUS " --> Tutorials in '${PROJECT_SOURCE_DIR}/code_examples' will NOT be built! (since PACKAGE_TYPE=${PACKAGE_TYPE}, but must be 'none')")
   endif()