sequenzo 0.1.18__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h

@@ -1,259 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Guillaume Saupin <guillaume.saupin@cea.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SKYLINE_STORAGE_H
-#define EIGEN_SKYLINE_STORAGE_H
-
-namespace Eigen { 
-
-/** Stores a skyline set of values in three structures :
- * The diagonal elements
- * The upper elements
- * The lower elements
- *
- */
-template<typename Scalar>
-class SkylineStorage {
-    typedef typename NumTraits<Scalar>::Real RealScalar;
-    typedef SparseIndex Index;
-public:
-
-    SkylineStorage()
-    : m_diag(0),
-    m_lower(0),
-    m_upper(0),
-    m_lowerProfile(0),
-    m_upperProfile(0),
-    m_diagSize(0),
-    m_upperSize(0),
-    m_lowerSize(0),
-    m_upperProfileSize(0),
-    m_lowerProfileSize(0),
-    m_allocatedSize(0) {
-    }
-
-    SkylineStorage(const SkylineStorage& other)
-    : m_diag(0),
-    m_lower(0),
-    m_upper(0),
-    m_lowerProfile(0),
-    m_upperProfile(0),
-    m_diagSize(0),
-    m_upperSize(0),
-    m_lowerSize(0),
-    m_upperProfileSize(0),
-    m_lowerProfileSize(0),
-    m_allocatedSize(0) {
-        *this = other;
-    }
-
-    SkylineStorage & operator=(const SkylineStorage& other) {
-        resize(other.diagSize(), other.m_upperProfileSize, other.m_lowerProfileSize, other.upperSize(), other.lowerSize());
-        memcpy(m_diag, other.m_diag, m_diagSize * sizeof (Scalar));
-        memcpy(m_upper, other.m_upper, other.upperSize() * sizeof (Scalar));
-        memcpy(m_lower, other.m_lower, other.lowerSize() * sizeof (Scalar));
-        memcpy(m_upperProfile, other.m_upperProfile, m_upperProfileSize * sizeof (Index));
-        memcpy(m_lowerProfile, other.m_lowerProfile, m_lowerProfileSize * sizeof (Index));
-        return *this;
-    }
-
-    void swap(SkylineStorage& other) {
-        std::swap(m_diag, other.m_diag);
-        std::swap(m_upper, other.m_upper);
-        std::swap(m_lower, other.m_lower);
-        std::swap(m_upperProfile, other.m_upperProfile);
-        std::swap(m_lowerProfile, other.m_lowerProfile);
-        std::swap(m_diagSize, other.m_diagSize);
-        std::swap(m_upperSize, other.m_upperSize);
-        std::swap(m_lowerSize, other.m_lowerSize);
-        std::swap(m_allocatedSize, other.m_allocatedSize);
-    }
-
-    ~SkylineStorage() {
-        delete[] m_diag;
-        delete[] m_upper;
-        if (m_upper != m_lower)
-            delete[] m_lower;
-        delete[] m_upperProfile;
-        delete[] m_lowerProfile;
-    }
-
-    void reserve(Index size, Index upperProfileSize, Index lowerProfileSize, Index upperSize, Index lowerSize) {
-        Index newAllocatedSize = size + upperSize + lowerSize;
-        if (newAllocatedSize > m_allocatedSize)
-            reallocate(size, upperProfileSize, lowerProfileSize, upperSize, lowerSize);
-    }
-
-    void squeeze() {
-        if (m_allocatedSize > m_diagSize + m_upperSize + m_lowerSize)
-            reallocate(m_diagSize, m_upperProfileSize, m_lowerProfileSize, m_upperSize, m_lowerSize);
-    }
-
-    void resize(Index diagSize, Index upperProfileSize, Index lowerProfileSize, Index upperSize, Index lowerSize, float reserveSizeFactor = 0) {
-        if (m_allocatedSize < diagSize + upperSize + lowerSize)
-            reallocate(diagSize, upperProfileSize, lowerProfileSize, upperSize + Index(reserveSizeFactor * upperSize), lowerSize + Index(reserveSizeFactor * lowerSize));
-        m_diagSize = diagSize;
-        m_upperSize = upperSize;
-        m_lowerSize = lowerSize;
-        m_upperProfileSize = upperProfileSize;
-        m_lowerProfileSize = lowerProfileSize;
-    }
-
-    inline Index diagSize() const {
-        return m_diagSize;
-    }
-
-    inline Index upperSize() const {
-        return m_upperSize;
-    }
-
-    inline Index lowerSize() const {
-        return m_lowerSize;
-    }
-
-    inline Index upperProfileSize() const {
-        return m_upperProfileSize;
-    }
-
-    inline Index lowerProfileSize() const {
-        return m_lowerProfileSize;
-    }
-
-    inline Index allocatedSize() const {
-        return m_allocatedSize;
-    }
-
-    inline void clear() {
-        m_diagSize = 0;
-    }
-
-    inline Scalar& diag(Index i) {
-        return m_diag[i];
-    }
-
-    inline const Scalar& diag(Index i) const {
-        return m_diag[i];
-    }
-
-    inline Scalar& upper(Index i) {
-        return m_upper[i];
-    }
-
-    inline const Scalar& upper(Index i) const {
-        return m_upper[i];
-    }
-
-    inline Scalar& lower(Index i) {
-        return m_lower[i];
-    }
-
-    inline const Scalar& lower(Index i) const {
-        return m_lower[i];
-    }
-
-    inline Index& upperProfile(Index i) {
-        return m_upperProfile[i];
-    }
-
-    inline const Index& upperProfile(Index i) const {
-        return m_upperProfile[i];
-    }
-
-    inline Index& lowerProfile(Index i) {
-        return m_lowerProfile[i];
-    }
-
-    inline const Index& lowerProfile(Index i) const {
-        return m_lowerProfile[i];
-    }
-
-    static SkylineStorage Map(Index* upperProfile, Index* lowerProfile, Scalar* diag, Scalar* upper, Scalar* lower, Index size, Index upperSize, Index lowerSize) {
-        SkylineStorage res;
-        res.m_upperProfile = upperProfile;
-        res.m_lowerProfile = lowerProfile;
-        res.m_diag = diag;
-        res.m_upper = upper;
-        res.m_lower = lower;
-        res.m_allocatedSize = res.m_diagSize = size;
-        res.m_upperSize = upperSize;
-        res.m_lowerSize = lowerSize;
-        return res;
-    }
-
-    inline void reset() {
-        memset(m_diag, 0, m_diagSize * sizeof (Scalar));
-        memset(m_upper, 0, m_upperSize * sizeof (Scalar));
-        memset(m_lower, 0, m_lowerSize * sizeof (Scalar));
-        memset(m_upperProfile, 0, m_diagSize * sizeof (Index));
-        memset(m_lowerProfile, 0, m_diagSize * sizeof (Index));
-    }
-
-    void prune(Scalar reference, RealScalar epsilon = dummy_precision<RealScalar>()) {
-        //TODO
-    }
-
-protected:
-
-    inline void reallocate(Index diagSize, Index upperProfileSize, Index lowerProfileSize, Index upperSize, Index lowerSize) {
-
-        Scalar* diag = new Scalar[diagSize];
-        Scalar* upper = new Scalar[upperSize];
-        Scalar* lower = new Scalar[lowerSize];
-        Index* upperProfile = new Index[upperProfileSize];
-        Index* lowerProfile = new Index[lowerProfileSize];
-
-        Index copyDiagSize = (std::min)(diagSize, m_diagSize);
-        Index copyUpperSize = (std::min)(upperSize, m_upperSize);
-        Index copyLowerSize = (std::min)(lowerSize, m_lowerSize);
-        Index copyUpperProfileSize = (std::min)(upperProfileSize, m_upperProfileSize);
-        Index copyLowerProfileSize = (std::min)(lowerProfileSize, m_lowerProfileSize);
-
-        // copy
-        memcpy(diag, m_diag, copyDiagSize * sizeof (Scalar));
-        memcpy(upper, m_upper, copyUpperSize * sizeof (Scalar));
-        memcpy(lower, m_lower, copyLowerSize * sizeof (Scalar));
-        memcpy(upperProfile, m_upperProfile, copyUpperProfileSize * sizeof (Index));
-        memcpy(lowerProfile, m_lowerProfile, copyLowerProfileSize * sizeof (Index));
-
-
-
-        // delete old stuff
-        delete[] m_diag;
-        delete[] m_upper;
-        delete[] m_lower;
-        delete[] m_upperProfile;
-        delete[] m_lowerProfile;
-        m_diag = diag;
-        m_upper = upper;
-        m_lower = lower;
-        m_upperProfile = upperProfile;
-        m_lowerProfile = lowerProfile;
-        m_allocatedSize = diagSize + upperSize + lowerSize;
-        m_upperSize = upperSize;
-        m_lowerSize = lowerSize;
-    }
-
-public:
-    Scalar* m_diag;
-    Scalar* m_upper;
-    Scalar* m_lower;
-    Index* m_upperProfile;
-    Index* m_lowerProfile;
-    Index m_diagSize;
-    Index m_upperSize;
-    Index m_lowerSize;
-    Index m_upperProfileSize;
-    Index m_lowerProfileSize;
-    Index m_allocatedSize;
-
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_SKYLINE_STORAGE_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h

@@ -1,89 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2009 Guillaume Saupin <guillaume.saupin@cea.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SKYLINEUTIL_H
-#define EIGEN_SKYLINEUTIL_H
-
-namespace Eigen { 
-
-#ifdef NDEBUG
-#define EIGEN_DBG_SKYLINE(X)
-#else
-#define EIGEN_DBG_SKYLINE(X) X
-#endif
-
-const unsigned int SkylineBit = 0x1200;
-template<typename Lhs, typename Rhs, int ProductMode> class SkylineProduct;
-enum AdditionalProductEvaluationMode {SkylineTimeDenseProduct, SkylineTimeSkylineProduct, DenseTimeSkylineProduct};
-enum {IsSkyline = SkylineBit};
-
-
-#define EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(Derived, Op) \
-template<typename OtherDerived> \
-EIGEN_STRONG_INLINE Derived& operator Op(const Eigen::SkylineMatrixBase<OtherDerived>& other) \
-{ \
-  return Base::operator Op(other.derived()); \
-} \
-EIGEN_STRONG_INLINE Derived& operator Op(const Derived& other) \
-{ \
-  return Base::operator Op(other); \
-}
-
-#define EIGEN_SKYLINE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(Derived, Op) \
-template<typename Other> \
-EIGEN_STRONG_INLINE Derived& operator Op(const Other& scalar) \
-{ \
-  return Base::operator Op(scalar); \
-}
-
-#define EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATORS(Derived) \
-  EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(Derived, =) \
-  EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(Derived, +=) \
-  EIGEN_SKYLINE_INHERIT_ASSIGNMENT_OPERATOR(Derived, -=) \
-  EIGEN_SKYLINE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(Derived, *=) \
-  EIGEN_SKYLINE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(Derived, /=)
-
-#define _EIGEN_SKYLINE_GENERIC_PUBLIC_INTERFACE(Derived, BaseClass) \
-  typedef BaseClass Base; \
-  typedef typename Eigen::internal::traits<Derived>::Scalar Scalar; \
-  typedef typename Eigen::NumTraits<Scalar>::Real RealScalar; \
-  typedef typename Eigen::internal::traits<Derived>::StorageKind StorageKind; \
-  typedef typename Eigen::internal::index<StorageKind>::type Index; \
-  enum {  Flags = Eigen::internal::traits<Derived>::Flags, };
-
-#define EIGEN_SKYLINE_GENERIC_PUBLIC_INTERFACE(Derived) \
-  _EIGEN_SKYLINE_GENERIC_PUBLIC_INTERFACE(Derived, Eigen::SkylineMatrixBase<Derived>)
-
-template<typename Derived> class SkylineMatrixBase;
-template<typename _Scalar, int _Flags = 0> class SkylineMatrix;
-template<typename _Scalar, int _Flags = 0> class DynamicSkylineMatrix;
-template<typename _Scalar, int _Flags = 0> class SkylineVector;
-template<typename _Scalar, int _Flags = 0> class MappedSkylineMatrix;
-
-namespace internal {
-
-template<typename Lhs, typename Rhs> struct skyline_product_mode;
-template<typename Lhs, typename Rhs, int ProductMode = skyline_product_mode<Lhs,Rhs>::value> struct SkylineProductReturnType;
-
-template<typename T> class eval<T,IsSkyline>
-{
-    typedef typename traits<T>::Scalar _Scalar;
-    enum {
-          _Flags = traits<T>::Flags
-    };
-
-  public:
-    typedef SkylineMatrix<_Scalar, _Flags> type;
-};
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_SKYLINEUTIL_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h

@@ -1,122 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SPARSE_BLOCKFORDYNAMICMATRIX_H
-#define EIGEN_SPARSE_BLOCKFORDYNAMICMATRIX_H
-
-namespace Eigen { 
-
-#if 0
-
-// NOTE Have to be reimplemented as a specialization of BlockImpl< DynamicSparseMatrix<_Scalar, _Options, _Index>, ... >
-// See SparseBlock.h for an example
-
-
-/***************************************************************************
-* specialisation for DynamicSparseMatrix
-***************************************************************************/
-
-template<typename _Scalar, int _Options, typename _Index, int Size>
-class SparseInnerVectorSet<DynamicSparseMatrix<_Scalar, _Options, _Index>, Size>
-  : public SparseMatrixBase<SparseInnerVectorSet<DynamicSparseMatrix<_Scalar, _Options, _Index>, Size> >
-{
-    typedef DynamicSparseMatrix<_Scalar, _Options, _Index> MatrixType;
-  public:
-
-    enum { IsRowMajor = internal::traits<SparseInnerVectorSet>::IsRowMajor };
-
-    EIGEN_SPARSE_PUBLIC_INTERFACE(SparseInnerVectorSet)
-    class InnerIterator: public MatrixType::InnerIterator
-    {
-      public:
-        inline InnerIterator(const SparseInnerVectorSet& xpr, Index outer)
-          : MatrixType::InnerIterator(xpr.m_matrix, xpr.m_outerStart + outer), m_outer(outer)
-        {}
-        inline Index row() const { return IsRowMajor ? m_outer : this->index(); }
-        inline Index col() const { return IsRowMajor ? this->index() : m_outer; }
-      protected:
-        Index m_outer;
-    };
-
-    inline SparseInnerVectorSet(const MatrixType& matrix, Index outerStart, Index outerSize)
-      : m_matrix(matrix), m_outerStart(outerStart), m_outerSize(outerSize)
-    {
-      eigen_assert( (outerStart>=0) && ((outerStart+outerSize)<=matrix.outerSize()) );
-    }
-
-    inline SparseInnerVectorSet(const MatrixType& matrix, Index outer)
-      : m_matrix(matrix), m_outerStart(outer), m_outerSize(Size)
-    {
-      eigen_assert(Size!=Dynamic);
-      eigen_assert( (outer>=0) && (outer<matrix.outerSize()) );
-    }
-
-    template<typename OtherDerived>
-    inline SparseInnerVectorSet& operator=(const SparseMatrixBase<OtherDerived>& other)
-    {
-      if (IsRowMajor != ((OtherDerived::Flags&RowMajorBit)==RowMajorBit))
-      {
-        // need to transpose => perform a block evaluation followed by a big swap
-        DynamicSparseMatrix<Scalar,IsRowMajor?RowMajorBit:0> aux(other);
-        *this = aux.markAsRValue();
-      }
-      else
-      {
-        // evaluate/copy vector per vector
-        for (Index j=0; j<m_outerSize.value(); ++j)
-        {
-          SparseVector<Scalar,IsRowMajor ? RowMajorBit : 0> aux(other.innerVector(j));
-          m_matrix.const_cast_derived()._data()[m_outerStart+j].swap(aux._data());
-        }
-      }
-      return *this;
-    }
-
-    inline SparseInnerVectorSet& operator=(const SparseInnerVectorSet& other)
-    {
-      return operator=<SparseInnerVectorSet>(other);
-    }
-
-    Index nonZeros() const
-    {
-      Index count = 0;
-      for (Index j=0; j<m_outerSize.value(); ++j)
-        count += m_matrix._data()[m_outerStart+j].size();
-      return count;
-    }
-
-    const Scalar& lastCoeff() const
-    {
-      EIGEN_STATIC_ASSERT_VECTOR_ONLY(SparseInnerVectorSet);
-      eigen_assert(m_matrix.data()[m_outerStart].size()>0);
-      return m_matrix.data()[m_outerStart].vale(m_matrix.data()[m_outerStart].size()-1);
-    }
-
-//     template<typename Sparse>
-//     inline SparseInnerVectorSet& operator=(const SparseMatrixBase<OtherDerived>& other)
-//     {
-//       return *this;
-//     }
-
-    EIGEN_STRONG_INLINE Index rows() const { return IsRowMajor ? m_outerSize.value() : m_matrix.rows(); }
-    EIGEN_STRONG_INLINE Index cols() const { return IsRowMajor ? m_matrix.cols() : m_outerSize.value(); }
-
-  protected:
-
-    const typename MatrixType::Nested m_matrix;
-    Index m_outerStart;
-    const internal::variable_if_dynamic<Index, Size> m_outerSize;
-
-};
-
-#endif
-
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSE_BLOCKFORDYNAMICMATRIX_H