sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h

@@ -1,98 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008 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_DOT_H
-#define EIGEN_SPARSE_DOT_H
-
-namespace Eigen { 
-
-template<typename Derived>
-template<typename OtherDerived>
-typename internal::traits<Derived>::Scalar
-SparseMatrixBase<Derived>::dot(const MatrixBase<OtherDerived>& other) const
-{
-  EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
-  EIGEN_STATIC_ASSERT_VECTOR_ONLY(OtherDerived)
-  EIGEN_STATIC_ASSERT_SAME_VECTOR_SIZE(Derived,OtherDerived)
-  EIGEN_STATIC_ASSERT((internal::is_same<Scalar, typename OtherDerived::Scalar>::value),
-    YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
-
-  eigen_assert(size() == other.size());
-  eigen_assert(other.size()>0 && "you are using a non initialized vector");
-
-  internal::evaluator<Derived> thisEval(derived());
-  typename internal::evaluator<Derived>::InnerIterator i(thisEval, 0);
-  Scalar res(0);
-  while (i)
-  {
-    res += numext::conj(i.value()) * other.coeff(i.index());
-    ++i;
-  }
-  return res;
-}
-
-template<typename Derived>
-template<typename OtherDerived>
-typename internal::traits<Derived>::Scalar
-SparseMatrixBase<Derived>::dot(const SparseMatrixBase<OtherDerived>& other) const
-{
-  EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)
-  EIGEN_STATIC_ASSERT_VECTOR_ONLY(OtherDerived)
-  EIGEN_STATIC_ASSERT_SAME_VECTOR_SIZE(Derived,OtherDerived)
-  EIGEN_STATIC_ASSERT((internal::is_same<Scalar, typename OtherDerived::Scalar>::value),
-    YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
-
-  eigen_assert(size() == other.size());
-
-  internal::evaluator<Derived> thisEval(derived());
-  typename internal::evaluator<Derived>::InnerIterator i(thisEval, 0);
-  
-  internal::evaluator<OtherDerived>  otherEval(other.derived());
-  typename internal::evaluator<OtherDerived>::InnerIterator j(otherEval, 0);
-
-  Scalar res(0);
-  while (i && j)
-  {
-    if (i.index()==j.index())
-    {
-      res += numext::conj(i.value()) * j.value();
-      ++i; ++j;
-    }
-    else if (i.index()<j.index())
-      ++i;
-    else
-      ++j;
-  }
-  return res;
-}
-
-template<typename Derived>
-inline typename NumTraits<typename internal::traits<Derived>::Scalar>::Real
-SparseMatrixBase<Derived>::squaredNorm() const
-{
-  return numext::real((*this).cwiseAbs2().sum());
-}
-
-template<typename Derived>
-inline typename NumTraits<typename internal::traits<Derived>::Scalar>::Real
-SparseMatrixBase<Derived>::norm() const
-{
-  using std::sqrt;
-  return sqrt(squaredNorm());
-}
-
-template<typename Derived>
-inline typename NumTraits<typename internal::traits<Derived>::Scalar>::Real
-SparseMatrixBase<Derived>::blueNorm() const
-{
-  return internal::blueNorm_impl(*this);
-}
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSE_DOT_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h

@@ -1,29 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2014 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_FUZZY_H
-#define EIGEN_SPARSE_FUZZY_H
-
-namespace Eigen {
-  
-template<typename Derived>
-template<typename OtherDerived>
-bool SparseMatrixBase<Derived>::isApprox(const SparseMatrixBase<OtherDerived>& other, const RealScalar &prec) const
-{
-  const typename internal::nested_eval<Derived,2,PlainObject>::type actualA(derived());
-  typename internal::conditional<bool(IsRowMajor)==bool(OtherDerived::IsRowMajor),
-    const typename internal::nested_eval<OtherDerived,2,PlainObject>::type,
-    const PlainObject>::type actualB(other.derived());
-
-  return (actualA - actualB).squaredNorm() <= prec * prec * numext::mini(actualA.squaredNorm(), actualB.squaredNorm());
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSE_FUZZY_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h

@@ -1,305 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2015 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_MAP_H
-#define EIGEN_SPARSE_MAP_H
-
-namespace Eigen {
-
-namespace internal {
-
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-struct traits<Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-  : public traits<SparseMatrix<MatScalar,MatOptions,MatIndex> >
-{
-  typedef SparseMatrix<MatScalar,MatOptions,MatIndex> PlainObjectType;
-  typedef traits<PlainObjectType> TraitsBase;
-  enum {
-    Flags = TraitsBase::Flags & (~NestByRefBit)
-  };
-};
-
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-struct traits<Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-  : public traits<SparseMatrix<MatScalar,MatOptions,MatIndex> >
-{
-  typedef SparseMatrix<MatScalar,MatOptions,MatIndex> PlainObjectType;
-  typedef traits<PlainObjectType> TraitsBase;
-  enum {
-    Flags = TraitsBase::Flags & (~ (NestByRefBit | LvalueBit))
-  };
-};
-
-} // end namespace internal
-
-template<typename Derived,
-         int Level = internal::accessors_level<Derived>::has_write_access ? WriteAccessors : ReadOnlyAccessors
-> class SparseMapBase;
-
-/** \ingroup SparseCore_Module
-  * class SparseMapBase
-  * \brief Common base class for Map and Ref instance of sparse matrix and vector.
-  */
-template<typename Derived>
-class SparseMapBase<Derived,ReadOnlyAccessors>
-  : public SparseCompressedBase<Derived>
-{
-  public:
-    typedef SparseCompressedBase<Derived> Base;
-    typedef typename Base::Scalar Scalar;
-    typedef typename Base::StorageIndex StorageIndex;
-    enum { IsRowMajor = Base::IsRowMajor };
-    using Base::operator=;
-  protected:
-    
-    typedef typename internal::conditional<
-                         bool(internal::is_lvalue<Derived>::value),
-                         Scalar *, const Scalar *>::type ScalarPointer;
-    typedef typename internal::conditional<
-                         bool(internal::is_lvalue<Derived>::value),
-                         StorageIndex *, const StorageIndex *>::type IndexPointer;
-
-    Index   m_outerSize;
-    Index   m_innerSize;
-    Array<StorageIndex,2,1>  m_zero_nnz;
-    IndexPointer  m_outerIndex;
-    IndexPointer  m_innerIndices;
-    ScalarPointer m_values;
-    IndexPointer  m_innerNonZeros;
-
-  public:
-
-    /** \copydoc SparseMatrixBase::rows() */
-    inline Index rows() const { return IsRowMajor ? m_outerSize : m_innerSize; }
-    /** \copydoc SparseMatrixBase::cols() */
-    inline Index cols() const { return IsRowMajor ? m_innerSize : m_outerSize; }
-    /** \copydoc SparseMatrixBase::innerSize() */
-    inline Index innerSize() const { return m_innerSize; }
-    /** \copydoc SparseMatrixBase::outerSize() */
-    inline Index outerSize() const { return m_outerSize; }
-    /** \copydoc SparseCompressedBase::nonZeros */
-    inline Index nonZeros() const { return m_zero_nnz[1]; }
-    
-    /** \copydoc SparseCompressedBase::isCompressed */
-    bool isCompressed() const { return m_innerNonZeros==0; }
-
-    //----------------------------------------
-    // direct access interface
-    /** \copydoc SparseMatrix::valuePtr */
-    inline const Scalar* valuePtr() const { return m_values; }
-    /** \copydoc SparseMatrix::innerIndexPtr */
-    inline const StorageIndex* innerIndexPtr() const { return m_innerIndices; }
-    /** \copydoc SparseMatrix::outerIndexPtr */
-    inline const StorageIndex* outerIndexPtr() const { return m_outerIndex; }
-    /** \copydoc SparseMatrix::innerNonZeroPtr */
-    inline const StorageIndex* innerNonZeroPtr() const { return m_innerNonZeros; }
-    //----------------------------------------
-
-    /** \copydoc SparseMatrix::coeff */
-    inline Scalar coeff(Index row, Index col) const
-    {
-      const Index outer = IsRowMajor ? row : col;
-      const Index inner = IsRowMajor ? col : row;
-
-      Index start = m_outerIndex[outer];
-      Index end = isCompressed() ? m_outerIndex[outer+1] : start + m_innerNonZeros[outer];
-      if (start==end)
-        return Scalar(0);
-      else if (end>0 && inner==m_innerIndices[end-1])
-        return m_values[end-1];
-      // ^^  optimization: let's first check if it is the last coefficient
-      // (very common in high level algorithms)
-
-      const StorageIndex* r = std::lower_bound(&m_innerIndices[start],&m_innerIndices[end-1],inner);
-      const Index id = r-&m_innerIndices[0];
-      return ((*r==inner) && (id<end)) ? m_values[id] : Scalar(0);
-    }
-
-    inline SparseMapBase(Index rows, Index cols, Index nnz, IndexPointer outerIndexPtr, IndexPointer innerIndexPtr,
-                              ScalarPointer valuePtr, IndexPointer innerNonZerosPtr = 0)
-      : m_outerSize(IsRowMajor?rows:cols), m_innerSize(IsRowMajor?cols:rows), m_zero_nnz(0,internal::convert_index<StorageIndex>(nnz)), m_outerIndex(outerIndexPtr),
-        m_innerIndices(innerIndexPtr), m_values(valuePtr), m_innerNonZeros(innerNonZerosPtr)
-    {}
-
-    // for vectors
-    inline SparseMapBase(Index size, Index nnz, IndexPointer innerIndexPtr, ScalarPointer valuePtr)
-      : m_outerSize(1), m_innerSize(size), m_zero_nnz(0,internal::convert_index<StorageIndex>(nnz)), m_outerIndex(m_zero_nnz.data()),
-        m_innerIndices(innerIndexPtr), m_values(valuePtr), m_innerNonZeros(0)
-    {}
-
-    /** Empty destructor */
-    inline ~SparseMapBase() {}
-
-  protected:
-    inline SparseMapBase() {}
-};
-
-/** \ingroup SparseCore_Module
-  * class SparseMapBase
-  * \brief Common base class for writable Map and Ref instance of sparse matrix and vector.
-  */
-template<typename Derived>
-class SparseMapBase<Derived,WriteAccessors>
-  : public SparseMapBase<Derived,ReadOnlyAccessors>
-{
-    typedef MapBase<Derived, ReadOnlyAccessors> ReadOnlyMapBase;
-    
-  public:
-    typedef SparseMapBase<Derived, ReadOnlyAccessors> Base;
-    typedef typename Base::Scalar Scalar;
-    typedef typename Base::StorageIndex StorageIndex;
-    enum { IsRowMajor = Base::IsRowMajor };
-    
-    using Base::operator=;
-
-  public:
-    
-    //----------------------------------------
-    // direct access interface
-    using Base::valuePtr;
-    using Base::innerIndexPtr;
-    using Base::outerIndexPtr;
-    using Base::innerNonZeroPtr;
-    /** \copydoc SparseMatrix::valuePtr */
-    inline Scalar* valuePtr()              { return Base::m_values; }
-    /** \copydoc SparseMatrix::innerIndexPtr */
-    inline StorageIndex* innerIndexPtr()   { return Base::m_innerIndices; }
-    /** \copydoc SparseMatrix::outerIndexPtr */
-    inline StorageIndex* outerIndexPtr()   { return Base::m_outerIndex; }
-    /** \copydoc SparseMatrix::innerNonZeroPtr */
-    inline StorageIndex* innerNonZeroPtr() { return Base::m_innerNonZeros; }
-    //----------------------------------------
-
-    /** \copydoc SparseMatrix::coeffRef */
-    inline Scalar& coeffRef(Index row, Index col)
-    {
-      const Index outer = IsRowMajor ? row : col;
-      const Index inner = IsRowMajor ? col : row;
-
-      Index start = Base::m_outerIndex[outer];
-      Index end = Base::isCompressed() ? Base::m_outerIndex[outer+1] : start + Base::m_innerNonZeros[outer];
-      eigen_assert(end>=start && "you probably called coeffRef on a non finalized matrix");
-      eigen_assert(end>start && "coeffRef cannot be called on a zero coefficient");
-      StorageIndex* r = std::lower_bound(&Base::m_innerIndices[start],&Base::m_innerIndices[end],inner);
-      const Index id = r - &Base::m_innerIndices[0];
-      eigen_assert((*r==inner) && (id<end) && "coeffRef cannot be called on a zero coefficient");
-      return const_cast<Scalar*>(Base::m_values)[id];
-    }
-    
-    inline SparseMapBase(Index rows, Index cols, Index nnz, StorageIndex* outerIndexPtr, StorageIndex* innerIndexPtr,
-                         Scalar* valuePtr, StorageIndex* innerNonZerosPtr = 0)
-      : Base(rows, cols, nnz, outerIndexPtr, innerIndexPtr, valuePtr, innerNonZerosPtr)
-    {}
-
-    // for vectors
-    inline SparseMapBase(Index size, Index nnz, StorageIndex* innerIndexPtr, Scalar* valuePtr)
-      : Base(size, nnz, innerIndexPtr, valuePtr)
-    {}
-
-    /** Empty destructor */
-    inline ~SparseMapBase() {}
-
-  protected:
-    inline SparseMapBase() {}
-};
-
-/** \ingroup SparseCore_Module
-  *
-  * \brief Specialization of class Map for SparseMatrix-like storage.
-  *
-  * \tparam SparseMatrixType the equivalent sparse matrix type of the referenced data, it must be a template instance of class SparseMatrix.
-  *
-  * \sa class Map, class SparseMatrix, class Ref<SparseMatrixType,Options>
-  */
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-class Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType>
-  : public SparseMapBase<Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-#else
-template<typename SparseMatrixType>
-class Map<SparseMatrixType>
-  : public SparseMapBase<Derived,WriteAccessors>
-#endif
-{
-  public:
-    typedef SparseMapBase<Map> Base;
-    EIGEN_SPARSE_PUBLIC_INTERFACE(Map)
-    enum { IsRowMajor = Base::IsRowMajor };
-
-  public:
-
-    /** Constructs a read-write Map to a sparse matrix of size \a rows x \a cols, containing \a nnz non-zero coefficients,
-      * stored as a sparse format as defined by the pointers \a outerIndexPtr, \a innerIndexPtr, and \a valuePtr.
-      * If the optional parameter \a innerNonZerosPtr is the null pointer, then a standard compressed format is assumed.
-      *
-      * This constructor is available only if \c SparseMatrixType is non-const.
-      *
-      * More details on the expected storage schemes are given in the \ref TutorialSparse "manual pages".
-      */
-    inline Map(Index rows, Index cols, Index nnz, StorageIndex* outerIndexPtr,
-               StorageIndex* innerIndexPtr, Scalar* valuePtr, StorageIndex* innerNonZerosPtr = 0)
-      : Base(rows, cols, nnz, outerIndexPtr, innerIndexPtr, valuePtr, innerNonZerosPtr)
-    {}
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-    /** Empty destructor */
-    inline ~Map() {}
-};
-
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-class Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType>
-  : public SparseMapBase<Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-{
-  public:
-    typedef SparseMapBase<Map> Base;
-    EIGEN_SPARSE_PUBLIC_INTERFACE(Map)
-    enum { IsRowMajor = Base::IsRowMajor };
-
-  public:
-#endif
-    /** This is the const version of the above constructor.
-      *
-      * This constructor is available only if \c SparseMatrixType is const, e.g.:
-      * \code Map<const SparseMatrix<double> >  \endcode
-      */
-    inline Map(Index rows, Index cols, Index nnz, const StorageIndex* outerIndexPtr,
-               const StorageIndex* innerIndexPtr, const Scalar* valuePtr, const StorageIndex* innerNonZerosPtr = 0)
-      : Base(rows, cols, nnz, outerIndexPtr, innerIndexPtr, valuePtr, innerNonZerosPtr)
-    {}
-
-    /** Empty destructor */
-    inline ~Map() {}
-};
-
-namespace internal {
-
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-struct evaluator<Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-  : evaluator<SparseCompressedBase<Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
-{
-  typedef evaluator<SparseCompressedBase<Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
-  typedef Map<SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;  
-  evaluator() : Base() {}
-  explicit evaluator(const XprType &mat) : Base(mat) {}
-};
-
-template<typename MatScalar, int MatOptions, typename MatIndex, int Options, typename StrideType>
-struct evaluator<Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> >
-  : evaluator<SparseCompressedBase<Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > >
-{
-  typedef evaluator<SparseCompressedBase<Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> > > Base;
-  typedef Map<const SparseMatrix<MatScalar,MatOptions,MatIndex>, Options, StrideType> XprType;  
-  evaluator() : Base() {}
-  explicit evaluator(const XprType &mat) : Base(mat) {}
-};
-
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSE_MAP_H