sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h

@@ -1,66 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@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 SPARSELU_IMPL_H
-#define SPARSELU_IMPL_H
-
-namespace Eigen {
-namespace internal {
-  
-/** \ingroup SparseLU_Module
-  * \class SparseLUImpl
-  * Base class for sparseLU
-  */
-template <typename Scalar, typename StorageIndex>
-class SparseLUImpl
-{
-  public:
-    typedef Matrix<Scalar,Dynamic,1> ScalarVector;
-    typedef Matrix<StorageIndex,Dynamic,1> IndexVector; 
-    typedef Matrix<Scalar,Dynamic,Dynamic,ColMajor> ScalarMatrix;
-    typedef Map<ScalarMatrix, 0,  OuterStride<> > MappedMatrixBlock;
-    typedef typename ScalarVector::RealScalar RealScalar; 
-    typedef Ref<Matrix<Scalar,Dynamic,1> > BlockScalarVector;
-    typedef Ref<Matrix<StorageIndex,Dynamic,1> > BlockIndexVector;
-    typedef LU_GlobalLU_t<IndexVector, ScalarVector> GlobalLU_t; 
-    typedef SparseMatrix<Scalar,ColMajor,StorageIndex> MatrixType; 
-    
-  protected:
-     template <typename VectorType>
-     Index expand(VectorType& vec, Index& length, Index nbElts, Index keep_prev, Index& num_expansions);
-     Index memInit(Index m, Index n, Index annz, Index lwork, Index fillratio, Index panel_size,  GlobalLU_t& glu); 
-     template <typename VectorType>
-     Index memXpand(VectorType& vec, Index& maxlen, Index nbElts, MemType memtype, Index& num_expansions);
-     void heap_relax_snode (const Index n, IndexVector& et, const Index relax_columns, IndexVector& descendants, IndexVector& relax_end); 
-     void relax_snode (const Index n, IndexVector& et, const Index relax_columns, IndexVector& descendants, IndexVector& relax_end); 
-     Index snode_dfs(const Index jcol, const Index kcol,const MatrixType& mat,  IndexVector& xprune, IndexVector& marker, GlobalLU_t& glu); 
-     Index snode_bmod (const Index jcol, const Index fsupc, ScalarVector& dense, GlobalLU_t& glu);
-     Index pivotL(const Index jcol, const RealScalar& diagpivotthresh, IndexVector& perm_r, IndexVector& iperm_c, Index& pivrow, GlobalLU_t& glu);
-     template <typename Traits>
-     void dfs_kernel(const StorageIndex jj, IndexVector& perm_r,
-                    Index& nseg, IndexVector& panel_lsub, IndexVector& segrep,
-                    Ref<IndexVector> repfnz_col, IndexVector& xprune, Ref<IndexVector> marker, IndexVector& parent,
-                    IndexVector& xplore, GlobalLU_t& glu, Index& nextl_col, Index krow, Traits& traits);
-     void panel_dfs(const Index m, const Index w, const Index jcol, MatrixType& A, IndexVector& perm_r, Index& nseg, ScalarVector& dense, IndexVector& panel_lsub, IndexVector& segrep, IndexVector& repfnz, IndexVector& xprune, IndexVector& marker, IndexVector& parent, IndexVector& xplore, GlobalLU_t& glu);
-    
-     void panel_bmod(const Index m, const Index w, const Index jcol, const Index nseg, ScalarVector& dense, ScalarVector& tempv, IndexVector& segrep, IndexVector& repfnz, GlobalLU_t& glu);
-     Index column_dfs(const Index m, const Index jcol, IndexVector& perm_r, Index maxsuper, Index& nseg,  BlockIndexVector lsub_col, IndexVector& segrep, BlockIndexVector repfnz, IndexVector& xprune, IndexVector& marker, IndexVector& parent, IndexVector& xplore, GlobalLU_t& glu);
-     Index column_bmod(const Index jcol, const Index nseg, BlockScalarVector dense, ScalarVector& tempv, BlockIndexVector segrep, BlockIndexVector repfnz, Index fpanelc, GlobalLU_t& glu); 
-     Index copy_to_ucol(const Index jcol, const Index nseg, IndexVector& segrep, BlockIndexVector repfnz ,IndexVector& perm_r, BlockScalarVector dense, GlobalLU_t& glu); 
-     void pruneL(const Index jcol, const IndexVector& perm_r, const Index pivrow, const Index nseg, const IndexVector& segrep, BlockIndexVector repfnz, IndexVector& xprune, GlobalLU_t& glu);
-     void countnz(const Index n, Index& nnzL, Index& nnzU, GlobalLU_t& glu); 
-     void fixupL(const Index n, const IndexVector& perm_r, GlobalLU_t& glu); 
-     
-     template<typename , typename >
-     friend struct column_dfs_traits;
-}; 
-
-} // end namespace internal
-} // namespace Eigen
-
-#endif

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h

@@ -1,226 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@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/.
-
-/* 
- 
- * NOTE: This file is the modified version of [s,d,c,z]memory.c files in SuperLU 
- 
- * -- SuperLU routine (version 3.1) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * August 1, 2008
- *
- * Copyright (c) 1994 by Xerox Corporation.  All rights reserved.
- *
- * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
- * EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
- *
- * Permission is hereby granted to use or copy this program for any
- * purpose, provided the above notices are retained on all copies.
- * Permission to modify the code and to distribute modified code is
- * granted, provided the above notices are retained, and a notice that
- * the code was modified is included with the above copyright notice.
- */
-
-#ifndef EIGEN_SPARSELU_MEMORY
-#define EIGEN_SPARSELU_MEMORY
-
-namespace Eigen {
-namespace internal {
-  
-enum { LUNoMarker = 3 };
-enum {emptyIdxLU = -1};
-inline Index LUnumTempV(Index& m, Index& w, Index& t, Index& b)
-{
-  return (std::max)(m, (t+b)*w);
-}
-
-template< typename Scalar>
-inline Index LUTempSpace(Index&m, Index& w)
-{
-  return (2*w + 4 + LUNoMarker) * m * sizeof(Index) + (w + 1) * m * sizeof(Scalar);
-}
-
-
-
-
-/** 
-  * Expand the existing storage to accommodate more fill-ins
-  * \param vec Valid pointer to the vector to allocate or expand
-  * \param[in,out] length  At input, contain the current length of the vector that is to be increased. At output, length of the newly allocated vector
-  * \param[in] nbElts Current number of elements in the factors
-  * \param keep_prev  1: use length  and do not expand the vector; 0: compute new_len and expand
-  * \param[in,out] num_expansions Number of times the memory has been expanded
-  */
-template <typename Scalar, typename StorageIndex>
-template <typename VectorType>
-Index  SparseLUImpl<Scalar,StorageIndex>::expand(VectorType& vec, Index& length, Index nbElts, Index keep_prev, Index& num_expansions) 
-{
-  
-  float alpha = 1.5; // Ratio of the memory increase 
-  Index new_len; // New size of the allocated memory
-  
-  if(num_expansions == 0 || keep_prev) 
-    new_len = length ; // First time allocate requested
-  else 
-    new_len = (std::max)(length+1,Index(alpha * length));
-  
-  VectorType old_vec; // Temporary vector to hold the previous values   
-  if (nbElts > 0 )
-    old_vec = vec.segment(0,nbElts); 
-  
-  //Allocate or expand the current vector
-#ifdef EIGEN_EXCEPTIONS
-  try
-#endif
-  {
-    vec.resize(new_len); 
-  }
-#ifdef EIGEN_EXCEPTIONS
-  catch(std::bad_alloc& )
-#else
-  if(!vec.size())
-#endif
-  {
-    if (!num_expansions)
-    {
-      // First time to allocate from LUMemInit()
-      // Let LUMemInit() deals with it.
-      return -1;
-    }
-    if (keep_prev)
-    {
-      // In this case, the memory length should not not be reduced
-      return new_len;
-    }
-    else 
-    {
-      // Reduce the size and increase again 
-      Index tries = 0; // Number of attempts
-      do 
-      {
-        alpha = (alpha + 1)/2;
-        new_len = (std::max)(length+1,Index(alpha * length));
-#ifdef EIGEN_EXCEPTIONS
-        try
-#endif
-        {
-          vec.resize(new_len); 
-        }
-#ifdef EIGEN_EXCEPTIONS
-        catch(std::bad_alloc& )
-#else
-        if (!vec.size())
-#endif
-        {
-          tries += 1; 
-          if ( tries > 10) return new_len; 
-        }
-      } while (!vec.size());
-    }
-  }
-  //Copy the previous values to the newly allocated space 
-  if (nbElts > 0)
-    vec.segment(0, nbElts) = old_vec;   
-   
-  
-  length  = new_len;
-  if(num_expansions) ++num_expansions;
-  return 0; 
-}
-
-/**
- * \brief  Allocate various working space for the numerical factorization phase.
- * \param m number of rows of the input matrix 
- * \param n number of columns 
- * \param annz number of initial nonzeros in the matrix 
- * \param lwork  if lwork=-1, this routine returns an estimated size of the required memory
- * \param glu persistent data to facilitate multiple factors : will be deleted later ??
- * \param fillratio estimated ratio of fill in the factors
- * \param panel_size Size of a panel
- * \return an estimated size of the required memory if lwork = -1; otherwise, return the size of actually allocated memory when allocation failed, and 0 on success
- * \note Unlike SuperLU, this routine does not support successive factorization with the same pattern and the same row permutation
- */
-template <typename Scalar, typename StorageIndex>
-Index SparseLUImpl<Scalar,StorageIndex>::memInit(Index m, Index n, Index annz, Index lwork, Index fillratio, Index panel_size,  GlobalLU_t& glu)
-{
-  Index& num_expansions = glu.num_expansions; //No memory expansions so far
-  num_expansions = 0;
-  glu.nzumax = glu.nzlumax = (std::min)(fillratio * (annz+1) / n, m) * n; // estimated number of nonzeros in U 
-  glu.nzlmax = (std::max)(Index(4), fillratio) * (annz+1) / 4; // estimated  nnz in L factor
-  // Return the estimated size to the user if necessary
-  Index tempSpace;
-  tempSpace = (2*panel_size + 4 + LUNoMarker) * m * sizeof(Index) + (panel_size + 1) * m * sizeof(Scalar);
-  if (lwork == emptyIdxLU) 
-  {
-    Index estimated_size;
-    estimated_size = (5 * n + 5) * sizeof(Index)  + tempSpace
-                    + (glu.nzlmax + glu.nzumax) * sizeof(Index) + (glu.nzlumax+glu.nzumax) *  sizeof(Scalar) + n; 
-    return estimated_size;
-  }
-  
-  // Setup the required space 
-  
-  // First allocate Integer pointers for L\U factors
-  glu.xsup.resize(n+1);
-  glu.supno.resize(n+1);
-  glu.xlsub.resize(n+1);
-  glu.xlusup.resize(n+1);
-  glu.xusub.resize(n+1);
-
-  // Reserve memory for L/U factors
-  do 
-  {
-    if(     (expand<ScalarVector>(glu.lusup, glu.nzlumax, 0, 0, num_expansions)<0)
-        ||  (expand<ScalarVector>(glu.ucol,  glu.nzumax,  0, 0, num_expansions)<0)
-        ||  (expand<IndexVector> (glu.lsub,  glu.nzlmax,  0, 0, num_expansions)<0)
-        ||  (expand<IndexVector> (glu.usub,  glu.nzumax,  0, 1, num_expansions)<0) )
-    {
-      //Reduce the estimated size and retry
-      glu.nzlumax /= 2;
-      glu.nzumax /= 2;
-      glu.nzlmax /= 2;
-      if (glu.nzlumax < annz ) return glu.nzlumax; 
-    }
-  } while (!glu.lusup.size() || !glu.ucol.size() || !glu.lsub.size() || !glu.usub.size());
-  
-  ++num_expansions;
-  return 0;
-  
-} // end LuMemInit
-
-/** 
- * \brief Expand the existing storage 
- * \param vec vector to expand 
- * \param[in,out] maxlen On input, previous size of vec (Number of elements to copy ). on output, new size
- * \param nbElts current number of elements in the vector.
- * \param memtype Type of the element to expand
- * \param num_expansions Number of expansions 
- * \return 0 on success, > 0 size of the memory allocated so far
- */
-template <typename Scalar, typename StorageIndex>
-template <typename VectorType>
-Index SparseLUImpl<Scalar,StorageIndex>::memXpand(VectorType& vec, Index& maxlen, Index nbElts, MemType memtype, Index& num_expansions)
-{
-  Index failed_size; 
-  if (memtype == USUB)
-     failed_size = this->expand<VectorType>(vec, maxlen, nbElts, 1, num_expansions);
-  else
-    failed_size = this->expand<VectorType>(vec, maxlen, nbElts, 0, num_expansions);
-
-  if (failed_size)
-    return failed_size; 
-  
-  return 0 ;  
-}
-
-} // end namespace internal
-
-} // end namespace Eigen
-#endif // EIGEN_SPARSELU_MEMORY

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h

@@ -1,110 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@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/.
-
-/* 
- * NOTE: This file comes from a partly modified version of files slu_[s,d,c,z]defs.h
- * -- SuperLU routine (version 4.1) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * November, 2010
- * 
- * Global data structures used in LU factorization -
- * 
- *   nsuper: #supernodes = nsuper + 1, numbered [0, nsuper].
- *   (xsup,supno): supno[i] is the supernode no to which i belongs;
- *  xsup(s) points to the beginning of the s-th supernode.
- *  e.g.   supno 0 1 2 2 3 3 3 4 4 4 4 4   (n=12)
- *          xsup 0 1 2 4 7 12
- *  Note: dfs will be performed on supernode rep. relative to the new 
- *        row pivoting ordering
- *
- *   (xlsub,lsub): lsub[*] contains the compressed subscript of
- *  rectangular supernodes; xlsub[j] points to the starting
- *  location of the j-th column in lsub[*]. Note that xlsub 
- *  is indexed by column.
- *  Storage: original row subscripts
- *
- *      During the course of sparse LU factorization, we also use
- *  (xlsub,lsub) for the purpose of symmetric pruning. For each
- *  supernode {s,s+1,...,t=s+r} with first column s and last
- *  column t, the subscript set
- *    lsub[j], j=xlsub[s], .., xlsub[s+1]-1
- *  is the structure of column s (i.e. structure of this supernode).
- *  It is used for the storage of numerical values.
- *  Furthermore,
- *    lsub[j], j=xlsub[t], .., xlsub[t+1]-1
- *  is the structure of the last column t of this supernode.
- *  It is for the purpose of symmetric pruning. Therefore, the
- *  structural subscripts can be rearranged without making physical
- *  interchanges among the numerical values.
- *
- *  However, if the supernode has only one column, then we
- *  only keep one set of subscripts. For any subscript interchange
- *  performed, similar interchange must be done on the numerical
- *  values.
- *
- *  The last column structures (for pruning) will be removed
- *  after the numercial LU factorization phase.
- *
- *   (xlusup,lusup): lusup[*] contains the numerical values of the
- *  rectangular supernodes; xlusup[j] points to the starting
- *  location of the j-th column in storage vector lusup[*]
- *  Note: xlusup is indexed by column.
- *  Each rectangular supernode is stored by column-major
- *  scheme, consistent with Fortran 2-dim array storage.
- *
- *   (xusub,ucol,usub): ucol[*] stores the numerical values of
- *  U-columns outside the rectangular supernodes. The row
- *  subscript of nonzero ucol[k] is stored in usub[k].
- *  xusub[i] points to the starting location of column i in ucol.
- *  Storage: new row subscripts; that is subscripts of PA.
- */
-
-#ifndef EIGEN_LU_STRUCTS
-#define EIGEN_LU_STRUCTS
-namespace Eigen {
-namespace internal {
-  
-typedef enum {LUSUP, UCOL, LSUB, USUB, LLVL, ULVL} MemType; 
-
-template <typename IndexVector, typename ScalarVector>
-struct LU_GlobalLU_t {
-  typedef typename IndexVector::Scalar StorageIndex; 
-  IndexVector xsup; //First supernode column ... xsup(s) points to the beginning of the s-th supernode
-  IndexVector supno; // Supernode number corresponding to this column (column to supernode mapping)
-  ScalarVector  lusup; // nonzero values of L ordered by columns 
-  IndexVector lsub; // Compressed row indices of L rectangular supernodes. 
-  IndexVector xlusup; // pointers to the beginning of each column in lusup
-  IndexVector xlsub; // pointers to the beginning of each column in lsub
-  Index   nzlmax; // Current max size of lsub
-  Index   nzlumax; // Current max size of lusup
-  ScalarVector  ucol; // nonzero values of U ordered by columns 
-  IndexVector usub; // row indices of U columns in ucol
-  IndexVector xusub; // Pointers to the beginning of each column of U in ucol 
-  Index   nzumax; // Current max size of ucol
-  Index   n; // Number of columns in the matrix  
-  Index   num_expansions; 
-};
-
-// Values to set for performance
-struct perfvalues {
-  Index panel_size; // a panel consists of at most <panel_size> consecutive columns
-  Index relax; // To control degree of relaxing supernodes. If the number of nodes (columns) 
-                // in a subtree of the elimination tree is less than relax, this subtree is considered 
-                // as one supernode regardless of the row structures of those columns
-  Index maxsuper; // The maximum size for a supernode in complete LU
-  Index rowblk; // The minimum row dimension for 2-D blocking to be used;
-  Index colblk; // The minimum column dimension for 2-D blocking to be used;
-  Index fillfactor; // The estimated fills factors for L and U, compared with A
-}; 
-
-} // end namespace internal
-
-} // end namespace Eigen
-#endif // EIGEN_LU_STRUCTS