sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.20__cp310-cp310-macosx_10_9_universal2.whl

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

@@ -1,137 +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 xpivotL.c file in SuperLU 
- 
- * -- SuperLU routine (version 3.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * October 15, 2003
- *
- * 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 SPARSELU_PIVOTL_H
-#define SPARSELU_PIVOTL_H
-
-namespace Eigen {
-namespace internal {
-  
-/**
- * \brief Performs the numerical pivotin on the current column of L, and the CDIV operation.
- * 
- * Pivot policy :
- * (1) Compute thresh = u * max_(i>=j) abs(A_ij);
- * (2) IF user specifies pivot row k and abs(A_kj) >= thresh THEN
- *           pivot row = k;
- *       ELSE IF abs(A_jj) >= thresh THEN
- *           pivot row = j;
- *       ELSE
- *           pivot row = m;
- * 
- *   Note: If you absolutely want to use a given pivot order, then set u=0.0.
- * 
- * \param jcol The current column of L
- * \param diagpivotthresh diagonal pivoting threshold
- * \param[in,out] perm_r Row permutation (threshold pivoting)
- * \param[in] iperm_c column permutation - used to finf diagonal of Pc*A*Pc'
- * \param[out] pivrow  The pivot row
- * \param glu Global LU data
- * \return 0 if success, i > 0 if U(i,i) is exactly zero 
- * 
- */
-template <typename Scalar, typename StorageIndex>
-Index SparseLUImpl<Scalar,StorageIndex>::pivotL(const Index jcol, const RealScalar& diagpivotthresh, IndexVector& perm_r, IndexVector& iperm_c, Index& pivrow, GlobalLU_t& glu)
-{
-  
-  Index fsupc = (glu.xsup)((glu.supno)(jcol)); // First column in the supernode containing the column jcol
-  Index nsupc = jcol - fsupc; // Number of columns in the supernode portion, excluding jcol; nsupc >=0
-  Index lptr = glu.xlsub(fsupc); // pointer to the starting location of the row subscripts for this supernode portion
-  Index nsupr = glu.xlsub(fsupc+1) - lptr; // Number of rows in the supernode
-  Index lda = glu.xlusup(fsupc+1) - glu.xlusup(fsupc); // leading dimension
-  Scalar* lu_sup_ptr = &(glu.lusup.data()[glu.xlusup(fsupc)]); // Start of the current supernode
-  Scalar* lu_col_ptr = &(glu.lusup.data()[glu.xlusup(jcol)]); // Start of jcol in the supernode
-  StorageIndex* lsub_ptr = &(glu.lsub.data()[lptr]); // Start of row indices of the supernode
-  
-  // Determine the largest abs numerical value for partial pivoting 
-  Index diagind = iperm_c(jcol); // diagonal index 
-  RealScalar pivmax(-1.0);
-  Index pivptr = nsupc; 
-  Index diag = emptyIdxLU; 
-  RealScalar rtemp;
-  Index isub, icol, itemp, k; 
-  for (isub = nsupc; isub < nsupr; ++isub) {
-    using std::abs;
-    rtemp = abs(lu_col_ptr[isub]);
-    if (rtemp > pivmax) {
-      pivmax = rtemp; 
-      pivptr = isub;
-    } 
-    if (lsub_ptr[isub] == diagind) diag = isub;
-  }
-  
-  // Test for singularity
-  if ( pivmax <= RealScalar(0.0) ) {
-    // if pivmax == -1, the column is structurally empty, otherwise it is only numerically zero
-    pivrow = pivmax < RealScalar(0.0) ? diagind : lsub_ptr[pivptr];
-    perm_r(pivrow) = StorageIndex(jcol);
-    return (jcol+1);
-  }
-  
-  RealScalar thresh = diagpivotthresh * pivmax; 
-  
-  // Choose appropriate pivotal element 
-  
-  {
-    // Test if the diagonal element can be used as a pivot (given the threshold value)
-    if (diag >= 0 ) 
-    {
-      // Diagonal element exists
-      using std::abs;
-      rtemp = abs(lu_col_ptr[diag]);
-      if (rtemp != RealScalar(0.0) && rtemp >= thresh) pivptr = diag;
-    }
-    pivrow = lsub_ptr[pivptr];
-  }
-  
-  // Record pivot row
-  perm_r(pivrow) = StorageIndex(jcol);
-  // Interchange row subscripts
-  if (pivptr != nsupc )
-  {
-    std::swap( lsub_ptr[pivptr], lsub_ptr[nsupc] );
-    // Interchange numerical values as well, for the two rows in the whole snode
-    // such that L is indexed the same way as A
-    for (icol = 0; icol <= nsupc; icol++)
-    {
-      itemp = pivptr + icol * lda; 
-      std::swap(lu_sup_ptr[itemp], lu_sup_ptr[nsupc + icol * lda]);
-    }
-  }
-  // cdiv operations
-  Scalar temp = Scalar(1.0) / lu_col_ptr[nsupc];
-  for (k = nsupc+1; k < nsupr; k++)
-    lu_col_ptr[k] *= temp; 
-  return 0;
-}
-
-} // end namespace internal
-} // end namespace Eigen
-
-#endif // SPARSELU_PIVOTL_H

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

@@ -1,136 +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]pruneL.c file in SuperLU 
- 
- * -- SuperLU routine (version 2.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * November 15, 1997
- *
- * 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 SPARSELU_PRUNEL_H
-#define SPARSELU_PRUNEL_H
-
-namespace Eigen {
-namespace internal {
-
-/**
- * \brief Prunes the L-structure.
- *
- * It prunes the L-structure  of supernodes whose L-structure contains the current pivot row "pivrow"
- * 
- * 
- * \param jcol The current column of L
- * \param[in] perm_r Row permutation
- * \param[out] pivrow  The pivot row
- * \param nseg Number of segments
- * \param segrep 
- * \param repfnz
- * \param[out] xprune 
- * \param glu Global LU data
- * 
- */
-template <typename Scalar, typename StorageIndex>
-void SparseLUImpl<Scalar,StorageIndex>::pruneL(const Index jcol, const IndexVector& perm_r, const Index pivrow, const Index nseg,
-                                               const IndexVector& segrep, BlockIndexVector repfnz, IndexVector& xprune, GlobalLU_t& glu)
-{
-  // For each supernode-rep irep in U(*,j]
-  Index jsupno = glu.supno(jcol); 
-  Index i,irep,irep1; 
-  bool movnum, do_prune = false; 
-  Index kmin = 0, kmax = 0, minloc, maxloc,krow; 
-  for (i = 0; i < nseg; i++)
-  {
-    irep = segrep(i); 
-    irep1 = irep + 1; 
-    do_prune = false; 
-    
-    // Don't prune with a zero U-segment 
-    if (repfnz(irep) == emptyIdxLU) continue; 
-    
-    // If a snode overlaps with the next panel, then the U-segment
-    // is fragmented into two parts -- irep and irep1. We should let 
-    // pruning occur at the rep-column in irep1s snode. 
-    if (glu.supno(irep) == glu.supno(irep1) ) continue; // don't prune 
-    
-    // If it has not been pruned & it has a nonz in row L(pivrow,i)
-    if (glu.supno(irep) != jsupno )
-    {
-      if ( xprune (irep) >= glu.xlsub(irep1) )
-      {
-        kmin = glu.xlsub(irep);
-        kmax = glu.xlsub(irep1) - 1; 
-        for (krow = kmin; krow <= kmax; krow++)
-        {
-          if (glu.lsub(krow) == pivrow) 
-          {
-            do_prune = true; 
-            break; 
-          }
-        }
-      }
-      
-      if (do_prune) 
-      {
-        // do a quicksort-type partition
-        // movnum=true means that the num values have to be exchanged
-        movnum = false; 
-        if (irep == glu.xsup(glu.supno(irep)) ) // Snode of size 1 
-          movnum = true; 
-        
-        while (kmin <= kmax)
-        {
-          if (perm_r(glu.lsub(kmax)) == emptyIdxLU)
-            kmax--; 
-          else if ( perm_r(glu.lsub(kmin)) != emptyIdxLU)
-            kmin++;
-          else 
-          {
-            // kmin below pivrow (not yet pivoted), and kmax
-            // above pivrow: interchange the two suscripts
-            std::swap(glu.lsub(kmin), glu.lsub(kmax)); 
-            
-            // If the supernode has only one column, then we 
-            // only keep one set of subscripts. For any subscript
-            // intercnahge performed, similar interchange must be 
-            // done on the numerical values. 
-            if (movnum) 
-            {
-              minloc = glu.xlusup(irep) + ( kmin - glu.xlsub(irep) ); 
-              maxloc = glu.xlusup(irep) + ( kmax - glu.xlsub(irep) ); 
-              std::swap(glu.lusup(minloc), glu.lusup(maxloc)); 
-            }
-            kmin++;
-            kmax--;
-          }
-        } // end while 
-        
-        xprune(irep) = StorageIndex(kmin);  //Pruning 
-      } // end if do_prune 
-    } // end pruning 
-  } // End for each U-segment
-}
-
-} // end namespace internal
-} // end namespace Eigen
-
-#endif // SPARSELU_PRUNEL_H

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

@@ -1,83 +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/.
-
-/* This file is a modified version of heap_relax_snode.c file in SuperLU
- * -- SuperLU routine (version 3.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * October 15, 2003
- *
- * 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 SPARSELU_RELAX_SNODE_H
-#define SPARSELU_RELAX_SNODE_H
-
-namespace Eigen {
-
-namespace internal {
- 
-/** 
- * \brief Identify the initial relaxed supernodes
- * 
- * This routine is applied to a column elimination tree. 
- * It assumes that the matrix has been reordered according to the postorder of the etree
- * \param n  the number of columns
- * \param et elimination tree 
- * \param relax_columns Maximum number of columns allowed in a relaxed snode 
- * \param descendants Number of descendants of each node in the etree
- * \param relax_end last column in a supernode
- */
-template <typename Scalar, typename StorageIndex>
-void SparseLUImpl<Scalar,StorageIndex>::relax_snode (const Index n, IndexVector& et, const Index relax_columns, IndexVector& descendants, IndexVector& relax_end)
-{
-  
-  // compute the number of descendants of each node in the etree
-  Index parent; 
-  relax_end.setConstant(emptyIdxLU);
-  descendants.setZero();
-  for (Index j = 0; j < n; j++) 
-  {
-    parent = et(j);
-    if (parent != n) // not the dummy root
-      descendants(parent) += descendants(j) + 1;
-  }
-  // Identify the relaxed supernodes by postorder traversal of the etree
-  Index snode_start; // beginning of a snode 
-  for (Index j = 0; j < n; )
-  {
-    parent = et(j);
-    snode_start = j; 
-    while ( parent != n && descendants(parent) < relax_columns ) 
-    {
-      j = parent; 
-      parent = et(j);
-    }
-    // Found a supernode in postordered etree, j is the last column 
-    relax_end(snode_start) = StorageIndex(j); // Record last column
-    j++;
-    // Search for a new leaf
-    while (descendants(j) != 0 && j < n) j++;
-  } // End postorder traversal of the etree
-  
-}
-
-} // end namespace internal
-
-} // end namespace Eigen
-#endif