debian/changelog

-sofa-framework (19.06.01+dfsg-1) UNRELEASED; urgency=medium
+sofa-framework (19.06.01+dfsg2-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * Point watch file to Github

debian/copyright

@@ -4,7 +4,6 @@ Debianized-By: Dominique Belhachemi <domibel@debian.org>
 Debianized-Date: Tue, 24 Jun 2008 20:51:56 +0200
 Source: https://github.com/sofa-framework/sofa/releases
 Files-Excluded: */libQGLViewer*
-                */csparse
                 */gtest
                 */qwt*
                 */eigen-3*
@@ -13,7 +12,6 @@ Files-Excluded: */libQGLViewer*
                 */tinyxml
                 */*.dll
                 */*.lib
-                */SuiteSparse
 
 Files: *
 Copyright: 2006-2008 MGH, INRIA, USTL, UJF, CNRS

debian/watch

 version=4
 
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
   https://github.com/sofa-framework/sofa/releases .*/archive/v@ANY_VERSION@@ARCHIVE_EXT@

extlibs/csparse/CMakeLists.txt

+cmake_minimum_required(VERSION 3.1)
+project(csparse VERSION 1.2.0)
+
+set(HEADER_FILES
+    csparse.h
+    ldl.h
+    UFconfig.h)
+
+set(SOURCE_FILES
+    csparse.c
+    ldl.c)
+
+# The code must be relocatable if we want to link a shared library against it.
+if("x${CMAKE_CXX_COMPILER_ID}" STREQUAL "xGNU" OR "x${CMAKE_CXX_COMPILER_ID}" STREQUAL "xClang")
+    add_compile_options(-fPIC)
+endif()
+
+add_library(${PROJECT_NAME} STATIC ${HEADER_FILES} ${SOURCE_FILES})
+target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>")
+target_include_directories(${PROJECT_NAME} PUBLIC "$<INSTALL_INTERFACE:include/extlibs/CSparse>")
+set_target_properties(${PROJECT_NAME} PROPERTIES PUBLIC_HEADER "${HEADER_FILES}")
+
+include(${SOFA_KERNEL_SOURCE_DIR}/SofaFramework/SofaMacros.cmake)
+sofa_generate_package(NAME CSparse VERSION ${PROJECT_VERSION} TARGETS ${PROJECT_NAME} INCLUDE_INSTALL_DIR "extlibs/CSparse")

extlibs/csparse/COPYING.txt

+CSPARSE: a Concise Sparse matrix package.
+Copyright (c) 2006, Timothy A. Davis.
+http://www.cise.ufl.edu/research/sparse/CSparse

extlibs/csparse/CSparseConfig.cmake.in

+# CMake package configuration file for the csparse library
+
+@PACKAGE_INIT@
+
+if(NOT TARGET csparse)
+	include("${CMAKE_CURRENT_LIST_DIR}/CSparseTargets.cmake")
+endif()
+
+check_required_components(csparse)
+
+set(CSparse_LIBRARIES csparse)
+set(CSparse_INCLUDE_DIRS @PACKAGE_CSPARSE_INCLUDE_DIR@)

extlibs/csparse/UFconfig.h

+/* ========================================================================== */
+/* === UFconfig.h =========================================================== */
+/* ========================================================================== */
+
+/* Configuration file for SuiteSparse: a Suite of Sparse matrix packages
+ * (AMD, COLAMD, CCOLAMD, CAMD, CHOLMOD, UMFPACK, CXSparse, and others).
+ *
+ * UFconfig.h provides the definition of the long integer.  On most systems,
+ * a C program can be compiled in LP64 mode, in which long's and pointers are
+ * both 64-bits, and int's are 32-bits.  Windows 64, however, uses the LLP64
+ * model, in which int's and long's are 32-bits, and long long's and pointers
+ * are 64-bits.
+ *
+ * SuiteSparse packages that include long integer versions are
+ * intended for the LP64 mode.  However, as a workaround for Windows 64
+ * (and perhaps other systems), the long integer can be redefined.
+ *
+ * If _WIN64 is defined, then the __int64 type is used instead of long.
+ *
+ * The long integer can also be defined at compile time.  For example, this
+ * could be added to UFconfig.mk:
+ *
+ * CFLAGS = -O -D'UF_long=long long' -D'UF_long_max=9223372036854775801' \
+ *   -D'UF_long_id="%lld"'
+ *
+ * This file defines UF_long as either long (on all but _WIN64) or
+ * __int64 on Windows 64.  The intent is that a UF_long is always a 64-bit
+ * integer in a 64-bit code.  ptrdiff_t might be a better choice than long;
+ * it is always the same size as a pointer.
+ *
+ * This file also defines the SUITESPARSE_VERSION and related definitions.
+ *
+ * Copyright (c) 2007, University of Florida.  No licensing restrictions
+ * apply to this file or to the UFconfig directory.  Author: Timothy A. Davis.
+ */
+
+#ifndef _UFCONFIG_H
+#define _UFCONFIG_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#include <limits.h>
+
+/* ========================================================================== */
+/* === UF_long ============================================================== */
+/* ========================================================================== */
+
+#ifndef UF_long
+
+#ifdef _WIN64
+
+#define UF_long __int64
+#define UF_long_max _I64_MAX
+#define UF_long_id "%I64d"
+
+#else
+
+#define UF_long long
+#define UF_long_max LONG_MAX
+#define UF_long_id "%ld"
+
+#endif
+#endif
+
+/* ========================================================================== */
+/* === SuiteSparse version ================================================== */
+/* ========================================================================== */
+
+/* SuiteSparse is not a package itself, but a collection of packages, some of
+ * which must be used together (UMFPACK requires AMD, CHOLMOD requires AMD,
+ * COLAMD, CAMD, and CCOLAMD, etc).  A version number is provided here for the
+ * collection itself.  The versions of packages within each version of
+ * SuiteSparse are meant to work together.  Combining one packge from one
+ * version of SuiteSparse, with another package from another version of
+ * SuiteSparse, may or may not work.
+ *
+ * SuiteSparse Version 3.2.0 contains the following packages:
+ *
+ *  AMD		    version 2.2.0
+ *  CAMD	    version 2.2.0
+ *  COLAMD	    version 2.7.1
+ *  CCOLAMD	    version 2.7.1
+ *  CHOLMOD	    version 1.7.0
+ *  CSparse	    version 2.2.1
+ *  CXSparse	    version 2.2.1
+ *  KLU		    version 1.0.1
+ *  BTF		    version 1.0.1
+ *  LDL		    version 2.0.1
+ *  UFconfig	    version number is the same as SuiteSparse
+ *  UMFPACK	    version 5.2.0
+ *  RBio	    version 1.1.1
+ *  UFcollection    version 1.1.1
+ *  LINFACTOR       version 1.1.0
+ *  MESHND          version 1.1.0
+ *  SSMULT          version 1.1.0
+ *  MATLAB_Tools    no specific version number
+ *  SuiteSparseQR   version 1.1.0
+ *
+ * Other package dependencies:
+ *  BLAS	    required by CHOLMOD and UMFPACK
+ *  LAPACK	    required by CHOLMOD
+ *  METIS 4.0.1	    required by CHOLMOD (optional) and KLU (optional)
+ */
+
+#define SUITESPARSE_DATE "Sept 20, 2008"
+#define SUITESPARSE_VER_CODE(main,sub) ((main) * 1000 + (sub))
+#define SUITESPARSE_MAIN_VERSION 3
+#define SUITESPARSE_SUB_VERSION 2
+#define SUITESPARSE_SUBSUB_VERSION 0
+#define SUITESPARSE_VERSION \
+    SUITESPARSE_VER_CODE(SUITESPARSE_MAIN_VERSION,SUITESPARSE_SUB_VERSION)
+
+#ifdef __cplusplus
+}
+#endif
+#endif

extlibs/csparse/csparse.h

+#ifndef _CS_H
+#define _CS_H
+
+#ifdef MATLAB_MEX_FILE
+#include "mex.h"
+#endif
+#define CS_VER 1		    /* CSparse Version 1.2.0 */
+#define CS_SUBVER 2
+#define CS_SUBSUB 0
+#define CS_DATE "Mar 6, 2006"	    /* CSparse release date */
+#define CS_COPYRIGHT "Copyright (c) Timothy A. Davis, 2006"
+
+#if defined(__cplusplus)
+extern "C" {
+#endif
+
+/* --- primary CSparse routines and data structures ------------------------- */
+typedef struct cs_sparse    /* matrix in compressed-column or triplet form */
+{
+    int nzmax ;	    /* maximum number of entries */
+    int m ;	    /* number of rows */
+    int n ;	    /* number of columns */
+    int *p ;	    /* column pointers (size n+1) or col indices (size nzmax) */
+    int *i ;	    /* row indices, size nzmax */
+    double *x ;	    /* numerical values, size nzmax */
+    int nz ;	    /* # of entries in triplet matrix, -1 for compressed-col */
+} cs ;
+
+cs *cs_add (const cs *A, const cs *B, double alpha, double beta) ;
+int cs_cholsol (const cs *A, double *b, int order) ;
+int cs_dupl (cs *A) ;
+int cs_entry (cs *T, int i, int j, double x) ;
+int cs_lusol (const cs *A, double *b, int order, double tol) ;
+int cs_gaxpy (const cs *A, const double *x, double *y) ;
+cs *cs_multiply (const cs *A, const cs *B) ;
+int cs_qrsol (const cs *A, double *b, int order) ;
+cs *cs_transpose (const cs *A, int values) ;
+cs *cs_triplet (const cs *T) ;
+double cs_norm (const cs *A) ;
+int cs_print (const cs *A, int brief) ;
+cs *cs_load (FILE *f) ;
+/* utilities */
+void *cs_calloc (int n, size_t size) ;
+void *cs_free (void *p) ;
+void *cs_realloc (void *p, int n, size_t size, int *ok) ;
+cs *cs_spalloc (int m, int n, int nzmax, int values, int triplet) ;
+cs *cs_spfree (cs *A) ;
+int cs_sprealloc (cs *A, int nzmax) ;
+void *cs_malloc (int n, size_t size) ;
+
+/* --- secondary CSparse routines and data structures ----------------------- */
+typedef struct cs_symbolic  /* symbolic Cholesky, LU, or QR analysis */
+{
+    int *Pinv ;	    /* inverse row perm. for QR, fill red. perm for Chol */
+    int *Q ;	    /* fill-reducing column permutation for LU and QR */
+    int *parent ;   /* elimination tree for Cholesky and QR */
+    int *cp ;	    /* column pointers for Cholesky, row counts for QR */
+    int m2 ;	    /* # of rows for QR, after adding fictitious rows */
+    int lnz ;	    /* # entries in L for LU or Cholesky; in V for QR */
+    int unz ;	    /* # entries in U for LU; in R for QR */
+} css ;
+
+typedef struct cs_numeric   /* numeric Cholesky, LU, or QR factorization */
+{
+    cs *L ;	    /* L for LU and Cholesky, V for QR */
+    cs *U ;	    /* U for LU, R for QR, not used for Cholesky */
+    int *Pinv ;	    /* partial pivoting for LU */
+    double *B ;	    /* beta [0..n-1] for QR */
+} csn ;
+
+typedef struct cs_dmperm_results    /* cs_dmperm or cs_scc output */
+{
+    int *P ;	    /* size m, row permutation */
+    int *Q ;	    /* size n, column permutation */
+    int *R ;	    /* size nb+1, block k is rows R[k] to R[k+1]-1 in A(P,Q) */
+    int *S ;	    /* size nb+1, block k is cols S[k] to S[k+1]-1 in A(P,Q) */
+    int nb ;	    /* # of blocks in fine dmperm decomposition */
+    int rr [5] ;    /* coarse row decomposition */
+    int cc [5] ;    /* coarse column decomposition */
+} csd ;
+
+int *cs_amd (const cs *A, int order) ;
+csn *cs_chol (const cs *A, const css *S) ;
+csd *cs_dmperm (const cs *A) ;
+int cs_droptol (cs *A, double tol) ;
+int cs_dropzeros (cs *A) ;
+int cs_happly (const cs *V, int i, double beta, double *x) ;
+int cs_ipvec (int n, const int *P, const double *b, double *x) ;
+int cs_lsolve (const cs *L, double *x) ;
+int cs_ltsolve (const cs *L, double *x) ;
+csn *cs_lu (const cs *A, const css *S, double tol) ;
+cs *cs_permute (const cs *A, const int *P, const int *Q, int values) ;
+int *cs_pinv (const int *P, int n) ;
+int cs_pvec (int n, const int *P, const double *b, double *x) ;
+csn *cs_qr (const cs *A, const css *S) ;
+css *cs_schol (const cs *A, int order) ;
+css *cs_sqr (const cs *A, int order, int qr) ;
+cs *cs_symperm (const cs *A, const int *Pinv, int values) ;
+int cs_usolve (const cs *U, double *x) ;
+int cs_utsolve (const cs *U, double *x) ;
+int cs_updown (cs *L, int sigma, const cs *C, const int *parent) ;
+/* utilities */
+css *cs_sfree (css *S) ;
+csn *cs_nfree (csn *N) ;
+csd *cs_dfree (csd *D) ;
+
+/* --- tertiary CSparse routines -------------------------------------------- */
+int *cs_counts (const cs *A, const int *parent, const int *post, int ata) ;
+int cs_cumsum (int *p, int *c, int n) ;
+int cs_dfs (int j, cs *L, int top, int *xi, int *pstack, const int *Pinv) ;
+int *cs_etree (const cs *A, int ata) ;
+int cs_fkeep (cs *A, int (*fkeep) (int, int, double, void *), void *other) ;
+double cs_house (double *x, double *beta, int n) ;
+int *cs_maxtrans (const cs *A) ;
+int *cs_post (int n, const int *parent) ;
+int cs_reach (cs *L, const cs *B, int k, int *xi, const int *Pinv) ;
+csd *cs_scc (cs *A) ;
+int cs_scatter (const cs *A, int j, double beta, int *w, double *x, int mark,
+    cs *C, int nz) ;
+int cs_splsolve (cs *L, const cs *B, int k, int *xi, double *x,
+    const int *Pinv) ;
+int cs_tdfs (int j, int k, int *head, const int *next, int *post,
+    int *stack) ;
+/* utilities */
+csd *cs_dalloc (int m, int n) ;
+cs *cs_done (cs *C, void *w, void *x, int ok) ;
+int *cs_idone (int *p, cs *C, void *w, int ok) ;
+csn *cs_ndone (csn *N, cs *C, void *w, void *x, int ok) ;
+csd *cs_ddone (csd *D, cs *C, void *w, int ok) ;
+
+#define CS_MAX(a,b) (((a) > (b)) ? (a) : (b))
+#define CS_MIN(a,b) (((a) < (b)) ? (a) : (b))
+#define CS_FLIP(i) (-(i)-2)
+#define CS_UNFLIP(i) (((i) < 0) ? CS_FLIP(i) : (i))
+#define CS_MARKED(Ap,j) (Ap [j] < 0)
+#define CS_MARK(Ap,j) { Ap [j] = CS_FLIP (Ap [j]) ; }
+#define CS_OVERFLOW(n,size) (n > INT_MAX / (int) size)
+
+
+#if defined(__cplusplus)
+} //extern "C"
+#endif
+
+#endif

extlibs/csparse/ldl.h

+/* ========================================================================== */
+/* === ldl.h:  include file for the LDL package ============================= */
+/* ========================================================================== */
+
+/* LDL Copyright (c) Timothy A Davis,
+ * University of Florida.  All Rights Reserved.  See README for the License.
+ */
+
+#include "UFconfig.h"
+
+#ifdef LDL_LONG
+#define LDL_int UF_long
+#define LDL_ID UF_long_id
+
+#define LDL_symbolic ldl_l_symbolic
+#define LDL_numeric ldl_l_numeric
+#define LDL_lsolve ldl_l_lsolve
+#define LDL_dsolve ldl_l_dsolve
+#define LDL_ltsolve ldl_l_ltsolve
+#define LDL_perm ldl_l_perm
+#define LDL_permt ldl_l_permt
+#define LDL_valid_perm ldl_l_valid_perm
+#define LDL_valid_matrix ldl_l_valid_matrix
+
+#else
+#define LDL_int int
+#define LDL_ID "%d"
+
+#define LDL_symbolic ldl_symbolic
+#define LDL_numeric ldl_numeric
+#define LDL_lsolve ldl_lsolve
+#define LDL_dsolve ldl_dsolve
+#define LDL_ltsolve ldl_ltsolve
+#define LDL_perm ldl_perm
+#define LDL_permt ldl_permt
+#define LDL_valid_perm ldl_valid_perm
+#define LDL_valid_matrix ldl_valid_matrix
+
+#endif
+
+#if defined(__cplusplus)
+extern "C" {
+#endif
+
+/* ========================================================================== */
+/* === int version ========================================================== */
+/* ========================================================================== */
+
+void ldl_symbolic (int n, int Ap [ ], int Ai [ ], int Lp [ ],
+    int Parent [ ], int Lnz [ ], int Flag [ ], int P [ ], int Pinv [ ]) ;
+
+int ldl_numeric (int n, int Ap [ ], int Ai [ ], double Ax [ ],
+    int Lp [ ], int Parent [ ], int Lnz [ ], int Li [ ], double Lx [ ],
+    double D [ ], double Y [ ], int Pattern [ ], int Flag [ ],
+    int P [ ], int Pinv [ ]) ;
+
+void ldl_lsolve (int n, double X [ ], int Lp [ ], int Li [ ],
+    double Lx [ ]) ;
+
+void ldl_dsolve (int n, double X [ ], double D [ ]) ;
+
+void ldl_ltsolve (int n, double X [ ], int Lp [ ], int Li [ ],
+    double Lx [ ]) ;
+
+void ldl_perm  (int n, double X [ ], double B [ ], int P [ ]) ;
+void ldl_permt (int n, double X [ ], double B [ ], int P [ ]) ;
+
+int ldl_valid_perm (int n, int P [ ], int Flag [ ]) ;
+int ldl_valid_matrix ( int n, int Ap [ ], int Ai [ ]) ;
+
+/* ========================================================================== */
+/* === long version ========================================================= */
+/* ========================================================================== */
+
+void ldl_l_symbolic (UF_long n, UF_long Ap [ ], UF_long Ai [ ], UF_long Lp [ ],
+    UF_long Parent [ ], UF_long Lnz [ ], UF_long Flag [ ], UF_long P [ ],
+    UF_long Pinv [ ]) ;
+
+UF_long ldl_l_numeric (UF_long n, UF_long Ap [ ], UF_long Ai [ ], double Ax [ ],
+    UF_long Lp [ ], UF_long Parent [ ], UF_long Lnz [ ], UF_long Li [ ],
+    double Lx [ ], double D [ ], double Y [ ], UF_long Pattern [ ],
+    UF_long Flag [ ], UF_long P [ ], UF_long Pinv [ ]) ;
+
+void ldl_l_lsolve (UF_long n, double X [ ], UF_long Lp [ ], UF_long Li [ ],
+    double Lx [ ]) ;
+
+void ldl_l_dsolve (UF_long n, double X [ ], double D [ ]) ;
+
+void ldl_l_ltsolve (UF_long n, double X [ ], UF_long Lp [ ], UF_long Li [ ],
+    double Lx [ ]) ;
+
+void ldl_l_perm  (UF_long n, double X [ ], double B [ ], UF_long P [ ]) ;
+void ldl_l_permt (UF_long n, double X [ ], double B [ ], UF_long P [ ]) ;
+
+UF_long ldl_l_valid_perm (UF_long n, UF_long P [ ], UF_long Flag [ ]) ;
+UF_long ldl_l_valid_matrix ( UF_long n, UF_long Ap [ ], UF_long Ai [ ]) ;
+
+/* ========================================================================== */
+/* === LDL version ========================================================== */
+/* ========================================================================== */
+
+#define LDL_DATE "Nov 1, 2007"
+#define LDL_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
+#define LDL_MAIN_VERSION 2
+#define LDL_SUB_VERSION 0
+#define LDL_SUBSUB_VERSION 1
+#define LDL_VERSION LDL_VERSION_CODE(LDL_MAIN_VERSION,LDL_SUB_VERSION)
+
+#if defined(__cplusplus)
+} //extern "C"
+#endif