merge with master

remove gmp-devel from Requires
2019-10-11 17:40:19 -04:00 · 2019-10-10 23:02:39 -04:00
7 changed files with 206 additions and 253 deletions
--- a/.gitignore
+++ b/.gitignore
@ -2,6 +2,3 @@
 /iso2mesh-1.9.1.tar.gz
 /meshfix-1.2.1.tar.gz
 /tetgen1.5.1.tar.gz
-/cork-0.9.1.tar.gz
-/iso2mesh-1.9.6.tar.gz
-/meshfix-1.2.2.tar.gz
--- a/iso2mesh-1.9.6-CMakeCMP0064.patch
+++ b/iso2mesh-1.9.6-CMakeCMP0064.patch
@ -1,113 +0,0 @@
-diff -up iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt~ iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt
--- iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt~	2020-09-05 21:56:08.000000000 +0200
-+++ iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt	2021-07-20 11:17:50.726256258 +0200
-@@ -4,12 +4,7 @@
- 
- project( Mesh_3_example )
- 
-cmake_minimum_required(VERSION 2.6.2)
-if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" VERSION_GREATER 2.8.3)
-  cmake_policy(VERSION 2.8.4)
-else()
-  cmake_policy(VERSION 2.6)
-endif()
-+cmake_minimum_required(VERSION 3.1...3.21)
- 
- include_directories(../../include)
- include_directories(../../../Triangulation_3/include)
-@@ -32,7 +27,7 @@ if ( CGAL_FOUND )
-   option(ACTIVATE_CONCURRENT_MESH_3
-     "Activate parallelism in Mesh_3"
-     OFF)
-    
-+
-   # And add -DCGAL_CONCURRENT_MESH_3 if that option is ON
-   if( ACTIVATE_CONCURRENT_MESH_3 OR ENV{ACTIVATE_CONCURRENT_MESH_3} )
-     add_definitions( -DCGAL_CONCURRENT_MESH_3 )
-@@ -45,7 +40,7 @@ if ( CGAL_FOUND )
-       find_package( TBB )
-     endif( LINK_WITH_TBB )
-   endif()
-  
-+
-   if( TBB_FOUND )
-     include(${TBB_USE_FILE})
-     list(APPEND CGAL_3RD_PARTY_LIBRARIES ${TBB_LIBRARIES})
-@@ -74,4 +69,3 @@ if ( CGAL_FOUND )
- else()
-   message(STATUS "This program requires the CGAL library, and will not be compiled.")
- endif()
-
-diff -up iso2mesh-1.9.6/tools/cgalsimp2/CMakeLists.txt~ iso2mesh-1.9.6/tools/cgalsimp2/CMakeLists.txt
--- iso2mesh-1.9.6/tools/cgalsimp2/CMakeLists.txt~	2020-09-05 21:56:08.000000000 +0200
-+++ iso2mesh-1.9.6/tools/cgalsimp2/CMakeLists.txt	2021-07-20 11:18:34.737708589 +0200
-@@ -4,22 +4,9 @@
- project( Surface_mesh_simplification )
- 
- 
-cmake_minimum_required(VERSION 2.6.2)
-if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}" VERSION_GREATER 2.6)
-  if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" VERSION_GREATER 2.8.3)
-    cmake_policy(VERSION 2.8.4)
-  else()
-    cmake_policy(VERSION 2.6)
-  endif()
-endif()
-+cmake_minimum_required(VERSION 3.1...3.21)
- 
- set( CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS true )
- 
-if ( COMMAND cmake_policy )
-
-  cmake_policy( SET CMP0003 NEW )  
-
-endif()
- 
- # CGAL and its components
- find_package( CGAL QUIET COMPONENTS  )
-@@ -27,7 +14,7 @@ find_package( CGAL QUIET COMPONENTS  )
- if ( NOT CGAL_FOUND )
- 
-   message(STATUS "This project requires the CGAL library, and will not be compiled.")
-  return()  
-+  return()
- 
- endif()
- 
-@@ -42,7 +29,7 @@ if ( NOT Boost_FOUND )
- 
-   message(STATUS "This project requires the Boost library, and will not be compiled.")
- 
-  return()  
-+  return()
- 
- endif()
- 
-diff -up iso2mesh-1.9.6/tools/cgalsurf/CMakeLists.txt~ iso2mesh-1.9.6/tools/cgalsurf/CMakeLists.txt
--- iso2mesh-1.9.6/tools/cgalsurf/CMakeLists.txt~	2020-09-05 21:56:08.000000000 +0200
-+++ iso2mesh-1.9.6/tools/cgalsurf/CMakeLists.txt	2021-07-20 11:18:16.986526147 +0200
-@@ -3,12 +3,7 @@
- 
- project( Surface_mesher_example )
- 
-cmake_minimum_required(VERSION 2.6.2)
-if("${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_PATCH_VERSION}" VERSION_GREATER 2.8.3)
-  cmake_policy(VERSION 2.8.4)
-else()
-  cmake_policy(VERSION 2.6)
-endif()
-+cmake_minimum_required(VERSION 3.1...3.21)
- 
- include_directories(../../include)
- 
-@@ -26,8 +21,7 @@ else()
-   if(RUNNING_CGAL_AUTO_TEST)
-     # Just to avoid a warning from CMake if that variable is set on the command line...
-   endif()
-  
-+
-   message(STATUS "NOTICE: This program requires the CGAL and CGAL ImageIO libraries, and will not be compiled.")
-  
-endif()
- 
-+endif()
--- a/iso2mesh-1.9.6-recent_Boost_version.patch
+++ b/iso2mesh-1.9.6-recent_Boost_version.patch
@ -1,12 +0,0 @@
-diff -up iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt~ iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt
--- iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt~	2021-07-20 11:24:07.950132510 +0200
-+++ iso2mesh-1.9.6/tools/cgalmesh/CMakeLists.txt	2021-07-20 11:25:30.913983853 +0200
-@@ -47,7 +47,7 @@ if ( CGAL_FOUND )
-   endif()
- 
- 
-  if ( Boost_FOUND AND Boost_VERSION GREATER 103400 )
-+  if ( Boost_FOUND )
-     include( CGAL_CreateSingleSourceCGALProgram )
- 
-     # Compilable examples
--- a/meshfix-remove-rpath.patch
+++ b/meshfix-remove-rpath.patch
@ -0,0 +1,14 @@
+diff -up a/CMakeLists.txt.orig b/CMakeLists.txt
+--- a/CMakeLists.txt.orig	2019-10-01 18:39:42.000000000 +0200
+++ b/CMakeLists.txt	2019-10-07 20:06:44.072901788 +0200
+@@ -8,10 +8,6 @@ include_directories(
+     contrib/OpenNL3.2.1/src
+     contrib/jrs_predicates
+ )
+-link_directories(
+-    ${LINK_DIRECTORIES}
+-    ${CMAKE_CURRENT_SOURCE_DIR}/contrib/JMeshLib/lib
+-)
+ file(GLOB meshfix_h include/*.h)
+ set(meshfix_src
+     contrib/jrs_predicates/jrs_predicates.c
--- a/octave-iso2mesh-c99.patch
+++ b/octave-iso2mesh-c99.patch
@ -1,36 +0,0 @@
-Avoid implicit function declarations: Declare lsame_ and
-xerbla_. Include <slu_ddefs.h> for dCreate_CompCol_Matrix,
-dCreate_Dense_Matrix, dgssv.  Prevents build failures with future
-compilers.
-
-Submitted upstream: <https://github.com/fangq/meshfix/pull/1>
-
-diff -ur iso2mesh-1.9.6.orig/tools/meshfix/contrib/OpenNL3.2.1/src/nl_single_file.c iso2mesh-1.9.6/tools/meshfix/contrib/OpenNL3.2.1/src/nl_single_file.c
--- iso2mesh-1.9.6.orig/tools/meshfix/contrib/OpenNL3.2.1/src/nl_single_file.c	2020-06-20 18:44:57.000000000 +0200
-+++ iso2mesh-1.9.6/tools/meshfix/contrib/OpenNL3.2.1/src/nl_single_file.c	2023-04-14 09:02:52.027673795 +0200
-@@ -1480,6 +1480,8 @@
- typedef NLboolean logical ;
- typedef NLint     ftnlen ;
- 
-+int NL_FORTRAN_WRAP(lsame)(char *ca, char *cb);
-+int NL_FORTRAN_WRAP(xerbla)(char *srname, int *info);
- 
- #ifndef max
- #define max(x,y) ((x) > (y) ? (x) : (y))
-@@ -3437,6 +3439,16 @@
- 
- /* SuperLU includes */
- #include <slu_cdefs.h>
-+
-+/* Hide the dgemv, gemv_ prototypes because the local definition is
-+   different (the n, m arguments are integers, not pointers to
-+   integers here). */
-+#define dgemv dgemv_hidden
-+#define dgemv_ dgemv__hidden
-+#include <slu_ddefs.h>
-+#undef dgemv
-+#undef dgemv_
-+
- #include <supermatrix.h>
- 
- /* Note: SuperLU is difficult to call, but it is worth it.    */
--- a/octave-iso2mesh.spec
+++ b/octave-iso2mesh.spec
@ -1,8 +1,8 @@
 %global octpkg iso2mesh

 Name:           octave-%{octpkg}
-Version:        1.9.6
-Release:        11%{?dist}
+Version:        1.9.1
+Release:        3%{?dist}
 Summary:        A 3D surface and volumetric mesh generator for MATLAB/Octave
 # Main package: GPLv3+
 # Meshfix: GPLv2+
@ -14,22 +14,13 @@ URL:            http://iso2mesh.sf.net
 # the following utilities are called internally by iso2mesh (stored under a private folder),
 # this is needed for making outputs reproducible
 Source0:        https://github.com/fangq/iso2mesh/archive/v%{version}/%{octpkg}-%{version}.tar.gz
-Source1:        https://github.com/fangq/cork/archive/v0.9.1/cork-0.9.1.tar.gz
-Source2:        https://github.com/fangq/meshfix/archive/v1.2.2/meshfix-1.2.2.tar.gz
+Source1:        https://github.com/fangq/cork/archive/v0.9/cork-0.9.tar.gz
+Source2:        https://github.com/fangq/meshfix/archive/v1.2.1/meshfix-1.2.1.tar.gz
 Source3:        http://ftp.mcs.anl.gov/pub/petsc/externalpackages/tetgen1.5.1.tar.gz
-
-#  Policy CMP0064 is not set: Support new TEST if() operator.
-# See also https://github.com/CGAL/cgal/issues/5857
-Patch0:         iso2mesh-1.9.6-CMakeCMP0064.patch
-
-# Fix the incorrect detection of Boost version
-# > -- NOTICE: This program requires Boost >= 1.34.1, and will not be compiled.
-Patch1:         iso2mesh-1.9.6-recent_Boost_version.patch
-Patch2:         octave-iso2mesh-c99.patch
+Patch0:         meshfix-remove-rpath.patch

 ExcludeArch:    armv7hl
-BuildRequires: make
-BuildRequires:  cmake CGAL-devel SuperLU-devel gcc-c++ zlib-devel octave-devel
+BuildRequires:  cmake CGAL-devel SuperLU-devel blas-static gcc-c++ zlib-devel octave-devel

 %if 0%{?fedora} >=32
 Requires:       octave mpfr-devel boost-devel SuperLU octave-jsonlab octave-jnifti octave-zmat
@ -65,21 +56,197 @@ This package contains the demo script and sample datasets for octave-%{octpkg}.

 %prep
 %setup -q -b 1 -n %{octpkg}-%{version}
-%setup -q -T -D -b 2 -n meshfix-1.2.2
+%setup -q -T -D -b 2 -n meshfix-1.2.1
+%patch0 -p1
 %setup -q -T -D -b 3 -n %{octpkg}-%{version}
-%patch -P 0 -z .bak -p1
-%patch -P 1 -z .bak -p1
 rm -rf tools/cork
 rm -rf tools/meshfix
 rm -rf tools/tetgen
-mv ../cork-0.9.1 tools/cork
-mv ../meshfix-1.2.2 tools/meshfix
+mv ../cork-0.9 tools/cork
+mv ../meshfix-1.2.1 tools/meshfix
 mv ../tetgen1.5.1 tools/tetgen
-%patch -P 2 -p1
 rm -rf bin/*.mex* bin/*.exe bin/*.dll

 cp COPYING.txt COPYING

+cat > DESCRIPTION << EOF
+Name: %{octpkg}
+Version: %{version}
+Date: %(date +"%Y-%d-%m")
+Title: %{summary}
+Author: Qianqian Fang <fangqq@gmail.com>
+Maintainer: Qianqian Fang <fangqq@gmail.com>
+Description: Iso2Mesh is a MATLAB/Octave-based mesh generation toolbox,
+ designed for easy creation of high quality surface and
+ tetrahedral meshes from 3D volumetric images. It contains
+ a rich set of mesh processing scripts/programs, working
+ either independently or interacting with external free
+ meshing utilities. Iso2Mesh toolbox can directly convert
+ a 3D image stack, including binary, segmented or gray-scale
+ images such as MRI or CT scans, into quality volumetric
+ meshes. This makes it particularly suitable for multi-modality
+ medical imaging data analysis and multi-physics modeling.
+ Iso2Mesh is cross-platform and is compatible with both MATLAB
+ and GNU Octave.
+URL: %{url}
+Depends: jnifti, jsonlab, zmat
+Categories: Mesh
+EOF
+
+cat > INDEX << EOF
+iso2mesh >> Iso2Mesh
+Iso2Mesh
+ advancefront
+ barydualmesh
+ bbxflatsegment
+ binsurface
+ bwislands
+ cgals2m
+ cgalv2m
+ deislands2d
+ deislands3d
+ delendelem
+ deletemeshfile
+ edgeneighbors
+ elemfacecenter
+ elemvolume
+ extractloops
+ extrudecurve
+ extrudesurf
+ faceneighbors
+ fallbackexeext
+ fillholes3d
+ fillsurf
+ finddisconnsurf
+ flatsegment
+ getexeext
+ getintersecttri
+ getoptkey
+ getplanefrom3pt
+ getvarfrom
+ highordertet
+ i2m
+ imedge3d
+ img2mesh
+ innersurf
+ insurface
+ internalpoint
+ iso2meshver
+ isoctavemesh
+ jsonopt
+ latticegrid
+ m2v
+ maskdist
+ maxsurf
+ mcpath
+ memmapstream
+ mergemesh
+ mergestruct
+ mergesurf
+ mesh2mask
+ mesh2vol
+ meshabox
+ meshacylinder
+ meshanellip
+ meshasphere
+ meshcentroid
+ meshcheckrepair
+ meshconn
+ meshcylinders
+ meshedge
+ mesheuler
+ meshface
+ meshgrid5
+ meshgrid6
+ meshinterp
+ meshquality
+ meshrefine
+ meshremap
+ meshreorient
+ meshresample
+ meshunitsphere
+ mwpath
+ neighborelem
+ nodevolume
+ orderloopedge
+ orthdisk
+ outersurf
+ plotedges
+ plotmesh
+ plotsurf
+ plottetra
+ qmeshcut
+ raysurf
+ raytrace
+ readasc
+ readgts
+ readinr
+ readmedit
+ readmptiff
+ readnirfast
+ readoff
+ readsmf
+ readtetgen
+ remeshsurf
+ removedupelem
+ removedupnodes
+ removeisolatednode
+ removeisolatedsurf
+ rotatevec3d
+ rotmat2vec
+ s2m
+ s2v
+ saveabaqus
+ saveasc
+ savebinstl
+ savedxf
+ savegts
+ saveinr
+ savejmesh
+ savejson
+ savemedit
+ savemphtxt
+ savemsh
+ savenirfast
+ saveoff
+ savesmf
+ savestl
+ savesurfpoly
+ savetetgenele
+ savetetgennode
+ savevrml
+ smoothbinvol
+ smoothsurf
+ sms
+ sortmesh
+ surf2mesh
+ surf2vol
+ surf2volz
+ surfaceclean
+ surfacenorm
+ surfboolean
+ surfdiffuse
+ surfedge
+ surfinterior
+ surfpart
+ surfplane
+ surfreorient
+ surfseeds
+ surfvolume
+ thickenbinvol
+ thinbinvol
+ uniqedges
+ uniqfaces
+ v2m
+ v2s
+ varargin2struct
+ vol2mesh
+ vol2restrictedtri
+ vol2surf
+ volface
+ volmap2mesh
+EOF
+
 mkdir -p inst/

 rm -rf base64decode base64encode fast_match_bracket gzipdecode gzipencode \
@ -92,28 +259,12 @@ savemsgpack savenifti saveubjson zlibdecode zlibencode
 mv *.m inst/
 mv img2mesh.fig inst/

-# Fix jmeshlib build flags
-sed -e "s|-Wall|%{optflags}|;s|^LIBS = |&$RPM_LD_FLAGS |" \
-    -i tools/meshfix/contrib/JMeshLib/test/Makefile
-
-# Link FlexiBLAS instead of BLAS
-sed -e "s| blas| flexiblas|" -i tools/meshfix/CMakeLists.txt
-
-# Fix tetgen build flags
-sed -e "s|^\(CXXFLAGS = \).*|\1%{optflags} $RPM_LD_FLAGS|" \
-    -e "s|-O0|%{optflags} $RPM_LD_FLAGS|" \
-    -i tools/tetgen/makefile
-
 %build
 %set_build_flags
-%if 0%{?__isa_bits} == 32
-# Reduce the debuginfo level to avoid virtual memory exhaustion
-CXXFLAGS="${CXXFLAGS-} -g1"
-%endif
 pushd tools
 # can't use make_build macro below because parallel make with CGAL exhausts
 # vm's memory and crash the building process, use sequential make instead
-make USERCCFLAGS="%{optflags}"
+make
 popd
 pushd bin
 ln -s tetgen1.5 tetgen
@ -167,54 +318,6 @@ install -m 0755 -vp  bin/* %{buildroot}%{_libexecdir}/%{octpkg}/
 %doc sample

 %changelog
-* Fri Apr 14 2023 Florian Weimer <fweimer@redhat.com> - 1.9.6-11
- Port to C99
-
-* Sun Apr 09 2023 Orion Poplawski <orion@nwra.com> - 1.9.6-10
- Rebuild for octave 8.1.0
-
-* Thu Jan 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.6-9
- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
-
-* Fri Jul 22 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.6-8
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
-
-* Wed Jun 01 2022 Orion Poplawski <orion@nwra.com> - 1.9.6-7
- Rebuild for octave 7.1
-
-* Fri May 06 2022 Iñaki Úcar <iucar@fedoraproject.org> - 1.9.6-6
- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
-
-* Thu Jan 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.6-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
-
-* Sat Oct 30 2021 Antonio Trande <sagitter@fedoraproject.org> - 1.9.6-3
- Rebuild for SuperLU-5.3.0
-
-* Thu Jul 22 2021 Qianqian Fang <fangqq@gmail.com> - 1.9.6-3
- Apply makefile patch by Laurent Rineau, fix CGAL build error on F35, fix #1917433
-
-* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.6-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
-
-* Fri Sep 04 2020 Qianqian Fang <fangqq@gmail.com> - 1.9.6-1
- New upstream release 1.9.6
-
-* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.1-7
- Fix cgal build error on F34
- Second attempt - Rebuilt for
-  https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
-
-* Tue Jul 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.1-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
-
-* Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.1-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
-
-* Mon Nov 25 2019 Jerry James <loganjerry@gmail.com> - 1.9.1-4
- Rebuild for mpfr 4
- Use Fedora build flags when building jmeshlib and tetgen
-
 * Fri Oct 11 2019 Qianqian Fang <fangqq@gmail.com> - 1.9.1-3
 - Define octave package-level dependency via the DESCRIPTION file
 - Remove gmp-devel from Requires
--- a/6
+++ b/6
@ -1,4 +1,4 @@
-SHA512 (cork-0.9.1.tar.gz) = fb7915c3f238978e4765c32173858768397fbf13e8b9be95cc1c17cf7bedb34b40b4b26feba0dc51c663f2dda33076ba29ae7b74460a4e39924b96eef145a458
-SHA512 (iso2mesh-1.9.6.tar.gz) = fb4799daf779e306b751b51237eb9b00f6c94df4efb7336bdd3690e913dd4f459b45d365c52915a3232568fa3e8100264bfc54ad014becf3b314ddf0abc35c90
-SHA512 (meshfix-1.2.2.tar.gz) = cd2cb2f4dfe0e8bcacafde1bb739e7db958e5a814c6bb7bcf318db029d482b56dda92c40aa72513cbc56c5f3948f9051d6772e76cd94dc828512d2710c46ce03
+SHA512 (cork-0.9.tar.gz) = 192ace02060519e39894fe33d481e86b84f996ece4db9ace02c5cfcaeafcb058f3e23950f3ee885c140978af71c81759f3eef0c5c2557f4eb215168b3c963506
+SHA512 (iso2mesh-1.9.1.tar.gz) = a317ed9c0c63fbccac7b1df15a5c7f64a7e26658616b397361e783da8042dbeb340588620955934ce3675634d7194f956afa7c4f4b76495548c4d62d46ef2a8e
+SHA512 (meshfix-1.2.1.tar.gz) = f4da936c74414d65641c4d3d4d60968edfa2baeb4cb3cd7d6be95fa6c7d94c703ea1b09442d27685411c3ebf8ccd94765952fb0b4fa31a7dffa9a98470556ead
 SHA512 (tetgen1.5.1.tar.gz) = dc485e67c4aba11c390152bc807f2572a95358e16fc76b147afd6cf00f70c4c4a57997b341e0432b06ba53d3e7e4b1961c0912a30454da4352e55c07051598ef
Author	SHA1	Message	Date
Qianqian Fang	5b32bb050b	merge with master	2019-10-11 17:40:19 -04:00
Qianqian Fang	06ae05eba5	remove gmp-devel from Requires	2019-10-10 23:02:39 -04:00