initial commit

2010-08-11 11:37:36 -07:00
16 changed files with 153 additions and 445 deletions
--- a/.gitignore
+++ b/.gitignore
@ -1,3 +1,2 @@
-/coot-0.8.7.tar.gz
-/reference-structures.tar.gz
-/coot-0.8.8.tar.gz
+coot-0.6.1-20100127svn2740.tar.gz
+coot-reference-structures.tar.gz
--- a/coot-configure.ac.patch
+++ b/coot-configure.ac.patch
@ -1,28 +0,0 @@
--- configure.ac.orig	2016-12-30 12:57:26.843081999 -0500
-+++ configure.ac	2016-12-30 12:58:11.963460565 -0500
-@@ -45,11 +45,11 @@
- 
- # AC_PROG_INTLTOOL, no, not today.  Mac compilation problems, no perl/ XML or something.
- # BL says Lets do some testing and use old style if needed
-AC_MSG_CHECKING([which libtool initialization strategy to adopt])
-AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])])
-m4_ifset([LT_INIT],
-[LT_INIT],
-[AC_PROG_LIBTOOL])
-+# AC_MSG_CHECKING([which libtool initialization strategy to adopt])
-+# AC_MSG_RESULT([m4_ifset([LT_INIT],[LT-INIT],[AC-PROG-LIBTOOL])])
-+# m4_ifset([LT_INIT],
-+# [LT_INIT],
-+# [AC_PROG_LIBTOOL])
- 
- GNOME_COMPILE_WARNINGS
- GNOME_CXX_WARNINGS
-@@ -148,7 +148,7 @@
- AM_WITH_GUILE(, [echo optional guile\?],,)
- if test x$coot_guile = xtrue ; then
-    GUILE_FLAGS
-   AM_GUILE_LIB
-+   # AM_GUILE_LIB
-    # guile-gui depends on a gui interface being present.  If it is, force check for guile-gui
-    if test x$with_guile_gtk != x ; then
-       AM_GUILE_GUI
--- a/coot-configure.in.patch
+++ b/coot-configure.in.patch
@ -0,0 +1,41 @@
+--- configure.in_orig	2010-01-27 16:15:51.387782244 -0800
+++ configure.in	2010-01-27 16:44:53.586783325 -0800
+@@ -132,13 +132,26 @@
+ AM_PATH_GLUT(, [echo You need the GLUT utility library; exit 1], AC_MSG_ERROR([Cannot find proper GLUT version]))
+ 
+ dnl Check for MMDB.
+-AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
+# AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,)
+ 
+-AM_WITH_MMDBSSM
+# AM_WITH_MMDBSSM
+PKG_CHECK_MODULES(MMDB, mmdb >= 1.12)
+MMDB_CXXFLAGS="-DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP $MMDB_CFLAGS"
+AC_SUBST(MMDB_CXXFLAGS)
+AC_SUBST(MMDB_LIBS)
+
+PKG_CHECK_MODULES(MMDBSSM, ssm >= 0.1)
+MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB $MMDBSSM_CFLAGS"
+AC_SUBST(MMDBSSM_CXXFLAGS)
+AC_SUBST(MMDBSSM_LIBS)
+ 
+ dnl Check for Clipper.  we exit if clipper is not found.
+ #
+-AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
+# AM_PATH_CLIPPER(, [echo Error locating Clipper - a CNS-enabled version of Clipper \(2.1-090520-ac or later\) is required now; exit 1],AC_MSG_ERROR([Cannot find Clipper]))
+PKG_CHECK_MODULES(CLIPPER, clipper >= 2.0)
+CLIPPER_CXXFLAGS=$CLIPPER_CFLAGS
+AC_SUBST(CLIPPER_CXXFLAGS)
+AC_SUBST(CLIPPER_LIBS)
+ 
+ # we set default coot_guile to true
+ coot_guile=true
+@@ -146,7 +159,7 @@
+ if test x$coot_guile = xtrue ; then
+    GUILE_FLAGS
+    AM_GUILE_LIB
+-   AM_GUILE_GUI
+#   AM_GUILE_GUI
+    GUILE_VERSION=$($ac_cv_path_GUILE_CONFIG --version  2>&1 | awk '{split($NF, arr, "[[.]]");  print arr[[1]] "." arr[[2]]}')
+    echo checking GUILE_VERSION: $GUILE_VERSION
+    AC_SUBST(GUILE_VERSION)
--- a/coot-guile.patch
+++ b/coot-guile.patch
@ -1,27 +0,0 @@
--- macros/guile_orig.m4	2013-07-31 00:25:19.715073145 -0700
-+++ macros/guile.m4	2013-07-31 00:27:01.763927099 -0700
-@@ -72,21 +72,21 @@
- # The variables are marked for substitution, as by @code{AC_SUBST}.
- #
- AC_DEFUN([GUILE_PROGS],
- [AC_PATH_PROG(GUILE,guile)
-+ [AC_PATH_PROG(GUILE,guile1.8)
-   if test x$with_guile = xyes ; then 
-      if test "$GUILE" = "" ; then
- 	AC_MSG_ERROR([guile required but not found])
-      fi
-   fi
-   AC_SUBST(GUILE)
-  AC_PATH_PROG(GUILE_CONFIG,guile-config)
-+  AC_PATH_PROG(GUILE_CONFIG,guile1.8-config)
-   if test x$with_guile = xyes ; then 
-      if test "$GUILE_CONFIG" = "" ; then
-         AC_MSG_ERROR([guile-config required but not found])
-      fi
-   fi
-   AC_SUBST(GUILE_CONFIG)
-  AC_PATH_PROG(GUILE_TOOLS,guile-tools)
-+  AC_PATH_PROG(GUILE_TOOLS,guile1.8-tools)
-   AC_SUBST(GUILE_TOOLS)
-  ])
- 
--- a/coot-lbg.patch
+++ b/coot-lbg.patch
@ -1,11 +0,0 @@
--- lbg/lbg.cc_orig	2016-11-09 21:27:32.074363190 -0500
-+++ lbg/lbg.cc	2016-11-09 21:27:47.836327788 -0500
-@@ -4873,7 +4873,7 @@
-       } 
-    } else {
- 
-      PyObject *pName = PyString_FromString("lidia.fetch");
-+      PyObject *pName = PyString_FromString("coot.lidia.fetch");
-       PyObject *pModule = PyImport_Import(pName);
-       if (pModule == NULL) {
- 	 std::cout << "NULL pModule" << std::endl;
--- a/coot-makefile.patch
+++ b/coot-makefile.patch
@ -1,35 +0,0 @@
--- src/Makefile.am_orig	2016-11-09 16:13:53.942706012 -0500
-+++ src/Makefile.am	2016-11-09 16:15:08.263956290 -0500
-@@ -457,7 +457,9 @@
-    EXTRA_DIST += coot_wrap_python_pre.cc 
- endif
- if COOT_USE_PYTHON
-   dist_python_PYTHON = coot.py coot.pth
-+   # dist_python_PYTHON = coot.py coot.pth
-+   pythondir = $(pkgdatadir)/python
-+   dist_pkgpython_SCRIPTS = coot.py
- endif
- 
- 
--- lbg/Makefile.am_orig	2016-11-09 16:46:09.161705178 -0500
-+++ lbg/Makefile.am	2016-11-09 21:51:45.630944576 -0500
-@@ -73,8 +73,8 @@
- # I don't understand.  Maybe the setting of wl should be done in configure?  But then
- # I have to force the output of libtool.  Bleugh.  Hmm...
- # Anyway, thankyou Gary Vaughan.
-wl=-Wl,
-lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
-+# wl=-Wl,
-+# lidia_LDFLAGS = $(EXPORT_DYNAMIC_FLAG_SPEC)
- 
- # res spec output operator means we include libcoot-coord-utils
- # (if that is annoying, then remove it and expand it by hand)
-@@ -106,7 +106,7 @@
- test_srs_standalone_SOURCES = test-srs-standalone.cc
- test_srs_standalone_LDADD = $(CCP4SRS_LIBS) $(MMDB_LIBS)
- 
-pkgpythondir=$(pythondir)/lidia
-+pkgpythondir=$(pythondir)/coot/lidia
- 
- dist_pkgpython_PYTHON = \
-     __init__.py fetch.py
--- a/coot-rdkit.patch
+++ b/coot-rdkit.patch
@ -1,11 +0,0 @@
--- lbg/lbg-search.cc_orig	2016-11-09 18:29:44.870809951 -0500
-+++ lbg/lbg-search.cc	2016-11-09 18:42:43.549933656 -0500
-@@ -34,7 +34,7 @@
- #include "geometry/srs-interface.hh"
- #ifdef RDKIT_HAS_CAIRO_SUPPORT
- #include <cairo.h>
-#include <MolDraw2DCairo.h>
-+#include <GraphMol/MolDraw2D/MolDraw2DCairo.h>
- #include "lidia-core/rdkit-interface.hh"
- #else
- #include "lidia-core/rdkit-interface.hh"
--- a/coot-user-manual.texi.patch
+++ b/coot-user-manual.texi.patch
@ -0,0 +1,24 @@
+--- doc/user-manual.texi_orig	2010-01-27 16:23:57.630783062 -0800
+++ doc/user-manual.texi	2010-01-27 16:50:48.507782342 -0800
+@@ -4470,10 +4470,10 @@
+ @c note that texi2html (and makeinfo) requires that this c-interface texi file be in the 
+ @c same directory as this file (user-manual.texi) NOT the directory that 
+ @c texi2html is run in.
+-@include c-interface.h.texi
+@include c-interface_8h.texi
+ @node    More Scripting Functions
+ @chapter More Scripting Functions
+-@include cc-interface.hh.texi
+@c @include cc-interface.hh.texi
+ 
+ 
+ 
+@@ -4491,7 +4491,7 @@
+ @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node
+ @c
+ 
+-@include ../../coot/scheme/coot-scheme-functions.texi
+@c @include ../../coot/scheme/coot-scheme-functions.texi
+ 
+ 
+ 
--- a/coot-utils.patch
+++ b/coot-utils.patch
@ -1,20 +0,0 @@
--- coot-utils/coot-shelx.hh_orig	2016-04-07 22:05:10.753625059 -0400
-+++ coot-utils/coot-shelx.hh	2016-04-07 22:05:43.366973568 -0400
-@@ -33,6 +33,7 @@
- 
- #include <mmdb2/mmdb_manager.h>
- #include "clipper/core/cell.h"
-+#include "coot-coord-utils.hh"
- 
- namespace coot {
- 
--- coot-utils/coot-hole.hh_orig	2016-04-07 22:05:55.561054355 -0400
-+++ coot-utils/coot-hole.hh	2016-04-07 22:06:16.954432665 -0400
-@@ -4,6 +4,7 @@
- #include "clipper/core/xmap.h"
- #include "clipper/core/nxmap.h"
- 
-+#include "coot-map-utils.hh"
- #include "utils/coot-utils.hh"
- #include "geometry/protein-geometry.hh"
- 
--- a/coot.desktop
+++ b/coot.desktop
@ -7,4 +7,4 @@ Exec=coot
 Icon=coot
 Terminal=false
 Type=Application
-Categories=Graphics;Science;Chemistry;
+Categories=Graphics;Science
--- a/coot.in
+++ b/coot.in
@ -5,9 +5,9 @@
 # written by Paul Emsley

 COOT_PREFIX="@prefix@"
-current_exe_dir="@libexecdir@"
+current_exe_dir="@bindir@"

-coot_real=$current_exe_dir/coot-bin
+coot_real=$current_exe_dir/coot-real
 # echo coot-real is at $coot_real

 # ----------------------------------------------------------------------------
--- a/coot.png
+++ b/coot.png
--- a/coot.spec
+++ b/coot.spec
@ -1,64 +1,55 @@
-%global refmac_dictionary %(rpm -q --queryformat '%%{name}-%%{version}' refmac-dictionary)
+%{!?python_sitelib: %define python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
+%define refmac_dictionary %(rpm -q --queryformat '%%{name}-%%{version}' refmac-dictionary)
+
 Name: coot
 Summary: The crystallographic object-oriented toolkit
-URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
-Version: 0.8.8
-Release: 5%{?dist}
-# source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown)
-License: GPLv3+
+URL: http://www.biop.ox.ac.uk/coot/
+Version: 0.6.1
+Release: 3.20100127svn2740%{?dist}
+# source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown)
+License: GPLv3+ and LGPLv2+
 Group: Applications/Engineering
-Source0: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/%{name}-%{version}.tar.gz
-# additional files for reference/libraries used in main binary
-Source1: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz
-Source2: coot.in
-Source3: %{name}.desktop
-Source4: __init__.py
-# don't use broken guile_lib autoconf macro
-Patch0: coot-configure.ac.patch
-# fix location of python files and remove hard coding of -Wl
-Patch1: coot-makefile.patch
-# fix to use guile1.8 config in autoconf script
-Patch2: coot-guile.patch
-# fix to includes so build completes
-Patch3: coot-utils.patch
-# proper include for rdkit
-Patch4: coot-rdkit.patch
-# Fix for moving python files to coot/lidia
-Patch5: coot-lbg.patch
+# The source for this package was pulled from upstream's vcs.  Use the
+# following commands to generate the tarball:
+#  svn co -r 2740 http://coot.googlecode.com/svn/trunk/ coot-0.6.1
+#  tar cvzf coot-0.6.1-20100127svn2740.tar.gz coot-0.6.1
+Source0: coot-0.6.1-20100127svn2740.tar.gz
+Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz
+Source2: svn-revision.cc
+Source3: coot.in
+Source4: %{name}.png
+Source5: %{name}.desktop
+Source6: __init__.py
+Patch0: coot-configure.in.patch
+Patch1: coot-user-manual.texi.patch
+BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 BuildRequires: autoconf
 BuildRequires: automake
 BuildRequires: clipper-devel >= 2.1-7
 BuildRequires: desktop-file-utils
-BuildRequires: doxygen
-BuildRequires: libappstream-glib
 BuildRequires: freeglut-devel
-BuildRequires: goocanvas-devel
 BuildRequires: gsl-devel
 BuildRequires: gtk2-devel
 BuildRequires: gtkglext-devel
-BuildRequires: compat-guile18-devel
+BuildRequires: guile-devel
 BuildRequires: guile-lib
 BuildRequires: imlib-devel
 BuildRequires: libcurl-devel
 BuildRequires: libgnomecanvas-devel
 BuildRequires: libtool
-BuildRequires: mmdb2-devel
-BuildRequires: python2-devel
-BuildRequires: python2-rdkit
+BuildRequires: mmdb-devel >= 1.19
+BuildRequires: python-devel
 BuildRequires: pygtk2-devel
-BuildRequires: rdkit-devel
 BuildRequires: refmac-dictionary
 BuildRequires: ssm-devel
 BuildRequires: swig
+%if 0%{?rhel}
+BuildRequires: tetex-latex
+%else
 BuildRequires: tex(latex)
+%endif
 BuildRequires: texinfo-tex
-BuildRequires: ghostscript
-Requires: compat-guile18
-Requires: hicolor-icon-theme
 Requires: refmac-dictionary
-Requires: %{name}-data = %{version}-%{release}
-Requires: lib%{name}%{?_isa} = %{version}-%{release}
-Requires: python2-%{name}%{?_isa} = %{version}-%{release}

 %description

@ -68,49 +59,20 @@ GUI builder glade), mmdb, clipper, and OpenGL, together with a new
 approach to map contouring and importing/creation and other modeling
 and building operations.

-%package data
-Summary: Data files for coot
-Group: Applications/Engineering
-BuildArch: noarch
-
-%description data
-
-The coot-data package contains all the support files for coot, such
-as reference structures, rotamer libraries, etc.
-
-%package -n libcoot
-Summary: Library files for coot
-Group: Development/Libraries
-
-%description -n libcoot
-
-This package contains library files needed for program development
-using the coot macromolecular model building package.
-
-%package -n libcoot-devel
+%package devel
 Summary: Header files and library for developing programs with coot
-Group: Development/Libraries
-Requires: lib%{name}%{?_isa} = %{version}-%{release}
-
-%description -n libcoot-devel
-
-This package contains header files needed for program development
-using the coot macromolecular model building package.
-
-%package -n python2-%{name}
-%{?python_provide:%python_provide python2-%{name}}
-Summary: Python support for coot
+Requires: %{name} = %{version}-%{release}
 Group: Development/Libraries

-%description -n python2-%{name}
+%description devel

-This package contains python specific library files needed for
-coot to provide support for and interface with the python shell
+This package contains libraries and header files needed for program
+development using the coot macromolecular model building package.

 %package doc
 Summary: documentation PDF files for coot
+Requires: %{name} = %{version}-%{release}
 Group: Applications/Engineering
-BuildArch: noarch

 %description doc

@ -122,284 +84,95 @@ package.
 %setup -q -a 1
 %patch0 -p0
 %patch1 -p0
-%patch2 -p0
-%patch3 -p0
-%patch4 -p0
-%patch5 -p0

 cp %{SOURCE2} ./src/
-cp %{SOURCE3} .
+cp %{SOURCE3} ./src/

 # various cleanups
+rm src/coot_wrap_guile_pre.cc
+rm src/coot_wrap_python_pre.cc
 iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
+find . -executable \( -name "*.cc" -o -name "*.cpp" -o -name "*.h" -o -name "*.hh" \) -exec chmod 644 {} \;

-rm macros/libtool.m4
 aclocal -I macros
 libtoolize --automake --copy
 autoconf
 automake --copy --add-missing --gnu

 %build
-mkdir guile
-%configure --with-guile --with-python --with-pygtk --disable-static CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" --with-enhanced-ligand-tools RDKIT_LIBS="-lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python -lpython2.7" RDKIT_CXXFLAGS="-I%{_includedir}/rdkit -DRDKIT_HAS_CAIRO_SUPPORT"
+%configure --with-gtk2 --with-guile --with-python --with-pygtk --with-gtkcanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing"

-# remove rpath, direct-shlib-dep
 sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
 sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
-sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool
-# sed -i "s|ofile='libtool'|ofile='libtool.foo'|" config.status
-sed -i 's|$(SHELL) ./config.status;; \\|echo "skipping";; \\|' Makefile
-cp libtool libtool.tdf

 make %{?_smp_mflags}
-pushd src
-doxygen coot-dox.cfg
-popd
 pushd doc
-make coot-user-manual.pdf
+texi2pdf user-manual.texi
 make coot-keys-and-buttons.pdf
 popd

 %install
+rm -rf %{buildroot}
 make install DESTDIR=%{buildroot} INSTALL='install -p'

 mv reference-structures %{buildroot}%{_datadir}/coot/
-
-sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=%{python2_sitelib}/coot|' src/coot
+sed -i 's|COOT_PYTHON_DIR=|COOT_PYTHON_DIR=%{python_sitelib}/coot|' src/coot
 sed -i 's|COOT_REFMAC_LIB_DIR=|COOT_REFMAC_LIB_DIR=%{_datadir}/%{refmac_dictionary}|' src/coot
 install -p -m 755 src/coot %{buildroot}%{_bindir}/

 # remove unpackaged files from the buildroot
 rm -f %{buildroot}%{_libdir}/*.la
-rm -f %{buildroot}%{python2_sitearch}/*.la
+
+# headers
+mkdir %{buildroot}%{_includedir}/coot
+mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/
+mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/

 # python stuff
-for lib in $(find %{buildroot}%{python2_sitelib}/coot/ -name "*.py"); do
- sed '/\/usr\/bin\/env/d' $lib > $lib.new &&
- touch -r $lib $lib.new &&
- mv $lib.new $lib
-done
-cp %{SOURCE4} %{buildroot}%{python2_sitelib}/coot/
-chmod 644 %{buildroot}%{python2_sitelib}/coot/coot.py
+mkdir -p %{buildroot}%{python_sitelib}/coot
+mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/
+cp %{SOURCE6} %{buildroot}%{python_sitelib}/coot/
+chmod 644 %{buildroot}%{python_sitelib}/coot/coot.py

 # desktop file
-desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications coot.desktop
-appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.appdata.xml
+desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications %{SOURCE5}
+mkdir -p %{buildroot}%{_datadir}/pixmaps
+install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/

-%post
-/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || :
+%clean
+rm -rf %{buildroot}

-%post -n libcoot -p /sbin/ldconfig
+%check
+# this fails - need to fix upstream
+# make check

-%postun
-if [ $1 -eq 0 ] ; then
-    /bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null
-    /usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || :
-fi
+%post -p /sbin/ldconfig

-%postun -n libcoot -p /sbin/ldconfig
-
-%posttrans
-/usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || :
+%postun -p /sbin/ldconfig

 %files
+%defattr(-,root,root,-)
+%doc AUTHORS README COPYING
 %{_bindir}/*
-%{_libexecdir}/*
-%{_datadir}/applications/%{name}.desktop
-%{_datadir}/appdata/%{name}.appdata.xml
-%{_datadir}/icons/hicolor/48x48/apps/coot.png
-%{_datadir}/icons/hicolor/64x64/apps/coot.png
-%{_datadir}/icons/hicolor/96x96/apps/coot.png
-%{_datadir}/icons/hicolor/256x256/apps/coot.png
-%{_datadir}/icons/hicolor/scalable/apps/coot.svg
-%{_mandir}/man1/*
-
-%files data
-%{_datadir}/coot/
-
-%files -n libcoot
-%doc AUTHORS README
-%license COPYING
-# GPLv3+ 
+# libccp4mg-utils.so* is LGPLv2+
+# libcoot-surface.so* is a mix of LGPLv2+ and GPLv3+
+# all others are GPLv3+ 
 %{_libdir}/*.so.*
+%{_datadir}/coot/
+%{_datadir}/applications/%{name}.desktop
+%{_datadir}/pixmaps/%{name}.png
+%{python_sitelib}/coot/

-%files -n python2-%{name}
-%{python2_sitelib}/coot/
-%{python2_sitearch}/*.so.*
-%{python2_sitearch}/*.so
-
-%files -n libcoot-devel
+%files devel
+%defattr(-,root,root,-)
 %{_libdir}/*.so
 %{_includedir}/coot/

 %files doc
-%license COPYING
-%doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf
+%defattr(-,root,root,-)
+%doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf

 %changelog
-* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.8.8-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
-
-* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.8.8-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
-
-* Mon Jul 24 2017 Björn Esser <besser82@fedoraproject.org> - 0.8.8-3
- Rebuilt for Boost 1.64
-
-* Mon May 15 2017 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.8.8-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild
-
-* Sat Mar 18 2017 Tim Fenn <tim.fenn@gmail.com> - 0.8.8-1
- update to 0.8.8
-
-* Thu Feb 09 2017 Tim Fenn <tim.fenn@gmail.com> - 0.8.7-6
- Fix to requires
-
-* Wed Feb 08 2017 Kalev Lember <klember@redhat.com> - 0.8.7-5
- Rebuilt for Boost 1.63
-
-* Sun Feb 05 2017 Tim Fenn <tim.fenn@gmail.com> - 0.8.7-4
- add missing patch
-
-* Thu Jan 26 2017 Tim Fenn <tim.fenn@gmail.com> - 0.8.7-3
- rename python2 package
- add python_provide macro
- remove hardcoded library path include
-
-* Sat Nov 12 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.7-2
- test build for fixing unused-shlib and weak-sybmol
-
-* Sun Nov 06 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.7-1
- update to 0.8.7
- fix requires in devel packages
- make coot-data noarch
- remove macros and lingering ldconfig calls
-
-* Tue Nov 01 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.6.2-2
- move license and doc files to libcoot
- remove spurious ldconfig
- split out python files and data to separate packages and add requires
-
-* Sat Oct 22 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.6.2-1
- update to 0.8.6.2
- add rdkit support (and patch to fix it)
- change define to global
- fix hicolor requires and png files
- fix shlib dep
- remove outdated autoconf macro
-
-* Fri Oct 14 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.6.1-3
- remove unecessary rhel only macros
- put doc in noarch
-
-* Fri Oct 07 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.6.1-2
- include description of patches
- python-devel to python2-devel BR
- remove python-sitelib macro (use system defined version)
-
-* Fri Aug 26 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.6.1-1
- update to 0.8.6.1
-
-* Sat Jul 30 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.5-1
- update to 0.8.5
-
-* Thu Apr 07 2016 Tim Fenn <tim.fenn@gmail.com> - 0.8.3-1
- Update to 0.8.3
-
-* Mon Feb 22 2016 Orion Poplawski <orion@cora.nwra.com> - 0.8.2-3
- Rebuild for gsl 2.1
-
-* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.8.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
-
-* Mon Sep 7 2015 Tim Fenn <tim.fenn@gmail.com> - 0.8.2-1
- update to 0.8.2
- add patch for coot-utils
-
-* Sun Jun 28 2015 Tim Fenn <tim.fenn@gmail.com> - 0.8.1-3
- fix to appdata.xml
- add all icon pixmaps, edit desktop file to match
-
-* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.8.1-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
-
-* Sat Jan 31 2015 Tim Fenn <tim.fenn@gmail.com> - 0.8.1-1
- update to 0.8.1
- update URL
- no sxml support in guile 1.8 (remove AM_GUILE_LIB check)
- add gtk update icon cache scriptlets
- add appdata xml file and additional app-data-validate scripts
-
-* Sat Aug 16 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.2-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
-
-* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7.2-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
-
-* Fri Dec 27 2013 Tim Fenn <tim.fenn@gmail.com> - 0.7.2-1
- update to 0.7.2
- update upstream URLs, no longer using vcs
-
-* Sun Aug 11 2013 Tim Fenn <tim.fenn@gmail.com> - 0.7-5.20120929svn4458
- add ghostscript to buildrequires
-
-* Fri Aug 09 2013 Tim Fenn <tim.fenn@gmail.com> - 0.7-4.20120929svn4458
- use xz instead of gz (BZ 982385)
- update for soname bump in deps (BZ 989141)
- use guile1.8-compat, add guile requires
-
-* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7-3.20120929svn4458
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
-
-* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.7-2.20120929svn4458
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
-
-* Sat Sep 29 2012 Tim Fenn <tim.fenn@gmail.com> - 0.7-1.20120929svn4458
- update to 0.7
-
-* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.2-14.20110715svn3566
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
-
-* Tue Feb 28 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.2-13.20110715svn3566
- Rebuilt for c++ ABI breakage
-
-* Sat Jan 14 2012 Tim Fenn <tim.fenn@gmail.com> - 0.6.2-12.20110715svn3566
- patches to fix unistd.h issue and compilation errors
-
-* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.2-11.20110715svn3566
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
-
-* Sat Dec 10 2011 Tim Fenn <tim.fenn@gmail.com> - 0.6.2-10.20110715svn3566
- patch for new libpng
-
-* Tue Dec 06 2011 Adam Jackson <ajax@redhat.com> - 0.6.2-9.20110715svn3566
- Rebuild for new libpng
-
-* Fri Jul 15 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-8.20110715svn3566
- update to SVN 3566 (0.6.2 final)
-
-* Tue Apr 26 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-7.20110421svn3461
- add reference structures source file
-
-* Tue Apr 26 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-6.20110421svn3461
- add missing source
-
-* Thu Apr 21 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-5.20110421svn3461
- update to SVN 3461
- fix missing Requires: guile-lib
-
-* Tue Mar 29 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-4.20110328svn3442
- update to SVN 3442 (should remove guile-gtk broken dependencies)
-
-* Fri Feb 25 2011 Tim Fenn <fenn@stanford.edu> - 0.6.2-3.20110225svn3399
- update to SVN 3399
-
-* Tue Feb 08 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.6.2-2.20101012svn3213
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
-
-* Tue Oct 12 2010 Tim Fenn <fenn@stanford.edu> - 0.6.2-1.20101012svn3213
- update to 0.6.2
-
 * Thu Aug 05 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-3.20100127svn2740
 - fix file attr
 - add comment to make check error
--- a/dead.package
+++ b/dead.package
@ -1,3 +0,0 @@
-2016-05-31: Retired because of broken deps in preparation of Fedora 24
-Reference: https://fedorahosted.org/rel-eng/ticket/6416
-
--- a/4
+++ b/4
@ -1,2 +1,2 @@
-SHA512 (coot-0.8.8.tar.gz) = 6d99e4bc0a5cd17b46bd52741b934e98e98eec9fe5a9fd108e891834256e17cc03eb12327aa6756beff4ce552456ae5e8a0ee459ecf3894a99809be218481b83
-SHA512 (reference-structures.tar.gz) = 7ebe28a619a577b18fc66e714f0bc8347121ebb12f372ac29c1d2d96013e608632921ea26caea3b62744252ae356949de8e04a6513f1a1e0ba30865708c26ffe
+ecf43a60294f660946f5a14b8bf98769  coot-0.6.1-20100127svn2740.tar.gz
+59df05751b1ab445a6517757a1ace302  coot-reference-structures.tar.gz
--- a/svn-revision.cc
+++ b/svn-revision.cc
@ -0,0 +1,6 @@
+extern "C" {
+int svn_revision() { 
+   return  2740;
+}
+}
+