%global 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: 1%{?dist}
# source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown)
License: GPLv3+
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
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-lib
BuildRequires: imlib-devel
BuildRequires: libcurl-devel
BuildRequires: libgnomecanvas-devel
BuildRequires: libtool
BuildRequires: mmdb2-devel
BuildRequires: python2-devel
BuildRequires: python2-rdkit
BuildRequires: pygtk2-devel
BuildRequires: rdkit-devel
BuildRequires: refmac-dictionary
BuildRequires: ssm-devel
BuildRequires: swig
BuildRequires: tex(latex)
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

Coot is a toolkit for Macromolecular Crystallography and
model-building.  Coot uses professional (and free) widgets (with the
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
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
Group: Development/Libraries

%description -n python2-%{name}

This package contains python specific library files needed for
coot to provide support for and interface with the python shell

%package doc
Summary: documentation PDF files for coot
Group: Applications/Engineering
BuildArch: noarch

%description doc

the coot-doc package contains information concerning the use and
button/key shortcuts for the coot macromolecular model building
package.

%prep
%setup -q -a 1
%patch0 -p0
%patch1 -p0
%patch2 -p0
%patch3 -p0
%patch4 -p0
%patch5 -p0

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

# various cleanups
iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README

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"

# 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
make coot-keys-and-buttons.pdf
popd

%install
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_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

# 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

# desktop file
desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications coot.desktop
appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.appdata.xml

%post
/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || :

%post -n libcoot -p /sbin/ldconfig

%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

%postun -n libcoot -p /sbin/ldconfig

%posttrans
/usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || :

%files
%{_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+ 
%{_libdir}/*.so.*

%files -n python2-%{name}
%{python2_sitelib}/coot/
%{python2_sitearch}/*.so.*
%{python2_sitearch}/*.so

%files -n libcoot-devel
%{_libdir}/*.so
%{_includedir}/coot/

%files doc
%license COPYING
%doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf

%changelog
* 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

* Tue Jul 20 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-2.20100127svn2740
- move some documentation to subpackage
- add check section

* Wed Jan 27 2010 Tim Fenn <fenn@stanford.edu> - 0.6.1-1.20100127svn2740
- update to SVN 2740, 0.6.1 release
- add curl buildrequires

* Thu Dec 03 2009 Tim Fenn <fenn@stanford.edu> - 0.6-6.20091203svn2545
- update to SVN 2545, 0.6 release

* Mon Nov 30 2009 Tim Fenn <fenn@stanford.edu> - 0.6-5.20091130svn2528
- fix texi, include user-manual
- update to SVN 2528
- remove net-http, guile-goosh and guile-gui

* Wed Oct 07 2009 Tim Fenn <fenn@stanford.edu> - 0.6-4.20091007svn2404
- update buildrequires
- use tetex-latex on EL builds
- update to SVN 2404 (fixes some licensing issues)

* Mon Oct 05 2009 Tim Fenn <fenn@stanford.edu> - 0.6-3.20091005svn2400
- update to SVN 2400

* Wed Sep 23 2009 Tim Fenn <fenn@stanford.edu> - 0.6-2.20090920svn2334
- edit summary
- update upstream URL
- make create_server.py non-executable
- chmod src to 644

* Sun Sep 20 2009 Tim Fenn <fenn@stanford.edu> - 0.6-1.20090920svn2334
- update to 0.6
- get source from VCS system

* Wed Mar 25 2009 Tim Fenn <fenn@stanford.edu> - 0.5.2-3
- fix summary
- add additional licensing information
- split guile-extras into original tarballs

* Sat Mar 14 2009 Tim Fenn <fenn@stanford.edu> - 0.5.2-2
- fix for desktop-file-install
- gcc 4.4 patch

* Mon Dec 15 2008 Tim Fenn <fenn@stanford.edu> - 0.5.2-1
- update to 0.5.2

* Thu Nov 27 2008 Tim Fenn <fenn@stanford.edu> - 0.5-3
- use consistent buildroot
- include gtkglext-devel, guile-lib, desktop-file-utils in buildrequires
- remove pyobject2 in buildrequires

* Tue Nov 18 2008 Tim Fenn <fenn@stanford.edu> - 0.5-2
- enable guile
- include extra guile modules

* Mon Nov 17 2008 Tim Fenn <fenn@stanford.edu> - 0.5-1
- initial build