From 2b07951fd69139415b70b9b4d7e74c772562ed3e Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Wed, 11 Aug 2010 10:57:32 -0700 Subject: [PATCH 01/43] initial commit --- .gitignore | 2 + __init__.py | 1 + coot-configure.in.patch | 41 +++++++ coot-user-manual.texi.patch | 24 ++++ coot.desktop | 10 ++ coot.in | 62 ++++++++++ coot.png | Bin 0 -> 1271 bytes coot.spec | 236 ++++++++++++++++++++++++++++++++++++ sources | 2 + svn-revision.cc | 6 + 10 files changed, 384 insertions(+) create mode 100644 __init__.py create mode 100644 coot-configure.in.patch create mode 100644 coot-user-manual.texi.patch create mode 100644 coot.desktop create mode 100755 coot.in create mode 100644 coot.png create mode 100644 coot.spec create mode 100644 svn-revision.cc diff --git a/.gitignore b/.gitignore index e69de29..0a061f3 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1,2 @@ +coot-0.6.1-20100127svn2740.tar.gz +coot-reference-structures.tar.gz diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..83d04e7 --- /dev/null +++ b/__init__.py @@ -0,0 +1 @@ +# File to allow this directory to be treated as a python package. diff --git a/coot-configure.in.patch b/coot-configure.in.patch new file mode 100644 index 0000000..f8501c2 --- /dev/null +++ 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: $GUILE_VERSION + AC_SUBST(GUILE_VERSION) diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch new file mode 100644 index 0000000..2f8df9a --- /dev/null +++ b/coot-user-manual.texi.patch @@ -0,0 +1,24 @@ +--- doc/user-manual.texi_orig 2010-01-27 16:23:57.630783062 -0800 ++++ doc/user-manual.texi 2010-01-27 16:50:48.507782342 -0800 +@@ -4470,10 +4470,10 @@ + @c note that texi2html (and makeinfo) requires that this c-interface texi file be in the + @c same directory as this file (user-manual.texi) NOT the directory that + @c texi2html is run in. +-@include c-interface.h.texi ++@include c-interface_8h.texi + @node More Scripting Functions + @chapter More Scripting Functions +-@include cc-interface.hh.texi ++@c @include cc-interface.hh.texi + + + +@@ -4491,7 +4491,7 @@ + @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node + @c + +-@include ../../coot/scheme/coot-scheme-functions.texi ++@c @include ../../coot/scheme/coot-scheme-functions.texi + + + diff --git a/coot.desktop b/coot.desktop new file mode 100644 index 0000000..79a76c6 --- /dev/null +++ b/coot.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Encoding=UTF-8 +Name=coot +GenericName=coot +Comment=macromolecular model builder +Exec=coot +Icon=coot +Terminal=false +Type=Application +Categories=Graphics;Science diff --git a/coot.in b/coot.in new file mode 100755 index 0000000..bff0148 --- /dev/null +++ b/coot.in @@ -0,0 +1,62 @@ +#!/bin/sh +# -*-shell-script-*- +# coot wrapper script +# Copyright 2004, 2005, 2006, 2007 University of York +# written by Paul Emsley + +COOT_PREFIX="@prefix@" +current_exe_dir="@bindir@" + +coot_real=$current_exe_dir/coot-real +# echo coot-real is at $coot_real + +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# If the COOT_PREFIX is correct, then these should not need modification +# i.e. nothing below here need be changed. +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# +prefix=$COOT_PREFIX + +SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib +COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme +COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb +COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps +COOT_DATA_DIR=$COOT_PREFIX/share/coot +COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc +COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures +COOT_PYTHON_DIR= +COOT_REFMAC_LIB_DIR= + +PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR + +GUILE_WARN_DEPRECATED=no + +if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then + GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH + export GUILE_LOAD_PATH +fi + +# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH + +export SYMINFO +export COOT_PREFIX +export COOT_STANDARD_RESIDUES +export COOT_REFMAC_LIB_DIR +export COOT_PYTHON_DIR +export PYTHONPATH +export COOT_SCHEME_DIR +export COOT_REF_STRUCTS +export COOT_RESOURCES_FILE +export COOT_PIXMAPS_DIR +export COOT_DATA_DIR + +echo $coot_real $* +$coot_real $* +status=$? + +if [ $status != 0 ] ; then + @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real +fi + diff --git a/coot.png b/coot.png new file mode 100644 index 0000000000000000000000000000000000000000..9e6ded7e24754bfa77ee5fe584fd2df36be6e86e GIT binary patch literal 1271 zcmVPx#24YJ`L;(K){{a7>y{D4^000SaNLh0L01FcU01FcV0GgZ_00007bV*G`2iOY| z7cwAl4qK}L00ehQL_t(o!|j$^h*nh;$A4?>v(Gv6&FyO@P0Y-$hK1E+NifDss}%$!X@howHXD-}g<^ zMNP{J@_#scpR@O7t^ZnkueBE(#$o&)AcFoYiX+_3UZNo{&YXx%@9BB$pHnVwiGr!r z-xkGYo;}STU-{@+2Q9SVS~^pSZ;A2iJgyvxS|nQbM4v{u6%M_DRN_?9$q~*JY&41M zF1^TON7f@&i(w5|1m8EKiB^n8-ZNBAi92Im9B=61>Gk7U2eB{5$nIHAPI} z^HYzT^umnOPJQD0_qOi(>a&mE`(>N<0iXCZt;9>fZZph-Aqa+H1Z?En>W2+Q37uf) z3epram=~jypPzMRM>hSA`GadeTKCe16>sg+Vi$Q|q+?zeom;yphAuj-NV|2=W^EL# zmDCC(mJ*Lx?s3*aVhORuBV&;{+y_m$eQ&P3;`RA+i@!doqtGqIg^{^An&}ip)i56j zy91#mAaTH4KpWNv0yJ6>q~Q|~X!yhs$eQvir~Gu(MNhppuvY@XtYFwU#W{f>NLA6A zVMBqC)QN;NAd#U`r=blBVU+S_YZzgu_u>0``lr@T7##ZXi0$7jJ7?T6i#9ZMjwA?C z*S&|K0mZlHSZhWo*2s#1kO-1H+_1;*^7tP-ezzm4*6mgl0krX@jnO6@R!zMArVqa! z;Elw$7q<^}9kXrQLsvfa>f$y471i!`S~s?aWM@pY+~d{bcYETUp0wX^S|xN>$;MX6 zj?4+I1}I7o?g}dc1h=52oPBa{Z*;m zswQ&;HwPFq;uWw6x5uGF0gH_gH+#k90gJQ|1NBy^|0|Ghtw}zYs+9pI-n8^xfU)iQ zg+*&dM+pTzsluE?$EO0h7}!d^d&_riUj4CM-Xzt z>awd%%Prgb+Xy?l>#MM3$ISjnIQHIWw$G41%y?SpX$^&Y5|T-Rgwb<`Y26DJ8^Jd{ zVpx=sWfiF|C|T*@y@mLL%V+tG{m&PlTzcdVnx|xM=%C}8lw^S*6C6>+p~H;`lYm7{ z0y%l1Lgmeplor;k)_XuV<$hPRYBVWv{dtnz-q+_pPC_!#6HRs!ohK$!%ajXMsm(51 zY5gI)+2%}R*}|)N@^`6P;iC0^ z?e@1Ib}~V0c79tYSA4OJS3*bHM^ zuUXBGHsyU8E?0@^6Bst5B{Q}>`?6e>rlx01Va=vZTwBh0>+d^+&6>b5y;ZquAaJKb z?jWtgE&+{T3ef9?We%oh#pWQhO( literal 0 HcmV?d00001 diff --git a/coot.spec b/coot.spec new file mode 100644 index 0000000..e48e755 --- /dev/null +++ b/coot.spec @@ -0,0 +1,236 @@ +%{!?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://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 +# 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: freeglut-devel +BuildRequires: gsl-devel +BuildRequires: gtk2-devel +BuildRequires: gtkglext-devel +BuildRequires: guile-devel +BuildRequires: guile-lib +BuildRequires: imlib-devel +BuildRequires: libcurl-devel +BuildRequires: libgnomecanvas-devel +BuildRequires: libtool +BuildRequires: mmdb-devel >= 1.19 +BuildRequires: python-devel +BuildRequires: pygtk2-devel +BuildRequires: refmac-dictionary +BuildRequires: ssm-devel +BuildRequires: swig +%if 0%{?rhel} +BuildRequires: tetex-latex +%else +BuildRequires: tex(latex) +%endif +BuildRequires: texinfo-tex +Requires: refmac-dictionary + +%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 devel +Summary: Header files and library for developing programs with coot +Requires: %{name} = %{version}-%{release} +Group: Development/Libraries + +%description devel + +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 + +%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 + +cp %{SOURCE2} ./src/ +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 {} \; + +aclocal -I macros +libtoolize --automake --copy +autoconf +automake --copy --add-missing --gnu + +%build +%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" + +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 + +make %{?_smp_mflags} +pushd doc +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=%{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 + +# headers +mkdir %{buildroot}%{_includedir}/coot +mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ +mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ + +# python stuff +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 %{SOURCE5} +mkdir -p %{buildroot}%{_datadir}/pixmaps +install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/ + +%clean +rm -rf %{buildroot} + +%check +# this fails - need to fix upstream +# make check + +%post -p /sbin/ldconfig + +%postun -p /sbin/ldconfig + +%files +%defattr(-,root,root,-) +%doc AUTHORS README COPYING +%{_bindir}/* +# 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 devel +%defattr(-,root,root,-) +%{_libdir}/*.so +%{_includedir}/coot/ + +%files doc +%defattr(-,root,root,-) +%doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf + +%changelog +* Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 +- fix file attr +- add comment to make check error + +* Tue Jul 20 2010 Tim Fenn - 0.6.1-2.20100127svn2740 +- move some documentation to subpackage +- add check section + +* Wed Jan 27 2010 Tim Fenn - 0.6.1-1.20100127svn2740 +- update to SVN 2740, 0.6.1 release +- add curl buildrequires + +* Thu Dec 03 2009 Tim Fenn - 0.6-6.20091203svn2545 +- update to SVN 2545, 0.6 release + +* Mon Nov 30 2009 Tim Fenn - 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 - 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 - 0.6-3.20091005svn2400 +- update to SVN 2400 + +* Wed Sep 23 2009 Tim Fenn - 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 - 0.6-1.20090920svn2334 +- update to 0.6 +- get source from VCS system + +* Wed Mar 25 2009 Tim Fenn - 0.5.2-3 +- fix summary +- add additional licensing information +- split guile-extras into original tarballs + +* Sat Mar 14 2009 Tim Fenn - 0.5.2-2 +- fix for desktop-file-install +- gcc 4.4 patch + +* Mon Dec 15 2008 Tim Fenn - 0.5.2-1 +- update to 0.5.2 + +* Thu Nov 27 2008 Tim Fenn - 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 - 0.5-2 +- enable guile +- include extra guile modules + +* Mon Nov 17 2008 Tim Fenn - 0.5-1 +- initial build diff --git a/sources b/sources index e69de29..73137a9 100644 --- a/sources +++ b/sources @@ -0,0 +1,2 @@ +ecf43a60294f660946f5a14b8bf98769 coot-0.6.1-20100127svn2740.tar.gz +59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc new file mode 100644 index 0000000..432f2c5 --- /dev/null +++ b/svn-revision.cc @@ -0,0 +1,6 @@ +extern "C" { +int svn_revision() { + return 2740; +} +} + From 73be485eb591b81113cc3aef75fefd88a175b028 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Wed, 11 Aug 2010 11:37:36 -0700 Subject: [PATCH 02/43] initial commit --- .gitignore | 2 + __init__.py | 1 + coot-configure.in.patch | 41 +++++++ coot-user-manual.texi.patch | 24 ++++ coot.desktop | 10 ++ coot.in | 62 ++++++++++ coot.png | Bin 0 -> 1271 bytes coot.spec | 236 ++++++++++++++++++++++++++++++++++++ sources | 2 + svn-revision.cc | 6 + 10 files changed, 384 insertions(+) create mode 100644 __init__.py create mode 100644 coot-configure.in.patch create mode 100644 coot-user-manual.texi.patch create mode 100644 coot.desktop create mode 100755 coot.in create mode 100644 coot.png create mode 100644 coot.spec create mode 100644 svn-revision.cc diff --git a/.gitignore b/.gitignore index e69de29..0a061f3 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1,2 @@ +coot-0.6.1-20100127svn2740.tar.gz +coot-reference-structures.tar.gz diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..83d04e7 --- /dev/null +++ b/__init__.py @@ -0,0 +1 @@ +# File to allow this directory to be treated as a python package. diff --git a/coot-configure.in.patch b/coot-configure.in.patch new file mode 100644 index 0000000..f8501c2 --- /dev/null +++ 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: $GUILE_VERSION + AC_SUBST(GUILE_VERSION) diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch new file mode 100644 index 0000000..2f8df9a --- /dev/null +++ b/coot-user-manual.texi.patch @@ -0,0 +1,24 @@ +--- doc/user-manual.texi_orig 2010-01-27 16:23:57.630783062 -0800 ++++ doc/user-manual.texi 2010-01-27 16:50:48.507782342 -0800 +@@ -4470,10 +4470,10 @@ + @c note that texi2html (and makeinfo) requires that this c-interface texi file be in the + @c same directory as this file (user-manual.texi) NOT the directory that + @c texi2html is run in. +-@include c-interface.h.texi ++@include c-interface_8h.texi + @node More Scripting Functions + @chapter More Scripting Functions +-@include cc-interface.hh.texi ++@c @include cc-interface.hh.texi + + + +@@ -4491,7 +4491,7 @@ + @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node + @c + +-@include ../../coot/scheme/coot-scheme-functions.texi ++@c @include ../../coot/scheme/coot-scheme-functions.texi + + + diff --git a/coot.desktop b/coot.desktop new file mode 100644 index 0000000..79a76c6 --- /dev/null +++ b/coot.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Encoding=UTF-8 +Name=coot +GenericName=coot +Comment=macromolecular model builder +Exec=coot +Icon=coot +Terminal=false +Type=Application +Categories=Graphics;Science diff --git a/coot.in b/coot.in new file mode 100755 index 0000000..bff0148 --- /dev/null +++ b/coot.in @@ -0,0 +1,62 @@ +#!/bin/sh +# -*-shell-script-*- +# coot wrapper script +# Copyright 2004, 2005, 2006, 2007 University of York +# written by Paul Emsley + +COOT_PREFIX="@prefix@" +current_exe_dir="@bindir@" + +coot_real=$current_exe_dir/coot-real +# echo coot-real is at $coot_real + +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# If the COOT_PREFIX is correct, then these should not need modification +# i.e. nothing below here need be changed. +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# +prefix=$COOT_PREFIX + +SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib +COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme +COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb +COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps +COOT_DATA_DIR=$COOT_PREFIX/share/coot +COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc +COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures +COOT_PYTHON_DIR= +COOT_REFMAC_LIB_DIR= + +PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR + +GUILE_WARN_DEPRECATED=no + +if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then + GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH + export GUILE_LOAD_PATH +fi + +# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH + +export SYMINFO +export COOT_PREFIX +export COOT_STANDARD_RESIDUES +export COOT_REFMAC_LIB_DIR +export COOT_PYTHON_DIR +export PYTHONPATH +export COOT_SCHEME_DIR +export COOT_REF_STRUCTS +export COOT_RESOURCES_FILE +export COOT_PIXMAPS_DIR +export COOT_DATA_DIR + +echo $coot_real $* +$coot_real $* +status=$? + +if [ $status != 0 ] ; then + @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real +fi + diff --git a/coot.png b/coot.png new file mode 100644 index 0000000000000000000000000000000000000000..9e6ded7e24754bfa77ee5fe584fd2df36be6e86e GIT binary patch literal 1271 zcmVPx#24YJ`L;(K){{a7>y{D4^000SaNLh0L01FcU01FcV0GgZ_00007bV*G`2iOY| z7cwAl4qK}L00ehQL_t(o!|j$^h*nh;$A4?>v(Gv6&FyO@P0Y-$hK1E+NifDss}%$!X@howHXD-}g<^ zMNP{J@_#scpR@O7t^ZnkueBE(#$o&)AcFoYiX+_3UZNo{&YXx%@9BB$pHnVwiGr!r z-xkGYo;}STU-{@+2Q9SVS~^pSZ;A2iJgyvxS|nQbM4v{u6%M_DRN_?9$q~*JY&41M zF1^TON7f@&i(w5|1m8EKiB^n8-ZNBAi92Im9B=61>Gk7U2eB{5$nIHAPI} z^HYzT^umnOPJQD0_qOi(>a&mE`(>N<0iXCZt;9>fZZph-Aqa+H1Z?En>W2+Q37uf) z3epram=~jypPzMRM>hSA`GadeTKCe16>sg+Vi$Q|q+?zeom;yphAuj-NV|2=W^EL# zmDCC(mJ*Lx?s3*aVhORuBV&;{+y_m$eQ&P3;`RA+i@!doqtGqIg^{^An&}ip)i56j zy91#mAaTH4KpWNv0yJ6>q~Q|~X!yhs$eQvir~Gu(MNhppuvY@XtYFwU#W{f>NLA6A zVMBqC)QN;NAd#U`r=blBVU+S_YZzgu_u>0``lr@T7##ZXi0$7jJ7?T6i#9ZMjwA?C z*S&|K0mZlHSZhWo*2s#1kO-1H+_1;*^7tP-ezzm4*6mgl0krX@jnO6@R!zMArVqa! z;Elw$7q<^}9kXrQLsvfa>f$y471i!`S~s?aWM@pY+~d{bcYETUp0wX^S|xN>$;MX6 zj?4+I1}I7o?g}dc1h=52oPBa{Z*;m zswQ&;HwPFq;uWw6x5uGF0gH_gH+#k90gJQ|1NBy^|0|Ghtw}zYs+9pI-n8^xfU)iQ zg+*&dM+pTzsluE?$EO0h7}!d^d&_riUj4CM-Xzt z>awd%%Prgb+Xy?l>#MM3$ISjnIQHIWw$G41%y?SpX$^&Y5|T-Rgwb<`Y26DJ8^Jd{ zVpx=sWfiF|C|T*@y@mLL%V+tG{m&PlTzcdVnx|xM=%C}8lw^S*6C6>+p~H;`lYm7{ z0y%l1Lgmeplor;k)_XuV<$hPRYBVWv{dtnz-q+_pPC_!#6HRs!ohK$!%ajXMsm(51 zY5gI)+2%}R*}|)N@^`6P;iC0^ z?e@1Ib}~V0c79tYSA4OJS3*bHM^ zuUXBGHsyU8E?0@^6Bst5B{Q}>`?6e>rlx01Va=vZTwBh0>+d^+&6>b5y;ZquAaJKb z?jWtgE&+{T3ef9?We%oh#pWQhO( literal 0 HcmV?d00001 diff --git a/coot.spec b/coot.spec new file mode 100644 index 0000000..e48e755 --- /dev/null +++ b/coot.spec @@ -0,0 +1,236 @@ +%{!?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://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 +# 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: freeglut-devel +BuildRequires: gsl-devel +BuildRequires: gtk2-devel +BuildRequires: gtkglext-devel +BuildRequires: guile-devel +BuildRequires: guile-lib +BuildRequires: imlib-devel +BuildRequires: libcurl-devel +BuildRequires: libgnomecanvas-devel +BuildRequires: libtool +BuildRequires: mmdb-devel >= 1.19 +BuildRequires: python-devel +BuildRequires: pygtk2-devel +BuildRequires: refmac-dictionary +BuildRequires: ssm-devel +BuildRequires: swig +%if 0%{?rhel} +BuildRequires: tetex-latex +%else +BuildRequires: tex(latex) +%endif +BuildRequires: texinfo-tex +Requires: refmac-dictionary + +%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 devel +Summary: Header files and library for developing programs with coot +Requires: %{name} = %{version}-%{release} +Group: Development/Libraries + +%description devel + +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 + +%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 + +cp %{SOURCE2} ./src/ +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 {} \; + +aclocal -I macros +libtoolize --automake --copy +autoconf +automake --copy --add-missing --gnu + +%build +%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" + +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 + +make %{?_smp_mflags} +pushd doc +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=%{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 + +# headers +mkdir %{buildroot}%{_includedir}/coot +mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ +mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ + +# python stuff +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 %{SOURCE5} +mkdir -p %{buildroot}%{_datadir}/pixmaps +install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/ + +%clean +rm -rf %{buildroot} + +%check +# this fails - need to fix upstream +# make check + +%post -p /sbin/ldconfig + +%postun -p /sbin/ldconfig + +%files +%defattr(-,root,root,-) +%doc AUTHORS README COPYING +%{_bindir}/* +# 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 devel +%defattr(-,root,root,-) +%{_libdir}/*.so +%{_includedir}/coot/ + +%files doc +%defattr(-,root,root,-) +%doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf + +%changelog +* Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 +- fix file attr +- add comment to make check error + +* Tue Jul 20 2010 Tim Fenn - 0.6.1-2.20100127svn2740 +- move some documentation to subpackage +- add check section + +* Wed Jan 27 2010 Tim Fenn - 0.6.1-1.20100127svn2740 +- update to SVN 2740, 0.6.1 release +- add curl buildrequires + +* Thu Dec 03 2009 Tim Fenn - 0.6-6.20091203svn2545 +- update to SVN 2545, 0.6 release + +* Mon Nov 30 2009 Tim Fenn - 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 - 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 - 0.6-3.20091005svn2400 +- update to SVN 2400 + +* Wed Sep 23 2009 Tim Fenn - 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 - 0.6-1.20090920svn2334 +- update to 0.6 +- get source from VCS system + +* Wed Mar 25 2009 Tim Fenn - 0.5.2-3 +- fix summary +- add additional licensing information +- split guile-extras into original tarballs + +* Sat Mar 14 2009 Tim Fenn - 0.5.2-2 +- fix for desktop-file-install +- gcc 4.4 patch + +* Mon Dec 15 2008 Tim Fenn - 0.5.2-1 +- update to 0.5.2 + +* Thu Nov 27 2008 Tim Fenn - 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 - 0.5-2 +- enable guile +- include extra guile modules + +* Mon Nov 17 2008 Tim Fenn - 0.5-1 +- initial build diff --git a/sources b/sources index e69de29..73137a9 100644 --- a/sources +++ b/sources @@ -0,0 +1,2 @@ +ecf43a60294f660946f5a14b8bf98769 coot-0.6.1-20100127svn2740.tar.gz +59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc new file mode 100644 index 0000000..432f2c5 --- /dev/null +++ b/svn-revision.cc @@ -0,0 +1,6 @@ +extern "C" { +int svn_revision() { + return 2740; +} +} + From 8f5dd3d2c30168e6ea7994c38aae740442538197 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 12 Oct 2010 12:00:43 -0700 Subject: [PATCH 03/43] - update to 0.6.2 --- .gitignore | 2 ++ coot.spec | 17 ++++++++++------- sources | 2 +- svn-revision.cc | 2 +- 4 files changed, 14 insertions(+), 9 deletions(-) diff --git a/.gitignore b/.gitignore index 0a061f3..be6ce24 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,4 @@ coot-0.6.1-20100127svn2740.tar.gz coot-reference-structures.tar.gz +/coot-reference-structures.tar.gz +/coot-0.6.2-20101012svn3213.tar.gz diff --git a/coot.spec b/coot.spec index e48e755..2d87a36 100644 --- a/coot.spec +++ b/coot.spec @@ -4,16 +4,16 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ -Version: 0.6.1 -Release: 3.20100127svn2740%{?dist} +Version: 0.6.2 +Release: 1.20101012svn3213%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # 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 +# svn co -r 3213 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 +# tar cvzf coot-0.6.2-20101012svn3213.tar.gz coot-0.6.2 +Source0: coot-0.6.2-20101012svn3213.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -143,8 +143,8 @@ install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/ rm -rf %{buildroot} %check -# this fails - need to fix upstream -# make check +make check +# %{buildroot}%{_bindir}/coot-real --no-graphics --script python-tests/coot_unittest.py %post -p /sbin/ldconfig @@ -173,6 +173,9 @@ rm -rf %{buildroot} %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Oct 12 2010 Tim Fenn - 0.6.2-1.20101012svn3213 +- update to 0.6.2 + * Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 - fix file attr - add comment to make check error diff --git a/sources b/sources index 73137a9..083104b 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -ecf43a60294f660946f5a14b8bf98769 coot-0.6.1-20100127svn2740.tar.gz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz +307876bc5d52c2073e45142dc325d912 coot-0.6.2-20101012svn3213.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc index 432f2c5..7f9aab6 100644 --- a/svn-revision.cc +++ b/svn-revision.cc @@ -1,6 +1,6 @@ extern "C" { int svn_revision() { - return 2740; + return 3213; } } From d916bcd93e8ae220ba7c0c8b44c57833763950b8 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Tue, 8 Feb 2011 05:27:08 -0600 Subject: [PATCH 04/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 2d87a36..4502879 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 1.20101012svn3213%{?dist} +Release: 2.20101012svn3213%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -173,6 +173,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Feb 08 2011 Fedora Release Engineering - 0.6.2-2.20101012svn3213 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild + * Tue Oct 12 2010 Tim Fenn - 0.6.2-1.20101012svn3213 - update to 0.6.2 From 1414a8383aaa20a495fee9d96a72fe05a5aa6903 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Fri, 25 Feb 2011 18:11:49 -0800 Subject: [PATCH 05/43] update to svn 3399 --- .gitignore | 1 + coot-configure.in.patch | 8 ++++---- coot-user-manual.texi.patch | 8 ++++---- coot.spec | 12 +++++++----- sources | 2 +- 5 files changed, 17 insertions(+), 14 deletions(-) diff --git a/.gitignore b/.gitignore index be6ce24..bf43229 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ coot-0.6.1-20100127svn2740.tar.gz coot-reference-structures.tar.gz /coot-reference-structures.tar.gz /coot-0.6.2-20101012svn3213.tar.gz +/coot-0.6.2-20110225svn3399.tar.gz diff --git a/coot-configure.in.patch b/coot-configure.in.patch index f8501c2..7b544d7 100644 --- a/coot-configure.in.patch +++ b/coot-configure.in.patch @@ -1,6 +1,6 @@ ---- 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 @@ +--- configure.in_orig 2011-02-25 17:50:58.794613856 -0800 ++++ configure.in 2011-02-25 17:51:09.905607373 -0800 +@@ -134,13 +134,26 @@ AM_PATH_GLUT(, [echo You need the GLUT utility library; exit 1], AC_MSG_ERROR([Cannot find proper GLUT version])) dnl Check for MMDB. @@ -30,7 +30,7 @@ # we set default coot_guile to true coot_guile=true -@@ -146,7 +159,7 @@ +@@ -148,7 +161,7 @@ if test x$coot_guile = xtrue ; then GUILE_FLAGS AM_GUILE_LIB diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch index 2f8df9a..cc5a13b 100644 --- a/coot-user-manual.texi.patch +++ b/coot-user-manual.texi.patch @@ -1,6 +1,6 @@ ---- 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 @@ +--- doc/user-manual.texi_orig 2011-02-25 17:52:45.549624699 -0800 ++++ doc/user-manual.texi 2011-02-25 17:52:52.772606944 -0800 +@@ -4819,10 +4819,10 @@ @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. @@ -13,7 +13,7 @@ -@@ -4491,7 +4491,7 @@ +@@ -4840,7 +4840,7 @@ @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node @c diff --git a/coot.spec b/coot.spec index 4502879..2628c8d 100644 --- a/coot.spec +++ b/coot.spec @@ -5,15 +5,15 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 2.20101012svn3213%{?dist} +Release: 3.20110225svn3399%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 3213 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 -# tar cvzf coot-0.6.2-20101012svn3213.tar.gz coot-0.6.2 -Source0: coot-0.6.2-20101012svn3213.tar.gz +# svn co -r 3399 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 +# tar cvzf coot-0.6.2-20110225svn3399.tar.gz coot-0.6.2 +Source0: coot-0.6.2-20110225svn3399.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -22,7 +22,6 @@ 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 @@ -173,6 +172,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Fri Feb 25 2011 Tim Fenn - 0.6.2-3.20110225svn3399 +- update to SVN 3399 + * Tue Feb 08 2011 Fedora Release Engineering - 0.6.2-2.20101012svn3213 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild diff --git a/sources b/sources index 083104b..3a0f756 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ +ce5c9bcf282059662e957809b56c7560 coot-0.6.2-20110225svn3399.tar.gz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz -307876bc5d52c2073e45142dc325d912 coot-0.6.2-20101012svn3213.tar.gz From ebc70ff70b7fcce60ee430289713097517948581 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 29 Mar 2011 12:10:09 -0700 Subject: [PATCH 06/43] - update to SVN 3442 (should fix guile-gtk dependency issues) --- .gitignore | 1 + coot.spec | 11 +++++++---- sources | 2 +- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index bf43229..367b274 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ coot-reference-structures.tar.gz /coot-reference-structures.tar.gz /coot-0.6.2-20101012svn3213.tar.gz /coot-0.6.2-20110225svn3399.tar.gz +/coot-0.6.2-20110328svn3442.tar.gz diff --git a/coot.spec b/coot.spec index 2628c8d..f72b812 100644 --- a/coot.spec +++ b/coot.spec @@ -5,15 +5,15 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 3.20110225svn3399%{?dist} +Release: 4.20110328svn3442%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 3399 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 -# tar cvzf coot-0.6.2-20110225svn3399.tar.gz coot-0.6.2 -Source0: coot-0.6.2-20110225svn3399.tar.gz +# svn co -r 3442 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 +# tar cvzf coot-0.6.2-20110328svn3442.tar.gz coot-0.6.2 +Source0: coot-0.6.2-20110328svn3442.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -172,6 +172,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Mar 29 2011 Tim Fenn - 0.6.2-4.20110328svn3442 +- update to SVN 3442 (should remove guile-gtk broken dependencies) + * Fri Feb 25 2011 Tim Fenn - 0.6.2-3.20110225svn3399 - update to SVN 3399 diff --git a/sources b/sources index 3a0f756..705d11b 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -ce5c9bcf282059662e957809b56c7560 coot-0.6.2-20110225svn3399.tar.gz +132dcd2487f5091ee59429820224a8ad coot-0.6.2-20110328svn3442.tar.gz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz From b17f0b8f9a87f04c2c5784d3a015a025a40773f5 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 26 Apr 2011 18:32:23 -0700 Subject: [PATCH 07/43] - update to SVN 3461 - fix missing Requires: guile-lib --- coot.spec | 13 +++++++++---- svn-revision.cc | 2 +- 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/coot.spec b/coot.spec index f72b812..fe74298 100644 --- a/coot.spec +++ b/coot.spec @@ -5,15 +5,15 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 4.20110328svn3442%{?dist} +Release: 5.20110421svn3461%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 3442 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 -# tar cvzf coot-0.6.2-20110328svn3442.tar.gz coot-0.6.2 -Source0: coot-0.6.2-20110328svn3442.tar.gz +# svn co -r 3461 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 +# tar cvzf coot-0.6.2-20110421svn3461.tar.gz coot-0.6.2 +Source0: coot-0.6.2-20110421svn3461.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -48,6 +48,7 @@ BuildRequires: tetex-latex BuildRequires: tex(latex) %endif BuildRequires: texinfo-tex +Requires: guile-lib Requires: refmac-dictionary %description @@ -172,6 +173,10 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Thu Apr 21 2011 Tim Fenn - 0.6.2-5.20110421svn3461 +- update to SVN 3461 +- fix missing Requires: guile-lib + * Tue Mar 29 2011 Tim Fenn - 0.6.2-4.20110328svn3442 - update to SVN 3442 (should remove guile-gtk broken dependencies) diff --git a/svn-revision.cc b/svn-revision.cc index 7f9aab6..be05d48 100644 --- a/svn-revision.cc +++ b/svn-revision.cc @@ -1,6 +1,6 @@ extern "C" { int svn_revision() { - return 3213; + return 3461; } } From bf41842f359b706aba44e2ba5ca17ceceabee08f Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 26 Apr 2011 19:06:50 -0700 Subject: [PATCH 08/43] - add missing source --- .gitignore | 1 + coot.spec | 5 ++++- sources | 3 +-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 367b274..4a8fe6a 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ coot-reference-structures.tar.gz /coot-0.6.2-20101012svn3213.tar.gz /coot-0.6.2-20110225svn3399.tar.gz /coot-0.6.2-20110328svn3442.tar.gz +/coot-0.6.2-20110421svn3461.tar.gz diff --git a/coot.spec b/coot.spec index fe74298..03f193d 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 5.20110421svn3461%{?dist} +Release: 6.20110421svn3461%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -173,6 +173,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Apr 26 2011 Tim Fenn - 0.6.2-6.20110421svn3461 +- add missing source + * Thu Apr 21 2011 Tim Fenn - 0.6.2-5.20110421svn3461 - update to SVN 3461 - fix missing Requires: guile-lib diff --git a/sources b/sources index 705d11b..d80d201 100644 --- a/sources +++ b/sources @@ -1,2 +1 @@ -132dcd2487f5091ee59429820224a8ad coot-0.6.2-20110328svn3442.tar.gz -59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz +7d9738af4cdc6589da6b53cdbc3f88f6 coot-0.6.2-20110421svn3461.tar.gz From f0b6da2a07db171a9cf1df73f35cdf1f4ffe2a4a Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 26 Apr 2011 19:20:56 -0700 Subject: [PATCH 09/43] - add reference structures source file --- coot.spec | 5 ++++- sources | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 03f193d..7234372 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 6.20110421svn3461%{?dist} +Release: 7.20110421svn3461%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -173,6 +173,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Apr 26 2011 Tim Fenn - 0.6.2-7.20110421svn3461 +- add reference structures source file + * Tue Apr 26 2011 Tim Fenn - 0.6.2-6.20110421svn3461 - add missing source diff --git a/sources b/sources index d80d201..b0be21d 100644 --- a/sources +++ b/sources @@ -1 +1,2 @@ 7d9738af4cdc6589da6b53cdbc3f88f6 coot-0.6.2-20110421svn3461.tar.gz +59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz From 9b0268fddee5fe54a922453a85e8c839cb910829 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Mon, 18 Jul 2011 11:54:33 -0700 Subject: [PATCH 10/43] * Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 - update to SVN 3566 (0.6.2 final) --- .gitignore | 1 + coot.spec | 11 +++++++---- sources | 2 +- svn-revision.cc | 2 +- 4 files changed, 10 insertions(+), 6 deletions(-) diff --git a/.gitignore b/.gitignore index 4a8fe6a..f5ae5ad 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ coot-reference-structures.tar.gz /coot-0.6.2-20110225svn3399.tar.gz /coot-0.6.2-20110328svn3442.tar.gz /coot-0.6.2-20110421svn3461.tar.gz +/coot-0.6.2-20110715svn3566.tar.gz diff --git a/coot.spec b/coot.spec index 7234372..4e28fef 100644 --- a/coot.spec +++ b/coot.spec @@ -5,15 +5,15 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 7.20110421svn3461%{?dist} +Release: 8.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 3461 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 -# tar cvzf coot-0.6.2-20110421svn3461.tar.gz coot-0.6.2 -Source0: coot-0.6.2-20110421svn3461.tar.gz +# svn co -r 3566 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 +# tar cvzf coot-0.6.2-20110715svn3566.tar.gz coot-0.6.2 +Source0: coot-0.6.2-20110715svn3566.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -173,6 +173,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 +- update to SVN 3566 (0.6.2 final) + * Tue Apr 26 2011 Tim Fenn - 0.6.2-7.20110421svn3461 - add reference structures source file diff --git a/sources b/sources index b0be21d..6a74466 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -7d9738af4cdc6589da6b53cdbc3f88f6 coot-0.6.2-20110421svn3461.tar.gz +c05e91fb2a93b9e84e35e2548e8d4992 coot-0.6.2-20110715svn3566.tar.gz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc index be05d48..196c17f 100644 --- a/svn-revision.cc +++ b/svn-revision.cc @@ -1,6 +1,6 @@ extern "C" { int svn_revision() { - return 3461; + return 3566; } } From d7fb565170e8d64ee5bdbf671bcf9ccd8f0c8443 Mon Sep 17 00:00:00 2001 From: Adam Jackson Date: Mon, 5 Dec 2011 22:50:48 -0500 Subject: [PATCH 11/43] Rebuild for new libpng --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 4e28fef..bd23c23 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 8.20110715svn3566%{?dist} +Release: 9.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -173,6 +173,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Dec 06 2011 Adam Jackson - 0.6.2-9.20110715svn3566 +- Rebuild for new libpng + * Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 - update to SVN 3566 (0.6.2 final) From 8cde1f0ae9ccefb2473edd6c1bb0f1dfda38fd26 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sat, 10 Dec 2011 17:10:37 -0800 Subject: [PATCH 12/43] * Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 - patch for new libpng --- coot-libpng15.patch | 29 +++++++++++++++++++++++++++++ coot.spec | 7 ++++++- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 coot-libpng15.patch diff --git a/coot-libpng15.patch b/coot-libpng15.patch new file mode 100644 index 0000000..bddd251 --- /dev/null +++ b/coot-libpng15.patch @@ -0,0 +1,29 @@ +--- ccp4mg-utils/ppmutil.cc ++++ ccp4mg-utils/ppmutil.cc +@@ -2494,15 +2494,21 @@ + + pixels = new unsigned char[width*height*colourspace]; + ++ png_colorp palette; ++ int num_trans; ++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4 ++ png_bytep trans_alpha; ++#endif ++ + for (int i=0; ipalette[row_pointers[i][j]].red; +- pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green; +- pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue; +- if(row_pointers[i][j]num_trans){ ++ pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; ++ pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green; ++ pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue; ++ if(row_pointers[i][j]= 1 && PNG_LIBPNG_VER_MINOR >=4 +- pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]]; ++ pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]]; + #else + pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]]; + #endif diff --git a/coot.spec b/coot.spec index bd23c23..7741dec 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 9.20110715svn3566%{?dist} +Release: 10.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -22,6 +22,7 @@ Source5: %{name}.desktop Source6: __init__.py Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch +Patch2: coot-libpng15.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 @@ -84,6 +85,7 @@ package. %setup -q -a 1 %patch0 -p0 %patch1 -p0 +%patch2 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} ./src/ @@ -173,6 +175,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 +- patch for new libpng + * Tue Dec 06 2011 Adam Jackson - 0.6.2-9.20110715svn3566 - Rebuild for new libpng From 34e0d60c56ad2d1ed86f71141afa345331ca4fa8 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Thu, 12 Jan 2012 17:52:50 -0600 Subject: [PATCH 13/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 7741dec..bb771ec 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 10.20110715svn3566%{?dist} +Release: 11.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -175,6 +175,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Thu Jan 12 2012 Fedora Release Engineering - 0.6.2-11.20110715svn3566 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild + * Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 - patch for new libpng From 01409c1dd94dfb9720c977d6cf00f295384038db Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sat, 14 Jan 2012 19:29:22 -0800 Subject: [PATCH 14/43] * Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 - patches to fix unistd.h issue and compilation errors --- coot-fixes.patch | 34 ++++++++++++++++++++++++++++++++++ coot-unistd.patch | 12 ++++++++++++ coot.spec | 9 ++++++++- 3 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 coot-fixes.patch create mode 100644 coot-unistd.patch diff --git a/coot-fixes.patch b/coot-fixes.patch new file mode 100644 index 0000000..bc6c5c4 --- /dev/null +++ b/coot-fixes.patch @@ -0,0 +1,34 @@ +--- coot-utils/coot-coord-utils.cc_orig 2012-01-14 15:37:13.659012534 -0800 ++++ coot-utils/coot-coord-utils.cc 2012-01-14 15:37:25.340287814 -0800 +@@ -180,7 +180,8 @@ + clipper::Coord_frac cf = coot::util::shift_to_origin(mol); + clipper::Coord_orth co = cf.coord_orth(csp.first); + for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) { +- int imod = 1; ++ // int imod = 1; ++ imod = 1; + CModel *model_p = mol->GetModel(imod); + CChain *chain_p; + int nchains = model_p->GetNumberOfChains(); +@@ -2644,7 +2645,8 @@ + short int whole_res_flag = 1; + + for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) { +- int imod = 1; ++ // int imod = 1; ++ imod = 1; + CModel *model_p = mol_in->GetModel(imod); + CModel *new_model_p = new CModel; + int nchains = model_p->GetNumberOfChains(); +--- src/molecule-class-info-residues.cc_orig 2012-01-14 15:58:26.111024446 -0800 ++++ src/molecule-class-info-residues.cc 2012-01-14 15:57:44.284039047 -0800 +@@ -131,7 +131,8 @@ + + int r = 0; + for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) { +- int imod = 1; ++ // int imod = 1; ++ imod = 1; + CModel *model_p = atom_sel.mol->GetModel(imod); + CChain *chain_p; + // run over chains of the existing mol diff --git a/coot-unistd.patch b/coot-unistd.patch new file mode 100644 index 0000000..352386f --- /dev/null +++ b/coot-unistd.patch @@ -0,0 +1,12 @@ +--- utils/coot-utils.cc_orig 2012-01-14 14:55:00.076247314 -0800 ++++ utils/coot-utils.cc 2012-01-14 14:55:16.310628650 -0800 +@@ -47,9 +47,7 @@ + + #include // for mkdir + #include +-#if defined WINDOWS_MINGW + #include // BL says: in windows needed for mkdir +-#endif // MINGW + + // #include "clipper/core/hkl_compute.h" + diff --git a/coot.spec b/coot.spec index bb771ec..6febc93 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 11.20110715svn3566%{?dist} +Release: 12.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -23,6 +23,8 @@ Source6: __init__.py Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch Patch2: coot-libpng15.patch +Patch3: coot-unistd.patch +Patch4: coot-fixes.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 @@ -86,6 +88,8 @@ package. %patch0 -p0 %patch1 -p0 %patch2 -p0 +%patch3 -p0 +%patch4 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} ./src/ @@ -175,6 +179,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 +- patches to fix unistd.h issue and compilation errors + * Thu Jan 12 2012 Fedora Release Engineering - 0.6.2-11.20110715svn3566 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild From ba35e119aed6698357453b72b31c7388f1466ede Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Tue, 28 Feb 2012 12:05:06 -0600 Subject: [PATCH 15/43] - Rebuilt for c++ ABI breakage --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 6febc93..ce0952d 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 12.20110715svn3566%{?dist} +Release: 13.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -179,6 +179,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Tue Feb 28 2012 Fedora Release Engineering - 0.6.2-13.20110715svn3566 +- Rebuilt for c++ ABI breakage + * Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 - patches to fix unistd.h issue and compilation errors From b65cb86aefa898cb9d3746383253a400d1dcd5e8 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 18 Jul 2012 14:40:49 -0500 Subject: [PATCH 16/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index ce0952d..6b75230 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.6.2 -Release: 13.20110715svn3566%{?dist} +Release: 14.20110715svn3566%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -179,6 +179,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf %changelog +* Wed Jul 18 2012 Fedora Release Engineering - 0.6.2-14.20110715svn3566 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild + * Tue Feb 28 2012 Fedora Release Engineering - 0.6.2-13.20110715svn3566 - Rebuilt for c++ ABI breakage From c8d6fa743b3b9b58ba8f1b5855cbf2d0568103a9 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 16 Oct 2012 22:02:52 -0700 Subject: [PATCH 17/43] * Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 - update to 0.7 --- .gitignore | 1 + coot-configure.in.patch | 19 ++++++------------- coot-fixes.patch | 34 ---------------------------------- coot-libpng15.patch | 29 ----------------------------- coot-unistd.patch | 6 +++--- coot-user-manual.texi.patch | 12 ++++++------ coot.spec | 31 ++++++++++++++++++------------- sources | 2 +- svn-revision.cc | 2 +- 9 files changed, 36 insertions(+), 100 deletions(-) delete mode 100644 coot-fixes.patch delete mode 100644 coot-libpng15.patch diff --git a/.gitignore b/.gitignore index f5ae5ad..a3d4dc4 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ coot-reference-structures.tar.gz /coot-0.6.2-20110328svn3442.tar.gz /coot-0.6.2-20110421svn3461.tar.gz /coot-0.6.2-20110715svn3566.tar.gz +/coot-0.7-20120929svn4458.tar.gz diff --git a/coot-configure.in.patch b/coot-configure.in.patch index 7b544d7..13d55f4 100644 --- a/coot-configure.in.patch +++ b/coot-configure.in.patch @@ -1,7 +1,7 @@ ---- configure.in_orig 2011-02-25 17:50:58.794613856 -0800 -+++ configure.in 2011-02-25 17:51:09.905607373 -0800 -@@ -134,13 +134,26 @@ - AM_PATH_GLUT(, [echo You need the GLUT utility library; exit 1], AC_MSG_ERROR([Cannot find proper GLUT version])) +--- configure.in_orig 2012-09-29 18:54:43.410146251 -0700 ++++ configure.in 2012-09-29 18:59:46.669993583 -0700 +@@ -104,13 +104,28 @@ + dnl Check for MMDB. -AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,) @@ -9,6 +9,7 @@ -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) @@ -23,6 +24,7 @@ # -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=$CLIPPER_CFLAGS +AC_SUBST(CLIPPER_CXXFLAGS) @@ -30,12 +32,3 @@ # we set default coot_guile to true coot_guile=true -@@ -148,7 +161,7 @@ - if test x$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) diff --git a/coot-fixes.patch b/coot-fixes.patch deleted file mode 100644 index bc6c5c4..0000000 --- a/coot-fixes.patch +++ /dev/null @@ -1,34 +0,0 @@ ---- coot-utils/coot-coord-utils.cc_orig 2012-01-14 15:37:13.659012534 -0800 -+++ coot-utils/coot-coord-utils.cc 2012-01-14 15:37:25.340287814 -0800 -@@ -180,7 +180,8 @@ - clipper::Coord_frac cf = coot::util::shift_to_origin(mol); - clipper::Coord_orth co = cf.coord_orth(csp.first); - for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) { -- int imod = 1; -+ // int imod = 1; -+ imod = 1; - CModel *model_p = mol->GetModel(imod); - CChain *chain_p; - int nchains = model_p->GetNumberOfChains(); -@@ -2644,7 +2645,8 @@ - short int whole_res_flag = 1; - - for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) { -- int imod = 1; -+ // int imod = 1; -+ imod = 1; - CModel *model_p = mol_in->GetModel(imod); - CModel *new_model_p = new CModel; - int nchains = model_p->GetNumberOfChains(); ---- src/molecule-class-info-residues.cc_orig 2012-01-14 15:58:26.111024446 -0800 -+++ src/molecule-class-info-residues.cc 2012-01-14 15:57:44.284039047 -0800 -@@ -131,7 +131,8 @@ - - int r = 0; - for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) { -- int imod = 1; -+ // int imod = 1; -+ imod = 1; - CModel *model_p = atom_sel.mol->GetModel(imod); - CChain *chain_p; - // run over chains of the existing mol diff --git a/coot-libpng15.patch b/coot-libpng15.patch deleted file mode 100644 index bddd251..0000000 --- a/coot-libpng15.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- ccp4mg-utils/ppmutil.cc -+++ ccp4mg-utils/ppmutil.cc -@@ -2494,15 +2494,21 @@ - - pixels = new unsigned char[width*height*colourspace]; - -+ png_colorp palette; -+ int num_trans; -+#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4 -+ png_bytep trans_alpha; -+#endif -+ - for (int i=0; ipalette[row_pointers[i][j]].red; -- pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green; -- pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue; -- if(row_pointers[i][j]num_trans){ -+ pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red; -+ pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green; -+ pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue; -+ if(row_pointers[i][j]= 1 && PNG_LIBPNG_VER_MINOR >=4 -- pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]]; -+ pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]]; - #else - pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]]; - #endif diff --git a/coot-unistd.patch b/coot-unistd.patch index 352386f..a91efcb 100644 --- a/coot-unistd.patch +++ b/coot-unistd.patch @@ -1,6 +1,6 @@ ---- utils/coot-utils.cc_orig 2012-01-14 14:55:00.076247314 -0800 -+++ utils/coot-utils.cc 2012-01-14 14:55:16.310628650 -0800 -@@ -47,9 +47,7 @@ +--- utils/coot-utils.cc_orig 2012-09-29 19:16:39.050470149 -0700 ++++ utils/coot-utils.cc 2012-09-29 19:18:01.609169266 -0700 +@@ -48,9 +48,7 @@ #include // for mkdir #include diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch index cc5a13b..fc2a45a 100644 --- a/coot-user-manual.texi.patch +++ b/coot-user-manual.texi.patch @@ -1,6 +1,6 @@ ---- doc/user-manual.texi_orig 2011-02-25 17:52:45.549624699 -0800 -+++ doc/user-manual.texi 2011-02-25 17:52:52.772606944 -0800 -@@ -4819,10 +4819,10 @@ +--- doc/coot-user-manual.texi_orig 2012-09-29 19:50:40.386652186 -0700 ++++ doc/coot-user-manual.texi 2012-09-30 15:42:36.830651836 -0700 +@@ -4942,10 +4942,10 @@ @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. @@ -13,12 +13,12 @@ -@@ -4840,7 +4840,7 @@ +@@ -4963,7 +4963,7 @@ @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 +-@include coot-scheme-functions.texi ++@c @include coot-scheme-functions.texi diff --git a/coot.spec b/coot.spec index 6b75230..32ba75b 100644 --- a/coot.spec +++ b/coot.spec @@ -4,16 +4,16 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ -Version: 0.6.2 -Release: 14.20110715svn3566%{?dist} +Version: 0.7 +Release: 1.20120929svn4458%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 3566 http://coot.googlecode.com/svn/branches/release-0.6.2 coot-0.6.2 -# tar cvzf coot-0.6.2-20110715svn3566.tar.gz coot-0.6.2 -Source0: coot-0.6.2-20110715svn3566.tar.gz +# svn co -r 4458 http://coot.googlecode.com/svn/trunk coot-0.7 +# tar cvzf coot-0.7-20120929svn4458.tar.gz coot-0.7 +Source0: coot-0.7-20120929svn4458.tar.gz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -22,14 +22,14 @@ Source5: %{name}.desktop Source6: __init__.py Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch -Patch2: coot-libpng15.patch -Patch3: coot-unistd.patch -Patch4: coot-fixes.patch +Patch2: coot-unistd.patch +Patch3: coot-makefile.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 BuildRequires: desktop-file-utils BuildRequires: freeglut-devel +BuildRequires: goocanvas-devel BuildRequires: gsl-devel BuildRequires: gtk2-devel BuildRequires: gtkglext-devel @@ -51,7 +51,6 @@ BuildRequires: tetex-latex BuildRequires: tex(latex) %endif BuildRequires: texinfo-tex -Requires: guile-lib Requires: refmac-dictionary %description @@ -89,7 +88,6 @@ package. %patch1 -p0 %patch2 -p0 %patch3 -p0 -%patch4 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} ./src/ @@ -98,7 +96,6 @@ cp %{SOURCE3} ./src/ 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 {} \; aclocal -I macros libtoolize --automake --copy @@ -113,7 +110,7 @@ sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool make %{?_smp_mflags} pushd doc -texi2pdf user-manual.texi +texi2pdf coot-user-manual.texi make coot-keys-and-buttons.pdf popd @@ -137,6 +134,11 @@ mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ # python stuff mkdir -p %{buildroot}%{python_sitelib}/coot mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/ +for lib in $(find %{buildroot}%{python_sitelib}/coot/ -name "*.py"); do + sed '/\/usr\/bin\/env/d' $lib > $lib.new && + touch -r $lib $lib.new && + mv $lib.new $lib +done cp %{SOURCE6} %{buildroot}%{python_sitelib}/coot/ chmod 644 %{buildroot}%{python_sitelib}/coot/coot.py @@ -176,9 +178,12 @@ make check %files doc %defattr(-,root,root,-) -%doc doc/coot-keys-and-buttons.pdf doc/user-manual.pdf +%doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 +- update to 0.7 + * Wed Jul 18 2012 Fedora Release Engineering - 0.6.2-14.20110715svn3566 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild diff --git a/sources b/sources index 6a74466..b66edf2 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -c05e91fb2a93b9e84e35e2548e8d4992 coot-0.6.2-20110715svn3566.tar.gz +58bef4c0c0661c770b5f3710692fca8a coot-0.7-20120929svn4458.tar.gz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc index 196c17f..772cd89 100644 --- a/svn-revision.cc +++ b/svn-revision.cc @@ -1,6 +1,6 @@ extern "C" { int svn_revision() { - return 3566; + return 4458; } } From 7fbcd057c8a7fe6d8bc884a3fb79a31d401aa145 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Tue, 16 Oct 2012 22:07:57 -0700 Subject: [PATCH 18/43] - add missing coot-makefile.patch --- coot-makefile.patch | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 coot-makefile.patch diff --git a/coot-makefile.patch b/coot-makefile.patch new file mode 100644 index 0000000..ea5c34e --- /dev/null +++ b/coot-makefile.patch @@ -0,0 +1,10 @@ +--- lbg/Makefile.am_orig 2012-09-30 15:59:54.245707927 -0700 ++++ lbg/Makefile.am 2012-09-30 16:04:07.908430902 -0700 +@@ -68,6 +68,7 @@ + $(top_builddir)/lidia-core/libcoot-lidia-core.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/utils/libcoot-utils.la \ ++ $(PYTHON_LIBS) \ + $(RDKIT_LIBS) + + From 41a0a4f9fa6c56e53953accf62592b02493739b9 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 13 Feb 2013 12:58:54 -0600 Subject: [PATCH 19/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 32ba75b..461adde 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7 -Release: 1.20120929svn4458%{?dist} +Release: 2.20120929svn4458%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -181,6 +181,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Feb 13 2013 Fedora Release Engineering - 0.7-2.20120929svn4458 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + * Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 - update to 0.7 From ecfd840c7e2595e4845c27aacefbc98935409842 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 3 Aug 2013 00:51:44 -0500 Subject: [PATCH 20/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 461adde..9c5a112 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7 -Release: 2.20120929svn4458%{?dist} +Release: 3.20120929svn4458%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -181,6 +181,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Aug 03 2013 Fedora Release Engineering - 0.7-3.20120929svn4458 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild + * Wed Feb 13 2013 Fedora Release Engineering - 0.7-2.20120929svn4458 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild From ce1bb5ebd67ae11586976d79ffedb112bf6bfa1c Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Fri, 9 Aug 2013 18:09:17 -0700 Subject: [PATCH 21/43] * Fri Aug 09 2013 Tim Fenn - 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 --- .gitignore | 1 + coot-guile.patch | 27 ++++ coot-ssm1.3.patch | 322 ++++++++++++++++++++++++++++++++++++++++++++++ coot.spec | 20 ++- sources | 2 +- 5 files changed, 366 insertions(+), 6 deletions(-) create mode 100644 coot-guile.patch create mode 100644 coot-ssm1.3.patch diff --git a/.gitignore b/.gitignore index a3d4dc4..7253be0 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ coot-reference-structures.tar.gz /coot-0.6.2-20110421svn3461.tar.gz /coot-0.6.2-20110715svn3566.tar.gz /coot-0.7-20120929svn4458.tar.gz +/coot-0.7-20120929svn4458.tar.xz diff --git a/coot-guile.patch b/coot-guile.patch new file mode 100644 index 0000000..e79a6a9 --- /dev/null +++ b/coot-guile.patch @@ -0,0 +1,27 @@ +--- 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) + ]) + diff --git a/coot-ssm1.3.patch b/coot-ssm1.3.patch new file mode 100644 index 0000000..0b78f02 --- /dev/null +++ b/coot-ssm1.3.patch @@ -0,0 +1,322 @@ +diff -crB ./src/graphics-info.h ../coot-patched/src/graphics-info.h +*** ./src/graphics-info.h 2013-04-27 16:04:58.000000000 +0200 +--- ../coot-patched/src/graphics-info.h 2013-07-25 04:09:17.861265837 +0200 +*************** +*** 3307,3313 **** + short int move_copy_of_imol2_flag); + + #ifdef HAVE_SSMLIB +! void print_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, +--- 3307,3313 ---- + short int move_copy_of_imol2_flag); + + #ifdef HAVE_SSMLIB +! void print_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, +*************** +*** 3315,3321 **** + int n_selected_atoms_1, int n_selected_atoms_2, + short int move_copy_of_imol2_flag); + +! void make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, +--- 3315,3321 ---- + int n_selected_atoms_1, int n_selected_atoms_2, + short int move_copy_of_imol2_flag); + +! void make_and_print_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, +*************** +*** 3325,3331 **** + void print_horizontal_ssm_sequence_alignment(std::pair aligned_sequences) const; + + std::pair +! get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +--- 3325,3331 ---- + void print_horizontal_ssm_sequence_alignment(std::pair aligned_sequences) const; + + std::pair +! get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +diff -crB ./src/graphics-info-superpose.cc ../coot-patched/src/graphics-info-superpose.cc +*** ./src/graphics-info-superpose.cc 2013-01-16 17:40:31.000000000 +0100 +--- ../coot-patched/src/graphics-info-superpose.cc 2013-07-25 04:42:47.876256551 +0200 +*************** +*** 22,27 **** +--- 22,31 ---- + #include "Python.h" // before system includes to stop "POSIX_C_SOURCE" redefined problems + #endif + ++ #ifdef HAVE_SSMLIB ++ #include "ssm_defs.h" ++ #endif ++ + #if defined _MSC_VER + #include + #endif +*************** +*** 168,179 **** + + #ifdef HAVE_SSMLIB + +! int precision = SSMP_Normal; +! int connectivity = CSSC_Flexible; + + // probably not necessary, not sure: +! SetSSConnectivityCheck ( CSSC_Flexible ); +! SetSSMatchPrecision ( SSMP_Normal ); + + if (asc_ref.n_selected_atoms > 0) { + if (asc_mov.n_selected_atoms > 0) { +--- 172,183 ---- + + #ifdef HAVE_SSMLIB + +! ssm::PRECISION precision = ssm::PREC_Normal; +! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible; + + // probably not necessary, not sure: +! ssm::SetConnectivityCheck ( ssm::CONNECT_Flexible ); +! ssm::SetMatchPrecision ( ssm::PREC_Normal ); + + if (asc_ref.n_selected_atoms > 0) { + if (asc_mov.n_selected_atoms > 0) { +*************** +*** 199,234 **** + + // Remove the pointer one day. + // +! CSSMAlign *SSMAlign = new CSSMAlign(); +! int rc = SSMAlign->Align(mol2, mol1, precision, connectivity, + asc_mov.SelectionHandle, + asc_ref.SelectionHandle); + + if (rc) { + std::string ws; + switch (rc) { +! case SSM_noHits : + std::cout << " *** secondary structure does not match.\n"; + ws = "secondary structure does not match"; + break; +! case SSM_noSPSN : + std::cout << " *** structures are too remote.\n"; + ws = "structures are too remote"; + break; +! case SSM_noGraph : + std::cout << " *** can't make graph for " << name1 << "\n"; + ws = "can't make graph for " + name1; + ws += " structure"; + break; +! case SSM_noVertices : + std::cout << " *** empty graph for " << name1 << "\n"; + ws = "empty graph for " + name1; + break; +! case SSM_noGraph2 : + std::cout << " *** can't make graph for " << name2 << "\n"; + ws = "can't make graph for " + name2; + break; +! case SSM_noVertices2 : + std::cout << " *** empty graph for " << name2 << "\n"; + ws = "empty graph for " + name2; + break; +--- 203,238 ---- + + // Remove the pointer one day. + // +! ssm::Align *SSMAlign = new ssm::Align(); +! int rc = SSMAlign->align(mol2, mol1, precision, connectivity, + asc_mov.SelectionHandle, + asc_ref.SelectionHandle); + + if (rc) { + std::string ws; + switch (rc) { +! case ssm::RC_NoHits : + std::cout << " *** secondary structure does not match.\n"; + ws = "secondary structure does not match"; + break; +! case ssm::RC_NoSuperposition : + std::cout << " *** structures are too remote.\n"; + ws = "structures are too remote"; + break; +! case ssm::RC_NoGraph : + std::cout << " *** can't make graph for " << name1 << "\n"; + ws = "can't make graph for " + name1; + ws += " structure"; + break; +! case ssm::RC_NoVertices : + std::cout << " *** empty graph for " << name1 << "\n"; + ws = "empty graph for " + name1; + break; +! case ssm::RC_NoGraph2 : + std::cout << " *** can't make graph for " << name2 << "\n"; + ws = "can't make graph for " + name2; + break; +! case ssm::RC_NoVertices2 : + std::cout << " *** empty graph for " << name2 << "\n"; + ws = "empty graph for " + name2; + break; +*************** +*** 298,304 **** + // mat44 tmat; + // realtype rmsdAchieved, seqIdentity, nCombs; + // int nAligned, nGaps, nMisD; +! // CSuperpose Superpose; type in class CSSMAlign + // + // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2, + // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity, +--- 302,308 ---- + // mat44 tmat; + // realtype rmsdAchieved, seqIdentity, nCombs; + // int nAligned, nGaps, nMisD; +! // CSuperpose Superpose; type in class ssm::Align + // + // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2, + // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity, +*************** +*** 331,337 **** + + #ifdef HAVE_SSMLIB + void +! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +--- 335,341 ---- + + #ifdef HAVE_SSMLIB + void +! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +*************** +*** 394,400 **** + + #ifdef HAVE_SSMLIB + std::pair +! graphics_info_t::get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +--- 398,404 ---- + + #ifdef HAVE_SSMLIB + std::pair +! graphics_info_t::get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +*************** +*** 483,489 **** + + #ifdef HAVE_SSMLIB + void +! graphics_info_t::print_ssm_sequence_alignment(CSSMAlign *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +--- 487,493 ---- + + #ifdef HAVE_SSMLIB + void +! graphics_info_t::print_ssm_sequence_alignment(ssm::Align *SSMAlign, + atom_selection_container_t asc_ref, + atom_selection_container_t asc_mov, + PCAtom *atom_selection1, PCAtom *atom_selection2, +diff -crB ./src/molecule-class-info-ncs.cc ../coot-patched/src/molecule-class-info-ncs.cc +*** ./src/molecule-class-info-ncs.cc 2013-01-16 17:40:31.000000000 +0100 +--- ../coot-patched/src/molecule-class-info-ncs.cc 2013-07-25 04:44:45.450071527 +0200 +*************** +*** 51,56 **** +--- 51,57 ---- + + #ifdef HAVE_SSMLIB + #include "ssm_align.h" ++ #include "ssm_defs.h" + #endif + + // This is called by make_bonds_type_checked(), which is called by +*************** +*** 514,546 **** + if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) { + #ifdef HAVE_SSMLIB + +! int precision = SSMP_Normal; +! int connectivity = CSSC_Flexible; +! CSSMAlign *SSMAlign = new CSSMAlign(); +! int rc = SSMAlign->Align(atom_sel.mol, atom_sel.mol, + precision, connectivity, SelHandle2, SelHandle1); + + if (rc) { + std::string ws; + switch (rc) { +! case SSM_noHits : + std::cout << " *** secondary structure does not match.\n"; + ws = "secondary structure does not match"; + break; +! case SSM_noSPSN : + std::cout << " *** structures are too remote.\n"; + ws = "structures are too remote"; + break; +! case SSM_noGraph : + std::cout << " *** can't make graph for 1\n"; + break; +! case SSM_noVertices : + std::cout << " *** empty graph for 1\n"; + break; +! case SSM_noGraph2 : + std::cout << " *** can't make graph for 2\n"; + break; +! case SSM_noVertices2 : + std::cout << " *** empty graph for 2\n"; + break; + default : +--- 515,547 ---- + if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) { + #ifdef HAVE_SSMLIB + +! ssm::PRECISION precision = ssm::PREC_Normal; +! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible; +! ssm::Align *SSMAlign = new ssm::Align(); +! int rc = SSMAlign->align(atom_sel.mol, atom_sel.mol, + precision, connectivity, SelHandle2, SelHandle1); + + if (rc) { + std::string ws; + switch (rc) { +! case ssm::RC_NoHits : + std::cout << " *** secondary structure does not match.\n"; + ws = "secondary structure does not match"; + break; +! case ssm::RC_NoSuperposition : + std::cout << " *** structures are too remote.\n"; + ws = "structures are too remote"; + break; +! case ssm::RC_NoGraph : + std::cout << " *** can't make graph for 1\n"; + break; +! case ssm::RC_NoVertices : + std::cout << " *** empty graph for 1\n"; + break; +! case ssm::RC_NoGraph2 : + std::cout << " *** can't make graph for 2\n"; + break; +! case ssm::RC_NoVertices2 : + std::cout << " *** empty graph for 2\n"; + break; + default : diff --git a/coot.spec b/coot.spec index 9c5a112..4e9e071 100644 --- a/coot.spec +++ b/coot.spec @@ -5,15 +5,15 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7 -Release: 3.20120929svn4458%{?dist} +Release: 4.20120929svn4458%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering # The source for this package was pulled from upstream's vcs. Use the # following commands to generate the tarball: -# svn co -r 4458 http://coot.googlecode.com/svn/trunk coot-0.7 -# tar cvzf coot-0.7-20120929svn4458.tar.gz coot-0.7 -Source0: coot-0.7-20120929svn4458.tar.gz +# svn export -r 4458 http://coot.googlecode.com/svn/trunk coot-0.7 +# tar cvJf coot-0.7-20120929svn4458.tar.xz coot-0.7 +Source0: coot-0.7-20120929svn4458.tar.xz Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz Source2: svn-revision.cc Source3: coot.in @@ -24,6 +24,8 @@ Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch Patch2: coot-unistd.patch Patch3: coot-makefile.patch +Patch4: coot-ssm1.3.patch +Patch5: coot-guile.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 @@ -33,7 +35,7 @@ BuildRequires: goocanvas-devel BuildRequires: gsl-devel BuildRequires: gtk2-devel BuildRequires: gtkglext-devel -BuildRequires: guile-devel +BuildRequires: compat-guile18-devel BuildRequires: guile-lib BuildRequires: imlib-devel BuildRequires: libcurl-devel @@ -51,6 +53,7 @@ BuildRequires: tetex-latex BuildRequires: tex(latex) %endif BuildRequires: texinfo-tex +Requires: compat-guile18 Requires: refmac-dictionary %description @@ -88,6 +91,8 @@ package. %patch1 -p0 %patch2 -p0 %patch3 -p0 +%patch4 -p0 +%patch5 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} ./src/ @@ -181,6 +186,11 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Fri Aug 09 2013 Tim Fenn - 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 - 0.7-3.20120929svn4458 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild diff --git a/sources b/sources index b66edf2..cc72b65 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -58bef4c0c0661c770b5f3710692fca8a coot-0.7-20120929svn4458.tar.gz +2f424c13248b98c23e7d5e0591fb3a28 coot-0.7-20120929svn4458.tar.xz 59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz From bde6e4f814358325abb446974958c7d4b37f2e0f Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sun, 11 Aug 2013 23:57:03 -0700 Subject: [PATCH 22/43] * Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 - add ghostscript to buildrequires --- coot.spec | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 4e9e071..8f4cee4 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7 -Release: 4.20120929svn4458%{?dist} +Release: 5.20120929svn4458%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -53,6 +53,7 @@ BuildRequires: tetex-latex BuildRequires: tex(latex) %endif BuildRequires: texinfo-tex +BuildRequires: ghostscript Requires: compat-guile18 Requires: refmac-dictionary @@ -186,6 +187,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 +- add ghostscript to buildrequires + * Fri Aug 09 2013 Tim Fenn - 0.7-4.20120929svn4458 - use xz instead of gz (BZ 982385) - update for soname bump in deps (BZ 989141) From b9eca4416c4124c957a6b68f14969ed8ee6dcb24 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sat, 28 Dec 2013 12:07:05 -0800 Subject: [PATCH 23/43] - update to 0.7.2 - update upstream URLs, no longer using vcs --- .gitignore | 2 + coot-configure.in.patch | 13 +- coot-ssm1.3.patch | 322 ------------------------------------ coot-user-manual.texi.patch | 19 ++- coot.spec | 22 +-- sources | 4 +- svn-revision.cc | 6 - 7 files changed, 31 insertions(+), 357 deletions(-) delete mode 100644 coot-ssm1.3.patch delete mode 100644 svn-revision.cc diff --git a/.gitignore b/.gitignore index 7253be0..12341f3 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,5 @@ coot-reference-structures.tar.gz /coot-0.6.2-20110715svn3566.tar.gz /coot-0.7-20120929svn4458.tar.gz /coot-0.7-20120929svn4458.tar.xz +/coot-0.7.2.tar.gz +/reference-structures.tar.gz diff --git a/coot-configure.in.patch b/coot-configure.in.patch index 13d55f4..0e5145d 100644 --- a/coot-configure.in.patch +++ b/coot-configure.in.patch @@ -1,6 +1,6 @@ ---- configure.in_orig 2012-09-29 18:54:43.410146251 -0700 -+++ configure.in 2012-09-29 18:59:46.669993583 -0700 -@@ -104,13 +104,28 @@ +--- configure.in_orig 2013-12-27 13:49:54.395522721 -0800 ++++ configure.in 2013-12-27 13:52:48.927324774 -0800 +@@ -108,14 +108,24 @@ dnl Check for MMDB. @@ -8,17 +8,14 @@ +# AM_PATH_MMDB(, [echo Error locating necessary mmdb; exit 1],,) -AM_WITH_MMDBSSM +-AM_WITH_CCP4SRS +# AM_WITH_MMDBSSM ++# AM_WITH_CCP4SRS + +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. # diff --git a/coot-ssm1.3.patch b/coot-ssm1.3.patch deleted file mode 100644 index 0b78f02..0000000 --- a/coot-ssm1.3.patch +++ /dev/null @@ -1,322 +0,0 @@ -diff -crB ./src/graphics-info.h ../coot-patched/src/graphics-info.h -*** ./src/graphics-info.h 2013-04-27 16:04:58.000000000 +0200 ---- ../coot-patched/src/graphics-info.h 2013-07-25 04:09:17.861265837 +0200 -*************** -*** 3307,3313 **** - short int move_copy_of_imol2_flag); - - #ifdef HAVE_SSMLIB -! void print_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, ---- 3307,3313 ---- - short int move_copy_of_imol2_flag); - - #ifdef HAVE_SSMLIB -! void print_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, -*************** -*** 3315,3321 **** - int n_selected_atoms_1, int n_selected_atoms_2, - short int move_copy_of_imol2_flag); - -! void make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, ---- 3315,3321 ---- - int n_selected_atoms_1, int n_selected_atoms_2, - short int move_copy_of_imol2_flag); - -! void make_and_print_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, -*************** -*** 3325,3331 **** - void print_horizontal_ssm_sequence_alignment(std::pair aligned_sequences) const; - - std::pair -! get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, ---- 3325,3331 ---- - void print_horizontal_ssm_sequence_alignment(std::pair aligned_sequences) const; - - std::pair -! get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, -diff -crB ./src/graphics-info-superpose.cc ../coot-patched/src/graphics-info-superpose.cc -*** ./src/graphics-info-superpose.cc 2013-01-16 17:40:31.000000000 +0100 ---- ../coot-patched/src/graphics-info-superpose.cc 2013-07-25 04:42:47.876256551 +0200 -*************** -*** 22,27 **** ---- 22,31 ---- - #include "Python.h" // before system includes to stop "POSIX_C_SOURCE" redefined problems - #endif - -+ #ifdef HAVE_SSMLIB -+ #include "ssm_defs.h" -+ #endif -+ - #if defined _MSC_VER - #include - #endif -*************** -*** 168,179 **** - - #ifdef HAVE_SSMLIB - -! int precision = SSMP_Normal; -! int connectivity = CSSC_Flexible; - - // probably not necessary, not sure: -! SetSSConnectivityCheck ( CSSC_Flexible ); -! SetSSMatchPrecision ( SSMP_Normal ); - - if (asc_ref.n_selected_atoms > 0) { - if (asc_mov.n_selected_atoms > 0) { ---- 172,183 ---- - - #ifdef HAVE_SSMLIB - -! ssm::PRECISION precision = ssm::PREC_Normal; -! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible; - - // probably not necessary, not sure: -! ssm::SetConnectivityCheck ( ssm::CONNECT_Flexible ); -! ssm::SetMatchPrecision ( ssm::PREC_Normal ); - - if (asc_ref.n_selected_atoms > 0) { - if (asc_mov.n_selected_atoms > 0) { -*************** -*** 199,234 **** - - // Remove the pointer one day. - // -! CSSMAlign *SSMAlign = new CSSMAlign(); -! int rc = SSMAlign->Align(mol2, mol1, precision, connectivity, - asc_mov.SelectionHandle, - asc_ref.SelectionHandle); - - if (rc) { - std::string ws; - switch (rc) { -! case SSM_noHits : - std::cout << " *** secondary structure does not match.\n"; - ws = "secondary structure does not match"; - break; -! case SSM_noSPSN : - std::cout << " *** structures are too remote.\n"; - ws = "structures are too remote"; - break; -! case SSM_noGraph : - std::cout << " *** can't make graph for " << name1 << "\n"; - ws = "can't make graph for " + name1; - ws += " structure"; - break; -! case SSM_noVertices : - std::cout << " *** empty graph for " << name1 << "\n"; - ws = "empty graph for " + name1; - break; -! case SSM_noGraph2 : - std::cout << " *** can't make graph for " << name2 << "\n"; - ws = "can't make graph for " + name2; - break; -! case SSM_noVertices2 : - std::cout << " *** empty graph for " << name2 << "\n"; - ws = "empty graph for " + name2; - break; ---- 203,238 ---- - - // Remove the pointer one day. - // -! ssm::Align *SSMAlign = new ssm::Align(); -! int rc = SSMAlign->align(mol2, mol1, precision, connectivity, - asc_mov.SelectionHandle, - asc_ref.SelectionHandle); - - if (rc) { - std::string ws; - switch (rc) { -! case ssm::RC_NoHits : - std::cout << " *** secondary structure does not match.\n"; - ws = "secondary structure does not match"; - break; -! case ssm::RC_NoSuperposition : - std::cout << " *** structures are too remote.\n"; - ws = "structures are too remote"; - break; -! case ssm::RC_NoGraph : - std::cout << " *** can't make graph for " << name1 << "\n"; - ws = "can't make graph for " + name1; - ws += " structure"; - break; -! case ssm::RC_NoVertices : - std::cout << " *** empty graph for " << name1 << "\n"; - ws = "empty graph for " + name1; - break; -! case ssm::RC_NoGraph2 : - std::cout << " *** can't make graph for " << name2 << "\n"; - ws = "can't make graph for " + name2; - break; -! case ssm::RC_NoVertices2 : - std::cout << " *** empty graph for " << name2 << "\n"; - ws = "empty graph for " + name2; - break; -*************** -*** 298,304 **** - // mat44 tmat; - // realtype rmsdAchieved, seqIdentity, nCombs; - // int nAligned, nGaps, nMisD; -! // CSuperpose Superpose; type in class CSSMAlign - // - // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2, - // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity, ---- 302,308 ---- - // mat44 tmat; - // realtype rmsdAchieved, seqIdentity, nCombs; - // int nAligned, nGaps, nMisD; -! // CSuperpose Superpose; type in class ssm::Align - // - // Superpose->GetSuperposition(Ca1, dist1, nCa1, Ca2, - // nCa2, tmat, rmsdAchieved, nAligned, nGaps, seqIdentity, -*************** -*** 331,337 **** - - #ifdef HAVE_SSMLIB - void -! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, ---- 335,341 ---- - - #ifdef HAVE_SSMLIB - void -! graphics_info_t::make_and_print_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, -*************** -*** 394,400 **** - - #ifdef HAVE_SSMLIB - std::pair -! graphics_info_t::get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, ---- 398,404 ---- - - #ifdef HAVE_SSMLIB - std::pair -! graphics_info_t::get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, -*************** -*** 483,489 **** - - #ifdef HAVE_SSMLIB - void -! graphics_info_t::print_ssm_sequence_alignment(CSSMAlign *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, ---- 487,493 ---- - - #ifdef HAVE_SSMLIB - void -! graphics_info_t::print_ssm_sequence_alignment(ssm::Align *SSMAlign, - atom_selection_container_t asc_ref, - atom_selection_container_t asc_mov, - PCAtom *atom_selection1, PCAtom *atom_selection2, -diff -crB ./src/molecule-class-info-ncs.cc ../coot-patched/src/molecule-class-info-ncs.cc -*** ./src/molecule-class-info-ncs.cc 2013-01-16 17:40:31.000000000 +0100 ---- ../coot-patched/src/molecule-class-info-ncs.cc 2013-07-25 04:44:45.450071527 +0200 -*************** -*** 51,56 **** ---- 51,57 ---- - - #ifdef HAVE_SSMLIB - #include "ssm_align.h" -+ #include "ssm_defs.h" - #endif - - // This is called by make_bonds_type_checked(), which is called by -*************** -*** 514,546 **** - if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) { - #ifdef HAVE_SSMLIB - -! int precision = SSMP_Normal; -! int connectivity = CSSC_Flexible; -! CSSMAlign *SSMAlign = new CSSMAlign(); -! int rc = SSMAlign->Align(atom_sel.mol, atom_sel.mol, - precision, connectivity, SelHandle2, SelHandle1); - - if (rc) { - std::string ws; - switch (rc) { -! case SSM_noHits : - std::cout << " *** secondary structure does not match.\n"; - ws = "secondary structure does not match"; - break; -! case SSM_noSPSN : - std::cout << " *** structures are too remote.\n"; - ws = "structures are too remote"; - break; -! case SSM_noGraph : - std::cout << " *** can't make graph for 1\n"; - break; -! case SSM_noVertices : - std::cout << " *** empty graph for 1\n"; - break; -! case SSM_noGraph2 : - std::cout << " *** can't make graph for 2\n"; - break; -! case SSM_noVertices2 : - std::cout << " *** empty graph for 2\n"; - break; - default : ---- 515,547 ---- - if (graphics_info_t::ncs_matrix_flag == coot::NCS_SSM) { - #ifdef HAVE_SSMLIB - -! ssm::PRECISION precision = ssm::PREC_Normal; -! ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible; -! ssm::Align *SSMAlign = new ssm::Align(); -! int rc = SSMAlign->align(atom_sel.mol, atom_sel.mol, - precision, connectivity, SelHandle2, SelHandle1); - - if (rc) { - std::string ws; - switch (rc) { -! case ssm::RC_NoHits : - std::cout << " *** secondary structure does not match.\n"; - ws = "secondary structure does not match"; - break; -! case ssm::RC_NoSuperposition : - std::cout << " *** structures are too remote.\n"; - ws = "structures are too remote"; - break; -! case ssm::RC_NoGraph : - std::cout << " *** can't make graph for 1\n"; - break; -! case ssm::RC_NoVertices : - std::cout << " *** empty graph for 1\n"; - break; -! case ssm::RC_NoGraph2 : - std::cout << " *** can't make graph for 2\n"; - break; -! case ssm::RC_NoVertices2 : - std::cout << " *** empty graph for 2\n"; - break; - default : diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch index fc2a45a..c4ad336 100644 --- a/coot-user-manual.texi.patch +++ b/coot-user-manual.texi.patch @@ -1,11 +1,20 @@ ---- doc/coot-user-manual.texi_orig 2012-09-29 19:50:40.386652186 -0700 -+++ doc/coot-user-manual.texi 2012-09-30 15:42:36.830651836 -0700 -@@ -4942,10 +4942,10 @@ +--- doc/coot-user-manual.texi_orig 2013-12-27 15:59:56.897931023 -0800 ++++ doc/coot-user-manual.texi 2013-12-27 16:22:22.207559590 -0800 +@@ -47,7 +47,7 @@ + + @vskip 10mm + +-@image{coot-plain-2,127mm} ++@c @image{coot-plain-2,127mm} + + + @c The following two commands start the copyright page. +@@ -4951,10 +4951,10 @@ @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 ++@c @include c-interface.h.texi @node More Scripting Functions @chapter More Scripting Functions -@include cc-interface.hh.texi @@ -13,7 +22,7 @@ -@@ -4963,7 +4963,7 @@ +@@ -4972,7 +4972,7 @@ @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node @c diff --git a/coot.spec b/coot.spec index 8f4cee4..489e77a 100644 --- a/coot.spec +++ b/coot.spec @@ -4,18 +4,13 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ -Version: 0.7 -Release: 5.20120929svn4458%{?dist} +Version: 0.7.2 +Release: 1%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering -# The source for this package was pulled from upstream's vcs. Use the -# following commands to generate the tarball: -# svn export -r 4458 http://coot.googlecode.com/svn/trunk coot-0.7 -# tar cvJf coot-0.7-20120929svn4458.tar.xz coot-0.7 -Source0: coot-0.7-20120929svn4458.tar.xz -Source1: http://www.ysbl.york.ac.uk/~emsley/software/%{name}-reference-structures.tar.gz -Source2: svn-revision.cc +Source0: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/%{name}-%{version}.tar.gz +Source1: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz Source3: coot.in Source4: %{name}.png Source5: %{name}.desktop @@ -24,7 +19,6 @@ Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch Patch2: coot-unistd.patch Patch3: coot-makefile.patch -Patch4: coot-ssm1.3.patch Patch5: coot-guile.patch BuildRequires: autoconf BuildRequires: automake @@ -92,15 +86,11 @@ package. %patch1 -p0 %patch2 -p0 %patch3 -p0 -%patch4 -p0 %patch5 -p0 -cp %{SOURCE2} ./src/ 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 aclocal -I macros @@ -187,6 +177,10 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Fri Dec 27 2013 Tim Fenn - 0.7.2-1 +- update to 0.7.2 +- update upstream URLs, no longer using vcs + * Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 - add ghostscript to buildrequires diff --git a/sources b/sources index cc72b65..fd5a2e7 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -2f424c13248b98c23e7d5e0591fb3a28 coot-0.7-20120929svn4458.tar.xz -59df05751b1ab445a6517757a1ace302 coot-reference-structures.tar.gz +0e240393b0e41bba71dc45045c266bb5 coot-0.7.2.tar.gz +257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz diff --git a/svn-revision.cc b/svn-revision.cc deleted file mode 100644 index 772cd89..0000000 --- a/svn-revision.cc +++ /dev/null @@ -1,6 +0,0 @@ -extern "C" { -int svn_revision() { - return 4458; -} -} - From 169f8d5fe53696396abad273e6bfcc8839997577 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 7 Jun 2014 00:53:18 -0500 Subject: [PATCH 24/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 489e77a..2b964ac 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7.2 -Release: 1%{?dist} +Release: 2%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -177,6 +177,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Jun 07 2014 Fedora Release Engineering - 0.7.2-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + * Fri Dec 27 2013 Tim Fenn - 0.7.2-1 - update to 0.7.2 - update upstream URLs, no longer using vcs From e4e57c79683e6219aa61c1dde193958fbca8ea13 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Sat, 16 Aug 2014 01:16:17 +0000 Subject: [PATCH 25/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 2b964ac..0f95ce2 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www.biop.ox.ac.uk/coot/ Version: 0.7.2 -Release: 2%{?dist} +Release: 3%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -177,6 +177,9 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Aug 16 2014 Fedora Release Engineering - 0.7.2-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + * Sat Jun 07 2014 Fedora Release Engineering - 0.7.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild From c53deb08fa8a031dce5b2528ddece24834e2177f Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sun, 1 Feb 2015 19:51:25 -0500 Subject: [PATCH 26/43] 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 --- .gitignore | 1 + coot-configure.in.patch | 42 +++++++----------------- coot-makefile.patch | 43 +++++++++++++++++++----- coot.desktop | 2 +- coot.in | 4 +-- coot.spec | 72 +++++++++++++++++++++++++---------------- sources | 2 +- 7 files changed, 96 insertions(+), 70 deletions(-) diff --git a/.gitignore b/.gitignore index 12341f3..d776400 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ coot-reference-structures.tar.gz /coot-0.7-20120929svn4458.tar.xz /coot-0.7.2.tar.gz /reference-structures.tar.gz +/coot-0.8.1.tar.gz diff --git a/coot-configure.in.patch b/coot-configure.in.patch index 0e5145d..134cad5 100644 --- a/coot-configure.in.patch +++ b/coot-configure.in.patch @@ -1,31 +1,11 @@ ---- configure.in_orig 2013-12-27 13:49:54.395522721 -0800 -+++ configure.in 2013-12-27 13:52:48.927324774 -0800 -@@ -108,14 +108,24 @@ - - - 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_CCP4SRS -+# AM_WITH_MMDBSSM -+# AM_WITH_CCP4SRS -+ -+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) - - 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=$CLIPPER_CFLAGS -+AC_SUBST(CLIPPER_CXXFLAGS) -+AC_SUBST(CLIPPER_LIBS) - - # we set default coot_guile to true - coot_guile=true +--- configure.in_orig 2015-01-31 15:55:07.102736249 -0500 ++++ configure.in 2015-02-01 13:23:47.715379636 -0500 +@@ -135,7 +135,7 @@ + AM_WITH_GUILE(, [echo optional guile\?],,) + if test x$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 diff --git a/coot-makefile.patch b/coot-makefile.patch index ea5c34e..bed8e58 100644 --- a/coot-makefile.patch +++ b/coot-makefile.patch @@ -1,10 +1,37 @@ ---- lbg/Makefile.am_orig 2012-09-30 15:59:54.245707927 -0700 -+++ lbg/Makefile.am 2012-09-30 16:04:07.908430902 -0700 -@@ -68,6 +68,7 @@ - $(top_builddir)/lidia-core/libcoot-lidia-core.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/utils/libcoot-utils.la \ -+ $(PYTHON_LIBS) \ - $(RDKIT_LIBS) +--- pixmaps/icons/Makefile.am_orig 2015-02-01 13:55:55.730388444 -0500 ++++ pixmaps/icons/Makefile.am 2015-02-01 13:59:40.274738333 -0500 +@@ -2,8 +2,10 @@ + EXTRA_DIST = hicolor_apps_48x48_coot.png \ + hicolor_apps_64x64_coot.png \ + hicolor_apps_96x96_coot.png \ +- hicolor_apps_256x256_coot.png \ +- hicolor_apps_scalable_coot.svg ++ hicolor_apps_256x256_coot.png ++ ++appicondir=$(datadir)/icons/hicolor/scalable/apps ++appicon_DATA=hicolor_apps_scalable_coot.svg + + install-data-local: + for icon in $(EXTRA_DIST); do \ +@@ -11,6 +13,6 @@ + CONTEXT=` echo $$icon | cut -d_ -f2`; \ + SIZE=` echo $$icon | cut -d_ -f3`; \ + ICONFILE=`echo $$icon | cut -d_ -f4`; \ +- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ +- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ ++ mkdir -p $(DESTDIR)$(pkgdatadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ ++ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(pkgdatadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ + done; +--- src/Makefile.am_orig 2015-02-01 16:22:23.022449682 -0500 ++++ src/Makefile.am 2015-02-01 16:34:38.213828758 -0500 +@@ -27,8 +27,8 @@ + #__init__.py: coot.py + # cp coot.py __init__.py + +- +-dist_python_SCRIPTS = coot.py coot.pth ++pythondir = $(pkgdatadir)/python ++dist_pkgpython_SCRIPTS = coot.py + endif diff --git a/coot.desktop b/coot.desktop index 79a76c6..885607d 100644 --- a/coot.desktop +++ b/coot.desktop @@ -4,7 +4,7 @@ Name=coot GenericName=coot Comment=macromolecular model builder Exec=coot -Icon=coot +Icon=hicolor_apps_scalable_coot.svg Terminal=false Type=Application Categories=Graphics;Science diff --git a/coot.in b/coot.in index bff0148..7c2b35f 100755 --- a/coot.in +++ b/coot.in @@ -5,9 +5,9 @@ # written by Paul Emsley COOT_PREFIX="@prefix@" -current_exe_dir="@bindir@" +current_exe_dir="@libexecdir@" -coot_real=$current_exe_dir/coot-real +coot_real=$current_exe_dir/coot-bin # echo coot-real is at $coot_real # ---------------------------------------------------------------------------- diff --git a/coot.spec b/coot.spec index 0f95ce2..78f373e 100644 --- a/coot.spec +++ b/coot.spec @@ -3,27 +3,26 @@ Name: coot Summary: The crystallographic object-oriented toolkit -URL: http://www.biop.ox.ac.uk/coot/ -Version: 0.7.2 -Release: 3%{?dist} +URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ +Version: 0.8.1 +Release: 1%{?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 Source1: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/reference-structures.tar.gz -Source3: coot.in -Source4: %{name}.png -Source5: %{name}.desktop -Source6: __init__.py +Source2: coot.in +Source3: %{name}.desktop +Source4: __init__.py Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch -Patch2: coot-unistd.patch -Patch3: coot-makefile.patch -Patch5: coot-guile.patch +Patch2: coot-makefile.patch +Patch3: coot-guile.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 BuildRequires: desktop-file-utils +BuildRequires: libappstream-glib BuildRequires: freeglut-devel BuildRequires: goocanvas-devel BuildRequires: gsl-devel @@ -35,7 +34,7 @@ BuildRequires: imlib-devel BuildRequires: libcurl-devel BuildRequires: libgnomecanvas-devel BuildRequires: libtool -BuildRequires: mmdb-devel >= 1.19 +BuildRequires: mmdb2-devel BuildRequires: python-devel BuildRequires: pygtk2-devel BuildRequires: refmac-dictionary @@ -86,9 +85,9 @@ package. %patch1 -p0 %patch2 -p0 %patch3 -p0 -%patch5 -p0 -cp %{SOURCE3} ./src/ +cp %{SOURCE2} ./src/ +cp %{SOURCE3} . # various cleanups iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README @@ -99,8 +98,8 @@ autoconf automake --copy --add-missing --gnu %build -%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" - +mkdir guile +%configure --with-guile --with-python --with-pygtk --with-goocanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb2 -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" GUILE_LOAD_PATH="$GUILE_LOAD_PATH:/tmp/guile" 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 @@ -115,6 +114,7 @@ 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=%{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}/ @@ -123,25 +123,24 @@ install -p -m 755 src/coot %{buildroot}%{_bindir}/ rm -f %{buildroot}%{_libdir}/*.la # headers -mkdir %{buildroot}%{_includedir}/coot -mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ -mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ +# mkdir %{buildroot}%{_includedir}/coot +# mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ +# mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ # python stuff -mkdir -p %{buildroot}%{python_sitelib}/coot -mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/ +# mkdir -p %{buildroot}%{python_sitelib}/coot +# mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/ for lib in $(find %{buildroot}%{python_sitelib}/coot/ -name "*.py"); do sed '/\/usr\/bin\/env/d' $lib > $lib.new && touch -r $lib $lib.new && mv $lib.new $lib done -cp %{SOURCE6} %{buildroot}%{python_sitelib}/coot/ +cp %{SOURCE4} %{buildroot}%{python_sitelib}/coot/ chmod 644 %{buildroot}%{python_sitelib}/coot/coot.py # desktop file -desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications %{SOURCE5} -mkdir -p %{buildroot}%{_datadir}/pixmaps -install -p -m 644 %{SOURCE4} %{buildroot}%{_datadir}/pixmaps/ +desktop-file-install --vendor='' --dir=%{buildroot}%{_datadir}/applications coot.desktop +appstream-util validate-relax --nonet %{buildroot}/%{_datadir}/appdata/*.appdata.xml %clean rm -rf %{buildroot} @@ -150,21 +149,33 @@ rm -rf %{buildroot} make check # %{buildroot}%{_bindir}/coot-real --no-graphics --script python-tests/coot_unittest.py -%post -p /sbin/ldconfig +%post +/sbin/ldconfig +/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || : -%postun -p /sbin/ldconfig +%postun +/sbin/ldconfig +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 + +%posttrans +/usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || : %files %defattr(-,root,root,-) %doc AUTHORS README COPYING %{_bindir}/* +%{_libexecdir}/* # 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 +%{_datadir}/appdata/%{name}.appdata.xml +%{_datadir}/icons/hicolor/scalable/apps/hicolor_apps_scalable_coot.svg %{python_sitelib}/coot/ %files devel @@ -177,6 +188,13 @@ make check %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Jan 31 2015 Tim Fenn - 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 - 0.7.2-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild diff --git a/sources b/sources index fd5a2e7..4cd430d 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -0e240393b0e41bba71dc45045c266bb5 coot-0.7.2.tar.gz +f6be9a46cd5927decd1ef0f4ace5da7a coot-0.8.1.tar.gz 257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz From 5a1e066879e06761642e8e1ded4aa2c3d0f97dd5 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 17 Jun 2015 03:14:22 +0000 Subject: [PATCH 27/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 78f373e..0f325b8 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.1 -Release: 1%{?dist} +Release: 2%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -188,6 +188,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Jun 17 2015 Fedora Release Engineering - 0.8.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + * Sat Jan 31 2015 Tim Fenn - 0.8.1-1 - update to 0.8.1 - update URL From 53c12983b575dacc6ead8183b874161457e88096 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Mon, 29 Jun 2015 23:49:58 -0400 Subject: [PATCH 28/43] fix to appdata.xml - add all icon pixmaps, edit desktop file to match --- coot-appdata.patch | 24 ++++++++++++++++++++++++ coot-makefile.patch | 44 ++++++++++++++++---------------------------- coot.desktop | 2 +- coot.spec | 10 ++++++++-- 4 files changed, 49 insertions(+), 31 deletions(-) create mode 100644 coot-appdata.patch diff --git a/coot-appdata.patch b/coot-appdata.patch new file mode 100644 index 0000000..d472d3d --- /dev/null +++ b/coot-appdata.patch @@ -0,0 +1,24 @@ +--- coot.appdata.xml_orig 2015-06-28 23:45:07.527132520 -0400 ++++ coot.appdata.xml 2015-06-29 23:44:38.374147150 -0400 +@@ -1,10 +1,11 @@ + + +- +- Coot.desktop ++ ++ coot.desktop + GFDL-1.3 +- GPL-2.0+ and GPL-3.0+ and LGPL-3.0+ +- Macromolecular model builder ++ GPLv3+ and LGPLv2+ ++ Coot ++ Protein model building and validation for X-ray crystallographic data + +

+ Coot is a powerful macromolecular model-building tool for +@@ -26,4 +27,4 @@ + + http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ + pemsley _at_ mrc dash lmb.cam.ac.uk +- ++ diff --git a/coot-makefile.patch b/coot-makefile.patch index bed8e58..4cf9922 100644 --- a/coot-makefile.patch +++ b/coot-makefile.patch @@ -1,37 +1,25 @@ ---- pixmaps/icons/Makefile.am_orig 2015-02-01 13:55:55.730388444 -0500 -+++ pixmaps/icons/Makefile.am 2015-02-01 13:59:40.274738333 -0500 -@@ -2,8 +2,10 @@ - EXTRA_DIST = hicolor_apps_48x48_coot.png \ - hicolor_apps_64x64_coot.png \ - hicolor_apps_96x96_coot.png \ -- hicolor_apps_256x256_coot.png \ -- hicolor_apps_scalable_coot.svg -+ hicolor_apps_256x256_coot.png -+ -+appicondir=$(datadir)/icons/hicolor/scalable/apps -+appicon_DATA=hicolor_apps_scalable_coot.svg - - install-data-local: - for icon in $(EXTRA_DIST); do \ -@@ -11,6 +13,6 @@ - CONTEXT=` echo $$icon | cut -d_ -f2`; \ - SIZE=` echo $$icon | cut -d_ -f3`; \ - ICONFILE=`echo $$icon | cut -d_ -f4`; \ -- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ -+ mkdir -p $(DESTDIR)$(pkgdatadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -+ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(pkgdatadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ - done; ---- src/Makefile.am_orig 2015-02-01 16:22:23.022449682 -0500 -+++ src/Makefile.am 2015-02-01 16:34:38.213828758 -0500 -@@ -27,8 +27,8 @@ +--- src/Makefile.am_orig 2015-06-29 23:10:49.500572880 -0400 ++++ src/Makefile.am 2015-06-29 23:11:33.041822617 -0400 +@@ -27,9 +27,8 @@ #__init__.py: coot.py # cp coot.py __init__.py - -dist_python_SCRIPTS = coot.py coot.pth +- +pythondir = $(pkgdatadir)/python +dist_pkgpython_SCRIPTS = coot.py - endif + +--- pixmaps/icons/Makefile.am_orig 2015-06-29 23:11:55.713911249 -0400 ++++ pixmaps/icons/Makefile.am 2015-06-29 23:26:22.902239461 -0400 +@@ -11,6 +11,6 @@ + CONTEXT=` echo $$icon | cut -d_ -f2`; \ + SIZE=` echo $$icon | cut -d_ -f3`; \ + ICONFILE=`echo $$icon | cut -d_ -f4`; \ +- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ +- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ ++ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ ++ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ + done; diff --git a/coot.desktop b/coot.desktop index 885607d..79a76c6 100644 --- a/coot.desktop +++ b/coot.desktop @@ -4,7 +4,7 @@ Name=coot GenericName=coot Comment=macromolecular model builder Exec=coot -Icon=hicolor_apps_scalable_coot.svg +Icon=coot Terminal=false Type=Application Categories=Graphics;Science diff --git a/coot.spec b/coot.spec index 0f325b8..dd5e368 100644 --- a/coot.spec +++ b/coot.spec @@ -5,7 +5,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.1 -Release: 2%{?dist} +Release: 3%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -18,6 +18,7 @@ Patch0: coot-configure.in.patch Patch1: coot-user-manual.texi.patch Patch2: coot-makefile.patch Patch3: coot-guile.patch +Patch4: coot-appdata.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 @@ -85,6 +86,7 @@ package. %patch1 -p0 %patch2 -p0 %patch3 -p0 +%patch4 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} . @@ -175,7 +177,7 @@ fi %{_datadir}/coot/ %{_datadir}/applications/%{name}.desktop %{_datadir}/appdata/%{name}.appdata.xml -%{_datadir}/icons/hicolor/scalable/apps/hicolor_apps_scalable_coot.svg +%{_datadir}/icons/hicolor/ %{python_sitelib}/coot/ %files devel @@ -188,6 +190,10 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sun Jun 28 2015 Tim Fenn - 0.8.1-3 +- fix to appdata.xml +- add all icon pixmaps, edit desktop file to match + * Wed Jun 17 2015 Fedora Release Engineering - 0.8.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild From 435229e22dc3a6af4fea58c54a081fc41a6d857e Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 24 Sep 2015 22:37:57 -0400 Subject: [PATCH 29/43] update to 0.8.2 - add patch for coot-utils --- .gitignore | 1 + ...figure.in.patch => coot-configure.ac.patch | 4 +-- coot-utils.patch | 31 +++++++++++++++++++ coot.spec | 14 ++++++--- sources | 3 +- 5 files changed, 45 insertions(+), 8 deletions(-) rename coot-configure.in.patch => coot-configure.ac.patch (73%) create mode 100644 coot-utils.patch diff --git a/.gitignore b/.gitignore index d776400..576b573 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,4 @@ coot-reference-structures.tar.gz /coot-0.7.2.tar.gz /reference-structures.tar.gz /coot-0.8.1.tar.gz +/coot-0.8.2.tar.gz diff --git a/coot-configure.in.patch b/coot-configure.ac.patch similarity index 73% rename from coot-configure.in.patch rename to coot-configure.ac.patch index 134cad5..c9a35b3 100644 --- a/coot-configure.in.patch +++ b/coot-configure.ac.patch @@ -1,5 +1,5 @@ ---- configure.in_orig 2015-01-31 15:55:07.102736249 -0500 -+++ configure.in 2015-02-01 13:23:47.715379636 -0500 +--- configure.ac_orig 2015-01-31 15:55:07.102736249 -0500 ++++ configure.ac 2015-02-01 13:23:47.715379636 -0500 @@ -135,7 +135,7 @@ AM_WITH_GUILE(, [echo optional guile\?],,) if test x$coot_guile = xtrue ; then diff --git a/coot-utils.patch b/coot-utils.patch new file mode 100644 index 0000000..458835e --- /dev/null +++ b/coot-utils.patch @@ -0,0 +1,31 @@ +--- coot-utils/Makefile.am_orig 2015-09-24 22:00:00.826912149 -0400 ++++ coot-utils/Makefile.am 2015-09-24 22:02:42.329117367 -0400 +@@ -116,7 +116,7 @@ + + + # test-agg-clust +-check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions test-tt-morph ++check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions + + # testshelxreader fails to link for some reason! coot::protein_geometry::get_h_bond_type + # testcootutils also. 20100812 Fixed now - added libcoot-geometry.la +--- coot-utils/coot-shelx.hh_orig 2015-09-24 22:00:31.889296059 -0400 ++++ coot-utils/coot-shelx.hh 2015-09-24 22:01:54.006864161 -0400 +@@ -33,6 +33,7 @@ + + #include + #include "clipper/core/cell.h" ++#include "coot-coord-utils.hh" + + namespace coot { + +--- coot-utils/coot-hole.hh_orig 2015-09-24 22:00:39.574533094 -0400 ++++ coot-utils/coot-hole.hh 2015-09-24 22:02:06.645417847 -0400 +@@ -3,6 +3,7 @@ + #include "clipper/core/coords.h" + #include "clipper/core/nxmap.h" + ++#include "coot-map-utils.hh" + #include "utils/coot-utils.hh" + #include "geometry/protein-geometry.hh" + diff --git a/coot.spec b/coot.spec index dd5e368..a690455 100644 --- a/coot.spec +++ b/coot.spec @@ -1,11 +1,10 @@ %{!?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: 0.8.1 -Release: 3%{?dist} +Version: 0.8.2 +Release: 1%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -14,11 +13,12 @@ Source1: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/refere Source2: coot.in Source3: %{name}.desktop Source4: __init__.py -Patch0: coot-configure.in.patch +Patch0: coot-configure.ac.patch Patch1: coot-user-manual.texi.patch Patch2: coot-makefile.patch Patch3: coot-guile.patch Patch4: coot-appdata.patch +Patch5: coot-utils.patch BuildRequires: autoconf BuildRequires: automake BuildRequires: clipper-devel >= 2.1-7 @@ -87,6 +87,7 @@ package. %patch2 -p0 %patch3 -p0 %patch4 -p0 +%patch5 -p0 cp %{SOURCE2} ./src/ cp %{SOURCE3} . @@ -101,6 +102,7 @@ automake --copy --add-missing --gnu %build mkdir guile +# -D_GLIBCXX_USE_CXX11_ABI=0 ? -std=c++11 %configure --with-guile --with-python --with-pygtk --with-goocanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb2 -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" GUILE_LOAD_PATH="$GUILE_LOAD_PATH:/tmp/guile" 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 @@ -190,6 +192,10 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon Sep 7 2015 Tim Fenn - 0.8.2-1 +- update to 0.8.2 +- add patch for coot-utils + * Sun Jun 28 2015 Tim Fenn - 0.8.1-3 - fix to appdata.xml - add all icon pixmaps, edit desktop file to match diff --git a/sources b/sources index 4cd430d..913a724 100644 --- a/sources +++ b/sources @@ -1,2 +1 @@ -f6be9a46cd5927decd1ef0f4ace5da7a coot-0.8.1.tar.gz -257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz +71a6653bedff7c764dea38289ef0e65c coot-0.8.2.tar.gz From 8c3862d0f8b1a764ae5b519ac1b4fdd605b86daf Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 24 Sep 2015 22:43:17 -0400 Subject: [PATCH 30/43] update to 0.8.2 - add patch for coot-utils --- sources | 1 + 1 file changed, 1 insertion(+) diff --git a/sources b/sources index 913a724..6037d9b 100644 --- a/sources +++ b/sources @@ -1 +1,2 @@ 71a6653bedff7c764dea38289ef0e65c coot-0.8.2.tar.gz +257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz From 25c883624833f2306a55899f8a49dcfa1119bafd Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 24 Sep 2015 23:18:12 -0400 Subject: [PATCH 31/43] update to 0.8.2 - add patch for coot-utils --- coot-makefile.patch | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/coot-makefile.patch b/coot-makefile.patch index 4cf9922..2188a96 100644 --- a/coot-makefile.patch +++ b/coot-makefile.patch @@ -23,3 +23,21 @@ + mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ + $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ done; +--- lbg/Makefile.am_orig 2015-09-24 23:04:49.843200580 -0400 ++++ lbg/Makefile.am 2015-09-24 23:10:03.355713678 -0400 +@@ -1,4 +1,3 @@ +- + lib_LTLIBRARIES=libcoot-lidia.la + + AM_CPPFLAGS = \ +@@ -53,8 +52,8 @@ + # 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) From 71e9a5fc73d89ba4fbf69c89f7fa8056395179e8 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Wed, 3 Feb 2016 18:06:43 +0000 Subject: [PATCH 32/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index a690455..3cc7d5d 100644 --- a/coot.spec +++ b/coot.spec @@ -4,7 +4,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.2 -Release: 1%{?dist} +Release: 2%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -192,6 +192,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Feb 03 2016 Fedora Release Engineering - 0.8.2-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + * Mon Sep 7 2015 Tim Fenn - 0.8.2-1 - update to 0.8.2 - add patch for coot-utils From 7475342a1d140c43fb5b6c5e195dda4e587844fa Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 22 Feb 2016 09:52:23 -0700 Subject: [PATCH 33/43] Rebuild for gsl 2.1 --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 3cc7d5d..a098b78 100644 --- a/coot.spec +++ b/coot.spec @@ -4,7 +4,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.2 -Release: 2%{?dist} +Release: 3%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see %files for breakdown) License: GPLv3+ and LGPLv2+ Group: Applications/Engineering @@ -192,6 +192,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon Feb 22 2016 Orion Poplawski - 0.8.2-3 +- Rebuild for gsl 2.1 + * Wed Feb 03 2016 Fedora Release Engineering - 0.8.2-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild From 576efa92af30657f4e13cbce855138dd6e8c422d Mon Sep 17 00:00:00 2001 From: Till Maas Date: Tue, 31 May 2016 23:19:12 +0200 Subject: [PATCH 34/43] 2016-05-31: Retired because of broken deps in preparation of Fedora 24 Reference: https://fedorahosted.org/rel-eng/ticket/6416 --- .gitignore | 14 -- __init__.py | 1 - coot-appdata.patch | 24 --- coot-configure.ac.patch | 11 -- coot-guile.patch | 27 --- coot-makefile.patch | 43 ----- coot-unistd.patch | 12 -- coot-user-manual.texi.patch | 33 ---- coot-utils.patch | 31 ---- coot.desktop | 10 -- coot.in | 62 ------- coot.png | Bin 1271 -> 0 bytes coot.spec | 349 ------------------------------------ dead.package | 3 + sources | 2 - 15 files changed, 3 insertions(+), 619 deletions(-) delete mode 100644 .gitignore delete mode 100644 __init__.py delete mode 100644 coot-appdata.patch delete mode 100644 coot-configure.ac.patch delete mode 100644 coot-guile.patch delete mode 100644 coot-makefile.patch delete mode 100644 coot-unistd.patch delete mode 100644 coot-user-manual.texi.patch delete mode 100644 coot-utils.patch delete mode 100644 coot.desktop delete mode 100755 coot.in delete mode 100644 coot.png delete mode 100644 coot.spec create mode 100644 dead.package delete mode 100644 sources diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 576b573..0000000 --- a/.gitignore +++ /dev/null @@ -1,14 +0,0 @@ -coot-0.6.1-20100127svn2740.tar.gz -coot-reference-structures.tar.gz -/coot-reference-structures.tar.gz -/coot-0.6.2-20101012svn3213.tar.gz -/coot-0.6.2-20110225svn3399.tar.gz -/coot-0.6.2-20110328svn3442.tar.gz -/coot-0.6.2-20110421svn3461.tar.gz -/coot-0.6.2-20110715svn3566.tar.gz -/coot-0.7-20120929svn4458.tar.gz -/coot-0.7-20120929svn4458.tar.xz -/coot-0.7.2.tar.gz -/reference-structures.tar.gz -/coot-0.8.1.tar.gz -/coot-0.8.2.tar.gz diff --git a/__init__.py b/__init__.py deleted file mode 100644 index 83d04e7..0000000 --- a/__init__.py +++ /dev/null @@ -1 +0,0 @@ -# File to allow this directory to be treated as a python package. diff --git a/coot-appdata.patch b/coot-appdata.patch deleted file mode 100644 index d472d3d..0000000 --- a/coot-appdata.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- coot.appdata.xml_orig 2015-06-28 23:45:07.527132520 -0400 -+++ coot.appdata.xml 2015-06-29 23:44:38.374147150 -0400 -@@ -1,10 +1,11 @@ - - -- -- Coot.desktop -+ -+ coot.desktop - GFDL-1.3 -- GPL-2.0+ and GPL-3.0+ and LGPL-3.0+ --

Macromolecular model builder -+ GPLv3+ and LGPLv2+ -+ Coot -+ Protein model building and validation for X-ray crystallographic data - -

- Coot is a powerful macromolecular model-building tool for -@@ -26,4 +27,4 @@ - - http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ - pemsley _at_ mrc dash lmb.cam.ac.uk -- -+ diff --git a/coot-configure.ac.patch b/coot-configure.ac.patch deleted file mode 100644 index c9a35b3..0000000 --- a/coot-configure.ac.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.ac_orig 2015-01-31 15:55:07.102736249 -0500 -+++ configure.ac 2015-02-01 13:23:47.715379636 -0500 -@@ -135,7 +135,7 @@ - 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 diff --git a/coot-guile.patch b/coot-guile.patch deleted file mode 100644 index e79a6a9..0000000 --- a/coot-guile.patch +++ /dev/null @@ -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) - ]) - diff --git a/coot-makefile.patch b/coot-makefile.patch deleted file mode 100644 index 2188a96..0000000 --- a/coot-makefile.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- src/Makefile.am_orig 2015-06-29 23:10:49.500572880 -0400 -+++ src/Makefile.am 2015-06-29 23:11:33.041822617 -0400 -@@ -27,9 +27,8 @@ - #__init__.py: coot.py - # cp coot.py __init__.py - -- --dist_python_SCRIPTS = coot.py coot.pth -- -+pythondir = $(pkgdatadir)/python -+dist_pkgpython_SCRIPTS = coot.py - - endif - ---- pixmaps/icons/Makefile.am_orig 2015-06-29 23:11:55.713911249 -0400 -+++ pixmaps/icons/Makefile.am 2015-06-29 23:26:22.902239461 -0400 -@@ -11,6 +11,6 @@ - CONTEXT=` echo $$icon | cut -d_ -f2`; \ - SIZE=` echo $$icon | cut -d_ -f3`; \ - ICONFILE=`echo $$icon | cut -d_ -f4`; \ -- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -- $(INSTALL_DATA) $(srcdir)/$$icon $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ -+ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \ -+ $(INSTALL_DATA) $(srcdir)/$$icon $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \ - done; ---- lbg/Makefile.am_orig 2015-09-24 23:04:49.843200580 -0400 -+++ lbg/Makefile.am 2015-09-24 23:10:03.355713678 -0400 -@@ -1,4 +1,3 @@ -- - lib_LTLIBRARIES=libcoot-lidia.la - - AM_CPPFLAGS = \ -@@ -53,8 +52,8 @@ - # 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) diff --git a/coot-unistd.patch b/coot-unistd.patch deleted file mode 100644 index a91efcb..0000000 --- a/coot-unistd.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- utils/coot-utils.cc_orig 2012-09-29 19:16:39.050470149 -0700 -+++ utils/coot-utils.cc 2012-09-29 19:18:01.609169266 -0700 -@@ -48,9 +48,7 @@ - - #include // for mkdir - #include --#if defined WINDOWS_MINGW - #include // BL says: in windows needed for mkdir --#endif // MINGW - - // #include "clipper/core/hkl_compute.h" - diff --git a/coot-user-manual.texi.patch b/coot-user-manual.texi.patch deleted file mode 100644 index c4ad336..0000000 --- a/coot-user-manual.texi.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- doc/coot-user-manual.texi_orig 2013-12-27 15:59:56.897931023 -0800 -+++ doc/coot-user-manual.texi 2013-12-27 16:22:22.207559590 -0800 -@@ -47,7 +47,7 @@ - - @vskip 10mm - --@image{coot-plain-2,127mm} -+@c @image{coot-plain-2,127mm} - - - @c The following two commands start the copyright page. -@@ -4951,10 +4951,10 @@ - @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 -+@c @include c-interface.h.texi - @node More Scripting Functions - @chapter More Scripting Functions --@include cc-interface.hh.texi -+@c @include cc-interface.hh.texi - - - -@@ -4972,7 +4972,7 @@ - @c nodes (mutate, povray) and (e.g.) `tips-gui', but has no menu entry for this node - @c - --@include coot-scheme-functions.texi -+@c @include coot-scheme-functions.texi - - - diff --git a/coot-utils.patch b/coot-utils.patch deleted file mode 100644 index 458835e..0000000 --- a/coot-utils.patch +++ /dev/null @@ -1,31 +0,0 @@ ---- coot-utils/Makefile.am_orig 2015-09-24 22:00:00.826912149 -0400 -+++ coot-utils/Makefile.am 2015-09-24 22:02:42.329117367 -0400 -@@ -116,7 +116,7 @@ - - - # test-agg-clust --check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions test-tt-morph -+check_PROGRAMS = test-h-bonds testshelxreader testcootutils test-hole test-elastic test-spherical glyco-torsions - - # testshelxreader fails to link for some reason! coot::protein_geometry::get_h_bond_type - # testcootutils also. 20100812 Fixed now - added libcoot-geometry.la ---- coot-utils/coot-shelx.hh_orig 2015-09-24 22:00:31.889296059 -0400 -+++ coot-utils/coot-shelx.hh 2015-09-24 22:01:54.006864161 -0400 -@@ -33,6 +33,7 @@ - - #include - #include "clipper/core/cell.h" -+#include "coot-coord-utils.hh" - - namespace coot { - ---- coot-utils/coot-hole.hh_orig 2015-09-24 22:00:39.574533094 -0400 -+++ coot-utils/coot-hole.hh 2015-09-24 22:02:06.645417847 -0400 -@@ -3,6 +3,7 @@ - #include "clipper/core/coords.h" - #include "clipper/core/nxmap.h" - -+#include "coot-map-utils.hh" - #include "utils/coot-utils.hh" - #include "geometry/protein-geometry.hh" - diff --git a/coot.desktop b/coot.desktop deleted file mode 100644 index 79a76c6..0000000 --- a/coot.desktop +++ /dev/null @@ -1,10 +0,0 @@ -[Desktop Entry] -Encoding=UTF-8 -Name=coot -GenericName=coot -Comment=macromolecular model builder -Exec=coot -Icon=coot -Terminal=false -Type=Application -Categories=Graphics;Science diff --git a/coot.in b/coot.in deleted file mode 100755 index 7c2b35f..0000000 --- a/coot.in +++ /dev/null @@ -1,62 +0,0 @@ -#!/bin/sh -# -*-shell-script-*- -# coot wrapper script -# Copyright 2004, 2005, 2006, 2007 University of York -# written by Paul Emsley - -COOT_PREFIX="@prefix@" -current_exe_dir="@libexecdir@" - -coot_real=$current_exe_dir/coot-bin -# echo coot-real is at $coot_real - -# ---------------------------------------------------------------------------- -# ---------------------------------------------------------------------------- -# If the COOT_PREFIX is correct, then these should not need modification -# i.e. nothing below here need be changed. -# ---------------------------------------------------------------------------- -# ---------------------------------------------------------------------------- -# -prefix=$COOT_PREFIX - -SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib -COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme -COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb -COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps -COOT_DATA_DIR=$COOT_PREFIX/share/coot -COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc -COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures -COOT_PYTHON_DIR= -COOT_REFMAC_LIB_DIR= - -PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR - -GUILE_WARN_DEPRECATED=no - -if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then - GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH - export GUILE_LOAD_PATH -fi - -# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH - -export SYMINFO -export COOT_PREFIX -export COOT_STANDARD_RESIDUES -export COOT_REFMAC_LIB_DIR -export COOT_PYTHON_DIR -export PYTHONPATH -export COOT_SCHEME_DIR -export COOT_REF_STRUCTS -export COOT_RESOURCES_FILE -export COOT_PIXMAPS_DIR -export COOT_DATA_DIR - -echo $coot_real $* -$coot_real $* -status=$? - -if [ $status != 0 ] ; then - @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real -fi - diff --git a/coot.png b/coot.png deleted file mode 100644 index 9e6ded7e24754bfa77ee5fe584fd2df36be6e86e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1271 zcmVPx#24YJ`L;(K){{a7>y{D4^000SaNLh0L01FcU01FcV0GgZ_00007bV*G`2iOY| z7cwAl4qK}L00ehQL_t(o!|j$^h*nh;$A4?>v(Gv6&FyO@P0Y-$hK1E+NifDss}%$!X@howHXD-}g<^ zMNP{J@_#scpR@O7t^ZnkueBE(#$o&)AcFoYiX+_3UZNo{&YXx%@9BB$pHnVwiGr!r z-xkGYo;}STU-{@+2Q9SVS~^pSZ;A2iJgyvxS|nQbM4v{u6%M_DRN_?9$q~*JY&41M zF1^TON7f@&i(w5|1m8EKiB^n8-ZNBAi92Im9B=61>Gk7U2eB{5$nIHAPI} z^HYzT^umnOPJQD0_qOi(>a&mE`(>N<0iXCZt;9>fZZph-Aqa+H1Z?En>W2+Q37uf) z3epram=~jypPzMRM>hSA`GadeTKCe16>sg+Vi$Q|q+?zeom;yphAuj-NV|2=W^EL# zmDCC(mJ*Lx?s3*aVhORuBV&;{+y_m$eQ&P3;`RA+i@!doqtGqIg^{^An&}ip)i56j zy91#mAaTH4KpWNv0yJ6>q~Q|~X!yhs$eQvir~Gu(MNhppuvY@XtYFwU#W{f>NLA6A zVMBqC)QN;NAd#U`r=blBVU+S_YZzgu_u>0``lr@T7##ZXi0$7jJ7?T6i#9ZMjwA?C z*S&|K0mZlHSZhWo*2s#1kO-1H+_1;*^7tP-ezzm4*6mgl0krX@jnO6@R!zMArVqa! 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Coot uses professional (and free) widgets (with the -GUI builder glade), mmdb, clipper, and OpenGL, together with a new -approach to map contouring and importing/creation and other modeling -and building operations. - -%package devel -Summary: Header files and library for developing programs with coot -Requires: %{name} = %{version}-%{release} -Group: Development/Libraries - -%description devel - -This package contains libraries and header files needed for program -development using the coot macromolecular model building package. - -%package doc -Summary: documentation PDF files for coot -Requires: %{name} = %{version}-%{release} -Group: Applications/Engineering - -%description doc - -the coot-doc package contains information concerning the use and -button/key shortcuts for the coot macromolecular model building -package. - -%prep -%setup -q -a 1 -%patch0 -p0 -%patch1 -p0 -%patch2 -p0 -%patch3 -p0 -%patch4 -p0 -%patch5 -p0 - -cp %{SOURCE2} ./src/ -cp %{SOURCE3} . - -# various cleanups -iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README - -aclocal -I macros -libtoolize --automake --copy -autoconf -automake --copy --add-missing --gnu - -%build -mkdir guile -# -D_GLIBCXX_USE_CXX11_ABI=0 ? -std=c++11 -%configure --with-guile --with-python --with-pygtk --with-goocanvas-prefix=/usr --disable-static CPPFLAGS="-I/usr/include/mmdb2 -I/usr/include/ssm" CXXFLAGS="$RPM_OPT_FLAGS -fno-strict-aliasing" GUILE_LOAD_PATH="$GUILE_LOAD_PATH:/tmp/guile" -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 - -make %{?_smp_mflags} -pushd doc -texi2pdf coot-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=%{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 - -# headers -# mkdir %{buildroot}%{_includedir}/coot -# mv %{buildroot}%{_includedir}/*.h %{buildroot}%{_includedir}/coot/ -# mv %{buildroot}%{_includedir}/*.hh %{buildroot}%{_includedir}/coot/ - -# python stuff -# mkdir -p %{buildroot}%{python_sitelib}/coot -# mv %{buildroot}%{_datadir}/coot/python/* %{buildroot}%{python_sitelib}/coot/ -for lib in $(find %{buildroot}%{python_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}%{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 - -%clean -rm -rf %{buildroot} - -%check -make check -# %{buildroot}%{_bindir}/coot-real --no-graphics --script python-tests/coot_unittest.py - -%post -/sbin/ldconfig -/bin/touch --no-create %{_datadir}/icons/hicolor &>/dev/null || : - -%postun -/sbin/ldconfig -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 - -%posttrans -/usr/bin/gtk-update-icon-cache %{_datadir}/icons/hicolor &>/dev/null || : - -%files -%defattr(-,root,root,-) -%doc AUTHORS README COPYING -%{_bindir}/* -%{_libexecdir}/* -# 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}/appdata/%{name}.appdata.xml -%{_datadir}/icons/hicolor/ -%{python_sitelib}/coot/ - -%files devel -%defattr(-,root,root,-) -%{_libdir}/*.so -%{_includedir}/coot/ - -%files doc -%defattr(-,root,root,-) -%doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf - -%changelog -* Mon Feb 22 2016 Orion Poplawski - 0.8.2-3 -- Rebuild for gsl 2.1 - -* Wed Feb 03 2016 Fedora Release Engineering - 0.8.2-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Mon Sep 7 2015 Tim Fenn - 0.8.2-1 -- update to 0.8.2 -- add patch for coot-utils - -* Sun Jun 28 2015 Tim Fenn - 0.8.1-3 -- fix to appdata.xml -- add all icon pixmaps, edit desktop file to match - -* Wed Jun 17 2015 Fedora Release Engineering - 0.8.1-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild - -* Sat Jan 31 2015 Tim Fenn - 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 - 0.7.2-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild - -* Sat Jun 07 2014 Fedora Release Engineering - 0.7.2-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild - -* Fri Dec 27 2013 Tim Fenn - 0.7.2-1 -- update to 0.7.2 -- update upstream URLs, no longer using vcs - -* Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 -- add ghostscript to buildrequires - -* Fri Aug 09 2013 Tim Fenn - 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 - 0.7-3.20120929svn4458 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild - -* Wed Feb 13 2013 Fedora Release Engineering - 0.7-2.20120929svn4458 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild - -* Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 -- update to 0.7 - -* Wed Jul 18 2012 Fedora Release Engineering - 0.6.2-14.20110715svn3566 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild - -* Tue Feb 28 2012 Fedora Release Engineering - 0.6.2-13.20110715svn3566 -- Rebuilt for c++ ABI breakage - -* Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 -- patches to fix unistd.h issue and compilation errors - -* Thu Jan 12 2012 Fedora Release Engineering - 0.6.2-11.20110715svn3566 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild - -* Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 -- patch for new libpng - -* Tue Dec 06 2011 Adam Jackson - 0.6.2-9.20110715svn3566 -- Rebuild for new libpng - -* Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 -- update to SVN 3566 (0.6.2 final) - -* Tue Apr 26 2011 Tim Fenn - 0.6.2-7.20110421svn3461 -- add reference structures source file - -* Tue Apr 26 2011 Tim Fenn - 0.6.2-6.20110421svn3461 -- add missing source - -* Thu Apr 21 2011 Tim Fenn - 0.6.2-5.20110421svn3461 -- update to SVN 3461 -- fix missing Requires: guile-lib - -* Tue Mar 29 2011 Tim Fenn - 0.6.2-4.20110328svn3442 -- update to SVN 3442 (should remove guile-gtk broken dependencies) - -* Fri Feb 25 2011 Tim Fenn - 0.6.2-3.20110225svn3399 -- update to SVN 3399 - -* Tue Feb 08 2011 Fedora Release Engineering - 0.6.2-2.20101012svn3213 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild - -* Tue Oct 12 2010 Tim Fenn - 0.6.2-1.20101012svn3213 -- update to 0.6.2 - -* Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 -- fix file attr -- add comment to make check error - -* Tue Jul 20 2010 Tim Fenn - 0.6.1-2.20100127svn2740 -- move some documentation to subpackage -- add check section - -* Wed Jan 27 2010 Tim Fenn - 0.6.1-1.20100127svn2740 -- update to SVN 2740, 0.6.1 release -- add curl buildrequires - -* Thu Dec 03 2009 Tim Fenn - 0.6-6.20091203svn2545 -- update to SVN 2545, 0.6 release - -* Mon Nov 30 2009 Tim Fenn - 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 - 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 - 0.6-3.20091005svn2400 -- update to SVN 2400 - -* Wed Sep 23 2009 Tim Fenn - 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 - 0.6-1.20090920svn2334 -- update to 0.6 -- get source from VCS system - -* Wed Mar 25 2009 Tim Fenn - 0.5.2-3 -- fix summary -- add additional licensing information -- split guile-extras into original tarballs - -* Sat Mar 14 2009 Tim Fenn - 0.5.2-2 -- fix for desktop-file-install -- gcc 4.4 patch - -* Mon Dec 15 2008 Tim Fenn - 0.5.2-1 -- update to 0.5.2 - -* Thu Nov 27 2008 Tim Fenn - 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 - 0.5-2 -- enable guile -- include extra guile modules - -* Mon Nov 17 2008 Tim Fenn - 0.5-1 -- initial build diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..67bbcda --- /dev/null +++ b/dead.package @@ -0,0 +1,3 @@ +2016-05-31: Retired because of broken deps in preparation of Fedora 24 +Reference: https://fedorahosted.org/rel-eng/ticket/6416 + diff --git a/sources b/sources deleted file mode 100644 index 6037d9b..0000000 --- a/sources +++ /dev/null @@ -1,2 +0,0 @@ -71a6653bedff7c764dea38289ef0e65c coot-0.8.2.tar.gz -257ab90d44f1c877ada96720dbb87c13 reference-structures.tar.gz From 92f74e81ce687d8a2062410e18c2a5d27bcb2e0c Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sun, 5 Feb 2017 22:19:24 -0500 Subject: [PATCH 35/43] rename python2 package add python_provide macro remove hardcoded library path include --- .gitignore | 2 + __init__.py | 1 + coot-configure.ac.patch | 28 +++ coot-guile.patch | 27 +++ coot-lbg.patch | 11 + coot-rdkit.patch | 11 + coot-utils.patch | 20 ++ coot.desktop | 10 + coot.in | 62 ++++++ coot.spec | 439 ++++++++++++++++++++++++++++++++++++++++ sources | 2 + 11 files changed, 613 insertions(+) create mode 100644 .gitignore create mode 100644 __init__.py create mode 100644 coot-configure.ac.patch create mode 100644 coot-guile.patch create mode 100644 coot-lbg.patch create mode 100644 coot-rdkit.patch create mode 100644 coot-utils.patch create mode 100644 coot.desktop create mode 100755 coot.in create mode 100644 coot.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..4841daa --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +/coot-0.8.7.tar.gz +/reference-structures.tar.gz diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..83d04e7 --- /dev/null +++ b/__init__.py @@ -0,0 +1 @@ +# File to allow this directory to be treated as a python package. diff --git a/coot-configure.ac.patch b/coot-configure.ac.patch new file mode 100644 index 0000000..54ea352 --- /dev/null +++ b/coot-configure.ac.patch @@ -0,0 +1,28 @@ +--- 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$with_guile_gtk != x ; then + AM_GUILE_GUI diff --git a/coot-guile.patch b/coot-guile.patch new file mode 100644 index 0000000..e79a6a9 --- /dev/null +++ b/coot-guile.patch @@ -0,0 +1,27 @@ +--- macros/guile_orig.m4 2013-07-31 00:25:19.715073145 -0700 ++++ macros/guile.m4 2013-07-31 00:27:01.763927099 -0700 +@@ -72,21 +72,21 @@ + # The variables are marked for substitution, as by @code{AC_SUBST}. + # + AC_DEFUN([GUILE_PROGS], +- [AC_PATH_PROG(GUILE,guile) ++ [AC_PATH_PROG(GUILE,guile1.8) + if test x$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) + ]) + diff --git a/coot-lbg.patch b/coot-lbg.patch new file mode 100644 index 0000000..312737b --- /dev/null +++ b/coot-lbg.patch @@ -0,0 +1,11 @@ +--- 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; diff --git a/coot-rdkit.patch b/coot-rdkit.patch new file mode 100644 index 0000000..d88e909 --- /dev/null +++ b/coot-rdkit.patch @@ -0,0 +1,11 @@ +--- 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 +-#include ++#include + #include "lidia-core/rdkit-interface.hh" + #else + #include "lidia-core/rdkit-interface.hh" diff --git a/coot-utils.patch b/coot-utils.patch new file mode 100644 index 0000000..6342f93 --- /dev/null +++ b/coot-utils.patch @@ -0,0 +1,20 @@ +--- 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 + #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" + diff --git a/coot.desktop b/coot.desktop new file mode 100644 index 0000000..79a76c6 --- /dev/null +++ b/coot.desktop @@ -0,0 +1,10 @@ +[Desktop Entry] +Encoding=UTF-8 +Name=coot +GenericName=coot +Comment=macromolecular model builder +Exec=coot +Icon=coot +Terminal=false +Type=Application +Categories=Graphics;Science diff --git a/coot.in b/coot.in new file mode 100755 index 0000000..7c2b35f --- /dev/null +++ b/coot.in @@ -0,0 +1,62 @@ +#!/bin/sh +# -*-shell-script-*- +# coot wrapper script +# Copyright 2004, 2005, 2006, 2007 University of York +# written by Paul Emsley + +COOT_PREFIX="@prefix@" +current_exe_dir="@libexecdir@" + +coot_real=$current_exe_dir/coot-bin +# echo coot-real is at $coot_real + +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# If the COOT_PREFIX is correct, then these should not need modification +# i.e. nothing below here need be changed. +# ---------------------------------------------------------------------------- +# ---------------------------------------------------------------------------- +# +prefix=$COOT_PREFIX + +SYMINFO=$COOT_PREFIX/share/coot/syminfo.lib +COOT_SCHEME_DIR=$COOT_PREFIX/share/coot/scheme +COOT_STANDARD_RESIDUES=$COOT_PREFIX/share/coot/standard-residues.pdb +COOT_PIXMAPS_DIR=$COOT_PREFIX/share/coot/pixmaps +COOT_DATA_DIR=$COOT_PREFIX/share/coot +COOT_RESOURCES_FILE=$COOT_PREFIX/share/coot/cootrc +COOT_REF_STRUCTS=$COOT_PREFIX/share/coot/reference-structures +COOT_PYTHON_DIR= +COOT_REFMAC_LIB_DIR= + +PYTHONPATH=${PYTHONPATH:+"${PYTHONPATH}:"}$COOT_PYTHON_DIR + +GUILE_WARN_DEPRECATED=no + +if [ -n "$LOCAL_GUILE_LOAD_PATH_EXTRAS" ] ; then + GUILE_LOAD_PATH=${LOCAL_GUILE_LOAD_PATH_EXTRAS}:$GUILE_LOAD_PATH + export GUILE_LOAD_PATH +fi + +# echo GUILE_LOAD_PATH is now $GUILE_LOAD_PATH + +export SYMINFO +export COOT_PREFIX +export COOT_STANDARD_RESIDUES +export COOT_REFMAC_LIB_DIR +export COOT_PYTHON_DIR +export PYTHONPATH +export COOT_SCHEME_DIR +export COOT_REF_STRUCTS +export COOT_RESOURCES_FILE +export COOT_PIXMAPS_DIR +export COOT_DATA_DIR + +echo $coot_real $* +$coot_real $* +status=$? + +if [ $status != 0 ] ; then + @bindir@/guile -s $COOT_PREFIX/share/coot/scheme/coot-crash-catcher.scm $coot_real +fi + diff --git a/coot.spec b/coot.spec new file mode 100644 index 0000000..0b47ebb --- /dev/null +++ b/coot.spec @@ -0,0 +1,439 @@ +%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: 0.8.7 +Release: 3%{?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-lib%{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 +* Thu Jan 26 2017 Tim Fenn - 0.8.7-3 +- rename python2 package +- add python_provide macro +- remove hardcoded library path include + +* Sat Nov 12 2016 Tim Fenn - 0.8.7-2 +- test build for fixing unused-shlib and weak-sybmol + +* Sun Nov 06 2016 Tim Fenn - 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 - 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 - 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 - 0.8.6.1-3 +- remove unecessary rhel only macros +- put doc in noarch + +* Fri Oct 07 2016 Tim Fenn - 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 - 0.8.6.1-1 +- update to 0.8.6.1 + +* Sat Jul 30 2016 Tim Fenn - 0.8.5-1 +- update to 0.8.5 + +* Thu Apr 07 2016 Tim Fenn - 0.8.3-1 +- Update to 0.8.3 + +* Mon Feb 22 2016 Orion Poplawski - 0.8.2-3 +- Rebuild for gsl 2.1 + +* Wed Feb 03 2016 Fedora Release Engineering - 0.8.2-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + +* Mon Sep 7 2015 Tim Fenn - 0.8.2-1 +- update to 0.8.2 +- add patch for coot-utils + +* Sun Jun 28 2015 Tim Fenn - 0.8.1-3 +- fix to appdata.xml +- add all icon pixmaps, edit desktop file to match + +* Wed Jun 17 2015 Fedora Release Engineering - 0.8.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + +* Sat Jan 31 2015 Tim Fenn - 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 - 0.7.2-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + +* Sat Jun 07 2014 Fedora Release Engineering - 0.7.2-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + +* Fri Dec 27 2013 Tim Fenn - 0.7.2-1 +- update to 0.7.2 +- update upstream URLs, no longer using vcs + +* Sun Aug 11 2013 Tim Fenn - 0.7-5.20120929svn4458 +- add ghostscript to buildrequires + +* Fri Aug 09 2013 Tim Fenn - 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 - 0.7-3.20120929svn4458 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild + +* Wed Feb 13 2013 Fedora Release Engineering - 0.7-2.20120929svn4458 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + +* Sat Sep 29 2012 Tim Fenn - 0.7-1.20120929svn4458 +- update to 0.7 + +* Wed Jul 18 2012 Fedora Release Engineering - 0.6.2-14.20110715svn3566 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild + +* Tue Feb 28 2012 Fedora Release Engineering - 0.6.2-13.20110715svn3566 +- Rebuilt for c++ ABI breakage + +* Sat Jan 14 2012 Tim Fenn - 0.6.2-12.20110715svn3566 +- patches to fix unistd.h issue and compilation errors + +* Thu Jan 12 2012 Fedora Release Engineering - 0.6.2-11.20110715svn3566 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild + +* Sat Dec 10 2011 Tim Fenn - 0.6.2-10.20110715svn3566 +- patch for new libpng + +* Tue Dec 06 2011 Adam Jackson - 0.6.2-9.20110715svn3566 +- Rebuild for new libpng + +* Fri Jul 15 2011 Tim Fenn - 0.6.2-8.20110715svn3566 +- update to SVN 3566 (0.6.2 final) + +* Tue Apr 26 2011 Tim Fenn - 0.6.2-7.20110421svn3461 +- add reference structures source file + +* Tue Apr 26 2011 Tim Fenn - 0.6.2-6.20110421svn3461 +- add missing source + +* Thu Apr 21 2011 Tim Fenn - 0.6.2-5.20110421svn3461 +- update to SVN 3461 +- fix missing Requires: guile-lib + +* Tue Mar 29 2011 Tim Fenn - 0.6.2-4.20110328svn3442 +- update to SVN 3442 (should remove guile-gtk broken dependencies) + +* Fri Feb 25 2011 Tim Fenn - 0.6.2-3.20110225svn3399 +- update to SVN 3399 + +* Tue Feb 08 2011 Fedora Release Engineering - 0.6.2-2.20101012svn3213 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild + +* Tue Oct 12 2010 Tim Fenn - 0.6.2-1.20101012svn3213 +- update to 0.6.2 + +* Thu Aug 05 2010 Tim Fenn - 0.6.1-3.20100127svn2740 +- fix file attr +- add comment to make check error + +* Tue Jul 20 2010 Tim Fenn - 0.6.1-2.20100127svn2740 +- move some documentation to subpackage +- add check section + +* Wed Jan 27 2010 Tim Fenn - 0.6.1-1.20100127svn2740 +- update to SVN 2740, 0.6.1 release +- add curl buildrequires + +* Thu Dec 03 2009 Tim Fenn - 0.6-6.20091203svn2545 +- update to SVN 2545, 0.6 release + +* Mon Nov 30 2009 Tim Fenn - 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 - 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 - 0.6-3.20091005svn2400 +- update to SVN 2400 + +* Wed Sep 23 2009 Tim Fenn - 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 - 0.6-1.20090920svn2334 +- update to 0.6 +- get source from VCS system + +* Wed Mar 25 2009 Tim Fenn - 0.5.2-3 +- fix summary +- add additional licensing information +- split guile-extras into original tarballs + +* Sat Mar 14 2009 Tim Fenn - 0.5.2-2 +- fix for desktop-file-install +- gcc 4.4 patch + +* Mon Dec 15 2008 Tim Fenn - 0.5.2-1 +- update to 0.5.2 + +* Thu Nov 27 2008 Tim Fenn - 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 - 0.5-2 +- enable guile +- include extra guile modules + +* Mon Nov 17 2008 Tim Fenn - 0.5-1 +- initial build diff --git a/sources b/sources new file mode 100644 index 0000000..51c668a --- /dev/null +++ b/sources @@ -0,0 +1,2 @@ +SHA512 (coot-0.8.7.tar.gz) = 25a316e3399685669259bd4b33103aead88566172f17a6bb061e9036fead3a7d2fcd9689c7c604fbc904278dab4591738705aadd98f09f9ce6710e085df8c7dc +SHA512 (reference-structures.tar.gz) = 7ebe28a619a577b18fc66e714f0bc8347121ebb12f372ac29c1d2d96013e608632921ea26caea3b62744252ae356949de8e04a6513f1a1e0ba30865708c26ffe From 1a2ead7ce0af14517becab72cd763fdbf04d59bc Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sun, 5 Feb 2017 22:24:37 -0500 Subject: [PATCH 36/43] add missing patch --- coot-makefile.patch | 35 +++++++++++++++++++++++++++++++++++ coot.spec | 5 ++++- 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 coot-makefile.patch diff --git a/coot-makefile.patch b/coot-makefile.patch new file mode 100644 index 0000000..316e044 --- /dev/null +++ b/coot-makefile.patch @@ -0,0 +1,35 @@ +--- 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 diff --git a/coot.spec b/coot.spec index 0b47ebb..c9db8a1 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.7 -Release: 3%{?dist} +Release: 4%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sun Feb 05 2017 Tim Fenn - 0.8.7-4 +- add missing patch + * Thu Jan 26 2017 Tim Fenn - 0.8.7-3 - rename python2 package - add python_provide macro From e82c29b1b9bab994dbb6cea1d9b26f047c40ff71 Mon Sep 17 00:00:00 2001 From: Kalev Lember Date: Wed, 8 Feb 2017 15:01:01 +0100 Subject: [PATCH 37/43] Rebuilt for Boost 1.63 --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index c9db8a1..ab8d7a7 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.7 -Release: 4%{?dist} +Release: 5%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Feb 08 2017 Kalev Lember - 0.8.7-5 +- Rebuilt for Boost 1.63 + * Sun Feb 05 2017 Tim Fenn - 0.8.7-4 - add missing patch From 01b41e3365ca475fee8dfb9e7d61069fe729826f Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Thu, 9 Feb 2017 14:42:26 -0500 Subject: [PATCH 38/43] Fix to requires --- coot.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/coot.spec b/coot.spec index ab8d7a7..8a9b8fe 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.7 -Release: 5%{?dist} +Release: 6%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -58,7 +58,7 @@ Requires: hicolor-icon-theme Requires: refmac-dictionary Requires: %{name}-data = %{version}-%{release} Requires: lib%{name}%{?_isa} = %{version}-%{release} -Requires: python2-lib%{name}%{?_isa} = %{version}-%{release} +Requires: python2-%{name}%{?_isa} = %{version}-%{release} %description @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Thu Feb 09 2017 Tim Fenn - 0.8.7-6 +- Fix to requires + * Wed Feb 08 2017 Kalev Lember - 0.8.7-5 - Rebuilt for Boost 1.63 From 0718a5b9acded5907057be24645c93b0ea2782d7 Mon Sep 17 00:00:00 2001 From: Tim Fenn Date: Sat, 18 Mar 2017 13:15:35 -0400 Subject: [PATCH 39/43] update to 0.8.8 --- .gitignore | 1 + coot.desktop | 2 +- coot.spec | 7 +++++-- sources | 2 +- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 4841daa..c9ff031 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ /coot-0.8.7.tar.gz /reference-structures.tar.gz +/coot-0.8.8.tar.gz diff --git a/coot.desktop b/coot.desktop index 79a76c6..97da05e 100644 --- a/coot.desktop +++ b/coot.desktop @@ -7,4 +7,4 @@ Exec=coot Icon=coot Terminal=false Type=Application -Categories=Graphics;Science +Categories=Graphics;Science;Chemistry; diff --git a/coot.spec b/coot.spec index 8a9b8fe..0aaef5b 100644 --- a/coot.spec +++ b/coot.spec @@ -2,8 +2,8 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ -Version: 0.8.7 -Release: 6%{?dist} +Version: 0.8.8 +Release: 1%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Sat Mar 18 2017 Tim Fenn - 0.8.8-1 +- update to 0.8.8 + * Thu Feb 09 2017 Tim Fenn - 0.8.7-6 - Fix to requires diff --git a/sources b/sources index 51c668a..93f1b0b 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (coot-0.8.7.tar.gz) = 25a316e3399685669259bd4b33103aead88566172f17a6bb061e9036fead3a7d2fcd9689c7c604fbc904278dab4591738705aadd98f09f9ce6710e085df8c7dc +SHA512 (coot-0.8.8.tar.gz) = 6d99e4bc0a5cd17b46bd52741b934e98e98eec9fe5a9fd108e891834256e17cc03eb12327aa6756beff4ce552456ae5e8a0ee459ecf3894a99809be218481b83 SHA512 (reference-structures.tar.gz) = 7ebe28a619a577b18fc66e714f0bc8347121ebb12f372ac29c1d2d96013e608632921ea26caea3b62744252ae356949de8e04a6513f1a1e0ba30865708c26ffe From 072e89cc6560409949d2f19c41d7c9252400727a Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 15 May 2017 20:35:26 +0000 Subject: [PATCH 40/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 0aaef5b..dba3168 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ 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} +Release: 2%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon May 15 2017 Fedora Release Engineering - 0.8.8-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild + * Sat Mar 18 2017 Tim Fenn - 0.8.8-1 - update to 0.8.8 From cc804d9af5f7546334f18b6b2e07009a274427cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Esser?= Date: Mon, 24 Jul 2017 14:20:40 +0200 Subject: [PATCH 41/43] Rebuilt for Boost 1.64 --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index dba3168..f31afb3 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 2%{?dist} +Release: 3%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Mon Jul 24 2017 Björn Esser - 0.8.8-3 +- Rebuilt for Boost 1.64 + * Mon May 15 2017 Fedora Release Engineering - 0.8.8-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_27_Mass_Rebuild From aae6b2b7f698d9ad14a92cfc7dbdbf021b2da35e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 26 Jul 2017 05:28:31 +0000 Subject: [PATCH 42/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index f31afb3..735e6be 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 3%{?dist} +Release: 4%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Jul 26 2017 Fedora Release Engineering - 0.8.8-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + * Mon Jul 24 2017 Björn Esser - 0.8.8-3 - Rebuilt for Boost 1.64 From d01dc8c1911996529c43483575dcd3b289d5b22d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 2 Aug 2017 19:10:04 +0000 Subject: [PATCH 43/43] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild --- coot.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/coot.spec b/coot.spec index 735e6be..b45849b 100644 --- a/coot.spec +++ b/coot.spec @@ -3,7 +3,7 @@ Name: coot Summary: The crystallographic object-oriented toolkit URL: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ Version: 0.8.8 -Release: 4%{?dist} +Release: 5%{?dist} # source code is mixed GPLv3+ and LGPLv2+ (see files for breakdown) License: GPLv3+ Group: Applications/Engineering @@ -237,6 +237,9 @@ fi %doc doc/coot-keys-and-buttons.pdf doc/coot-user-manual.pdf %changelog +* Wed Aug 02 2017 Fedora Release Engineering - 0.8.8-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + * Wed Jul 26 2017 Fedora Release Engineering - 0.8.8-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild