Initial commit

8 files changed, 299 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..1d252658acd6
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,52 @@
+# Generated by mksrcinfo v8
+# Tue Jan 12 02:54:27 UTC 2016
+pkgbase = coot
+	pkgdesc = Crystallographic Object-Oriented Toolkit for model building, completion and validation
+	pkgver = 0.8.2
+	pkgrel = 2
+	url = http://lmb.bioch.ox.ac.uk/coot/
+	arch = i686
+	arch = x86_64
+	license = GPL
+	depends = guile1.8
+	depends = guile1.8-lib
+	depends = guile1.8-gtk
+	depends = guile1.8-gui
+	depends = gtkglext
+	depends = libccp4
+	depends = clipper
+	depends = goocanvas1
+	depends = gsl
+	depends = libgnomecanvas
+	depends = imlib
+	depends = swig
+	depends = freeglut
+	depends = libgl
+	depends = gtk2
+	depends = cairo
+	depends = libssm>=1.4
+	depends = zlib
+	depends = curl
+	depends = python2
+	depends = pygtk
+	depends = gtkglarea
+	depends = which
+	depends = bc
+	depends = sqlite
+	source = http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-0.8.2.tar.gz
+	source = coot-0.8.2-desktop.patch
+	source = coot-0.8.2-libguile.patch
+	source = coot-0.8.2-libtool.patch
+	source = coot-0.8.2-sandbox-icons.patch
+	source = coot-0.8.2-python.patch
+	source = coot-0.8.2-guile.patch
+	sha256sums = 2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee
+	sha256sums = 6558c17da028f47bec3480afbf85d8457e4c34bb50a6285bf0522de922a6bc89
+	sha256sums = aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b
+	sha256sums = e4ba02ad24330e3df3f32772275db47caeb4f36d77d57de882f7a73d7e11e5bf
+	sha256sums = b93756a9ab1244573ac24427954c53ac9f14a82e7ec1f115b178897abcab42a8
+	sha256sums = f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099
+	sha256sums = c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911
+
+pkgname = coot
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..9e36f5ccfffa
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,98 @@
+# Maintainer: Alexander Minges <alexander.minges@gmail.com>
+pkgname=coot
+pkgver=0.8.2
+pkgrel=2
+pkgdesc="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+arch=('i686' 'x86_64')
+url="http://lmb.bioch.ox.ac.uk/coot/"
+license=('GPL')
+depends=('guile1.8' 'guile1.8-lib' 'guile1.8-gtk' 'guile1.8-gui' 'gtkglext' 'libccp4' 'clipper' 'goocanvas1' 'gsl' 'libgnomecanvas' 'imlib' 'swig'
+         'freeglut' 'libgl' 'gtk2' 'cairo' 'libssm>=1.4' 'zlib' 'curl' 'python2' 'pygtk' 'gtkglarea' 'which' 'bc' 'sqlite')
+source=(http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/$pkgname-$pkgver.tar.gz
+        coot-0.8.2-desktop.patch
+        coot-0.8.2-libguile.patch
+        coot-0.8.2-libtool.patch
+        coot-0.8.2-sandbox-icons.patch
+        coot-0.8.2-python.patch
+        coot-0.8.2-guile.patch)
+#	coot-configure.in.patch
+#	coot-user-manual.texi.patch
+#	coot-makefile.patch
+#        coot-guile.patch
+#        coot-python.patch
+#        coot-icons.patch
+#        coot-lidia.patch)
+sha256sums=('2f5961ded7f2cf06b887560afe964c239aba94f9c4bf8a2a80b3ca4fbc471eee'
+            '6558c17da028f47bec3480afbf85d8457e4c34bb50a6285bf0522de922a6bc89'
+            'aa1e18d4ef43fb61e85aba05d13797f9aa2beb1da220405f1eb6058ac36eb60b'
+            'e4ba02ad24330e3df3f32772275db47caeb4f36d77d57de882f7a73d7e11e5bf'
+            'b93756a9ab1244573ac24427954c53ac9f14a82e7ec1f115b178897abcab42a8'
+            'f4747e1fc7a3387f42b6c40358f999404761a0282ee6be3c621091d9d5d88099'
+            'c15e844536f512c2d5524391dbc046a889a0d5f8c23336b854508e453e226911')
+
+build() {
+
+  cd "$srcdir/$pkgname-$pkgver"
+  
+  patch -Np1 -i "$srcdir/coot-0.8.2-desktop.patch"
+  patch -Np1 -i "$srcdir/coot-0.8.2-libguile.patch"
+  patch -Np1 -i "$srcdir/coot-0.8.2-libtool.patch"
+  patch -Np1 -i "$srcdir/coot-0.8.2-sandbox-icons.patch"
+  patch -Np0 -i "$srcdir/coot-0.8.2-python.patch"
+  patch -Np0 -i "$srcdir/coot-0.8.2-guile.patch"
+  
+  iconv -f iso8859-1 -t utf-8 README > README.conv && mv -f README.conv README
+  
+  aclocal -I macros
+  libtoolize --automake --copy
+  autoconf
+  automake --copy --add-missing --gnu
+  
+  # Work around coot's code not beeing completely standart compliant
+  CXXFLAGS="${CXXFLAGS} -fpermissive"
+  
+  ./configure --prefix=/usr \
+              --without-guile \
+              --with-python \
+              --with-guile \
+              --with-guile-gtk \
+              --with-pygtk \
+              --with-sqlite3 \
+              --with-boost \
+              --with-boost-python \
+              --disable-static
+
+  make
+
+#  patch -Np0 -i "$srcdir/coot-configure.in.patch"
+
+# patch -Np0 -i "$srcdir/coot-user-manual.texi.patch"
+# patch -Np0 -i "$srcdir/coot-guile.patch"
+# patch -Np0 -i "$srcdir/coot-python.patch"
+# patch -Np0 -i "$srcdir/coot-icons.patch"
+# patch -Np0 -i "$srcdir/coot-lidia.patch"
+
+#  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
+#  
+#  CXXFLAGS="${CXXFLAGS} -fpermissive"
+#  CFLAGS="${CFLAGS} -fpermissive"
+#
+#  ./configure --prefix=/usr \
+#              --includedir=/usr/include/coot \
+#              --with-guile \
+#              --with-python \
+#              --with-pygtk \
+#              --disable-static
+#  
+#  make
+}
+
+package() {
+  cd "$srcdir/$pkgname-$pkgver"
+  make DESTDIR="$pkgdir/" install
+} 
diff --git a/coot-0.8.2-desktop.patch b/coot-0.8.2-desktop.patch
new file mode 100644
index 000000000000..c264dd5a7628
--- /dev/null
+++ b/coot-0.8.2-desktop.patch
@@ -0,0 +1,21 @@
+ coot.desktop | 7 +++----
+ 1 file changed, 3 insertions(+), 4 deletions(-)
+
+diff --git a/coot.desktop b/coot.desktop
+index 74aecf3..8668018 100644
+--- a/coot.desktop
++++ b/coot.desktop
+@@ -1,10 +1,9 @@
+ [Desktop Entry]
+ Type=Application
+-Encoding=UTF-8
+ Name=Coot
+ Comment=Macromolecular model builder
+ Exec=coot
+-Icon=coot.png
++Icon=coot
+ Terminal=true
+-Categories=Science;Graphics
+-MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile
++Categories=Science;Graphics;
++MimeType=chemical/x-pdb;chemical/x-mmcif;chemical/x-mdl-molfile;
diff --git a/coot-0.8.2-guile.patch b/coot-0.8.2-guile.patch
new file mode 100644
index 000000000000..44dd1462a020
--- /dev/null
+++ b/coot-0.8.2-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,guile-config1.8)
+   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,guile-tools1.8)
+   AC_SUBST(GUILE_TOOLS)
+  ])
+ 
diff --git a/coot-0.8.2-libguile.patch b/coot-0.8.2-libguile.patch
new file mode 100644
index 000000000000..cbaccefb2947
--- /dev/null
+++ b/coot-0.8.2-libguile.patch
@@ -0,0 +1,29 @@
+ src/graphics-info-modelling.cc | 1 +
+ src/graphics-info.cc           | 2 ++
+ 2 files changed, 3 insertions(+)
+
+diff --git a/src/graphics-info-modelling.cc b/src/graphics-info-modelling.cc
+index 05a63ad..4b7d129 100644
+--- a/src/graphics-info-modelling.cc
++++ b/src/graphics-info-modelling.cc
+@@ -102,6 +102,7 @@
+ 
+ #include "utils/coot-utils.hh"
+ 
++#include <libguile.h>
+ 
+ // Idealize the geometry without considering the map.
+ //
+diff --git a/src/graphics-info.cc b/src/graphics-info.cc
+index e2f9d52..76b6769 100644
+--- a/src/graphics-info.cc
++++ b/src/graphics-info.cc
+@@ -92,6 +92,8 @@
+ #include "cc-interface-scripting.hh"
+ #endif
+ 
++#include <libguile.h>
++
+ // A few non-class members - should be somewhere else, I guess.
+ // 
+ void initialize_graphics_molecules() { 
diff --git a/coot-0.8.2-libtool.patch b/coot-0.8.2-libtool.patch
new file mode 100644
index 000000000000..10c43ad55594
--- /dev/null
+++ b/coot-0.8.2-libtool.patch
@@ -0,0 +1,39 @@
+ configure.ac    |  2 +-
+ lbg/Makefile.am | 11 -----------
+ 2 files changed, 1 insertion(+), 12 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 73d6ed7..b04dcd6 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,7 +69,7 @@ AC_LIB_PREPARE_MULTILIB
+ 
+ AC_SUBST(COOT_STDTYPES)
+ 
+-EXPORT_DYNAMIC_FLAG_SPEC=$export_dynamic_flag_spec
++eval EXPORT_DYNAMIC_FLAG_SPEC=\"$export_dynamic_flag_spec\"
+ AC_SUBST(EXPORT_DYNAMIC_FLAG_SPEC)
+ 
+ 
+diff --git a/lbg/Makefile.am b/lbg/Makefile.am
+index 1277afe..a79ebe0 100644
+--- a/lbg/Makefile.am
++++ b/lbg/Makefile.am
+@@ -43,17 +43,6 @@ pkginclude_HEADERS = lbg.hh wmolecule.hh  flev-annotations.hh graphics-c-interfa
+ 	lbg-drag-and-drop.hh qed-interface.hh alerts.hh pi-stacking.hh
+ pkgincludedir = $(includedir)/coot/lbg
+ 
+-# 20140521
+-# lidia_LDFLAGS = -Wl,--export-dynamic
+-# 
+-# Now we use EXPORT_DYNAMIC_FLAG_SPEC which usually evaluates to ${wl}--export-dynamic
+-# (but not for MacOSX, where it Does The Right Thing (hopefully)).
+-# We manually set the value of wl here, but maybe the Right Thing To Do for that is 
+-# run (eval) $($LIBTOOL --config | grep ^wl).  How do I do that here though?  
+-# 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)
+ 
+ # res spec output operator means we include libcoot-coord-utils
diff --git a/coot-0.8.2-python.patch b/coot-0.8.2-python.patch
new file mode 100644
index 000000000000..f163ed7b794b
--- /dev/null
+++ b/coot-0.8.2-python.patch
@@ -0,0 +1,17 @@
+--- macros/with-python.m4.orig	2013-08-17 11:46:15.000000000 +0200
++++ macros/with-python.m4	2013-09-10 11:45:57.205754025 +0200
+@@ -41,12 +41,12 @@
+    # be $PYTHON:
+    #
+    if test x$PYTHON = x ; then
+-      PYTHON=python
++      PYTHON=python2
+    fi
+    # Similar for python-config
+    #
+    if test x$PYTHON_CONFIG = x ; then
+-      PYTHON_CONFIG=python-config
++      PYTHON_CONFIG=python2-config
+    fi
+ 
+    # Check to see if python exists:
diff --git a/coot-0.8.2-sandbox-icons.patch b/coot-0.8.2-sandbox-icons.patch
new file mode 100644
index 000000000000..2a9ff2d7177c
--- /dev/null
+++ b/coot-0.8.2-sandbox-icons.patch
@@ -0,0 +1,16 @@
+ pixmaps/icons/Makefile.am | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
+index 0c183ae..dddc11a 100644
+--- a/pixmaps/icons/Makefile.am
++++ b/pixmaps/icons/Makefile.am
+@@ -11,6 +11,6 @@ install-data-local:
+ 		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;