A new graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. Very strange build system; takes lots of hacking and tweaking to get working. Doesn't work with python-2.4, only 2.3.

(Portage version: 2.0.53)

6 files changed, 372 insertions, 0 deletions

diff --git a/sci-chemistry/sparky/ChangeLog b/sci-chemistry/sparky/ChangeLog
new file mode 100644
index 000000000000..467e2cb5bfc3
--- /dev/null
+++ b/sci-chemistry/sparky/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/sparky
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/sparky/ChangeLog,v 1.1 2005/12/18 18:59:48 spyderous Exp $
+
+*sparky-3.111 (18 Dec 2005)
+
+  18 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>;
+  +files/fix-install.patch, +metadata.xml, +sparky-3.111.ebuild:
+  A new graphical NMR assignment and integration program for proteins, nucleic
+  acids, and other polymers. Very strange build system; takes lots of hacking
+  and tweaking to get working. Doesn't work with python-2.4, only 2.3.
+
diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest
new file mode 100644
index 000000000000..7912fad3f37b
--- /dev/null
+++ b/sci-chemistry/sparky/Manifest
@@ -0,0 +1,6 @@
+MD5 58d459eacbeaa84c039bad48bb30baf5 files/digest-sparky-3.111 72
+MD5 4be84fed797386cc8986d1b3e4b579d8 files/fix-install-working.patch 7992
+MD5 53c15336a39923c3345a2f7dd841db27 files/fix-install-working2.patch 9131
+MD5 edd4cafd319052b6792fe4918f0bfaa4 files/fix-install.patch 10206
+MD5 d380a123f668307505d6e516408ad685 files/sparky.patch 10038
+MD5 0d9ee98ebeefaa098fe9adb383eeb5e9 sparky-3.111.ebuild 2846
diff --git a/sci-chemistry/sparky/files/digest-sparky-3.111 b/sci-chemistry/sparky/files/digest-sparky-3.111
new file mode 100644
index 000000000000..7e9c6af4ea3b
--- /dev/null
+++ b/sci-chemistry/sparky/files/digest-sparky-3.111
@@ -0,0 +1 @@
+MD5 f437420748bcb86dbfd1ca33a948ebc7 sparky-source-3.111.tar.gz 3820709
diff --git a/sci-chemistry/sparky/files/fix-install.patch b/sci-chemistry/sparky/files/fix-install.patch
new file mode 100644
index 000000000000..a9d10a3f5aeb
--- /dev/null
+++ b/sci-chemistry/sparky/files/fix-install.patch
@@ -0,0 +1,259 @@
+diff -ur -x make-sparky sparky.orig/bin/sparky sparky/bin/sparky
+--- sparky.orig/bin/sparky	2004-03-05 11:32:10.000000000 -0800
++++ sparky/bin/sparky	2005-12-17 17:36:51.000000000 -0800
+@@ -4,22 +4,10 @@
+ #
+ 
+ # -----------------------------------------------------------------------------
+-# Figure out Sparky installation directory from $0.
+-#
+-set sparky_exe = $0
+-while (-l $sparky_exe)
+-  set ls_sparky_exe = `ls -l "$sparky_exe"`
+-  set sparky_exe = `echo "$ls_sparky_exe" | sed 's/.* -> //'`
+-end
+-set sparky_bin = `dirname "$sparky_exe"`
+-set sparky_bin = `cd "$sparky_bin"; pwd`
+-set sparky_inst = `dirname "$sparky_bin"`
+-
+-# -----------------------------------------------------------------------------
+ # Sparky uses the SPARKY_INSTALL environment variable to find its
+ # application resource file and print prolog file.
+ #
+-setenv SPARKY_INSTALL		$sparky_inst
++setenv SPARKY_INSTALL		/usr/lib/sparky
+ 
+ # -----------------------------------------------------------------------------
+ # If Python is available start Sparky as a Python extension.
+diff -ur -x make-sparky sparky.orig/c++/Makefile sparky/c++/Makefile
+--- sparky.orig/c++/Makefile	2004-02-03 15:56:24.000000000 -0800
++++ sparky/c++/Makefile	2005-12-18 10:49:08.000000000 -0800
+@@ -22,6 +22,7 @@
+ PYTHON_PREFIX	= /usr/local
+ PYTHON_LIB	= $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
+ PYTHON_INC	= $(PYTHON_PREFIX)/include/python$(PYTHON_VERSION)
++PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
+ TCLTK_VERSION	= 8.4
+ TCLTK_VER_WIN32	= 84
+ TK_PREFIX	= /usr/local
+@@ -113,21 +114,20 @@
+ 
+ nopython: $(EXECUTABLES)
+ 
+-install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python \
+-  $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk
+-	$(INSTALL) $(SPY_PYMOD) $(SPARKY_INSTALL)/python/sparky
+-	chmod 755 $(SPARKY_INSTALL)/python/sparky/$(SPY_PYMOD)
+-	$(INSTALL) $(TKINTER_PYMOD) $(SPARKY_INSTALL)/python/lib-tk
+-	chmod 755 $(SPARKY_INSTALL)/python/lib-tk/$(TKINTER_PYMOD)
++install-python: $(SPY_PYMOD) $(TKINTER_PYMOD) $(PYDIR) \
++	$(PYDIR)/sparky $(PYDIR)/lib-tk
++	$(INSTALL) $(SPY_PYMOD) $(PYDIR)/sparky
++	chmod 755 $(PYDIR)/sparky/$(SPY_PYMOD)
++	$(INSTALL) $(TKINTER_PYMOD) $(PYDIR)/lib-tk
++	chmod 755 $(PYDIR)/lib-tk/$(TKINTER_PYMOD)
+ 
+ install-nopython: $(EXECUTABLES) $(SPARKY_INSTALL)/bin
+ 	$(INSTALL) $(EXECUTABLES) $(SPARKY_INSTALL)/bin
+ 	cd $(SPARKY_INSTALL)/bin ; \
+ 	chmod 755 $(EXECUTABLES)
+ 
+-$(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python \
+-$(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
+-	mkdir $@
++$(SPARKY_INSTALL)/bin $(PYDIR) $(PYDIR)/sparky $(PYDIR)/lib-tk:
++	mkdir -p $@
+ 	chmod 755 $@
+ 
+ sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
+diff -ur -x make-sparky sparky.orig/c++/paths.h sparky/c++/paths.h
+--- sparky.orig/c++/paths.h	2002-01-17 19:15:06.000000000 -0800
++++ sparky/c++/paths.h	2005-12-17 20:57:15.000000000 -0800
+@@ -19,7 +19,7 @@
+ // Installation subdirectories and files
+ //
+ #define SPARKY_MANUAL		"manual"
+-#define SPARKY_LIB		"lib"
++#define SPARKY_LIB		""
+ #define SPARKY_PRINT		"print-prolog.ps"	// under lib directory
+ #define SPARKY_RESOURCE		"Sparky"		// under lib directory
+ #define SPARKY_SAMPLE_DATA	"example"
+diff -ur -x make-sparky sparky.orig/c++/system-unix.cc sparky/c++/system-unix.cc
+--- sparky.orig/c++/system-unix.cc	2004-02-26 10:57:54.000000000 -0800
++++ sparky/c++/system-unix.cc	2005-12-17 20:56:58.000000000 -0800
+@@ -95,7 +95,7 @@
+ //
+ Stringy default_sparky_install_path()
+ {
+-  return file_path(file_path(file_path("", "usr"), "local"), "sparky");
++  return file_path(file_path(file_path("", "usr"), "lib"), "sparky");
+ }
+ 
+ // ----------------------------------------------------------------------------
+diff -ur -x make-sparky sparky.orig/lib/Makefile sparky/lib/Makefile
+--- sparky.orig/lib/Makefile	2004-02-18 10:53:29.000000000 -0800
++++ sparky/lib/Makefile	2005-12-17 16:03:21.000000000 -0800
+@@ -18,9 +18,9 @@
+ TCL_SHLIB	= lib$(TCL_VERSION)$(TCLTK_SHLIB_SUFFIX)
+ TK_SHLIB	= lib$(TK_VERSION)$(TCLTK_SHLIB_SUFFIX)
+ 
+-install: $(SPARKY_INSTALL)/lib install-tcl-tk
+-	$(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib
+-	cd $(SPARKY_INSTALL)/lib ; \
++install: $(SPARKY_INSTALL)/lib
++	$(INSTALL) Sparky print-prolog.ps $(SPARKY_INSTALL)/lib/sparky
++	cd $(SPARKY_INSTALL)/lib/sparky ; \
+ 	chmod 644 Sparky print-prolog.ps
+ 
+ install-tcl-tk: $(SPARKY_INSTALL)/lib
+diff -ur -x make-sparky sparky.orig/Makefile sparky/Makefile
+--- sparky.orig/Makefile	2004-02-18 10:40:04.000000000 -0800
++++ sparky/Makefile	2005-12-17 19:40:48.000000000 -0800
+@@ -40,18 +40,22 @@
+ 
+ PYTHON_VERSION	= 2.3
+ PYTHON_DIR	= 
++PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
+ 
+ PYMOD_SUFFIX	= .so
+ SPY_PYMOD	= spy$(PYMOD_SUFFIX)
+ TKINTER_PYMOD	= _tkinter$(PYMOD_SUFFIX)
+ 
++PYDIR       = $(SPARKY_INSTALL)/lib/sparky/python
++DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
++
+ all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
+ 	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
+ 
+ Makefile.dep TAGS: force
+ 	cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
+ 
+-install: install-nopython $(SPARKY_INSTALL) install-python
++install: install-nopython $(SPARKY_INSTALL)
+ 	cd $(SPARKY_OBJ) && \
+ 	$(MAKE) -f $(SPARKY_SRC)/Makefile -e install-python
+ 	cd $(SPARKY)/python && $(MAKE) -f Makefile -e install
+@@ -67,7 +71,8 @@
+ 	chmod 755 sparky$(SCRIPT_SUFFIX)
+ 
+ install-example: $(SPARKY_INSTALL)
+-	cd $(SPARKY) ; $(INSTALLDIR) example $(SPARKY_INSTALL)
++	mkdir -p $(DOCDIR)/example
++	cd $(SPARKY) ; $(INSTALLDIR) example $(DOCDIR)
+ 
+ install-lib: $(SPARKY_INSTALL)
+ 	cd $(SPARKY)/lib && $(MAKE) -f Makefile -e install
+@@ -76,21 +81,14 @@
+ 	cd $(SPARKY)/manual && $(MAKE) -f Makefile -e install
+ 
+ install-misc: $(SPARKY_INSTALL)
+-	cd $(SPARKY) ; $(INSTALL) LICENSE README $(SPARKY_INSTALL)
+-	cd $(SPARKY_INSTALL) ; chmod 644 LICENSE README
+-
+-install-python: $(SPARKY_INSTALL) $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
+-ifdef PYTHON_DIR
+-	$(INSTALLDIR) $(PYTHON_DIR)/* $(SPARKY_INSTALL)/python$(PYTHON_VERSION)
+-else
+-	echo "Not packaging Python with Sparky."
+-endif
++	cd $(SPARKY) ; $(INSTALL) LICENSE README $(DOCDIR)
++	cd $(DOCDIR) ; chmod 644 LICENSE README
+ 
+ install-mac:
+ 	cd $(SPARKY)/mac && $(MAKE) -f Makefile -e install
+ 
+-$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(SPARKY_INSTALL)/python$(PYTHON_VERSION):
+-	mkdir $@
++$(SPARKY_INSTALL) $(SPARKY_INSTALL)/bin $(PYDIR):
++	mkdir -p $@
+ 	chmod 755 $@
+ 
+ force:
+diff -ur -x make-sparky sparky.orig/manual/Makefile sparky/manual/Makefile
+--- sparky.orig/manual/Makefile	2004-03-08 15:40:06.000000000 -0800
++++ sparky/manual/Makefile	2005-12-17 19:37:45.000000000 -0800
+@@ -13,6 +13,8 @@
+ 
+ SPARKY_INSTALL	= /usr/local/sparky
+ MANUAL_WWW	= /usr/local/html/cgl/sparky/manual
++DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
++MANUAL_LOC = $(DOCDIR)/manual
+ 
+ MANUAL_SECTIONS = overview.html intro.html views.html peaks.html \
+ 		  extensions.html autoassign.html misc.html \
+@@ -45,17 +47,17 @@
+ 
+ all: $(MANUAL_FILES)
+ 
+-install: $(MANUAL_FILES) $(SPARKY_INSTALL)/manual \
+-		$(SPARKY_INSTALL)/manual/images
+-	$(INSTALL) $(MANUAL_FILES) $(SPARKY_INSTALL)/manual
+-	cd $(SPARKY_INSTALL)/manual ; \
++install: $(MANUAL_FILES) $(MANUAL_LOC) \
++		$(MANUAL_LOC)/images
++	$(INSTALL) $(MANUAL_FILES) $(MANUAL_LOC)
++	cd $(MANUAL_LOC) ; \
+ 	chmod 644 $(MANUAL_FILES)
+ 	cd images ; \
+-	$(INSTALL) $(IMAGE_FILES) $(SPARKY_INSTALL)/manual/images
+-	cd $(SPARKY_INSTALL)/manual/images ; \
++	$(INSTALL) $(IMAGE_FILES) $(MANUAL_LOC)/images
++	cd $(MANUAL_LOC)/images ; \
+ 	chmod 644 $(IMAGE_FILES)
+ 
+-$(SPARKY_INSTALL)/manual $(SPARKY_INSTALL)/manual/images:
++$(MANUAL_LOC) $(MANUAL_LOC)/images:
+ 	mkdir $@
+ 	chmod 755 $@
+ 
+Only in sparky/manual: manual-postscript.gz
+diff -ur -x make-sparky sparky.orig/python/Makefile sparky/python/Makefile
+--- sparky.orig/python/Makefile	2004-02-18 10:51:06.000000000 -0800
++++ sparky/python/Makefile	2005-12-17 19:43:06.000000000 -0800
+@@ -9,6 +9,8 @@
+ PYTHON_VERSION	= 2.3
+ PYTHON		= $(PYTHON_PREFIX)/bin/python$(PYTHON_VERSION)
+ PYTHON_LIB	= $(PYTHON_PREFIX)/lib/python$(PYTHON_VERSION)
++PYDIR		= $(SPARKY_INSTALL)/lib/python$(PYTHON_VERSION)/site-packages
++DOCDIR		= $(SPARKY_INSTALL)/share/doc/sparky
+ 
+ PYTHON_CODE	= __init__.py align.py assigngraph.py atomnames.py \
+ 		  atoms.py autoassign.py axes.py \
+@@ -27,18 +29,13 @@
+ 		  sputil.py start_in_chimera.py strips.py subprocess.py \
+ 		  tkutil.py volumeerror.py xeasy.py xplor.py
+ 
+-install: $(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
+-		$(SPARKY_INSTALL)/python/lib-tk
+-	$(INSTALL) README $(SPARKY_INSTALL)/python
+-	$(INSTALL) $(PYTHON_CODE) $(SPARKY_INSTALL)/python/sparky
+-	$(INSTALL) lib-tk/*.py $(SPARKY_INSTALL)/python/lib-tk
+-	chmod 644 $(SPARKY_INSTALL)/python/README
+-	cd $(SPARKY_INSTALL)/python/sparky ; chmod 644 $(PYTHON_CODE)
+-	chmod 644 $(SPARKY_INSTALL)/python/lib-tk/*.py
+-	$(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/sparky
+-	$(PYTHON) $(PYTHON_LIB)/compileall.py $(SPARKY_INSTALL)/python/lib-tk
++install: $(PYDIR) $(PYDIR)/sparky $(DOCDIR)/python
++	$(INSTALL) README $(DOCDIR)/python
++	$(INSTALL) $(PYTHON_CODE) $(PYDIR)/sparky
++	chmod 644 $(DOCDIR)/python/README
++	cd $(PYDIR)/sparky ; chmod 644 $(PYTHON_CODE)
+ 
+-$(SPARKY_INSTALL)/python $(SPARKY_INSTALL)/python/sparky \
+-  $(SPARKY_INSTALL)/python/lib-tk:
++$(PYDIR) $(PYDIR)/sparky \
++  $(PYDIR)/lib-tk $(DOCDIR)/python:
+ 	mkdir $@
+ 	chmod 755 $@
+diff -ur -x make-sparky sparky.orig/python/spingraph.py sparky/python/spingraph.py
+--- sparky.orig/python/spingraph.py	2001-12-17 10:51:10.000000000 -0800
++++ sparky/python/spingraph.py	2005-12-17 22:09:17.000000000 -0800
+@@ -831,7 +831,7 @@
+                'by creating a file specifying atom positions, colors,\n' +
+                'sizes, and text label positions.  Sparky provides a\n' +
+                'default layout file\n' +
+-               '\n\t/usr/local/sparky/python/spinlayout.py\n\n' +
++               '\n\t/usr/lib/python2.4/site-packages/sparky/python/spinlayout.py\n\n' +
+                'You override this file by making your own copy\n' +
+                '\n\t~/Sparky/Python/spinlayout.py\n\n' +
+                'You can create the desired template on the screen\n'
diff --git a/sci-chemistry/sparky/metadata.xml b/sci-chemistry/sparky/metadata.xml
new file mode 100644
index 000000000000..211b8bd0f0a4
--- /dev/null
+++ b/sci-chemistry/sparky/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer>
+<email>spyderous@gentoo.org</email>
+<name>Donnie Berkholz</name>
+</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/sparky/sparky-3.111.ebuild b/sci-chemistry/sparky/sparky-3.111.ebuild
new file mode 100644
index 000000000000..7220f4f657c6
--- /dev/null
+++ b/sci-chemistry/sparky/sparky-3.111.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/sparky/sparky-3.111.ebuild,v 1.1 2005/12/18 18:59:48 spyderous Exp $
+
+inherit eutils toolchain-funcs multilib python
+
+DESCRIPTION="Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers"
+HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/"
+SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib/${PN}-source-${PV}.tar.gz"
+LICENSE="sparky"
+SLOT="0"
+# Note: this package will probably require significant work for lib{32,64},
+# including parts of the patch.
+KEYWORDS="~x86"
+IUSE=""
+RDEPEND="=dev-lang/python-2.3*
+	=dev-lang/tk-8.4*
+	|| ( app-shells/tcsh app-shells/csh )"
+DEPEND="${RDEPEND}
+	>=app-shells/bash-3
+	net-misc/rsync"
+S="${WORKDIR}/${PN}"
+
+pkg_setup() {
+# Install for specific pythons instead of whatever's newest.
+# We build against 2.3, because sparky binary builds include 2.3.
+# 2.4 returns an error message:
+#Traceback (most recent call last):
+#  File "<string>", line 1, in ?
+#  File "/usr/lib/python2.4/site-packages/sparky/__init__.py", line 44, in start_session
+#    tk = tkutil.initialize_tk(argv)
+#  File "/usr/lib/python2.4/site-packages/sparky/tkutil.py", line 919, in initialize_tk
+#    tk = Tkinter.Tk(display, program_name, program_class)
+#  File "/usr/lib/python2.4/lib-tk/Tkinter.py", line 1569, in __init__
+#    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
+#TypeError: create() takes at most 5 arguments (8 given)
+
+	python="/usr/bin/python2.3"
+	python_version
+
+	arguments=( SPARKY="${S}" \
+		SPARKY_INSTALL_MAC="" \
+		SPARKY_INSTALL="${D}/usr" \
+		PYTHON_PREFIX="${ROOT}usr" \
+		PYTHON_VERSION="${PYVER}" \
+		TK_PREFIX="${ROOT}usr" \
+		TCLTK_VERSION="8.4" \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		INSTALL="rsync -avz" \
+		INSTALLDIR="rsync -avz" )
+
+	# It would be nice to get the docs versioned, but not critical
+	#	DOCDIR="\$(SPARKY_INSTALL)/share/doc/${PN}" \
+	# To get libdir working properly, we need to get makefiles respecting this
+	#	PYDIR="\$(SPARKY_INSTALL)/$(get_libdir)/python\$(PYTHON_VERSION)/site-packages" \
+}
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+
+	epatch ${FILESDIR}/fix-install.patch
+
+	sed -i \
+		-e "s:^\(set PYTHON[[:space:]]*=\).*:\1 ${ROOT}usr/bin/python${PYVER}:g" \
+		-e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${ROOT}usr/$(get_libdir):g" \
+		${S}/bin/sparky
+}
+
+src_compile() {
+	emake "${arguments[@]}" || die "make failed"
+}
+
+src_install() {
+	make "${arguments[@]}" install || die "install failed"
+	# Make internal help work
+	dosym ../../share/doc/sparky/manual /usr/lib/sparky/manual
+	# It returns a weird threading error message without this
+	dosym ../python${PYVER}/site-packages /usr/lib/sparky/python
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/lib/python${PYVER}/site-packages/sparky
+}