proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

10 files changed, 602 insertions, 0 deletions

diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest
new file mode 100644
index 000000000000..1e8514f6cde8
--- /dev/null
+++ b/sci-chemistry/sparky/Manifest
@@ -0,0 +1 @@
+DIST sparky-source-3.115.tar.gz 4103686 SHA256 c187546aaec3d6489c533c3a778e1fe6fa634a931dcaf245c1e13f5720a002b6 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 WHIRLPOOL 8557a525eab51150da437f78cb8e404adad4f41ed0884498601887e832f78bb316e4847cc3b3a7147ec66bcddd4e06064323bb2ce76452b37d504a809feee7ff
diff --git a/sci-chemistry/sparky/files/3.115-fpic.patch b/sci-chemistry/sparky/files/3.115-fpic.patch
new file mode 100644
index 000000000000..37725aa029e2
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-fpic.patch
@@ -0,0 +1,42 @@
+diff --git a/c++/Makefile b/c++/Makefile
+index 421ff77..7442ed3 100644
+--- a/c++/Makefile
++++ b/c++/Makefile
+@@ -158,7 +158,7 @@ winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc
+ 	$(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc
+ 
+ python.o: python.cc
+-	$(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
++	$(CXX) $(CXXFLAGS) -fPIC $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
+ 
+ _tkinter.so: _tkinter.o
+ 	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS)
+diff --git a/c++/Makefile b/c++/Makefile
+index 353122d..84b0c24 100644
+--- a/c++/Makefile
++++ b/c++/Makefile
+@@ -168,7 +168,7 @@ _tkinter.o: _tkinter.c
+ 
+ Makefile.dep: force
+ 	cd $(SPARKY_SRC) ; \
+-	$(CXX) $(DEPEND) $(CXXFLAGS) $(TKFLAGS) $(PYFLAGS) \
++	$(CXX) $(DEPEND) $(CXXFLAGS) -fPIC $(TKFLAGS) $(PYFLAGS) \
+ 		$(SPARKY_OBJS:.o=.cc) $(OTHER_OBJS:.o=.cc) > $@
+ 
+ TAGS: force
+diff --git a/c++/Makefile b/c++/Makefile
+index 84b0c24..933f347 100644
+--- a/c++/Makefile
++++ b/c++/Makefile
+@@ -30,9 +30,9 @@ TCL_LIBNAME	= tcl$(TCLTK_VERSION)
+ PLATFORM	= unix
+ 
+ CXX		= g++
+-CXXFLAGS	= 
++CXXFLAGS	+= -fPIC
+ CC		= gcc
+-CFLAGS		=
++CFLAGS		+= -fPIC
+ PYFLAGS		= -I$(PYTHON_INC) -I$(PYTHON_LIB)/config
+ TKFLAGS		= -I$(TK_PREFIX)/include
+ TKLIBS		= -L$(TK_PREFIX)/lib -l$(TK_LIBNAME) -l$(TCL_LIBNAME) -lX11
diff --git a/sci-chemistry/sparky/files/3.115-ldflags.patch b/sci-chemistry/sparky/files/3.115-ldflags.patch
new file mode 100644
index 000000000000..bd4020387682
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-ldflags.patch
@@ -0,0 +1,61 @@
+diff --git a/c++/Makefile b/c++/Makefile
+index aeb4daa..5cab356 100644
+--- a/c++/Makefile
++++ b/c++/Makefile
+@@ -131,28 +131,28 @@ $(SPARKY_INSTALL)/python/sparky $(SPARKY_INSTALL)/python/lib-tk:
+ 	chmod 755 $@
+ 
+ sparky-no-python$(EXE_SUFFIX): main.o $(SPARKY_OBJS)
+-	$(CXX) -o $@ main.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ main.o $(SPARKY_OBJS) $(LDLIBS)
+ 
+ ucsfdata$(EXE_SUFFIX): ucsfdata.o $(NMR_OBJS)
+-	$(CXX) -o $@ ucsfdata.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ ucsfdata.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ pipe2ucsf$(EXE_SUFFIX): pipe2ucsf.o $(NMR_OBJS)
+-	$(CXX) -o $@ pipe2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ pipe2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ vnmr2ucsf$(EXE_SUFFIX): vnmr2ucsf.o $(NMR_OBJS)
+-	$(CXX) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ vnmr2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ bruk2ucsf$(EXE_SUFFIX): bruk2ucsf.o $(NMR_OBJS)
+-	$(CXX) -o $@ bruk2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ bruk2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ peaks2ucsf$(EXE_SUFFIX): peaks2ucsf.o $(NMR_OBJS)
+-	$(CXX) -o $@ peaks2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ peaks2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ matrix2ucsf$(EXE_SUFFIX): matrix2ucsf.o $(NMR_OBJS)
+-	$(CXX) -o $@ matrix2ucsf.o $(NMR_OBJS) $(LDFLAGS) $(SYSLIBS) $(EXTRALIBS)
++	$(CXX) $(LDFLAGS) -o $@ matrix2ucsf.o $(NMR_OBJS) $(SYSLIBS) $(EXTRALIBS)
+ 
+ spy.so: python.o $(SPARKY_OBJS)
+-	$(CXX) $(LDSHARED) -o $@ python.o $(SPARKY_OBJS) $(LDFLAGS) $(LDLIBS)
++	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ python.o $(SPARKY_OBJS) $(LDLIBS)
+ 
+ winsystem-$(PLATFORM).o: winsystem-$(PLATFORM).cc
+ 	$(CXX) $(CXXFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/winsystem-$(PLATFORM).cc
+@@ -161,7 +161,7 @@ python.o: python.cc
+ 	$(CXX) $(CXXFLAGS) $(PYFLAGS) $(TKFLAGS) -c $(SPARKY_SRC)/python.cc
+ 
+ _tkinter.so: _tkinter.o
+-	$(CXX) $(LDSHARED) -o $@ _tkinter.o $(LDFLAGS) $(TKLIBS)
++	$(CXX) $(LDSHARED) $(LDFLAGS) -o $@ _tkinter.o $(TKLIBS)
+ 
+ _tkinter.o: _tkinter.c
+ 	$(CC) $(CFLAGS) $(TKFLAGS) $(PYFLAGS) -c $(SPARKY_SRC)/_tkinter.c
+@@ -188,8 +188,8 @@ PYLDFLAGS	= -L$(PYTHON_LIB)/config -lpython$(PYTHON_VERSION)
+ PYIFLAGS	= -I$(PYTHON_INC)
+ 
+ debug-sparky: main-debug.o python.o _tkinter.o $(SPARKY_OBJS)
+-	$(CXX) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
+-		$(LDFLAGS) $(PYLDFLAGS) $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ main-debug.o python.o _tkinter.o $(SPARKY_OBJS) \
++		$(PYLDFLAGS) $(LDLIBS)
+ 
+ main-debug.o: main-debug.cc
+ 	$(CXX) $(CXXFLAGS) $(PYIFLAGS) -c $(SPARKY_SRC)/main-debug.cc
diff --git a/sci-chemistry/sparky/files/3.115-makefile.patch b/sci-chemistry/sparky/files/3.115-makefile.patch
new file mode 100644
index 000000000000..7c810dcbd8ae
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-makefile.patch
@@ -0,0 +1,17 @@
+diff --git a/Makefile b/Makefile
+index bb27034..30979bd 100644
+--- a/Makefile
++++ b/Makefile
+@@ -48,6 +48,12 @@ TKINTER_PYMOD	= _tkinter$(PYMOD_SUFFIX)
+ all nopython $(SPY_PYMOD) $(TKINTER_PYMOD) $(EXECUTABLES) debug-sparky clean: force
+ 	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $@
+ 
++libraries:
++	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(SPY_PYMOD) $(TKINTER_PYMOD)
++
++binaries:
++	cd $(SPARKY_OBJ) && $(MAKE) -f $(SPARKY_SRC)/Makefile -e $(EXECUTABLES) debug-sparky
++
+ Makefile.dep TAGS: force
+ 	cd $(SPARKY_SRC) && $(MAKE) -f Makefile -e $@
+ 
diff --git a/sci-chemistry/sparky/files/3.115-paths.patch b/sci-chemistry/sparky/files/3.115-paths.patch
new file mode 100644
index 000000000000..20d9a801ecd6
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-paths.patch
@@ -0,0 +1,13 @@
+diff --git a/c++/paths.h b/c++/paths.h
+index 2a21366..38aff52 100644
+--- a/c++/paths.h
++++ b/c++/paths.h
+@@ -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 --git a/sci-chemistry/sparky/files/3.115-wrapper-r1.patch b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
new file mode 100644
index 000000000000..d83b5b8510cc
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-wrapper-r1.patch
@@ -0,0 +1,41 @@
+diff --git a/bin/sparky b/bin/sparky
+index 8b51212..270723a 100644
+--- a/bin/sparky
++++ b/bin/sparky
+@@ -4,18 +4,6 @@
+ #
+ 
+ # -----------------------------------------------------------------------------
+-# 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 "$sparky_bin"`
+-
+-# -----------------------------------------------------------------------------
+ # Sparky uses the SPARKY_INSTALL environment variable to find its
+ # application resource file and print prolog file.
+ #
+@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL		"$sparky_inst"
+ # If Python is available start Sparky as a Python extension.
+ # Otherwise the standalone version of Sparky is started.
+ #
+-set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5"
++set PYTHON = GENTOO_PYTHON
+ if (! -e "$PYTHON") then
+   set PYTHON = python2.5
+ endif
+@@ -79,7 +67,7 @@ if ($status == 0) then
+   # ---------------------------------------------------------------------------
+   # Add the Sparky package and Tkinter to the Python path
+   #
+-  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk"
++  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky"
+   if ($?PYTHONPATH) then
+     setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH"
+   else
diff --git a/sci-chemistry/sparky/files/3.115-wrapper.patch b/sci-chemistry/sparky/files/3.115-wrapper.patch
new file mode 100644
index 000000000000..9498c0bec837
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-wrapper.patch
@@ -0,0 +1,41 @@
+diff --git a/bin/sparky b/bin/sparky
+index 8b51212..270723a 100644
+--- a/bin/sparky
++++ b/bin/sparky
+@@ -4,18 +4,6 @@
+ #
+ 
+ # -----------------------------------------------------------------------------
+-# 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 "$sparky_bin"`
+-
+-# -----------------------------------------------------------------------------
+ # Sparky uses the SPARKY_INSTALL environment variable to find its
+ # application resource file and print prolog file.
+ #
+@@ -25,7 +13,7 @@ setenv SPARKY_INSTALL		"$sparky_inst"
+ # If Python is available start Sparky as a Python extension.
+ # Otherwise the standalone version of Sparky is started.
+ #
+-set PYTHON = "$SPARKY_INSTALL/python2.5/bin/python2.5"
++set PYTHON = "@GENTOO_PORTAGE_EPREFIX@/usr/bin/python"
+ if (! -e "$PYTHON") then
+   set PYTHON = python2.5
+ endif
+@@ -79,7 +67,7 @@ if ($status == 0) then
+   # ---------------------------------------------------------------------------
+   # Add the Sparky package and Tkinter to the Python path
+   #
+-  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/lib-tk"
++  set SPARKY_PYTHONPATH = "$SPARKY_INSTALL/python:$SPARKY_INSTALL/python/sparky"
+   if ($?PYTHONPATH) then
+     setenv PYTHONPATH "${SPARKY_PYTHONPATH}:$PYTHONPATH"
+   else
diff --git a/sci-chemistry/sparky/files/fix-install.patch b/sci-chemistry/sparky/files/fix-install.patch
new file mode 100644
index 000000000000..4eefaa891f99
--- /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		@GENTOO_PORTAGE_EPREFIX@/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/python*/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..ae9ec7c5f6a4
--- /dev/null
+++ b/sci-chemistry/sparky/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/sparky/sparky-3.115-r1.ebuild b/sci-chemistry/sparky/sparky-3.115-r1.ebuild
new file mode 100644
index 000000000000..b28e5351dc5b
--- /dev/null
+++ b/sci-chemistry/sparky/sparky-3.115-r1.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
+
+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-${PV}/${PN}-source-${PV}.tar.gz"
+
+LICENSE="sparky"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	app-shells/tcsh
+	dev-lang/tcl:0=
+	dev-lang/tk:0="
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-ldflags.patch
+	"${FILESDIR}"/${PV}-wrapper-r1.patch
+	"${FILESDIR}"/${PV}-paths.patch
+	"${FILESDIR}"/${PV}-makefile.patch
+	)
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	TKVER=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+	PYVER=${EPYTHON#python}
+}
+
+src_prepare() {
+	epatch ${PATCHES[@]}
+
+	sed -i \
+		-e "s:^\(set PYTHON =\).*:\1 ${EPREFIX}/usr/bin/${EPYTHON}:g" \
+		-e "s:^\(setenv SPARKY_INSTALL[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir)/${PN}:g" \
+		-e "s:tcl8.4:tcl${TKVER}:g" \
+		-e "s:tk8.4:tk${TKVER}:g" \
+		-e "s:^\(setenv TCLTK_LIB[[:space:]]*\).*:\1 ${EPREFIX}/usr/$(get_libdir):g" \
+		"${S}"/bin/sparky || die
+	eprefixify "${S}"/bin/sparky
+}
+
+src_compile() {
+	emake \
+		SPARKY="${S}" \
+		PYTHON_VERSION="${PYVER}" \
+		PYTHON_PREFIX="${EPREFIX}/usr" \
+		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
+		PYTHON_INC="${EPREFIX}/usr/include/${EPYTHON}" \
+		TK_PREFIX="${EPREFIX}/usr" \
+		TCLTK_VERSION="${TKVER}" \
+		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		LDSHARED="-shared" \
+		binaries
+
+	rm c++/*.o || die
+
+	emake \
+		SPARKY="${S}" \
+		PYTHON_VERSION="${PYVER}" \
+		PYTHON_PREFIX="${EPREFIX}/usr" \
+		PYTHON_LIB="${EPREFIX}/usr/$(get_libdir)" \
+		PYTHON_INC="${EPREFIX}/usr/include/${EPYTHON}" \
+		TK_PREFIX="${EPREFIX}/usr" \
+		TCLTK_VERSION="${TKVER}" \
+		TKLIBS="-L${EPREFIX}/usr/$(get_libdir)/ -ltk -ltcl -lX11" \
+		CXX="$(tc-getCXX)" \
+		CC="$(tc-getCC)" \
+		CXXFLAGS="${CXXFLAGS} -fPIC" \
+		CFLAGS="${CFLAGS} -fPIC" \
+		LDSHARED="-shared -fPIC" \
+		libraries
+}
+
+src_install() {
+	# The symlinks are needed to avoid hacking the complete code to fix the locations
+
+	dobin c++/{{bruk,matrix,peaks,pipe,vnmr}2ucsf,ucsfdata,sparky-no-python} bin/${PN}
+
+	insinto /usr/share/${PN}/
+	doins lib/{print-prolog.ps,Sparky}
+	dosym ../../share/${PN}/print-prolog.ps /usr/$(get_libdir)/${PN}/print-prolog.ps
+	dosym ../../share/${PN}/Sparky /usr/$(get_libdir)/${PN}/Sparky
+
+	dohtml -r manual/*
+	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual
+
+	python_moduleinto ${PN}
+	python_domodule python/*.py c++/{spy.so,_tkinter.so}
+
+	python_optimize
+
+	dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python
+
+	if use examples; then
+		insinto /usr/share/doc/${PF}/
+		doins -r example || die
+		dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example
+	fi
+
+	dodoc README
+	newdoc python/README README.python
+}