reinit the tree, so we can have metadata

8 files changed, 299 insertions, 0 deletions

diff --git a/sci-chemistry/sparky/Manifest b/sci-chemistry/sparky/Manifest
new file mode 100644
index 000000000000..97fa4139999e
--- /dev/null
+++ b/sci-chemistry/sparky/Manifest
@@ -0,0 +1,10 @@
+AUX 3.115-fix-c++14.patch 849 SHA256 69498ca78090e575aa1e8637cc0d6dd12298cdc66fdbcbad02bbc3a73672f664 SHA512 80bbfe8a2e853f8be84ed48da99605805a42bb05b091c851ddbefb5513745cdf51c5396e97ad4e3be7dd199270fb069e239e0c24f6642d956fd6571d8b14a7e1 WHIRLPOOL ca4c9f6940808207fb5d411395ef13a528d5e698f3d1511b400271ba765e5b299d2ac48913f457bfc8839a510bfac608ca8bc0fa513bd0db2becfabb78532374
+AUX 3.115-ldflags.patch 2713 SHA256 227c4ca0deb0a98a6ce40f03065c68a8ac433772ef3d318adb6d69705fedfefe SHA512 1c439cc04af3e8e403257ccd45eecb16f0e36d4b51a28ab5ddda269bde271d23a20bb453cda48e03f58c31a9a614d4b19ca2b6aa7f75bdfec1f79b70e8c361de WHIRLPOOL d5d96703d1450abfca4a70c5dae6971664bc9e844d869d83928b1e21f4da4bce2093b9478c4d23ac47f711d0a412a85c13c4c55f02eeabfdb0b6a91fff37cf49
+AUX 3.115-makefile.patch 580 SHA256 c265b6114c826c8c88b7e7256ef281cfefba00997f8c719146000f95017139a5 SHA512 9ddd99de93656301f307aabb3284e86fe68f4c7957f0b5ff81da4615f850fc36b686908de84816f0ff8a3d75169ccd0d4d7cb5bb8afd88d96c913f766e7ee19a WHIRLPOOL ac85d055252a82373b781ebb60eca7cf33e3d40e248c866238bb9395555679d20e88a81b307962e89654660a24290274fac45e5257a1fb915be6437e62919c8c
+AUX 3.115-paths.patch 415 SHA256 8a38226eb0b6cbf1cd5af9d4aad2a17da11897e8c8c027bfb18d9dac24d87b47 SHA512 44c44c99cf2c5c51c8e506267efc4efc50eb2277ccdab362943da0c45c63f9e797ae699e99eda3ce6ca0b4e0a886393d1917ce8614eea3086e97446fc3c0c674 WHIRLPOOL d7f1fad28bb51b03c30e61a6fbde8725cfb9602f78f3e494184beee1398d177b9d48ef024cd024554066e13eefbe5397221aff245e62f6fa11848a0f7f972ec2
+AUX 3.115-wrapper-r1.patch 1518 SHA256 e99acd1e5d735ee027361fda5d4c0652c729e2a02eedc80253fbc8b3654e89ea SHA512 be2c18a40ceabdb1c25a7849e1ee00438092f264c486e93b3bfb412fc417902a3b22b672d28a6cc104fedc5477ea2c0de66bc40dd5d4d607ed0201eee4d368a7 WHIRLPOOL 731d9511f3224399db3f108b9c8de8dfdda30a333389766d67610eb15c0196cda26464bc164aff3757c5af0bcb0414cf50b73b49dc9027bedae67360a46e395e
+DIST sparky-source-3.115.tar.gz 4103686 SHA256 c187546aaec3d6489c533c3a778e1fe6fa634a931dcaf245c1e13f5720a002b6 SHA512 33b0fd368f15bf4d091d7152a189f57279aea54fb89a12f15314f2a1414b073f7bd282afedeb72e79192195b0b6ac212ca74da3def513592af5400c118ac8e89 WHIRLPOOL 8557a525eab51150da437f78cb8e404adad4f41ed0884498601887e832f78bb316e4847cc3b3a7147ec66bcddd4e06064323bb2ce76452b37d504a809feee7ff
+EBUILD sparky-3.115-r2.ebuild 3192 SHA256 7f6a628c6056e9813558755f0298c47dd5a085658d7f177c429ffa86f19b0627 SHA512 f2f5fe11666e85feca9d90c5fb6c9d93f42b9bde269f311a943c37b334d617d7dcdbc5ee45cb555fb6af278a648c0c0ab4ec28027143675ee0cc2c77dc41c10a WHIRLPOOL 4b5fae4301f184c8c041f39a7c86b3c5d197ff0b2249cb1fc24ad3a5e2c2928e72fb51c61f799ac0a7a09a1460832639abc5b91effa5e5a5e5d60ed6ceb7e60b
+MISC ChangeLog 3430 SHA256 fb5967bd22cef4fab1fa90f3e1a3e172b04fcbe992ac15c770a8a2bc824730b0 SHA512 14176a5d6f72e01337637ccdf402861638aecbba820c081c0aa6b350046cb60c0440378095db0686654434a3a432f6fc2ffc3944d1616868e48011e8ca7f52ab WHIRLPOOL 0d388824720b03aa771ae240a3595d58009f6b388806011752af7fb84e479e5928f99170e3e4b3dab0aa6181d115c050af93acc79b8161f5572d24dc22f1e406
+MISC ChangeLog-2015 3615 SHA256 ca930454305a6c0a819f94c74357aa75f93971b0427880550a7a3c0cc9b01d42 SHA512 ba7e788c591eed7e3a61ac8650757557ba44adf5265e0dabad54e0802dc68a5091f15300f6dd5e6f08aacc4b6b66f2b65f815acd14504c624dc5c60b9b0a3ec2 WHIRLPOOL 357f7369e9a0eae7d9f23c92fced2f8da8b63f598e6218f87b2405c76993800bfc6a07867e30cd3e9ffebc0a906c06108667db0aa736fee8e92f74dc5c37fa42
+MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269
diff --git a/sci-chemistry/sparky/files/3.115-fix-c++14.patch b/sci-chemistry/sparky/files/3.115-fix-c++14.patch
new file mode 100644
index 000000000000..3a05ea7d85ce
--- /dev/null
+++ b/sci-chemistry/sparky/files/3.115-fix-c++14.patch
@@ -0,0 +1,32 @@
+Fix the custom new/new[] operators in order to account for changed
+noexcept semantics in C++11.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=596012
+
+Patch by Peter Levine
+
+--- a/c++/memalloc.cc
++++ b/c++/memalloc.cc
+@@ -39,7 +39,10 @@
+ 
+ // ----------------------------------------------------------------------------
+ //
+-void *operator new(size_t size) throw(std::bad_alloc)
++void *operator new(size_t size)
++#if __cplusplus < 201103L
++throw(std::bad_alloc)
++#endif
+ {
+   void *value = allocate(size);
+   if (tracking_memory)
+@@ -72,7 +75,10 @@
+ 
+ // ----------------------------------------------------------------------------
+ //
+-void *operator new[](size_t size) throw(std::bad_alloc)
++void *operator new[](size_t size)
++#if __cplusplus < 201103L
++throw(std::bad_alloc)
++#endif
+ {
+   void *value = allocate(size);
+   if (tracking_memory)
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/metadata.xml b/sci-chemistry/sparky/metadata.xml
new file mode 100644
index 000000000000..8937bad0b175
--- /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>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/sparky/sparky-3.115-r2.ebuild b/sci-chemistry/sparky/sparky-3.115-r2.ebuild
new file mode 100644
index 000000000000..e664747fea13
--- /dev/null
+++ b/sci-chemistry/sparky/sparky-3.115-r2.ebuild
@@ -0,0 +1,117 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="tk"
+
+inherit flag-o-matic prefix python-single-r1 toolchain-funcs
+
+DESCRIPTION="Graphical NMR assignment and integration program for large polymers"
+HOMEPAGE="http://www.cgl.ucsf.edu/home/sparky/"
+SRC_URI="http://www.cgl.ucsf.edu/home/sparky/distrib-${PV}/${PN}-source-${PV}.tar.gz"
+
+LICENSE="sparky"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="${PYTHON_DEPS}
+	app-shells/tcsh
+	dev-lang/tcl:0=
+	dev-lang/tk:0="
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/${PN}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-ldflags.patch
+	"${FILESDIR}"/${PV}-wrapper-r1.patch
+	"${FILESDIR}"/${PV}-paths.patch
+	"${FILESDIR}"/${PV}-makefile.patch
+	"${FILESDIR}"/${PV}-fix-c++14.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() {
+	default
+
+	sed -i \
+		-e "s:^\(set PYTHON =\).*:\1 ${PYTHON}: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/$(get_libdir)" \
+		PYTHON_INC="$(python_get_includedir)" \
+		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/$(get_libdir)" \
+		PYTHON_INC="$(python_get_includedir)" \
+		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
+
+	python_moduleinto ${PN}
+	python_domodule python/*.py c++/{spy.so,_tkinter.so}
+	dosym ../${EPYTHON}/site-packages /usr/$(get_libdir)/${PN}/python
+
+	rm manual/{pkzip.cfg,Makefile} || die
+	mv {manual/,}manual.ps || die
+	local DOCS=( README manual.ps )
+	local HTML_DOCS=( manual/. )
+	einstalldocs
+	newdoc python/README README.python
+	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/manual
+
+	if use examples; then
+		dodoc -r example
+		dosym ../../share/doc/${PF}/example /usr/$(get_libdir)/${PN}/example
+	fi
+}