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

7 files changed, 306 insertions, 0 deletions

diff --git a/sci-chemistry/eden/Manifest b/sci-chemistry/eden/Manifest
new file mode 100644
index 000000000000..c0087f8f962b
--- /dev/null
+++ b/sci-chemistry/eden/Manifest
@@ -0,0 +1 @@
+DIST eden_V5.3.tar.gz 1139981 SHA256 249447f507ace3e188ce0d76796c6e307c043592405db1f6c24f3e90917ec524 SHA512 c59d08004bdb72ef39fe205aef546fbcff9c57ee42942c0391052de9c501c7793ed3bd280569020c2b9ec6133a87362d184a2012b61c6be18b5f6ba9b59716c5 WHIRLPOOL f0329805ab1d3b75febcc07c87583ee30f2ca44d5b5ae5c3512d4891a8763bf45ab7dc94abed831c0326cdbc35502f4bc3904ccb7447b090100b2f7d52b1156b
diff --git a/sci-chemistry/eden/eden-5.3-r2.ebuild b/sci-chemistry/eden/eden-5.3-r2.ebuild
new file mode 100644
index 000000000000..8dc430e329b1
--- /dev/null
+++ b/sci-chemistry/eden/eden-5.3-r2.ebuild
@@ -0,0 +1,87 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+MY_P="${PN}_V${PV}"
+
+DESCRIPTION="A crystallographic real-space electron-density refinement and optimization program"
+HOMEPAGE="http://www.gromacs.org/pipermail/eden-users/"
+SRC_URI="mirror://gentoo/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="double-precision"
+
+RDEPEND="
+	sci-libs/fftw:2.1
+	sci-libs/gsl"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}/${PN}"
+
+SRC="${S}/source"
+
+pkg_setup() {
+	export EDENHOME="${EPREFIX}/usr/$(get_libdir)/${PN}"
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-makefile-fixes.patch \
+		"${FILESDIR}"/${P}-impl-dec.patch \
+		"${FILESDIR}"/${P}-format-security.patch
+
+	sed -i \
+		-e "s:^\(FFTW.*=\).*:\1 ${EPREFIX}/usr:g" \
+		-e "s:^\(LIB.*=.*\$(FFTW)/\).*:\1$(get_libdir):g" \
+		-e "s:^\(BIN.*=\).*:\1 ${D}usr/bin:g" \
+		-e "s:^\(CFLAGS.*=\).*:\1 ${CFLAGS}:g" \
+		-e "s:-lgsl -lgslcblas:$($(tc-getPKG_CONFIG) --libs gsl):g" \
+		${SRC}/Makefile || die
+
+	if ! use double-precision; then
+		sed -i -e "s:^\(DOUBLESWITCH.*=\).*:\1 OFF:g" ${SRC}/Makefile || die
+		EDEN_EXE="s${PN}"
+	else
+		EDEN_EXE="d${PN}"
+	fi
+}
+
+src_compile() {
+	emake CC=$(tc-getCC) -C ${SRC}
+}
+
+src_install() {
+	emake -C ${SRC} install
+
+	python_foreach_impl python_newscript python/${PN}.py i${PN}
+	python_foreach_impl python_domodule python/FileListDialog.py
+
+	rm python/*py || die
+	insinto ${EDENHOME}/python
+	doins python/*
+
+	insinto ${EDENHOME}/help
+	doins help/*
+
+	insinto ${EDENHOME}/tools
+	doins tools/*
+
+	dodoc manual/UserManual.pdf
+
+	cat >> "${T}"/60${PN} <<- EOF
+	EDENHOME="${EDENHOME}"
+	EOF
+
+	doenvd "${T}"/60${PN}
+
+	dosym ${EDEN_EXE} /usr/bin/${PN}
+}
diff --git a/sci-chemistry/eden/files/5.3-makefile-fixes.patch b/sci-chemistry/eden/files/5.3-makefile-fixes.patch
new file mode 100644
index 000000000000..632358341784
--- /dev/null
+++ b/sci-chemistry/eden/files/5.3-makefile-fixes.patch
@@ -0,0 +1,60 @@
+ source/Makefile |   17 ++++++++++-------
+ 1 files changed, 10 insertions(+), 7 deletions(-)
+
+diff --git a/source/Makefile b/source/Makefile
+index 46d89cc..aa751c7 100644
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -78,8 +78,10 @@ CFLAGS		=   -Wall -pipe -g3
+ #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
+ #CFLAGS		=   -Wall -O3 -march=i686 
+ ifneq ($(FFTW),/usr/local)
++ifneq ($(FFTW),/usr)
+ CFLAGS		+= -I$(INC)
+ endif
++endif
+ 
+ #			NOTE:
+ # DOUBLESWITCH = ON	for double precision;
+@@ -91,15 +93,15 @@ endif
+ DOUBLESWITCH 	= ON
+ 
+ ifeq ($(DOUBLESWITCH),ON)
+-LDFLAGS	 = -L$(LIB) -ldfftw -lm  
++LIBS	 = -L$(LIB) -ldfftw -lm  
+ CFLAGS	+= -DDOUBLE 
+ TARGET	 = deden
+ else
+-LDFLAGS	 = -L$(LIB) -lsfftw -lm  
++LIBS	 = -L$(LIB) -lsfftw -lm  
+ TARGET	 = seden
+ endif
+ 
+-LDFLAGS += -g -lgsl -lgslcblas 
++LIBS += -lgsl -lgslcblas 
+ 
+ # GSL_PREFIX:= /sw/lib
+ # LDFLAGS += -l$(GSL_PREFIX)/libgsl.a -l$(GSL_PREFIX)/libgslcblas.a 
+@@ -120,17 +122,18 @@ OBJ	= 	addmaps.o   apodfc.o   apodfo.o     back.o     cadhkl.o  \
+ all:		eden	fbyteswap 
+ 
+ eden:  		eden.o   $(OBJ)
+-		$(CC)  $^ $(LDFLAGS) -o $@
++		$(CC)  $(LDFLAGS) -o $@ $^ $(LIBS)
+ 
+ fbyteswap:	fbyteswap.c		
+-		$(CC) -o $@ $^
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
+ 
+ install:	all
++		mkdir -p $(BIN)
+ 		mv fbyteswap $(BIN)
+ 		mv eden $(BIN)/$(TARGET)
+ 		chmod 751 $(BIN)/$(TARGET)
+-		chmod +x mkeden.csh
+-		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
++#		chmod +x mkeden.csh
++#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
+ 
+ dist:		clean
+ 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/files/eden-5.3-format-security.patch b/sci-chemistry/eden/files/eden-5.3-format-security.patch
new file mode 100644
index 000000000000..04b5ecfddebb
--- /dev/null
+++ b/sci-chemistry/eden/files/eden-5.3-format-security.patch
@@ -0,0 +1,96 @@
+ source/back.c     | 2 +-
+ source/concosts.c | 4 ++--
+ source/count.c    | 4 ++--
+ source/eden.c     | 2 +-
+ source/util.c     | 4 ++--
+ 5 files changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/source/back.c b/source/back.c
+index fd517b9..185a02b 100644
+--- a/source/back.c
++++ b/source/back.c
+@@ -112,7 +112,7 @@ void	back_main(int argc, char *argv[])
+           ballpark(caller) ;
+ 
+      if (argc > optind+2)
+-	  sprintf(sf_filename, argv[optind+2]) ;
++	  sprintf(sf_filename, "%s", argv[optind+2]) ;
+ 
+   /*********************************************
+   Pull off prefix defining whereabouts of input 
+diff --git a/source/concosts.c b/source/concosts.c
+index d62d2e3..590f073 100644
+--- a/source/concosts.c
++++ b/source/concosts.c
+@@ -452,7 +452,7 @@ void	prepare_singlets(char *filename)
+                       sprintf(message, 
+ 		      "s=%d, p=%d, n=%d, phase=%g, old phase=%g, delta=%g\n", 
+                       s, p, n, phase, *(checks+n), phase-*(checks+n)) ;
+-                      fprintf(fp_log, message) ;
++                      fprintf(fp_log, "%s", message) ;
+                  }
+               } 
+ 		/***********************************************
+@@ -556,7 +556,7 @@ void	prepare_triplets(char *filename)
+ 		 sprintf(message, 
+ "Triplet (%d %d %d) from input (%d %d %d) corresponds to point w/o fobs info!\n",
+ 		   newh, newk, newl, t_h[q], t_k[q], t_l[q]) ;
+-		 fprintf(fp_log, message) ;
++		 fprintf(fp_log, "%s", message) ;
+ 		 legal_triplet = FALSE ;
+               }
+            }
+diff --git a/source/count.c b/source/count.c
+index c3bc390..ca13008 100644
+--- a/source/count.c
++++ b/source/count.c
+@@ -460,12 +460,12 @@ void	print_el_count(char *filename,
+      }
+ 
+      sprintf(message, "\nTotal no. of electrons is %g\n", totnump*volvox) ;
+-     fprintf(fp, message) ;
++     fprintf(fp, "%s", message) ;
+      printTwice(message) ;
+ 
+      sprintf(message, "Count of all remaining electrons: %g %g %g\n", 
+      remainder0*volvox, remainder1*volvox, remainder2*volvox) ;
+-     fprintf(fp, message) ;
++     fprintf(fp, "%s", message) ;
+      printTwice(message) ;
+ 
+      fclose(fp) ;
+diff --git a/source/eden.c b/source/eden.c
+index dea3246..5a9b389 100644
+--- a/source/eden.c
++++ b/source/eden.c
+@@ -319,7 +319,7 @@ int	main(int argc, char *argv[])
+ 
+      get_unique_logname() ;
+ 
+-     sprintf(command_line, argv[0]) ;
++     sprintf(command_line, "%s", argv[0]) ;
+ 
+      for (k = 1; k < argc; k++) { 
+          strcat(command_line, " ") ;
+diff --git a/source/util.c b/source/util.c
+index 6fff179..41c624c 100644
+--- a/source/util.c
++++ b/source/util.c
+@@ -266,7 +266,7 @@ void	printTwice(char *mess)	/* send info to terminal (stdout) and to log */
+  
+ void	prompt(char *mess)	/* Send message to user, await reply */
+ {
+-    fprintf(stdout, mess) ;
++    fprintf(stdout, "%s", mess) ;
+ 
+     while (fgets(terminp, MAXSTRING, stdin) != NULL)  {
+ 	if ((int)strlen(terminp) > 0) 
+@@ -722,7 +722,7 @@ void	start_record()
+      int	k ;
+ 
+      rec_length = k = sprintf(record, "\n") ;
+-     rec_length += sprintf(record+k, timestamp()) ;
++     rec_length += sprintf(record+k, "%s", timestamp()) ;
+      k = rec_length ;
+ 
+      if ((cwd = getcwd(NULL, 120)) == NULL) 
diff --git a/sci-chemistry/eden/files/eden-5.3-impl-dec.patch b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
new file mode 100644
index 000000000000..af67508d090e
--- /dev/null
+++ b/sci-chemistry/eden/files/eden-5.3-impl-dec.patch
@@ -0,0 +1,28 @@
+ source/fbyteswap.c |    1 +
+ source/util.c      |    1 +
+ 2 files changed, 2 insertions(+), 0 deletions(-)
+
+diff --git a/source/fbyteswap.c b/source/fbyteswap.c
+index 83015b9..c9033c3 100644
+--- a/source/fbyteswap.c
++++ b/source/fbyteswap.c
+@@ -39,6 +39,7 @@ and shall not be used for advertising or product endorsement purposes.
+ 
+ #include <stdio.h>
+ #include <fcntl.h>
++#include <unistd.h>
+ #include <sys/stat.h>
+ #include <sys/types.h>
+ void byteswap();
+diff --git a/source/util.c b/source/util.c
+index 6fff179..ca7a957 100644
+--- a/source/util.c
++++ b/source/util.c
+@@ -89,6 +89,7 @@ and shall not be used for advertising or product endorsement purposes.
+ 
+ *******************************************************************************/
+ #include  <sys/time.h>	/* ... for picking up date & time	*/
++#include <time.h>
+ #include  <signal.h>	/* ... for capturing kill		*/
+ #include  "util.h"
+ 
diff --git a/sci-chemistry/eden/files/makefile-fixes.patch b/sci-chemistry/eden/files/makefile-fixes.patch
new file mode 100644
index 000000000000..4cfff3f515df
--- /dev/null
+++ b/sci-chemistry/eden/files/makefile-fixes.patch
@@ -0,0 +1,25 @@
+diff -ur eden.orig/source/Makefile eden/source/Makefile
+--- eden.orig/source/Makefile	2004-10-18 10:40:03.000000000 -0700
++++ eden/source/Makefile	2005-12-15 22:32:45.000000000 -0800
+@@ -78,8 +78,10 @@
+ #CFLAGS		=   -Wall -pipe -marchi686 -pedantic  -gdwarf-2 -g3
+ #CFLAGS		=   -Wall -O3 -march=i686 
+ ifneq ($(FFTW),/usr/local)
++ifneq ($(FFTW),/usr)
+ CFLAGS		+= -I$(INC)
+ endif
++endif
+ 
+ #			NOTE:
+ # DOUBLESWITCH = ON	for double precision;
+@@ -129,8 +131,8 @@
+ 		mv fbyteswap $(BIN)
+ 		mv eden $(BIN)/$(TARGET)
+ 		chmod 751 $(BIN)/$(TARGET)
+-		chmod +x mkeden.csh
+-		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
++#		chmod +x mkeden.csh
++#		./mkeden.csh $(BIN) $(BIN)/$(TARGET)
+ 
+ dist:		clean
+ 		cd ../..; tar -cvf eden_$(VERSION).tar --exclude CVS --exclude \#\*\# --exclude \*~ --exclude Misc --exclude .\* eden; gzip -f eden_$(VERSION).tar
diff --git a/sci-chemistry/eden/metadata.xml b/sci-chemistry/eden/metadata.xml
new file mode 100644
index 000000000000..732277b2b750
--- /dev/null
+++ b/sci-chemistry/eden/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-chemistry</herd>
+  <use>
+    <flag name="double-precision">More precise calculations at the expense of
+    speed</flag>
+  </use>
+</pkgmetadata>