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, 307 insertions, 0 deletions

diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest
new file mode 100644
index 00000000000..e082cb44f7f
--- /dev/null
+++ b/sci-chemistry/ccp4i/Manifest
@@ -0,0 +1,3 @@
+DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
+DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
+DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8
diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
new file mode 100644
index 00000000000..f5ac55ef17f
--- /dev/null
+++ b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild
@@ -0,0 +1,99 @@
+# 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-single-r1 virtualx
+
+MY_PN="${PN%i}"
+MY_P="${MY_PN}-${PV}"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC_URI="
+	${SRC}/${PV}/${MY_P}-core-src.tar.gz
+	mirror://gentoo/${P}-arpwarp.patch.bz2
+	http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
+[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux"
+LICENSE="ccp4"
+IUSE=""
+
+RDEPEND="
+	app-shells/tcsh
+	media-gfx/graphviz
+	>=dev-lang/tk-8.3:0
+	>=dev-tcltk/blt-2.4
+	sci-libs/ccp4-libs"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-fix-baubles.patch
+	"${WORKDIR}"/${P}-arpwarp.patch
+	)
+
+src_prepare() {
+	epatch ${PATCHES[@]}
+
+	[[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
+	python_fix_shebang ccp4i/ share/dbccp4i/
+}
+
+src_configure() {
+	:
+}
+
+src_compile() {
+	:
+}
+
+src_install() {
+	# rm imosflm stuff
+	rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die
+
+	rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die
+
+	# This is installed by mrbump
+	rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die
+
+	# CCP4Interface - GUI
+	insinto /usr/$(get_libdir)/ccp4
+	doins -r "${S}"/ccp4i
+	exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin
+	doexe "${S}"/ccp4i/bin/*
+	dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i
+
+	dodir /usr/$(get_libdir)/ccp4/ccp4i/unix
+
+	# dbccp4i
+	insinto /usr/share/ccp4
+	doins -r "${S}"/share/dbccp4i
+}
+
+pkg_postinst() {
+	_ccp4-setup() {
+		source "${EPREFIX}/etc/profile"
+		export USER=root
+		bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null
+	}
+	VIRTUALX_COMMAND="_ccp4-setup" virtualmake
+	echo ""
+	elog "ccp4i needs some enviromental settings. So please"
+	elog "\t source ${EPREFIX}/etc/profile"
+	echo ""
+}
diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
new file mode 100644
index 00000000000..2c5f659b801
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch
@@ -0,0 +1,22 @@
+--- ccp4i/etc/configure.def.dist	2009-01-09 16:45:08.000000000 +0100
++++ ccp4i/etc/configure.def.dist.new	2009-07-07 23:17:26.000000000 +0200
+@@ -53,8 +53,8 @@
+ RUN_IMOSFLM               _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]"
+ RUN_CCP4MG                _text                     "ccp4mg"
+ RUN_COOT                  _text                     "coot"
+-RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share smartie baubles.py]"
+-RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]"
++RUN_BAUBLES               _text                     "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]"
++RUN_DBVIEWER              _text                     "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]"
+ ENABLE_BUBBLE_HELP        _logical                  1
+ DISABLE_TASKS             _logical                  1
+ CCP4_SETUP_COMMAND        _text                     setup_ccp4
+@@ -62,7 +62,7 @@
+ BLT_LIBRARY               _text                     ""
+ MENU_LENGTH               _positiveint              25
+ HYPERTEXT_VIEWER          _text                     firefox
+-START_NETSCAPE	          _text			    netscape
++START_NETSCAPE	          _text			    firefox
+ O_MAPMAN                  _text                     mapman
+ MAPMAN_MAXSIZE		  _positiveint		    4194304
+ QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
new file mode 100644
index 00000000000..9f5cfb4b635
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch
@@ -0,0 +1,61 @@
+diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script
+index def44bc..dd4bb7e 100755
+--- a/ccp4i/scripts/check.script
++++ b/ccp4i/scripts/check.script
+@@ -24,7 +24,7 @@
+   if $RUN_RAMPAGE {
+ 
+     # Generate command line
+-    set cmd "[BinPath rapper]"
++    set cmd "[BinPath rappermc]"
+ 
+     set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
+     set paramsfile [FileJoin $rapperdatadir params.xml]
+diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script
+index cdae1e2..faae226 100755
+--- a/ccp4i/scripts/rapper.script
++++ b/ccp4i/scripts/rapper.script
+@@ -17,7 +17,7 @@
+ 
+ #set up command line 
+ 
+-set cmd "[BinPath rapper]"
++set cmd "[BinPath rappermc]"
+ 
+ set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper]
+ set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml]
+@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT"
+ 
+ # Run RAPPER to join loop back to framework and out put to defined pdb file
+ # Also need to sort out multimodel files join - FIX ME
+-set cmd2 "[BinPath rapper]"
++set cmd2 "[BinPath rappermc]"
+ append cmd2 " $paramsfile joinpdb "
+ append cmd2 " --pdb2 \"$root\-loop.pdb\" "
+ append cmd2 " --pdb  \"$root\-framework.pdb\" "
+diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl
+index ae88ff2..ee3307b 100755
+--- a/ccp4i/tasks/check.tcl
++++ b/ccp4i/tasks/check.tcl
+@@ -46,7 +46,7 @@ proc check_run { arrayname } {
+  # Check for Rampage program. If it is not found, we switch off the option.
+  # If it was the only option, script will fail with next check.
+  if { $array(RUN_RAMPAGE) == 1 } {
+-   if { [FindExecutable "rapper"] == "" } {
++   if { [FindExecutable "rappermc"] == "" } {
+       WarningMessage "Input Error: Rapper_Rampage program not found in system path."
+       set array(RUN_RAMPAGE) 0
+     }
+diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl
+index e299057..8843a3f 100755
+--- a/ccp4i/tasks/rapper.tcl
++++ b/ccp4i/tasks/rapper.tcl
+@@ -28,7 +28,7 @@ proc rapper_run { arrayname } {
+  # Check for RAPPER program. If it is not found, we switch off the option.
+  # If it was the only option, script will fail with next check.
+   if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} {
+-   if { [FindExecutable "rapper"] == "" } {
++   if { [FindExecutable "rappermc"] == "" } {
+       WarningMessage "Input Error: RAPPER program not found in system path."
+       set build_type 0
+     }
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
new file mode 100644
index 00000000000..74cd2b94660
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch
@@ -0,0 +1,26 @@
+diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script
+index 3483c97..5027536 100755
+--- a/ccp4i/scripts/superpose.script
++++ b/ccp4i/scripts/superpose.script
+@@ -21,7 +21,7 @@
+ 
+   if { [regexp SSM $SUPERPOSE_MODE ] } {
+ 
+-    set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
++    set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\""
+     set status [Execute $cmd "" program_status report ]
+ 
+   } elseif { [regexp TOP $SUPERPOSE_MODE ] } {
+diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl
+index 748bf6e..c92122a 100755
+--- a/ccp4i/tasks/superpose.tcl
++++ b/ccp4i/tasks/superpose.tcl
+@@ -100,7 +100,7 @@ proc superpose_run { arrayname } {
+ # If user is match equivalent named residues/atoms then fit in the match fields
+   switch [GetValue $arrayname SUPERPOSE_MODE] \
+   SSM {
+-    if { ![file exists [FindExecutable superpose]] } {
++    if { ![file exists [FindExecutable superpose-ccp4]] } {
+        WarningMessage "The program \"superpose\" is not on your path. 
+ Check your installation for \"superpose\" program and \"ssm\" library."
+        return 0
diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
new file mode 100644
index 00000000000..9af60b7c515
--- /dev/null
+++ b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch
@@ -0,0 +1,91 @@
+diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl
+index 7d05905..d01f1dc 100755
+--- a/ccp4i/crank/plugins/prep/crank_prep.tcl
++++ b/ccp4i/crank/plugins/prep/crank_prep.tcl
+@@ -226,7 +226,7 @@ proc run_truncate { i j } {
+     set script "$script\n$labout"
+     set script "$script\nEND\n"
+ 	
+-    set run_command "truncate $command << \"$script\""
++    set run_command "ftruncate $command << \"$script\""
+     puts $run_command
+     catch {eval exec $run_command } output 
+     puts $output
+diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script
+index e74aa0d..a2a1adb 100755
+--- a/ccp4i/scripts/dtrek2mtz.script
++++ b/ccp4i/scripts/dtrek2mtz.script
+@@ -36,7 +36,7 @@
+     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
+ 
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script
+index 90cba83..1c90c33 100755
+--- a/ccp4i/scripts/import.script
++++ b/ccp4i/scripts/import.script
+@@ -144,7 +144,7 @@ if { $FORMAT ==  "MTZ" } {
+ 
+     set truncatemtz [GetTmpFileName -ext mtz ]
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
++    set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+ 
+diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script
+index dcc619b..7250513 100755
+--- a/ccp4i/scripts/import_scaled.script
++++ b/ccp4i/scripts/import_scaled.script
+@@ -62,7 +62,7 @@
+ 
+     } else {
+       CreateComScript truncate truncate_script
+-      set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++      set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+       set status [Execute $cmd $truncate_script program_status report]
+ 
+       HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script
+index 6940ccd..bde10d6 100755
+--- a/ccp4i/scripts/scala.script
++++ b/ccp4i/scripts/scala.script
+@@ -275,7 +275,7 @@ END"
+ 
+       } else {
+         CreateComScript truncate truncate_script
+-        set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
++        set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""  
+         set status [Execute $cmd $truncate_script $LOG_FILE  program_status report  ]
+       }
+           
+diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script
+index 986e06c..a1947a6 100755
+--- a/ccp4i/scripts/scalepack2mtz.script
++++ b/ccp4i/scripts/scalepack2mtz.script
+@@ -35,7 +35,7 @@
+ 
+     set HKL_TRUNCATE [GetTmpFileName -ext mtz]
+     CreateComScript truncate truncate_script
+-    set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
++    set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\""
+     set status [Execute $cmd $truncate_script program_status report]
+ 
+     HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate
+diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script
+index e0e09ce..2d448a2 100755
+--- a/ccp4i/scripts/truncate.script
++++ b/ccp4i/scripts/truncate.script
+@@ -45,7 +45,7 @@
+ 
+   CreateComScript truncate truncate_script
+ 
+-  set cmd "[BinPath truncate] HKLIN \"$HKLIN\""
++  set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\""
+   if { ![StringSame $INPUT_DATA AMPLITUDES] } {
+     append cmd " HKLOUT \"$HKL_TRUNCATE\""
+   }
diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml
new file mode 100644
index 00000000000..51fdedab1b3
--- /dev/null
+++ b/sci-chemistry/ccp4i/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+</pkgmetadata>