New features in WebMO version 7.0 include:

Package-Manager: portage-2.1.2.5

5 files changed, 196 insertions, 6 deletions

diff --git a/sci-chemistry/webmo/ChangeLog b/sci-chemistry/webmo/ChangeLog
index b92a13306e1b..ec03856c4d57 100644
--- a/sci-chemistry/webmo/ChangeLog
+++ b/sci-chemistry/webmo/ChangeLog
@@ -1,6 +1,19 @@
 # ChangeLog for sci-chemistry/webmo
-# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/ChangeLog,v 1.11 2006/09/20 05:08:59 dberkholz Exp $
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/ChangeLog,v 1.12 2007/05/08 06:43:35 dberkholz Exp $
+
+*webmo-7.0.003 (08 May 2007)
+
+  08 May 2007; Donnie Berkholz <dberkholz@gentoo.org>;
+  +files/7.0.003-gentoo-locations.patch, +webmo-7.0.003.ebuild:
+  New features in WebMO version 7.0 include:
+    * Improved molecular mechanics for generating initial geometries
+    * Improved Editor clean-up for charged species and/or octet rule exceptions
+    * Automatic diagnosis and reporting of common causes of job failure
+    * JPEG image capture of molecular and spectral images
+    * Database storage of jobs and users for improved performance and scalability
+    * New administrative interface
+    * Many user interface enhancements and bug fixes
 
   20 Sep 2006; Donnie Berkholz <dberkholz@gentoo.org>; metadata.xml:
   (#148281) Change herd to sci-chemistry from sci.
diff --git a/sci-chemistry/webmo/Manifest b/sci-chemistry/webmo/Manifest
index ca917a8d6f00..00948519e03a 100644
--- a/sci-chemistry/webmo/Manifest
+++ b/sci-chemistry/webmo/Manifest
@@ -1,3 +1,7 @@
+AUX 7.0.003-gentoo-locations.patch 1936 RMD160 32aa3271b88c1404f9bc14c3abd43f571d3e6e66 SHA1 7e2b58918c714dc557685387c6f1e5f6cfce3815 SHA256 a6511aa4a2dbc065959b67e994077bdb218a347b55be436c09f2798a4b2b0a99
+MD5 739fe362241f07f6ce1a196c22922a6d files/7.0.003-gentoo-locations.patch 1936
+RMD160 32aa3271b88c1404f9bc14c3abd43f571d3e6e66 files/7.0.003-gentoo-locations.patch 1936
+SHA256 a6511aa4a2dbc065959b67e994077bdb218a347b55be436c09f2798a4b2b0a99 files/7.0.003-gentoo-locations.patch 1936
 AUX add-gamess-data-directory.patch 2112 RMD160 1cb6afe72d077b8e53c958276da054e581dffb80 SHA1 4b1d0fa9a2e38e1644969eed0d727fed6c03be2a SHA256 3f22a700679e762296593816a6ddac3fe048a069921dd890176b0a5863b0323d
 MD5 8e94349e3989b4b0219b8b5d8616ff4a files/add-gamess-data-directory.patch 2112
 RMD160 1cb6afe72d077b8e53c958276da054e581dffb80 files/add-gamess-data-directory.patch 2112
@@ -15,14 +19,19 @@ MD5 17c5529a4765b4a96aab284f55752cc0 files/reconfig 1957
 RMD160 68c3eac15df2acebdeeb9dd82938e5a3d5bc1aa9 files/reconfig 1957
 SHA256 86faf48c67355367ca6d68a1b1e992602b760857b50ced0f2be78a9da9395ba5 files/reconfig 1957
 DIST WebMO.6.1.010.tar.gz 1221074 RMD160 2ed4385229b3c094891cc31131ca0f313eba59e5 SHA1 63440398ddb3daf591fa260a30204519889a7ab0 SHA256 99f53a346b32ee7b9ec9c0c7a4368b5c3e744e8dd960e57a776867558e35ec7b
+DIST WebMO.7.0.003.tar.gz 1491250 RMD160 42a73223370ad5e6e5b0baca95c9b3a1b01a8a09 SHA1 63f125d118610a9e40cea8fa14200675d5be1c6a SHA256 41018522a78f752bf07ad4ae6798c9eac0d678aba7d1f71f7c6dd5c4f00b2435
 EBUILD webmo-6.1.010.ebuild 3447 RMD160 e3abbd76b154325f34dc9171b385b2b600417275 SHA1 25e6c4b8c91a26050162c01773a8fd3c686d4537 SHA256 3e7055a4531a11ea372231262bd72d6fa0bed50800adba30bea815adaf13f30d
 MD5 7505ab4addd0a63830fe371a05a8e415 webmo-6.1.010.ebuild 3447
 RMD160 e3abbd76b154325f34dc9171b385b2b600417275 webmo-6.1.010.ebuild 3447
 SHA256 3e7055a4531a11ea372231262bd72d6fa0bed50800adba30bea815adaf13f30d webmo-6.1.010.ebuild 3447
-MISC ChangeLog 2380 RMD160 5b660f58e58080a385b884313299ba46b47c1ed9 SHA1 7024e0ce47be6cd66def152e83851bfbf5dd4082 SHA256 98c95ba9dcb6aa7da8850a4054e4680dcc8ee09da67ffb5b3f01c98df566275c
-MD5 cf1c28e130dca9377cddd8eeb4444e75 ChangeLog 2380
-RMD160 5b660f58e58080a385b884313299ba46b47c1ed9 ChangeLog 2380
-SHA256 98c95ba9dcb6aa7da8850a4054e4680dcc8ee09da67ffb5b3f01c98df566275c ChangeLog 2380
+EBUILD webmo-7.0.003.ebuild 3453 RMD160 56fbdb979bbf4d978d1940d5a6dce5ec6ec7b751 SHA1 a8c3658dd4f787b7160d6ebe8897dcea031b4bb1 SHA256 34410c5cdc29f189a91f657263ec380b7da2bbecab7ec8bebc5944cda27f1edc
+MD5 4c87bb629e1a00ef8f26b41ff6393625 webmo-7.0.003.ebuild 3453
+RMD160 56fbdb979bbf4d978d1940d5a6dce5ec6ec7b751 webmo-7.0.003.ebuild 3453
+SHA256 34410c5cdc29f189a91f657263ec380b7da2bbecab7ec8bebc5944cda27f1edc webmo-7.0.003.ebuild 3453
+MISC ChangeLog 3024 RMD160 1f58a9231b4e670c99cbafe8e6c950143cdc6bbc SHA1 341703c410499bc33e081585e1ec8a8a17ac3651 SHA256 2e2c388fd962bb619e8d612d8572f444fb4ef569239d963ebf8e0de275dcf78d
+MD5 f3c3508f9e05884299cf3d3792bcab76 ChangeLog 3024
+RMD160 1f58a9231b4e670c99cbafe8e6c950143cdc6bbc ChangeLog 3024
+SHA256 2e2c388fd962bb619e8d612d8572f444fb4ef569239d963ebf8e0de275dcf78d ChangeLog 3024
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166
 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166
@@ -30,3 +39,6 @@ SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 metadata
 MD5 f5f9e87168b357da498cf69c14379595 files/digest-webmo-6.1.010 244
 RMD160 e20bf9b04c01ddd272aedd988598a8af065399cd files/digest-webmo-6.1.010 244
 SHA256 e53b2180f0ed15f57bafeb8bb148a8930231ad050db51610746f81a9d58fa486 files/digest-webmo-6.1.010 244
+MD5 f9c16f5331bc7683a1ffdcfdf249a3d6 files/digest-webmo-7.0.003 244
+RMD160 23199a2c39acb97e351d0d058e307e8d83963310 files/digest-webmo-7.0.003 244
+SHA256 46de69f5b392964a905fa87c265f5e4fa8ceb11d419057e93d535a190ac4fd11 files/digest-webmo-7.0.003 244
diff --git a/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch b/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch
new file mode 100644
index 000000000000..1190c648a677
--- /dev/null
+++ b/sci-chemistry/webmo/files/7.0.003-gentoo-locations.patch
@@ -0,0 +1,42 @@
+diff -urN WebMO.install.orig/cgi-bin/interfaces/gamess.int.disabled WebMO.install/cgi-bin/interfaces/gamess.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/gamess.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/gamess.int.disabled	2007-05-07 23:32:19.000000000 -0700
+@@ -2,7 +2,7 @@
+ interfaceDescription{'gamess_admin'}="Edit preferences specific to Gamess"
+ interfaceDescription{'gamess_name'}="Gamess"
+ gamessVersion="2006"
+-gamessGMSPATH="/usr/local/gamess"
++gamessGMSPATH="/usr/bin"
+ gamessBinary="gamess.00.x"
+ gamessDdikick="ddikick.x"
+ cpuMin="0"
+diff -urN WebMO.install.orig/cgi-bin/interfaces/mopac.int.disabled WebMO.install/cgi-bin/interfaces/mopac.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/mopac.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/mopac.int.disabled	2007-05-07 23:31:43.000000000 -0700
+@@ -2,8 +2,8 @@
+ interfaceDescription{'mopac_admin'}="Edit preferences specific to Mopac"
+ interfaceDescription{'mopac_name'}="Mopac"
+ mopacVersion="7"
+-mopacPath="/usr/local/mopac7/mopac.exe"
+-mopacScratch="/scratch"
++mopacPath="/usr/bin/mopac7"
++mopacScratch="/tmp"
+ mopacExternal="/usr/local/mopac7"
+ cpuMin="0"
+ cpuMax="100"
+diff -urN WebMO.install.orig/cgi-bin/interfaces/tinker.int.disabled WebMO.install/cgi-bin/interfaces/tinker.int.disabled
+--- WebMO.install.orig/cgi-bin/interfaces/tinker.int.disabled	2007-05-07 23:31:24.000000000 -0700
++++ WebMO.install/cgi-bin/interfaces/tinker.int.disabled	2007-05-07 23:31:43.000000000 -0700
+@@ -2,9 +2,9 @@
+ interfaceDescription{'tinker_admin'}="Edit preferences specific to Tinker"
+ interfaceDescription{'tinker_name'}="Tinker"
+ tinkerVersion="4.2"
+-tinkerBinDir="/usr/local/tinker/bin"
+-tinkerBinExt="x"
+-tinkerParamDir="/usr/local/tinker/params"
++tinkerBinDir="/usr/bin"
++tinkerBinExt=""
++tinkerParamDir="/usr/share/tinker/params"
+ cpuMin="0"
+ cpuMax="100"
+ cpuDefault="100"
diff --git a/sci-chemistry/webmo/files/digest-webmo-7.0.003 b/sci-chemistry/webmo/files/digest-webmo-7.0.003
new file mode 100644
index 000000000000..2c74be1a7a43
--- /dev/null
+++ b/sci-chemistry/webmo/files/digest-webmo-7.0.003
@@ -0,0 +1,3 @@
+MD5 29d65a5b0182775ccd9f6e6c2d6fcef1 WebMO.7.0.003.tar.gz 1491250
+RMD160 42a73223370ad5e6e5b0baca95c9b3a1b01a8a09 WebMO.7.0.003.tar.gz 1491250
+SHA256 41018522a78f752bf07ad4ae6798c9eac0d678aba7d1f71f7c6dd5c4f00b2435 WebMO.7.0.003.tar.gz 1491250
diff --git a/sci-chemistry/webmo/webmo-7.0.003.ebuild b/sci-chemistry/webmo/webmo-7.0.003.ebuild
new file mode 100644
index 000000000000..0a884a3eddce
--- /dev/null
+++ b/sci-chemistry/webmo/webmo-7.0.003.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/webmo/webmo-7.0.003.ebuild,v 1.1 2007/05/08 06:43:35 dberkholz Exp $
+
+inherit eutils webapp
+
+MY_SRC_PN="WebMO"
+MY_SRC_P="${MY_SRC_PN}.${PV}"
+DESCRIPTION="Web-based interface to computational chemistry packages"
+HOMEPAGE="http://webmo.net/"
+SRC_URI="${MY_SRC_P}.tar.gz"
+LICENSE="WebMO"
+SLOT="${PVR}"
+KEYWORDS="~x86"
+RESTRICT="fetch"
+IUSE=""
+RDEPEND="dev-lang/perl
+	net-www/apache"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${MY_SRC_PN}.install"
+
+pkg_nofetch() {
+	einfo "Go to http://webmo.net/ and register for a free license."
+	einfo "Download ${SRC_URI} and place it in ${DISTDIR}."
+}
+
+src_unpack() {
+	# We need a license number to proceed
+	if [[ -z ${WEBMO_LICENSE} ]]; then
+		msg="You must set WEBMO_LICENSE to your license number in make.conf."
+		ewarn "$msg"
+		die "$msg"
+	fi
+
+	# Check for invalid license values. Valid are dddd-dddd-dddd
+	if [[ ${WEBMO_LICENSE} != [0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9]-[0-9][0-9][0-9][0-9] ]]; then
+		msg="Invalid license format. Licenses should be DDDD-DDDD-DDDD (D is a digit)."
+		ewarn "$msg"
+		die "$msg"
+	fi
+
+	unpack ${A}
+
+	# Set up program locations to match where portage installs them
+	epatch ${FILESDIR}/${PV}-gentoo-locations.patch
+
+	# Add a data directory for gamess, because WebMO expects everything
+	# in one directory instead of FHS
+	# (Depends on gentoo-locations.patch)
+	epatch ${FILESDIR}/add-gamess-data-directory.patch
+
+	# Don't run diagnose.pl or ask about being root user
+	epatch ${FILESDIR}/dont-be-interactive-or-diagnose.patch
+
+	# Make setup.conf
+	create_setup_conf
+}
+
+src_install() {
+	webapp_src_preinst
+
+	# Install everything
+	perl setup.pl || die "Check ${S}/diagnose.html for errors"
+
+	# Get ${D} out of main config file
+	dosed "${MY_CGIBINDIR}/webmo/interfaces/globals.int"
+
+	webapp_hook_script ${FILESDIR}/reconfig
+
+	local files=$(find ${D}${MY_HOSTROOTDIR}/webmo ${D}${MY_CGIBINDIR}/webmo/interfaces)
+	# Add the directories themselves
+	files="${files} ${MY_HOSTROOTDIR}/webmo ${MY_CGIBINDIR}/webmo/interfaces"
+	files=${files//${D}/}
+	for file in ${files}; do
+		webapp_configfile "${file}"
+		webapp_serverowned "${file}"
+	done
+
+	ebegin "Fixing permissions"
+	pushd "${D}" > /dev/null
+	find . -perm /o+w -type f | xargs fperms 664
+	find . -perm /o+w -type d | xargs fperms 775
+	popd > /dev/null
+	eend 0
+
+	webapp_src_install
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Be sure that this line is uncommented in httpd.conf:"
+	einfo "AddHandle cgi-scripts .cgi"
+	einfo
+	einfo "The diagnose.pl script can be run if WebMO doesn't work properly."
+	einfo
+	ewarn "Be careful never to overwrite your user, group or job databases"
+	ewarn "when using etc-update after an upgrade."
+
+	webapp_pkg_postinst
+}
+
+create_setup_conf() {
+	local SETUP_CONF="${S}/setup.conf"
+
+	echo_setup perlPath /usr/bin/perl "${SETUP_CONF}"
+	echo_setup htmlBase "${D}${MY_HTDOCSDIR}" "${SETUP_CONF}"
+	echo_setup url_htmlBase /webmo "${SETUP_CONF}"
+	echo_setup cgiBase "${D}${MY_CGIBINDIR}/webmo" "${SETUP_CONF}"
+	echo_setup url_cgiBase /cgi-bin/webmo "${SETUP_CONF}"
+	echo_setup userBase "${D}${MY_HOSTROOTDIR}/webmo" "${SETUP_CONF}"
+	echo_setup license "${WEBMO_LICENSE}" "${SETUP_CONF}"
+}
+
+# Takes three arguments:
+# 1: variable, 2: value, 3: file to echo them to
+echo_setup() {
+	# All values must be double-quoted, so escape the inner quotes.
+	echo "${1}=\"${2}\"" >> ${3}
+}