Fixes for Python ABIs, #316167

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

7 files changed, 32 insertions, 229 deletions

diff --git a/sci-chemistry/arp-warp-bin/ChangeLog b/sci-chemistry/arp-warp-bin/ChangeLog
index f737b3434a5c..652deba273ac 100644
--- a/sci-chemistry/arp-warp-bin/ChangeLog
+++ b/sci-chemistry/arp-warp-bin/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/arp-warp-bin
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/ChangeLog,v 1.4 2010/03/20 18:07:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/ChangeLog,v 1.5 2010/04/22 20:03:33 jlec Exp $
+
+  22 Apr 2010; Justin Lecher <jlec@gentoo.org> -files/7.0.1-setup.patch,
+  -files/7.0.1-source-ccp4-if-needed.patch, files/7.1-setup.patch,
+  arp-warp-bin-7.1.ebuild:
+  Fixes for Python ABIs, #316167
 
 *arp-warp-bin-7.1 (20 Mar 2010)
 
diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest
index 67dbb07f8f9b..d3d23a2dfc15 100644
--- a/sci-chemistry/arp-warp-bin/Manifest
+++ b/sci-chemistry/arp-warp-bin/Manifest
@@ -1,17 +1,15 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX 7.0.1-setup.patch 6390 RMD160 64b0a1e4186294ed3a5dac58d073c25f706c39c6 SHA1 64417d3ff647f6d3d24deccfe3c212c0a6342116 SHA256 568059bea41429cc217c0246f2294cbf15d1a756f8bd2d7803c4c49bbc040b68
-AUX 7.0.1-source-ccp4-if-needed.patch 1252 RMD160 90856aafee9823ea45dbd5f3c2ab88bed9cfe77d SHA1 1d74549cd991bcbcf0687a2760cf71013489150f SHA256 33344b351ea53844fbfca00dc98fe1f5959a30b29f157f2f61f4be550e356c65
-AUX 7.1-setup.patch 6267 RMD160 b41ecc05594f0d2284daf1f6251ab30921766386 SHA1 269a5791162fc3951d50ac1afe826ff0a2aad7e3 SHA256 d6a595a2f4dfd91ce058ebf52ba5389f1abf6429d1050134f5a2f0f72c59ae21
+AUX 7.1-setup.patch 6277 RMD160 0113b56d57a00d2daa625c540282c2e047890abf SHA1 11774b738401dcda1badfaed5614c7e620160e8b SHA256 4d4ae302589270ee73fc41d6f8231ba64969e2828578528a1bc06ff926507d06
 DIST arp_warp_7.1.tar.gz 195970881 RMD160 16698d4d81c1380f0b9f0aa012dba2689c1faec0 SHA1 bcd033194770153c6ce130e18676d6d3d3a44316 SHA256 e3496283eb1d63ce0ce84b32812ababe0ac266a270918f93f333d036ba36f8c3
-EBUILD arp-warp-bin-7.1.ebuild 2435 RMD160 dcea8c7750981adf645131fc89f0f2230e71d9d8 SHA1 baec472808d1bf301df87f587460341372a139c7 SHA256 0fe485b1335a74fc86f57fd6c8fed3c315e442cb746c9a163e0c7604fb29ef4d
-MISC ChangeLog 1189 RMD160 a4ed4cc08337e801fdd3c4231d90ce9b4f1f8086 SHA1 41945c96eb10917b0cdc0c82a09910bf3048841c SHA256 1476b6b27f62e24f941711ef6412b8bf9efde26af75cac6892b6978e4690e99d
+EBUILD arp-warp-bin-7.1.ebuild 2626 RMD160 e8182f81317430da5b89967c50c2a665f55e8c6a SHA1 2818dd62d436bb17fc9be6c46d01ab825b0e4523 SHA256 b4fa462cdbe23b9d77c80070c88f836036182651625298fd36642309536b9e37
+MISC ChangeLog 1390 RMD160 ebb2d1129473f1a0ab6ac6877b5c371b31213eed SHA1 f75d586d7c6c26a4d71b979a67975c8f59d16bbe SHA256 cd137ed3d5c750e1f459e5e4c059e1ba42e0f8f95e3b28ff80d18d447aefc0e1
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
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+iEYEARECAAYFAkvQq5oACgkQgAnW8HDreRZOwQCeLhjeKVzPLN1t0XjGbwtHDCn9
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diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild
index 71cdfa661944..f6ea268c5d97 100644
--- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild
+++ b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild,v 1.1 2010/03/20 18:07:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/arp-warp-bin/arp-warp-bin-7.1.ebuild,v 1.2 2010/04/22 20:03:33 jlec Exp $
 
 EAPI="3"
 
@@ -36,9 +36,15 @@ pkg_nofetch(){
 	elog "and place ${A} in ${DISTDIR}"
 }
 
+pkg_setup() {
+	python_set_active_version 2
+}
+
 src_prepare() {
 	epatch "${FILESDIR}"/${PV}-setup.patch
 	eprefixify "${S}"/share/arpwarp_setup_base.*
+	sed "s:PYVER:$(python_get_version):g" -i "${S}"/share/arpwarp_setup_base.*
+	python_convert_shebangs $(python_get_version) flex-wARP-src-354/*py
 }
 
 src_install(){
diff --git a/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch b/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch
deleted file mode 100644
index 23dda9760bae..000000000000
--- a/sci-chemistry/arp-warp-bin/files/7.0.1-setup.patch
+++ /dev/null
@@ -1,170 +0,0 @@
-diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash arp_warp_7.0.1/share/arpwarp_setup_base.bash
---- arp_warp_7.0.1.orig/share/arpwarp_setup_base.bash	2007-10-21 21:46:13.000000000 +0200
-+++ arp_warp_7.0.1/share/arpwarp_setup_base.bash	2008-04-06 13:33:05.000000000 +0200
-@@ -13,10 +13,10 @@
-     identifier=${nameprocessor}'-'${namesystem}
- fi
- #
--arpwarphome="$1X"
-+arpwarphome="/opt/arp-warp-bin"
- #
- export warpbin=${arpwarphome}/bin/bin-${identifier}
--export warpdoc=${arpwarphome}/manual
-+export warpdoc=/usr/share/doc/arp-warp-bin-7.0.1/html/
- export PATH=${warpbin}:${PATH}
- #
- testccp='0'
-@@ -49,7 +49,7 @@
-     fi
- 
- ##    2. Complement by other potential places for python :
--    search_list="${search_list} /usr/local/bin/python /usr/bin/python"
-+    search_list="${search_list} /usr/bin/python"
-     flex_wARP_python="/dev/null"
- 
- ##    3. Pick up the first one of the list which seems reasonable :
-@@ -73,30 +73,6 @@
-             export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
-             break
-         fi
--#        3.c Otherwise, we should be able to create the byte-code using the python.
--        /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1
--        if [ 0 != $? ] ; then
--            /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} 1> /dev/null 2>&1
--            export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
--        else
--            export flex_wARP_bin=${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2}
--        fi
--        pushd ${flex_wARP_bin} 1> /dev/null 2>&1
--        if [ 0 != $? ] ; then 
--            export flex_wARP_bin=${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
--            /bin/mkdir -p ${flex_wARP_bin} 1> /dev/null 2>&1
--            pushd ${flex_wARP_bin} 1> /dev/null 2>&1
--        fi
--        /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py .
--        ${python_to_test} ./compile.py
--        /bin/rm -f *.py
--        popd 1> /dev/null 2>&1
--        if [ -e ${flex_wARP_bin}/CPyWARP.pyc ] ; then
--            export flex_wARP_python=${python_to_test}
--            echo "Created a new set of flex-wARP byte code in the directory :"
--            echo "  '${flex_wARP_bin}'"
--            break
--        fi
-     done
- ##    4. If nothing is available, print out a message.
-     if [ "/dev/null" != ${flex_wARP_python} ] ; then
-@@ -107,6 +83,7 @@
-         echo "WARNING while setting up ARP/wARP"
-         echo "No valid 'python' command was found"
-         echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available."
-+	echo "Did you upgrade your python? Please run 'emerge sci-chemistry/arp-warp-bin!'"
-         echo
-         export flex_wARP_warpbin="Unavailable"
-         export flex_wARP_cbin="Unavailable"
-@@ -115,17 +92,3 @@
-     fi
- fi
- 
--#
--# Setting up library path for SGI
--if [[ "${namesystem}" = 'IRIX64' || "${namesystem}" = 'IRIX' ]]; then
--    if test "$LD_LIBRARY_PATH"; then
--        export LD_LIBRARY_PATH=${warpbin}:${LD_LIBRARY_PATH}
--    else
--        export LD_LIBRARY_PATH=${warpbin}
--    fi
--fi
--#   echo
--#   echo 'ARP/wARP Version 7.0.1 has been setup'
--#
--
--
-diff -Nu -Nu -uarN arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh arp_warp_7.0.1/share/arpwarp_setup_base.csh
---- arp_warp_7.0.1.orig/share/arpwarp_setup_base.csh	2007-10-21 21:46:13.000000000 +0200
-+++ arp_warp_7.0.1/share/arpwarp_setup_base.csh	2008-04-06 13:32:48.000000000 +0200
-@@ -13,10 +13,10 @@
-     set identifier = ${nameprocessor}'-'${namesystem}
- endif
- #
--set arpwarphome = '$1X'
-+set arpwarphome = '/opt/arp-warp-bin'
- #
- setenv warpbin ${arpwarphome}/bin/bin-${identifier}
--setenv warpdoc ${arpwarphome}/manual
-+setenv warpdoc /usr/share/doc/arp-warp-bin-7.0.1/html/
- set path = ( $warpbin $path )
- #
- # Settings for python
-@@ -47,7 +47,7 @@
- endif
- 
- ##    2. Complement by other potential places for python :
--set search_list = "${search_list} /usr/local/bin/python /usr/bin/python"
-+set search_list = "${search_list} /usr/bin/python"
- setenv flex_wARP_python "/dev/null"
- 
- ##    3. Pick up the first one of the list which seems reasonable :
-@@ -71,30 +71,6 @@
-         setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
-         break
-     endif
--#        3.c Otherwise, we should be able to create the byte-code using the python.
--    /bin/mkdir -p ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2} >& /dev/null
--    if ( 0 != $status ) then
--        /bin/mkdir -p ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2} >& /dev/null
--        setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
--    else
--        setenv flex_wARP_bin ${arpwarphome}/byte-code/python-${pythonvrs1}.${pythonvrs2}
--    endif
--    pushd ${flex_wARP_bin} >& /dev/null
--    if ( 0 != $status ) then
--        setenv flex_wARP_bin ${HOME}/.flex-wARP/python-${pythonvrs1}.${pythonvrs2}
--        /bin/mkdir -p ${flex_wARP_bin} >& /dev/null
--        pushd ${flex_wARP_bin} >& /dev/null
--    endif
--    /bin/cp -p ${arpwarphome}/flex-wARP-src/*.py .
--    ${python_to_test} ./compile.py
--    /bin/rm -f *.py
--    popd >& /dev/null
--    if ( -e ${flex_wARP_bin}/CPyWARP.pyc ) then
--        setenv flex_wARP_python ${python_to_test}
--        echo "Created a new set of flex-wARP byte code in the directory :"
--        echo "  '${flex_wARP_bin}'"
--        break
--    endif
- end
- ##    4. If nothing is available, print out a message.
- if ( "/dev/null" != ${flex_wARP_python} ) then
-@@ -105,22 +81,13 @@
-     echo "WARNING while setting up ARP/wARP"
-     echo "No valid 'python' command was found"
-     echo "flex-warp ('ARP/wARP Expert System' in the GUI) will not be available."
-+    echo "Did you upgrade your python? Please run 'emerge sci-chemistry/arp-warp-bin!'"
-     echo
-     setenv flex_wARP_warpbin "Unavailable"
-     setenv flex_wARP_cbin "Unavailable"
-     setenv flex_wARP_python "/dev/null"
-     setenv flex_wARP_bin "Unavailable"
- endif
--
--#
--# Setting up library path for SGI
--if ( ${namesystem} == 'IRIX64' || ${namesystem} == 'IRIX' ) then
--    if ( ${?LD_LIBRARY_PATH} ) then
--        setenv LD_LIBRARY_PATH ${warpbin}:${LD_LIBRARY_PATH}
--    else
--        setenv LD_LIBRARY_PATH ${warpbin}
--    endif
--endif
- #
- goto endsetup
- #
-@@ -132,7 +99,4 @@
- #
- endsetup:
- #
--#echo
--#echo 'ARP/wARP Version 7.0.1 has been setup'
--#
- 
diff --git a/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch b/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch
deleted file mode 100644
index aa6f67f845f2..000000000000
--- a/sci-chemistry/arp-warp-bin/files/7.0.1-source-ccp4-if-needed.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- share.orig/arpwarp_setup_base.bash	2008-08-03 16:50:03.000000000 -0700
-+++ share/arpwarp_setup_base.bash	2008-08-03 16:51:20.000000000 -0700
-@@ -23,11 +23,13 @@
- #
- # Checks for CBIN variable
- if [ "$CBIN" = "" ]; then
--    echo
--    echo "Cannot setup ARP/wARP"
--    echo 'Variable $CBIN is not defined'
--    echo "Please install CCP4 first"
--    testccp='1'
-+    if [ "$CBIN" = "" ]; then
-+        echo
-+        echo "Cannot setup ARP/wARP"
-+        echo 'Variable $CBIN is not defined'
-+        echo "Please install CCP4 first"
-+        testccp='1'
-+    fi
- fi
- if [ "$testccp" = '0' ]; then
-     if [ ! -d $CBIN ]; then
---- share.orig/arpwarp_setup_base.csh	2008-08-03 16:50:06.000000000 -0700
-+++ share/arpwarp_setup_base.csh	2008-08-03 16:52:03.000000000 -0700
-@@ -22,11 +22,13 @@
- # Settings for python
- # Checks for CBIN variable
- if ( ! $?CBIN ) then
--    echo
--    echo 'Cannot setup ARP/wARP'
--    echo 'Variable $CBIN is not defined'
--    echo 'Please install CCP4 first'
--    goto errorsetup
-+    if ( ! $?CBIN ) then
-+        echo
-+        echo 'Cannot setup ARP/wARP'
-+        echo 'Variable $CBIN is not defined'
-+        echo 'Please install CCP4 first'
-+        goto errorsetup
-+    endif
- endif
- if ( ! -d $CBIN ) then
-     echo
diff --git a/sci-chemistry/arp-warp-bin/files/7.1-setup.patch b/sci-chemistry/arp-warp-bin/files/7.1-setup.patch
index 9ccc816732bb..639e6621ad81 100644
--- a/sci-chemistry/arp-warp-bin/files/7.1-setup.patch
+++ b/sci-chemistry/arp-warp-bin/files/7.1-setup.patch
@@ -20,7 +20,7 @@ index 29e769c..0b8a51e 100644
  
  ##    2. Complement by other potential places for python :
 -    search_list="${search_list} /usr/local/bin/python /usr/bin/python"
-+    search_list="${search_list} @GENTOO_PORTAGE_EPREFIX@/usr/bin/python"
++    search_list="${search_list} @GENTOO_PORTAGE_EPREFIX@/usr/bin/pythonPYVER"
      flex_wARP_python="/dev/null"
  
  ##    3. Pick up the first one of the list which seems reasonable :
@@ -101,7 +101,7 @@ index 41b11e9..a4edcff 100644
  
  ##    2. Complement by other potential places for python :
 -set search_list = "${search_list} /usr/local/bin/python /usr/bin/python"
-+set search_list = "${search_list} @GENTOO_PORTAGE_EPREFIX@/usr/bin/python"
++set search_list = "${search_list} @GENTOO_PORTAGE_EPREFIX@/usr/bin/pythonPYVER"
  setenv flex_wARP_python "/dev/null"
  
  ##    3. Pick up the first one of the list which seems reasonable :
diff --git a/sci-chemistry/caver/Manifest b/sci-chemistry/caver/Manifest
index e1625c7bf825..5969c1f2ec4b 100644
--- a/sci-chemistry/caver/Manifest
+++ b/sci-chemistry/caver/Manifest
@@ -1,12 +1,18 @@
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+Hash: SHA1
+
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 DIST caver2_0-v003_pymol_plugin.zip 3605820 RMD160 ab937f9090c31dbf078b08fdf582d2cad7717658 SHA1 b18ae1b011c906fe7fe5d94f6ee3bac185c352c6 SHA256 af82aff17103d31385b401edd4fc2c5da91d5ddef7d96b41e0b6e37b5adaef08
-DIST caverPLUG_unix_v0.99.2.tar.gz 81270 RMD160 58a5b2b7a1efe41a86d507831f754419ae912b12 SHA1 9ee32cd88bf83c99f7e59bd93d4cdb9fd16d1647 SHA256 5b7ca30f26023e2ed9eda6a5430ca5db0ebef7b34f7f8d2391a49182ec0663b1
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-DIST caver_unix_v0.99.2.tar.gz 1152263 RMD160 01b877bef15d0f0e1ccce8a3dbcda83826ba76c5 SHA1 d2c4e107e6a977ed7498be843852358c2bf3e428 SHA256 9934b5e80f375159132c5327df1fa8bd19ce90682c04c4cd9b91e62476e0f98b
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 EBUILD caver-0.99.4.ebuild 1779 RMD160 e18932af22a2d5926ab94b5fb819623f4dc0bdd2 SHA1 864b2d832d506f5955583519110b1347f4e8e28c SHA256 655eeb60534c3334ae40d895b5b66fdd384f095128390916b0eda8bf2dd8933f
 EBUILD caver-2.0.003-r1.ebuild 1784 RMD160 5e3262139d49085710e85d0d969fd5ab04921375 SHA1 fd3b9c1b1e1f7e45ba0bbaebd290094e69f540fa SHA256 481a985d8189625521251e71ce6cc793dc7ddd158b57abc4581d8ffe61f9ed98
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