124611 2006-03-02 01:15 0000 pymol 0.99 version bump, approximate ebuild enclosed 2006-03-03 09:33:08 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED P2 enhancement --- 1 hodak@nemo.physics.ncsu.edu sci@gentoo.org hodak@nemo.physics.ncsu.edu 2006-03-02 01:15:39 0000 PyMOL v0.99 is released, portage version bump should be in order. In a moment I will attach almost working ebuild for new pymol version. hodak@nemo.physics.ncsu.edu 2006-03-02 01:50:28 0000 Created an attachment (id=81095) pymol 0.99 ebuild I am submitting almost working ebuild, I need some help to make it fully functional. Changes from 0.98: Tarball name is pymol-0_99rc1-src.tgz (note rc1, even though this is the actual release, not just release candidate) Added dependencies: dev-lang/tcl media-libs/freetype Now the problems I am having: In 0.98 there was pymol.com thatp was filtered through sed and became the pymol binary. In 0.99 there is no pymol.com there are several files pymol.com.* in setup subdirectory. pymol.com.basic seems to be working but it needs to be changed. Original pymol.com.basic looks like this: #!/bin/sh PYMOL_PATH=${HOME}/pymol export PYMOL_PATH if [ "$PYTHONPATH" == "" ]; then PYTHONPATH=${PYMOL_PATH}/modules else PYTHONPATH=${PYMOL_PATH}/modules:${PYTHONPATH} fi export PYTHONPATH # python $PYMOL_PATH/modules/pymol/__init__.py "$@" The PYMOL_PATH is obviously wrong ($HOME ?) This file needs to be chnaging to this: #!/bin/sh PYMOL_PATH=/usr/share/doc/pymol-0.99/ export PYMOL_PATH /usr/bin/python /usr/lib/python2.4/site-packages/pymol/__init__.py "$@" Unfortunately, I do not know enough sed/ebuild to accomplish this, I really do not know how to find python version and setup path /usr/lib/python2.4. There is one more important change in 0.99: In 0.98 during installation the following directory is created: /usr/lib/python2.4/site-packages/pymol/pymol_path/ This containts 4 subdirectories and a file: data examples LICENSE scripts test I am not sure if examples, scripts or test are good for something, but data is important since it contains demo files. In 0.99 the pymol_path dir is not created during installation and thus demo files are missing. Looking into 0.98 ebuild, it turns out that there is special handling for examples subdirectories, it is copied into /usr/share/doc/pymol-0.99/examples/. Therefore I moved content of the other subdirectories into /usr/share/doc/pymol-0.99/ as well. Once PYMOL_PATH is setup to /usr/share/doc/pymol-0.99/ everything works as expected. To sum up, what is required is write couple of lines that will convert pymol.com.basic to the form I specified above, or just create pymol script with the three lines from scratch. The only tricky part (for me) is to figure out python2.4. In my case, I changed pymol script by hand and everything seems to be working fine. je_fro@gentoo.org 2006-03-02 06:16:12 0000 I did about the same thing as you, only after I "ebuild pymol-0.99.ebuild unpack" I edited /var/tmp/portage/pymol-0.99/work/pymol-0.99/setup/pymol.com.basic to the following: #!/bin/sh # # PyMOL startup script for "ext"-based installs # # ============================================================== # Set PYMOL_PATH to point at the correct location on your system # PYMOL_PATH=/usr/lib64/python2.4/site-packages/pymol export PYMOL_PATH # # ============================================================== # (no changes usually required below here) # # python modules # if [ "$PYTHONPATH" == "" ]; then PYTHONPATH=${PYMOL_PATH}/modules else PYTHONPATH=${PYMOL_PATH}/modules:${PYTHONPATH} fi export PYTHONPATH # python $PYMOL_PATH/__init__.py "$@" So far everything is working okay...I have some scripts from the pymol wiki that are running fine, (in /usr/lib64/python2.4/site-packages) and /usr/share/doc/pymol-0.99 was created (with CHANGES.gz DEVELOPERS.gz README.gz). Looks good.... dberkholz@gentoo.org 2006-03-02 06:33:10 0000 You get the python version from python.eclass. First run python_version(), then $PYVER is set to the major.minor (e.g., 2.3, 2.4). hodak@nemo.physics.ncsu.edu 2006-03-02 15:02:51 0000 je_fro: I think that for your configuration demos do not work. Can you test it? hodak@nemo.physics.ncsu.edu 2006-03-02 15:15:42 0000 Created an attachment (id=81151) Updated pymol ebuild Here is updated ebuild, it does everything I wanted and works for me without problems. The only thing is that I would prefer that examples, data, tests and scripts would go to /usr/lib/python2.4/site-packages/pymol/ instead of /usr/share/doc/, but when I try this I get "permission denied": mv: cannot move `data' to `/usr/lib/python2.4/site-packages/pymol/data': Permission denied Is there something that can be done about this? dberkholz@gentoo.org 2006-03-03 09:33:08 0000 Added 0.99 to portage. If you'd like, take a look at how I've done things differently. 81095 2006-03-02 01:50 0000 pymol 0.99 ebuild pymol-0.99.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1jaGVtaXN0cnkvcHltb2wvcHltb2wtMC45 OC5lYnVpbGQsdiAxLjQgMjAwNS8xMi8xOSAxODo1NToxMSBzcHlkZXJvdXMgRXhwICQKCmluaGVy aXQgZGlzdHV0aWxzIGV1dGlscyBtdWx0aWxpYgoKREVTQ1JJUFRJT049IkEgUHl0aG9uLWV4dGVu c2libGUgbW9sZWN1bGFyIGdyYXBoaWNzIHN5c3RlbS4iCkhPTUVQQUdFPSJodHRwOi8vcHltb2wu c291cmNlZm9yZ2UubmV0LyIKU1JDX1VSST0ibWlycm9yOi8vc291cmNlZm9yZ2UvcHltb2wvJHtQ Tn0tJHtQVi8uL199cmMxLXNyYy50Z3oiCgpMSUNFTlNFPSJQU0YtMi4yIgpJVVNFPSIiClNMT1Q9 IjAiCktFWVdPUkRTPSJ+YW1kNjQgcHBjIHg4NiIKCkRFUEVORD0iZGV2LWxhbmcvcHl0aG9uCglk ZXYtcHl0aG9uL3BtdwoJZGV2LXB5dGhvbi9udW1lcmljCglkZXYtbGFuZy90awoJZGV2LWxhbmcv dGNsCgltZWRpYS1saWJzL2ZyZWV0eXBlCgltZWRpYS1saWJzL2xpYnBuZwoJc3lzLWxpYnMvemxp YgoJdmlydHVhbC9nbHV0IgoKc3JjX3VucGFjaygpIHsKCXVucGFjayAke0F9CgljZCAke1N9Cgkj IFR1cm4gb2ZmIHNwbGFzaCBzY3JlZW4uICBQbGVhc2UgZG8gbWFrZSBhIHByb2plY3QgY29udHJp YnV0aW9uCgkjIGlmIHlvdSBhcmUgYWJsZSB0aG91Z2guCglbWyAtbiAiJFdBTlRfTk9TUExBU0gi IF1dICYmIGVwYXRjaCAke0ZJTEVTRElSfS9ub3NwbGFzaC1nZW50b28ucGF0Y2gKfQoKc3JjX2lu c3RhbGwoKSB7CglkaXN0dXRpbHNfc3JjX2luc3RhbGwKCWNkICR7U30KCQoJI1RoZSBmb2xsb3dp bmcgdGhyZWUgbGluZXMgcHJvYmFibHkgZG8gbm90IGRvIHRoZWlyIGpvYnMgYW5kIHNob3VsZCBi ZQoJI2NoYW5nZWQKCVBZVEhPTlBBVEg9JChmaW5kICR7RH0vdXNyLyQoZ2V0X2xpYmRpcikgLXR5 cGUgZCAtbmFtZSBzaXRlLXBhY2thZ2VzKSAke3B5dGhvbn0gc2V0dXAyLnB5Cglsb2NhbCBzZWRl eHA9InM6JHtEJS99OjpnIgoJc2VkIC1lICR7c2VkZXhwfSBzZXR1cC9weW1vbC5jb20uYmFzaWMg PiBweW1vbAoJCglleGVpbnRvIC91c3IvYmluCglkb2V4ZSBweW1vbAoJZG9kb2MgREVWRUxPUEVS UyBDSEFOR0VTCgkjaW5zdGFsbCBleGFtcGxlcwoJbXYgZXhhbXBsZXMgJHtEfS91c3Ivc2hhcmUv ZG9jLyR7UEZ9CgkKCSNpbnN0YWxsIGRhdGEgCgkjaW4gMC45OCBkYXRhIHdlbnQgdG8gL3Vzci9s aWIvcHl0aG9uMi40L3NpdGUtcGFja2FnZXMvcHltb2wvcHltb2xfcGF0aC9kYXRhLwoJbXYgZGF0 YSAke0R9L3Vzci9zaGFyZS9kb2MvJHtQRn0KCQoJI2luc3RhbGwgdGVzdCAKCSNpbiAwLjk4IHRl c3Qgd2VudCB0byAvdXNyL2xpYi9weXRob24yLjQvc2l0ZS1wYWNrYWdlcy9weW1vbC9weW1vbF9w YXRoL3Rlc3QKCW12IHRlc3QgJHtEfS91c3Ivc2hhcmUvZG9jLyR7UEZ9CgkKCSNpbnN0YWxsIHNj cmlwdHMgCgkjaW4gMC45OCBzY3JpcHRzIHdlbnQgdG8gL3Vzci9saWIvcHl0aG9uMi40L3NpdGUt cGFja2FnZXMvcHltb2wvcHltb2xfcGF0aC9zY3JpcHRzCgltdiBzY3JpcHRzICR7RH0vdXNyL3No YXJlL2RvYy8ke1BGfQp9Cg== 81151 2006-03-02 15:15 0000 Updated pymol 0.99 ebuild pymol-0.99.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1jaGVtaXN0cnkvcHltb2wvcHltb2wtMC45 OC5lYnVpbGQsdiAxLjQgMjAwNS8xMi8xOSAxODo1NToxMSBzcHlkZXJvdXMgRXhwICQKCmluaGVy aXQgZGlzdHV0aWxzIGV1dGlscyBtdWx0aWxpYgoKREVTQ1JJUFRJT049IkEgUHl0aG9uLWV4dGVu c2libGUgbW9sZWN1bGFyIGdyYXBoaWNzIHN5c3RlbS4iCkhPTUVQQUdFPSJodHRwOi8vcHltb2wu c291cmNlZm9yZ2UubmV0LyIKU1JDX1VSST0ibWlycm9yOi8vc291cmNlZm9yZ2UvcHltb2wvJHtQ Tn0tJHtQVi8uL199cmMxLXNyYy50Z3oiCgpMSUNFTlNFPSJQU0YtMi4yIgpJVVNFPSIiClNMT1Q9 IjAiCktFWVdPUkRTPSJ+YW1kNjQgcHBjIHg4NiIKCkRFUEVORD0iZGV2LWxhbmcvcHl0aG9uCglk ZXYtcHl0aG9uL3BtdwoJZGV2LXB5dGhvbi9udW1lcmljCglkZXYtbGFuZy90awoJZGV2LWxhbmcv dGNsCgltZWRpYS1saWJzL2ZyZWV0eXBlCgltZWRpYS1saWJzL2xpYnBuZwoJc3lzLWxpYnMvemxp YgoJdmlydHVhbC9nbHV0IgoKc3JjX3VucGFjaygpIHsKCXVucGFjayAke0F9CgljZCAke1N9Cgkj IFR1cm4gb2ZmIHNwbGFzaCBzY3JlZW4uICBQbGVhc2UgZG8gbWFrZSBhIHByb2plY3QgY29udHJp YnV0aW9uCgkjIGlmIHlvdSBhcmUgYWJsZSB0aG91Z2guCglbWyAtbiAiJFdBTlRfTk9TUExBU0gi IF1dICYmIGVwYXRjaCAke0ZJTEVTRElSfS9ub3NwbGFzaC1nZW50b28ucGF0Y2gKfQoKc3JjX2lu c3RhbGwoKSB7CglkaXN0dXRpbHNfc3JjX2luc3RhbGwKCWNkICR7U30KCgoJI0ZpbmQgcHl0aG9u IHZlcnNpb24KCXB5dGhvbl92ZXJzaW9uCgoJUFlNT0xfUEFUSD0vdXNyLyQoZ2V0X2xpYmRpcikv cHl0aG9uJHtQWVZFUn0vc2l0ZS1wYWNrYWdlcy9weW1vbAoKCglsb2NhbCBzZWRleHAxPSJzOl5Q WU1PTF9QQVRILiokOlBZTU9MX1BBVEg9L3Vzci9zaGFyZS9kb2MvJHtQRn06ZyIKCWxvY2FsIHNl ZGV4cDI9InM6XnB5dGhvbi4qJDovdXNyL2Jpbi9weXRob24gJHtQWU1PTF9QQVRIfS9fX2luaXRf Xy5weSBcIlwkXEBcIjpnIgoJCglzZWQgLWUgJHtzZWRleHAxfSAtZSAiJHtzZWRleHAyfSIgc2V0 dXAvcHltb2wuY29tLmJhc2ljID4gcHltb2wKCQoJCgkKCWV4ZWludG8gL3Vzci9iaW4KCWRvZXhl IHB5bW9sCglkb2RvYyBERVZFTE9QRVJTIENIQU5HRVMKCgkjaW5zdGFsbCBleGFtcGxlcwoJbXYg ZXhhbXBsZXMgJHtEfS91c3Ivc2hhcmUvZG9jLyR7UEZ9CgkKCSNpbnN0YWxsIGRhdGEgCgkjaW4g MC45OCBkYXRhIHdlbnQgdG8gL3Vzci9saWIvcHl0aG9uMi40L3NpdGUtcGFja2FnZXMvcHltb2wv cHltb2xfcGF0aC9kYXRhLwoJbXYgZGF0YSAke0R9L3Vzci9zaGFyZS9kb2MvJHtQRn0KCQoJI2lu c3RhbGwgdGVzdCAKCSNpbiAwLjk4IHRlc3Qgd2VudCB0byAvdXNyL2xpYi9weXRob24yLjQvc2l0 ZS1wYWNrYWdlcy9weW1vbC9weW1vbF9wYXRoL3Rlc3QKCW12IHRlc3QgJHtEfS91c3Ivc2hhcmUv ZG9jLyR7UEZ9CgkKCSNpbnN0YWxsIHNjcmlwdHMgCgkjaW4gMC45OCBzY3JpcHRzIHdlbnQgdG8g L3Vzci9saWIvcHl0aG9uMi40L3NpdGUtcGFja2FnZXMvcHltb2wvcHltb2xfcGF0aC9zY3JpcHRz CgltdiBzY3JpcHRzICR7RH0vdXNyL3NoYXJlL2RvYy8ke1BGfQp9Cg==