Camelia, the Perl 6 bug

IRC log for #cdk, 2009-09-10

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All times shown according to UTC.

Time Nick Message
00:56 poseidon joined #cdk
04:56 egonw joined #cdk
05:26 slyrus_ joined #cdk
05:27 slyrus_ evening
05:27 slyrus_ egonw, why all the different projects on that uu.se git server rather than making those branches of a single tree?
05:34 egonw you mean 0-unsorted, 1-foo, 2-bar, etc?
05:44 slyrus_ no, I mean cdk.git, jchempaint-primary.git, rajarshi.git
05:44 slyrus_ etc...
05:44 egonw write access, history, ...
05:44 egonw no particular reason
05:45 egonw jcp-primary is for example separate is it undergoed rebasing often...
05:45 egonw which will freak out the general user
05:45 slyrus_ yeah, but couldn't that all be done with branches of a single tree?
05:45 egonw yes, it could
05:46 slyrus_ the argument for a single tree is that there are nice trees for diffing/merging/etc... between branches
05:46 slyrus_ not so much with trees...
05:46 slyrus_ s/the/one/
05:46 egonw no, but you can easily pull in different trees into your local clone
05:46 egonw and then do the diffing
05:46 slyrus_ and why does jcp need such a different tree? (don't mean to sound like I'm complaining, just curious...)
05:47 * slyrus_ goes to try that
05:48 egonw ah, because the jchempaint app/applet is a quite different project...
05:48 egonw it's a user of the CDK library
05:48 slyrus_ yes, but surely it can use the same version of CDK as the other app/applets out there, no?
05:49 slyrus_ also, what are the git clone incantations for the uu.se git projects? I can see the git web, but not sure what I should use to clone that repo
05:50 egonw oh, but it is
05:50 egonw well, to some extend
05:50 egonw it needs some extra patches which have not been merged into the main cdk branch yet
05:51 egonw git clone a subfolder of: http://pele.farmbio.uu.se/git/
05:51 zarah egonw's link is also http://tinyurl.com/kvpo6d
05:51 egonw would be nice if those links were in the cgi-bin html view too...
05:53 slyrus_ thanks
05:55 slyrus_ just out of curiosity, why are the patches required by jchempaint not on the main branch? has it just not happened or are there technical reasons why it can't happen?
05:57 egonw no, they just need to be reviewed and approved first
06:08 egonw and the cdk project is a bit short on good reviewers
06:08 slyrus_ this is testing the limits of my git-fu :(
06:09 egonw who know and understand the cdk coding rules for code stability
06:09 egonw no worries... it does for all of us...
06:09 slyrus_ ok, now the question "what are the 0-other, 1-render, etc... branches all about"?
06:09 egonw the effort is just worth it...
06:09 egonw it pays off on my side when reviewing and merging patches
06:10 slyrus_ it's certainly better than the alternatives
06:10 bag joined #cdk
06:10 egonw 0-other, 1-render, etc are about code review again
06:10 egonw at some point, the jcp-prim patch against the cdk needs to be merged with the cdk
06:10 slyrus_ ok, so these are temporary branches that git set up for code review and then go away then?
06:10 egonw and thus be reviewed
06:11 egonw so, we split up the larger patch into smaller patches
06:11 egonw to make the whole thing understandable for the reviewer
06:11 egonw yes
06:11 egonw they will go away
06:12 slyrus_ my reading of the git repo is that the jcp-primary master is the same as the sf.net git repo, right?
06:12 slyrus_ s/repo/repo master/
06:14 egonw yes
06:17 slyrus_ ok, at least I'm not losing my mind ... completely anyway
06:17 egonw :)
06:17 egonw sorry for the complexity
06:18 slyrus_ ok, so now that I've got the jcp-primary stuff, what do I need to do to build jchempaint? do i have to download jchempaint sources separately?
06:18 egonw yes, and those come from svn :)
06:18 egonw see that wiki page I gave earlier
06:22 slyrus_ ah, perhaps this is what I want:
06:22 slyrus_ git svn clone https://cdk.svn.sourceforge​.net/svnroot/cdk/jchempaint
06:24 egonw yes, that sounds about right
06:25 egonw and yes, git-svn is a good choice :)
06:29 slyrus_ ok, so which branch of the jcp-primary tree do I need to build to get jcp to work?
06:30 egonw ah...
06:30 egonw you got me there...
06:31 egonw ebiStage
06:31 egonw but I have not all patches in yet...
06:31 egonw please pull from this branch into your jcp-primary clone:
06:32 egonw http://www.ebi.ac.uk/steinbeck-sr​v/git/jchempaint-primary-public/
06:32 zarah egonw's link is also http://tinyurl.com/muwgqp
06:32 egonw and use the ebiPatches branch
06:32 egonw the current applet code from SVN is using patched from the EBI not merged into jchempaint-primary  yet
06:33 egonw I'm in the process of doing that right now
06:33 egonw but needed to make an involved patch for the CDK first...
06:33 egonw which I am now finishing...
06:39 egonw_ joined #cdk
06:39 egonw_ sorry... was relocating to a different room
06:39 egonw_ did I miss anything?
06:45 slyrus_ nope. managed to build cdk from the master branch and to pull from the ebi repo. building from that and building jcp will have to wait until the morning.
06:45 slyrus_ thanks for your help!
06:46 slyrus_ btw, in case your curious, I'm considering abandoning my common-lisp based cheminformatics library I was trying to put together and instead using cdk from clojure
06:54 egonw that sounds very interesting
06:54 egonw we had a clojure unconference at the last cdk workshop
06:54 egonw and rajarshi has been doing some cdk/clojure stuff
06:56 slyrus_ ah nice. well, I'll check back tomorrow. thanks again and good night
07:02 Gpox joined #cdk
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08:12 shk3 joined #cdk
08:16 jbrefort joined #cdk
08:24 jonalv joined #cdk
09:06 CIA-78 cdk: shk3 * r14810 /jchempaint/trunk/build.xml: changed the build process to keep io-formats.set
09:32 CIA-78 cdk: shk3 * r14811 /jchempaint/trunk/META-INF/ (applet-core.files applet-editor.files): updated class lists
10:06 CIA-78 cdk: mark_rynbeek * r14812 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/action/NewAction.java:
10:06 CIA-78 cdk: if you paste a SMILES, the molecule is fully selected. If you then click New, this selection remained.
10:06 CIA-78 cdk: I added an explicit NONE selection for this
11:19 shk3 joined #cdk
11:29 CIA-78 cdk: shk3 * r14813 /jchempaint/trunk/META-INF/a​pplet-resources-core.files: added inactive buttons to core resources
12:46 jpansane1 moin
12:46 zarah ni hao jpansane1
13:04 CIA-78 cdk: shk3 * r14814 /jchempaint/trunk/ (3 files in 3 dirs): the isotope menu changes dynamically dependent on atom in selection
14:01 CIA-78 cdk: shk3 * r14815 /jchempaint/trunk/src/main/​org/openscience/jchempaint/ (12 files in 5 dirs): unified the options/settings to "Options"
14:02 slyrus_ joined #cdk
15:20 CIA-78 cdk: mark_rynbeek * r14816 /jchempaint/trunk/build.xml: removed qsar and modeling jar files from being built
17:01 slyrus_ joined #cdk

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