Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-21

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Time Nick Message
05:38 sneumann joined #bioclipse
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06:46 olass moin
06:46 zarah saluton olass
06:56 egonw moin
06:56 zarah privet egonw
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08:20 jonalv joined #bioclipse
08:57 jonalv zarah: @pz bioclipse 2.4 is not released
08:57 zarah jonalv: I'm just a bot, you expect me to understand that?
08:57 jonalv zarah: yes
08:57 zarah jonalv: I see.
08:57 jonalv zarah: no you don't
08:57 zarah jonalv: I see.
08:57 jonalv bah
08:58 jonalv @pz bioclipse 2.4 is not released
08:58 zarah [1634] Bioclipse 2.4.0 is not yet rel... http://tinyurl.com/3ad2mdl
08:58 zarah Entire list at http://tinyurl.com/35y8yfj
08:59 egonw zarah--
08:59 jonalv @pz bioclipse 2.6 is not released
08:59 zarah jonalv: I couldn't find anything on 'bioclipse 2.6 is not released' in the database.
09:00 sneumann egonw: did you succed in adapting the MetFrag plugin to 2.4 ?
09:00 egonw no, not yet...
09:00 sneumann what's missing ?
09:00 egonw need to copy in the new MetFrag source code
09:00 egonw I think that will solve all remaining problems
09:00 egonw but no time yet :(
09:00 egonw damn book chapters
09:01 sneumann ack. Was just looking at  @pz 1651
09:01 egonw @pz 1651
09:01 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1651
09:01 jonalv zarah--
09:01 egonw indeed...
09:02 egonw sneumann: hoping to get it online on Experimental for 2.4
09:02 egonw with some preview stuff...
09:02 egonw major thing missing is basically a proper spreadsheet thingy
09:02 jonalv egonw: what 2.4 blockers do you have? Could you update bug 1634?
09:03 egonw or so...
09:03 jonalv @pz 1634
09:03 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1634
09:03 egonw @pz 1634
09:03 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1634
09:03 sneumann swolf now has a (not yet deployed on the public site) MetFrag which gives SDF for all fragments
09:03 sneumann and also an *.xls (sic!) for the results table
09:11 egonw jonalv: about 1868... yes, it really does... because these patches can have bug fixes, which are otherwise lost...
09:12 egonw jonalv: but I can live with 1868 being unblockered
09:12 jonalv egonw: but wasn't it for upstream? I mean the patches doesn't have to pe pushed upstream for Bioclipse 2.4 to be releasable, or do they?
09:13 egonw it's not like that...
09:13 egonw yes, they need to be pushed upstream
09:13 egonw but
09:13 egonw as soon as we update from upstream, those patches are lost
09:13 egonw possibly causing regressions
09:13 jonalv okey
09:14 sneumann Then make a unit test for / against updated upstream and make its failure a blocker :-)
09:14 egonw yes, ideally ...
09:15 egonw I mean, rephrased, this is just: make a unit test for fixes you make
09:21 egonw jonalv: thanx for reprioritizating 2.4 !
09:21 egonw jonalv++
09:21 jonalv egonw: is 1999 a 2.4 blocker?
09:21 jonalv @pz 1999
09:21 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1999
09:22 egonw I don't really know...
09:22 egonw it seems all to be working fine...
09:22 * jonalv is not even sure he understands the problem
09:22 egonw but I do not know the scope of this problem
09:23 egonw from the message, I would say the editor is not bound to CML files with 0D, 2D, or 5D coordinates
09:23 egonw which sounds bad...
09:23 egonw but at the same time, I can open CML files in JCP
09:23 egonw so, files it anyway
09:23 jonalv egonw: are we talking about the same bug?
09:24 jonalv @pz 1999
09:24 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1999
09:26 egonw that's the one I am looking at
09:27 jonalv okey
09:36 jonalv egonw: You have 70 bugs with target 2.4, I don't think it is realistic that we can have all those fixed for 2.4. I am trying to get a grip of things and I was wondering if you could go through them and move some (or actually many) of them to 2.6?
09:37 egonw jonalv: cannot do that right now
09:37 egonw will do that in time
09:37 egonw btw, target 2.4 does not mean 2.4.0, or does it?
09:37 jonalv egonw: can you give me an estimate of when you can have them reprioritixed?
09:37 egonw that's not a rethorical question
09:38 egonw jonalv: august
09:38 jonalv egonw: well there is something called 2.4 release
09:38 egonw late august, likely
09:38 egonw jonalv: yes, I heard about that
09:38 jonalv okey then I am confused, what is the list for 2.4.0?
09:39 egonw do we have such a list? I guess those are the blockers
09:39 jonalv right, I think I want to redo things here
09:39 egonw jonalv: I don't think it makes sense to have targets, if we are not targeting for something
09:40 jonalv egonw: what do you mean? Aren't we targeting for something?
09:40 jonalv egonw: I want some kind of way to get a feeling for how far away the 2.4 release is
09:40 egonw I think those are the blockers
09:40 egonw if all blockers are gone, we have a release
09:41 jonalv intresting view
09:41 jonalv I don't really care which system we use as long as we use one and people are aware of it
09:41 egonw how so?
09:41 jonalv egonw: I hadn't thought of it
09:41 egonw what is your view then?
09:41 jonalv right now my view is that there is a chaos
09:42 egonw it would be futile to wait for all bugs to be fixed
09:42 jonalv And I am trying to create a better view
09:42 jonalv for myself that is
09:42 egonw jonalv: yeah, duh ... but it is organized chaos :)
09:42 egonw jonalv++
09:42 * egonw is pleased to see jonalv starting thinking as a release manager
09:42 egonw well done!
09:43 * jonalv decided to take vacation when 2.4 is out so he has a big carrot :)
09:43 egonw ouch...
09:44 egonw that mistake have many made...
09:44 egonw dump something on the community and then leave :)
09:44 jonalv hang on in what way was it a misstake?
09:45 egonw because half of the time, a release has some blocker...
09:45 egonw like the RC2 did
09:45 egonw as in, it does not boot
09:45 egonw or zip is corrupted
09:45 egonw ok, not 50%
09:45 egonw but very often :)
09:48 * egonw is quite amused about gmail speed... the email about bug tracker changes arrive much sooner than the SF html page can refresh :)
09:52 jonalv google++
09:56 masak joined #bioclipse
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11:39 egonw Gpox: ping
11:39 egonw Gpox: should I pull in both commits in the bug1973 branch?
11:46 Gpox yes
11:51 CIA-71 bioclipse.cheminformatics: Arvid Berg 2.4.x * rdac2570 / (4 files in 2 dirs):
11:51 CIA-71 bioclipse.cheminformatics: Added classes for Jmol rendering in MolTable
11:51 CIA-71 bioclipse.cheminformatics: Rendering is not turned on yet. - http://bit.ly/cf6w5R
11:51 CIA-71 bioclipse.cheminformatics: Arvid Berg 2.4.x * r940f5fa / plugins/net.bioclipse.cdk.ui.sdfeditor​/src/net/bioclipse/cdk/ui/sdfeditor/ed​itor/MultiPageMoleculesEditorPart.java :
11:51 CIA-71 bioclipse.cheminformatics: Use index 0 if no molecule is selected when switching from JCP-tab to structure-tab in SDFEditor
11:51 CIA-71 bioclipse.cheminformatics: Solves bug 1973 - http://bit.ly/9zalai
11:51 zarah bug #1973 | http://tinyurl.com/37qgvbm
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12:48 CIA-71 bioclipse.core: jonalv 2.4.x * r3f7914f / plugins/net.bioclipse.business.test/src​/net/bioclipse/business/test/AbstractBi​oclipsePlatformManagerPluginTest.java :
12:48 CIA-71 bioclipse.core: refactored tests into multiple methods
12:48 CIA-71 bioclipse.core: Fixes bug: #2001 - http://bit.ly/b1VS4N
12:48 zarah bug #2001 | http://tinyurl.com/2als65c
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13:33 CIA-71 bioclipse.chembl: annzi master * r7af1bbc / plugins/net.bioclipse.chembl.moss.u​i/src/net/bioclipse/chembl/moss/ui/​wizard/ChemblMossWizardPage2.java : updated page 2 in moss wizard (+10 more commits...) - http://bit.ly/dyIRxt
13:36 annzi jonalv: nu har jag med fruktansvärt mkt pirr i magen uppdaterat chembl:)
13:36 jonalv annzi++
13:36 jonalv annzi: oh this is where we speak english btw
13:37 annzi o sorry, thought it was farmbio
13:37 annzi english it is
13:37 egonw hi annzi
13:37 annzi hi egonw
13:37 egonw I
13:37 egonw I'll be at BMC tomorrow at around 8:15
13:37 egonw can we meet somewhere tomorrow?
13:37 egonw I really like to see that script
13:38 egonw this is my last week before holiday
13:38 egonw and we have some things to work out before I leave
13:38 egonw if not mistaken
13:39 annzi oh yes about that script I laid that one behind other things, so that is something to discuss
13:39 annzi :)
13:39 annzi I can be at bmc tomorrow at 8 as well
13:39 egonw good
13:40 egonw the bus is typically a bit late, but I should be there at 8:15
13:40 annzi for how long will you be away?
13:41 egonw 3 weeks
13:41 annzi egonw: I will sit in the lunchroom upstairs so we could sit there perhaps?
13:42 egonw let's see if Stephy is there... if not, we just use our room, ok?
13:42 annzi ok, if i send you my report today do you think we could discuss it tomorrow then?
13:43 egonw will try :)
13:43 egonw don't send it too late, please :)
13:44 annzi I could send it now ,but then you have to bare with me that I refer to figures as x and neither result or discussion is finished..
13:44 egonw no, please fix as much as possible first
13:44 egonw but please do send before 20:00
13:45 egonw how's that blog coming along for the chembl(og) ?
13:48 * egonw feels like one of those professors you try to hide from... because when they walk in, they always mean more work :)
13:51 annzi haha sorry the phone rang
13:51 annzi egonw: oh shoot forgot about that blogpost
13:51 annzi end of the week?
13:52 annzi so sorry
13:52 edrin olass: available?
13:54 egonw annzi: wednesday?
13:54 egonw annzi: then we can discuss it on Thu?
13:54 egonw Fri is midsommar
13:55 egonw annzi: and would not deprive you of that
13:56 annzi egonw: sound ok
13:56 annzi no my lovely midsommar, aren't you going to celebrate?
13:57 egonw yes, probably
13:57 egonw depends a bit on the deadline progress
13:57 annzi egonw: so meeting tomorrow at 8.15, report in at latest 20 today(will not be earlier have a spinning class in between;) blog in on Wed an discuss on Thu..
13:57 egonw right
13:58 annzi great
13:58 annzi egonw: any guidelines for the  blog post?
13:58 egonw assume your reader is an idiot
13:59 egonw explain everything
13:59 egonw take advantage of hyperlinking
13:59 egonw give one or two screenshots
13:59 egonw check the blog for earlier content, and perhaps use that as context
13:59 egonw keep it short...
14:00 egonw first one is most important :)
14:00 annzi nice guidelines, thanx
14:00 annzi :)
14:17 jonalv @pz zarah cdk icon
14:17 zarah jonalv: I couldn't find anything on 'zarah cdk icon' in the database.
14:17 jonalv @pz cdk icon
14:17 zarah [779] CDK icon 16x16                     http://tinyurl.com/caob23
14:17 zarah [1605] Run alignment as job              http://tinyurl.com/yf8a7rx
14:17 zarah [1994] Clean up icons and action name... http://tinyurl.com/2ua6ty6
14:17 zarah [1965] Unable to clear properties on ... http://tinyurl.com/39aan4p
14:17 zarah Entire list at http://tinyurl.com/d48mfx
14:45 * jonalv reboots this piece of crap
15:03 jonalv joined #bioclipse
15:06 jonalv egonw: what have you amde with my commit?
15:06 egonw huh?
15:06 jonalv for bioclipse.cheminformatics
15:06 jonalv When I pull I get merge conflicts
15:06 egonw dunno
15:06 egonw it does not look good?
15:06 egonw ah... don't pull...
15:06 egonw never pull
15:06 jonalv and my message is there but with another hash
15:06 jonalv in you branch that is
15:06 egonw fetch, rebase...
15:07 egonw that would be "git cherry-pick"
15:07 jonalv but I can't rebase, I have pushed it to you
15:07 jonalv and I can't pull
15:07 jonalv so basically I can't get updates
15:07 jonalv I need help
15:08 egonw git rebase egonw/2.4.x
15:08 egonw after: git fetch egonw
15:08 jonalv but that will rewrite my commits
15:09 jonalv egonw: I have pushed them, they are public
15:09 egonw where did you push them?
15:09 * masak .oO( the clash of cultures... )
15:09 jonalv to github?
15:10 egonw jonalv: don't ask me... I don't know where you pushed it
15:10 jonalv egonw: What am I supposed to do when you rewrite my commits then?
15:11 egonw what commit are you talking about (hashes please) and how did I rewrite them?
15:11 egonw some context please
15:11 jonalv http://github.com/jonalv/bioclipse.cheminformatic​s/commit/f8b871fd5a847c204239098a47867244391bb1cf
15:11 zarah jonalv's link is also http://tinyurl.com/3ynsujc
15:12 jonalv http://github.com/egonw/bioclipse.cheminformatics​/commit/de960fe9fd3b73e463200a65b26a67c550710afa
15:12 zarah jonalv's link is also http://tinyurl.com/34q3rab
15:13 jonalv egonw: and the set version one you don't seem to have pulled at all
15:13 jonalv egonw: http://github.com/egonw/biocl​ipse.cheminformatics/network
15:13 zarah jonalv's link is also http://tinyurl.com/nz6cg2
15:13 egonw I don't see any differences...
15:13 egonw what of that patch did I rewrite ?
15:14 masak possibly none.
15:14 masak might be it was just rebased into master.
15:14 egonw ok, just the hash changed?
15:14 jonalv doesn't that mean that it has changed?
15:14 egonw yes, that is, I think, because I use 'git cherry-pick'
15:14 egonw moreover, a signed off the patch
15:14 egonw jonalv: no, don't think so
15:15 egonw well...
15:15 masak right. git cherry-pick would give you another hash if master had moved since the base of the branch.
15:15 jonalv anyway the real problem is that we have diverged
15:15 masak jonalv: only a problem because you have pushed :)
15:15 egonw theoretically, one sees that where the patch applies is slightly different
15:15 egonw because of other changes elsewhere...
15:16 jonalv masak: If I hadn't pushed then we wouldn't have diverged now would we?
15:16 egonw jonalv: the best thing to do, is never push to your copy of 'upstream' branches
15:16 masak jonalv: that's what I'm saying.
15:16 egonw jonalv: but instead, push to development branches
15:16 jonalv egonw: HOW THE FUCK DO I GET MY CODE TO YOU THEN?
15:16 jonalv delepment branches?
15:16 masak (1) don't use capitals
15:17 egonw jonalv: yes
15:17 egonw masak: git can be frustrating...
15:17 masak aye.
15:17 masak it's all the freedom that does it.
15:17 egonw indeed
15:17 jonalv I am not sure I understand what you mean
15:18 jonalv could someone explain as they would to a four year old?
15:18 jonalv or maybe a couple of years older...
15:18 jonalv (I think I need vacation)
15:18 egonw jonalv (6yr old): you messed up
15:18 masak jonalv: when two branches like each other very, very much...
15:18 egonw jonalv (6yr old): now, go clean your room
15:19 egonw that's what I would say to my 6yr old son
15:19 egonw but it feels a bit weird putting jonalv down like that :(
15:19 jonalv egonw: well, that wasn't really explaining it now was it?
15:19 egonw no, but I would never try to explain git to a 6yr old :)
15:19 masak here's Linus's email again. http://www.mail-archive.com/dri-devel​@lists.sourceforge.net/msg39091.html
15:20 zarah masak's link is also http://tinyurl.com/kl6ue7
15:20 egonw jonalv: ok, here goes
15:20 egonw what happened indeed that we diverged...
15:20 egonw therefore, one best practice is to not let once branch diverge from upstream
15:20 egonw instead
15:20 * jonalv is beginning to think that he will never give commits to and cdk related stuff if it's goign to be this complicated
15:20 egonw you would use development branches
15:20 masak jonalv: it would seem to me one has very restricted options with a publicly pushed branch.
15:21 egonw those development branches just branch from the upstream branch
15:21 egonw and you push this branch to github
15:21 egonw just like this branch:
15:21 jonalv it's becomming frustrating that egonw is just cherry picking from my bnranch and leaving m e trying to keep it up to date with his stuff
15:21 jonalv how do I know which stuff made it in and whcihc stuff did not?
15:22 jonalv I feel it is very easy to loose commits...
15:22 jonalv I must be missing something here...
15:22 egonw http://github.com/egonw/cdk/tree/160-cip
15:22 zarah egonw's link is also http://tinyurl.com/353lzt5
15:22 egonw or this development branch:
15:22 egonw http://github.com/egonw/cdk/tree/155-signatures
15:22 zarah egonw's link is also http://tinyurl.com/3y3mo2t
15:23 masak the number indicates it's a dev branch?
15:23 egonw if you put all your stuff in branches, it will not get lost
15:23 egonw masak: practically, it does
15:23 masak ok.
15:23 jonalv egonw: what are the numbers?
15:23 egonw masak: I picked up that habit somewhere; the number basically indicates when I started it
15:23 masak oh, ok.
15:23 * masak never tried using numbers
15:23 egonw masak: it's a quick identifier for some historic info
15:24 jonalv so it's jsut a counter?
15:24 egonw jonalv: yes
15:24 jonalv ah
15:24 egonw btw, I overlooked the version number patch...
15:25 masak 'oversaw'?
15:25 egonw the cherry-pick primarily refered to the git command
15:25 egonw masak: possibly... did you see the English Langauge StackExchange proposal?
15:25 egonw masak: you might like that...
15:25 * masak didn't
15:25 egonw http://area51.stackexchange.com/pro​posals/1269/english-language-usage
15:25 zarah egonw's link is also http://tinyurl.com/3akdgrr
15:26 egonw "http://area51.stackexchange.com/pro​posals/1269/english-language-usage"
15:26 zarah egonw's link is also http://tinyurl.com/3akdgrr
15:26 egonw masak: perhaps start one for that made up language with an E of which I can't come up with the name
15:26 egonw or S?
15:26 egonw not Spanish... but Esperanto
15:26 egonw that one
15:26 egonw got it
15:26 masak egonw: :)
15:27 egonw jonalv: are we friends again?
15:27 masak we should totally have a hugbot on the channel.
15:27 jonalv egonw: the question is just, what do I do now?
15:27 masak zarah: hug jonalv
15:27 egonw ah. ok good
15:27 * zarah hugs jonalv and blushes
15:27 masak :)
15:27 egonw zarah: hug jonalv
15:27 * zarah hugs jonalv and blushes
15:27 * jonalv blushes
15:28 egonw ummm...
15:28 egonw 1. check if there are important commits you must save
15:28 masak zarah: you're a smart girl, you know that?
15:28 zarah masak: I'm so smart I scare myself.
15:28 egonw (should I merge in the version number commit?)
15:28 egonw 2. if you have interesting patches -> write down the hashes
15:28 egonw better, do in either case:
15:29 egonw git checkout -b 1-savedCopyOfMyDiverged2.4.x 2.4.x
15:29 jonalv egonw: yes please add that version patch
15:29 masak egonw: do you use 'git pull --rebase' a lot?
15:29 egonw masak: never done that, no
15:29 egonw jonalv: ack
15:29 egonw jonalv: after that git checkout command you do:
15:29 egonw git branch -D 2.4.x
15:29 masak egonw: it's another way to avoid merges.
15:29 egonw git checkout -b 2.4.x egonw/2.4.x
15:29 egonw git push -f github 2.4.x
15:30 egonw jonalv: assumptions:
15:30 egonw egonw is the alias for my github
15:30 egonw github is the alias for *your* github
15:30 egonw masak: ah, make sense: I have seen it as this equivalent, which I do use now and then:
15:30 jonalv egonw: yea I see how you mean, I just wonder if I force push how will you find the version patch?
15:30 egonw masak: git fetch upstream 2.4.x; git rebase upstream/2.4.x
15:31 egonw jonalv: I got the commit hash :)
15:31 masak egonw: yes, I believe those are equivalent.
15:31 jonalv egonw: well then that was all
15:31 * jonalv throws away his branch
15:34 egonw jonalv: I did: $ gcp fe17166094c8ad00b214
15:34 CIA-71 bioclipse.cheminformatics: jonalv 2.4.x * ra55ad95 / (2 files in 2 dirs): Set version to 2.4.0.RC2 - http://bit.ly/9Oz2xk
15:34 egonw notice the new commit hash
15:34 egonw btw, 'git rebase' will still recognize that the patch is the same
15:34 egonw the commit hash *must* be different, because the parent is different
15:34 jonalv egonw: what\s 'gcp'?
15:35 egonw oh, umm... a local alias for: git cherry-pick
15:35 egonw sorry
15:35 jonalv okey
15:35 egonw the commit is not a hash for the content
15:35 egonw but a pointer to the history tree
15:35 egonw I'm sure the blob will have a hash too...
15:35 masak aye.
15:35 egonw but would to need to read 'from the bottom up' once more
15:36 jonalv well the reason I got confused was that I had a merge conflict and two very different versions of that same code in the merge
15:36 masak the blob might actually be the same for both commits :)
15:36 jonalv that surely looked like you had changed the contents of the commit
15:36 jonalv but I guess there was some other merge conflict
15:42 egonw ok, will be afk for dinner and sorts...
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