Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-28

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All times shown according to UTC.

Time Nick Message
06:35 egonw joined #bioclipse
06:42 egonw moin
06:42 zarah oh hai egonw
07:22 Gpox joined #bioclipse
07:39 egonw Gpox: ping
07:39 egonw I cannot fetch the IEditRefactoring branch ...
07:39 egonw all other branches show up, but not that one ....
07:40 Gpox odd
07:40 egonw the refs are set on the server side...
07:40 egonw refs/heads/IEditRefactoring is present
07:40 egonw very odd
07:40 egonw can you push a branch 14-iedit ?
07:41 egonw just equal to IEditRefactoring...
07:41 egonw and run on pele: git-server-update-info
07:45 Gpox sure
07:45 Gpox I have some fixes i should merge in there first
07:46 Gpox I played around with the cdk-eclipse script on friday
07:48 egonw ok
08:03 jonalv joined #bioclipse
08:07 Gpox egonw: done
08:08 egonw Gpox: tack
08:10 shk3 joined #bioclipse
08:19 olass joined #bioclipse
08:22 olass hola
08:22 zarah hello olass, you fantastic person you
08:23 olass egonw: I had problems running QSAR due to some RDF problem parsing the ontology file..
08:23 egonw olass: file a bug report please
08:23 olass I did
08:23 egonw good
08:23 olass you marked it as accepted
08:23 egonw and working on xml / rdf validation
08:24 egonw in between bloody grant writing...
08:24 olass I wish to release a devel version this week
08:24 olass hmm.. I _must_ release a new devel version this week
08:25 olass would be great if you could look at that RDF thingy
08:25 olass when you have time
08:41 olass egonw: ping
08:42 egonw pong
08:42 olass If I have a mol open in JCP, can I be sure that aromaticity has been parceived on it?
08:42 egonw not sure, would need to check the source
08:43 olass this is quite important
08:43 olass I need to know what I am working on
08:43 olass and calling a ne wperceiveAromaticity just to be sure requires cloning
08:43 egonw if you draw benzene...
08:43 olass so a clone + perceive is rather time-consuming for large mol coolections
08:43 egonw does it draw a ring?
08:43 olass hmm
08:44 olass yes
08:44 egonw then it is automatically perceived
08:45 olass on load too?
08:45 olass of all mols?
08:45 olass including cml?
08:47 egonw no, not upon CML
08:47 egonw because CML already has that info
08:47 egonw if you don't trust the CML, you can recalculate
08:48 olass right
08:48 olass how about implicit hydrogens?
08:48 olass same thing?
08:48 egonw sorry, I do not have time for a tutorial right now
08:48 egonw check the source, please
08:49 olass egonw: one of the most important things we need to do is how we handle molecules in JCP
08:49 egonw and file a bug report against the appropriate classes for lack of JavaDoc
08:49 olass this cannot be "unsure"
08:49 olass "read the source"
08:49 olass it needs to be on a wiki page with clear rules
08:49 olass so we know what to expect
08:49 olass you disagree with me on that?
08:50 egonw about the wiki, yes
08:50 egonw it should be in Bioclipse instead
08:50 egonw and I agree there is a lack of documentation
08:50 olass so now we release 2.0.x with status "unknown" about aromaticity in JCP, is that so?
08:50 olass we honestly donät know?
08:50 egonw sure we "know"
08:50 edrin joined #bioclipse
08:51 egonw it just that we too lazy to look it up
08:51 egonw and we want it written down just before our nose
08:51 olass where do I look it up please?
08:51 olass in CDKManager?
08:51 egonw bioclipse.svn.sf.net
08:51 olass in CDKManager?
08:51 olass or somewhere else?
08:51 olass JCPManager?
08:53 egonw I don't know... and I don't have time too look up that info right now...
08:53 egonw like I said...
08:53 egonw [09/28/09 10:49] <egonw> and file a bug report against the appropriate classes for lack of JavaDoc
08:54 egonw and maybe you can start thinking about a scalable system for such info
08:54 egonw wiki does not work
08:54 olass egonw: when will you have time to help me with this important thing blocking today's release?
08:54 egonw wrong place
08:54 egonw not scalable
08:54 olass tomorrow?
08:54 egonw can't say
08:54 olass this week?
08:54 egonw Thu is more grant deadlines
08:55 egonw hopefully
08:55 egonw if you stop asking, and can get back to work
08:55 olass egonw: thanks for your help
08:55 olass left #bioclipse
08:58 masak joined #bioclipse
08:58 edrin hi
08:58 zarah saluton edrin
08:59 masak saluton edrin
08:59 jonalv saluton edrin
08:59 zarah saluton edrin
09:04 * egonw just impressed himself...
09:05 egonw bu answering the 4-year old of next door in *Swedish* :)
09:05 masak egonw++
09:05 egonw and he actually understood what I said!
09:06 masak \o/
09:06 egonw Gpox: I still can't get my local repos to learn about the upstream patches ... :(
09:06 egonw Gpox: can you do me a favor, and email me a bunch of *.patch ?
09:06 egonw with 'git format-patch' ?
09:10 egonw interesting spike of BC downloads on 15 Sept
09:10 egonw 140 against ~30 normally
09:10 egonw Gpox: tack
09:19 jonalv egonw: we normally have 30 downloads a day?
09:19 egonw yes
09:19 egonw apparently
09:20 egonw well, maybe a bit less in the last week...
09:20 egonw put differently... per month (you do the math)
09:20 egonw Aug: 854
09:20 egonw Jul: 1259
09:20 egonw Jun: 785
09:21 egonw May: 549
09:21 egonw Apr: 602
09:21 egonw Sep: 834 so far
09:21 egonw ok, so 20-30
09:21 egonw but Jul raises the bar
09:21 egonw but, not bad at all...
09:22 egonw let's settle for 50-a-day to close #1 ?
09:28 masak bah, #1 is unclosable anyway.
09:28 egonw but it is...
09:28 egonw it's just difficult
09:29 masak :)
09:29 egonw but nothing wrong with far away goals
09:29 egonw we just need another 6B converts
09:29 egonw ummm... that would be...
09:29 egonw 6T I guess?
09:29 egonw k, M, G, T, right?
09:29 egonw ah... no, stupid me
09:30 masak I have no idea what you're talking about. :)
09:30 egonw 6G converts should do :)
09:30 egonw 6 billion people
09:30 masak oh.
09:30 masak there are inherent problems in that new people are being born all the while.
09:31 egonw ok, good one!
09:31 egonw so, not 50 downloads a day...
09:32 egonw but let's set the score at babies born == bioclipse downloads
09:32 masak that only lets us keep a status quo.
09:33 egonw oh, you want more bioclipse users than people on earth
09:33 egonw yes, makes sense...
09:33 egonw there is the ISS
09:33 egonw hey, and who as talking about just humans anyway :)
09:34 masak "preparing for the new bioengineering era..."
09:55 olass joined #bioclipse
09:55 olass damn, 2.0.x has several core flaws :(
09:55 olass sad
09:55 jonalv olass: like what?
09:56 olass well, implicit hydrogens for example changes the same molecule differently
09:56 olass depending on how aromaticity was detected
09:56 jonalv olass: adding implicit hydrogens_
09:56 olass very strange
09:57 jonalv ?
09:57 olass hm
09:57 olass "update implicit hydrogens"
09:57 olass I filed a bug
09:57 egonw olass: that's a CDK bug
09:57 egonw I have been trying to pinpoint the cause, but have not found it yet
09:57 olass oh, did not know that was a known bug
09:58 olass ok
09:58 olass it seems to depend on order of aromatic bonds, if they are single aromatic or double aromatic
09:59 egonw you can check if atom typing works as aspected
09:59 egonw which it does not
09:59 jonalv seems like aromaticity is not yet solved :(
09:59 egonw they all should be C.sp2
09:59 egonw olass: please compare atom types for both SMILES
09:59 egonw they should give the same list
10:00 olass doing it as wek speak
10:00 olass yes, all are C.sp2
10:00 olass here is the SMILES: CN(C)CCC1=CNc2c1cc(cc2)CC1NC(=O)OC1
10:00 olass filed a bug about it
10:00 egonw yes, saw it
11:07 samuell joined #bioclipse
11:52 egonw Gpox: "using the former fro calrity" ??
11:54 Gpox using the former for calirty
11:54 egonw what's a calirty?
11:54 egonw mm... dict:calirty
11:55 egonw clarity
11:55 egonw ah, ok :)
11:55 egonw found it
12:00 egonw OK, one method in the new XMLManager left
12:00 egonw I can now validate XML against: DTD, XML Schema, RelaxNG, and Schematron 1.5
12:01 * egonw is pretty impressed that it all worked
12:15 egonw bbl
12:16 jonalv KIL WORD
12:16 jonalv it crashed
12:16 jonalv gah
12:18 masak I'm in the same office. jonalv is audibly not happy right now.
15:06 olass @ping
15:06 zarah olass: pong
15:06 olass just so silent today...
15:10 masak no-one here except us chickens.
15:12 masak hm, should be "there ain't nobody here but us chickens". :)
15:19 samuell Yup, not everything is better in the internet-era...
15:25 masak samuell: what you say‽
15:26 samuell Just that offices get silent in the office era
15:26 masak I think it's more of a case of the Mondays...
15:27 samuell Ah... good point :)
15:27 samuell (Ooops, not "office era" but "internet era")
15:44 * jonalv is in labb report correction mode
15:44 jonalv *lab
15:50 olass star-lab?
15:50 olass star-lite?
15:50 masak welcome to STAR LAB!
15:50 olass starring: JONALV
15:51 masak as himself.
15:51 jonalv olass: yea star lab at interationatol space station
15:51 olass dont STARt
15:51 masak :)
15:51 masak
15:51 jonalv olass: no I use * ot | (depending on whether I am on swedish or english keyboard layout) to signal a correction.
15:52 jonalv *or
15:52 jonalv masak: nice
15:52 olass ok, so what does ******* mean?
15:52 jonalv olass: no idea
15:52 masak olass: it's a password.
15:52 olass masak++ //correct
15:52 olass ok, next Q
15:53 masak olass: you know, if you type your password in an IRC session, it comes up as stars for everyone else.
15:53 olass whatis the following: ______
15:53 masak olass: that's Larry Wall in the mornings.
15:53 olass lol
15:53 masak olass: it's a puddle, waving.
15:53 olass it's a very calm sea
15:53 olass surface of a calm sea
15:53 jonalv *******
15:54 masak jonalv: it works!
15:54 jonalv masak: did it come up as stars?
15:54 masak jonalv: yes! wow!
15:54 olass Hk8%37/6&&
15:54 olass NO
15:54 olass MY PWD!
15:54 olass damn
15:54 olass better change fast...
15:54 masak olass: it looks like stars from here...
15:54 olass hmm, not here..
15:54 masak no, because it's your password.
15:54 olass *phew*
15:55 olass no need to change it then
15:55 masak amazing, isn't it?
15:55 olass yea
15:55 masak no, no need at all.
15:55 olass thanks
15:55 masak np
15:56 olass` joined #bioclipse
15:56 olass` olass: I think you should change that password...
15:56 olass wow
15:57 masak olass: http://bash.org/?244321
15:57 olass very funny!
15:58 masak ...if it happens to someone else, right?
15:58 olass right
15:59 masak olass`: still there?
15:59 olass masak: 45 is farmbio subnet..
16:00 masak hm...
16:00 olass @slap olass`
16:00 * zarah smashes a lamp on olass`'s head
16:00 olass @kill olass`
16:01 olass HAHA!
16:01 masak haha.
16:01 olass found the traitor!
16:01 masak :)
16:01 jonalv joined #bioclipse
16:01 jonalv oh hai
16:01 zarah hello jonalv, you fantastic person you
16:02 jonalv zarah: you are the fantastic one
16:02 zarah jonalv: no, YOU are the fantastic one! :)
16:02 olass grmf
16:02 jonalv olass: _
16:02 jonalv ?
16:02 olass *morr*
16:02 jonalv olass: "grmf"?
16:02 jonalv olass: "morr"?
16:03 olass jonalv: you are busted
16:03 olass jonalv: see the logs..
16:03 jonalv olass: okej I admit. I wanted to check if that really was you password and if it were alert you to the fact that you jsut posted you password to the world. I am not sure that is a bad thing though...
16:04 olass what?
16:04 masak the question whether it really was the right password remains unresolved, however.
16:04 jonalv olass: "what" about which part?
16:04 olass the stars or the calm sea surface?
16:05 olass or the *morr*?
16:06 egonw joined #bioclipse
16:12 * edrin is going home
16:12 edrin ciao
16:12 edrin cu later
16:12 edrin left #bioclipse
16:24 samuell egonw: Regarding "project plan", should I use the the planned week-schedule  from the initial project plan, or is it OK with some adjustments because of the swith to Blipkit?
16:25 samuell (adjustments which I will check with you of course)
17:03 egonw some adjustments are ok
17:03 samuell Ok!
17:16 egonw Gpox: ping
17:54 Gpox egonw: pong
17:55 egonw hej
17:55 egonw wondering why you removed the GraphModelRendere
17:56 egonw which is really a 2D graph plotting  thingy
17:59 Gpox though it was old code, it didn't compile iirc
17:59 Gpox feel free to ignore that commit
18:02 egonw will do...
18:02 egonw I guess it should be removed...
18:02 egonw but it's not for the JCP patch to do...
18:07 samuell egonw: Mail is on it's way.
18:07 egonw ah, ok
18:08 samuell I'm not ready yet, but slides 1-6 are modified so far...
18:08 samuell working on with the rest...
18:11 samuell Suppose I should skip the comparison with Pellet, as that is anyway something I have to learn more about.
18:13 samuell (Ah, that's what you had suggested already)
18:14 egonw do you want comments now?
18:14 egonw I only have one
18:14 samuell Yes, sure
18:14 egonw (which overshadows all others)
18:14 samuell Ok
18:14 egonw you have too much content on each slide
18:15 egonw this will get people reading the slides, instead of listening to you
18:15 egonw do not write on the slide what you want to tell...
18:15 egonw but tell people what you want them to hear
18:15 egonw and use the slides to help you and your audience see the thread
18:15 samuell Good point
18:15 samuell Will fix
18:16 samuell BTW, what is a "Next steps" slide supposed to contain? Next steps right now, in the project, or after this project?
18:19 egonw well, you're time line says it all...
18:20 samuell Ok
18:20 egonw you can copy the timeline again...
18:20 egonw makes the presentation nicely round too
18:20 egonw getting you back where you started...
18:26 samuell Yes
18:30 egonw Gpox: splitting up patch 0007
18:30 egonw according to module...
18:30 egonw was interesting experience :)
18:34 Gpox ah sorry about that, it was such a simple change didn't realize it was split over a lot of modules
18:34 egonw no worries
18:34 Gpox patch 0011 is probably that same when i think about it
18:35 egonw fine
18:35 egonw I'll only start complaining the next time
18:36 egonw :)
18:37 Gpox I guess the edits should be spit over different modules as well, except the basic set of operations
18:37 egonw ouch
18:37 egonw merge conflict in 0008
18:38 Gpox shouldn't be too hard all i have done is moved a big chunk to an other interface
18:39 egonw indeed
18:40 Gpox there is more stuff from the IChemModelRelay that should be moved out
18:58 egonw Gpox: the last merge was actually trickier...
18:58 egonw because your patch failed because it changed bits in a patch later on...
18:59 egonw causing the patch to fail for each branch...
18:59 egonw fair enough... as a simple --skip was enough...
18:59 egonw but I strongly suggest to apply patches in the right patch...
18:59 egonw so, changes to classes in the cdk control module, should go as patch directly in the 6-control branch
19:00 egonw etc
19:00 egonw that does require extensive rebasing, but a script helps there...
19:03 egonw mmm..... 0009 looks complex too
19:04 samuell egonw: R2 is on mail.
19:05 samuell Have tried to shorten down things. Tell if it is still too much.
19:06 Gpox hm shouldn't be that hard most of those classes is new
19:08 samuell brb
19:08 Gpox there are a few that existed before from the stuff i did before the summer that might cause a little trouble
19:10 egonw :)
19:12 egonw samuell: looks better
19:12 egonw but I think you need to explain better how prolog programming relates to reasoning...
19:22 samuell egonw: Ok, yeah, that's probably true.
19:25 egonw your audience will know zero about reasoning...
19:25 egonw let alone that there are different types of reasoning
19:25 egonw really, even I don't understand the differences between DL reasoning and alternatives...
19:28 samuell Well, me neither. Hmm... I just know an example of what is possible in prolog, but not DL.
19:34 samuell Just found a good article where PROLOG vs DL seem to be compared. Will read, and modify slides.
19:35 egonw well, that would be a nice thing for a slide...
19:35 egonw that example of what Prolog can do and DL not...
19:35 egonw and then explain why that is...
19:36 samuell Yep
19:37 samuell Will try to eat dinner while reading, so will be back later. Otherwise, will there be time for last adjustments tomorrow if I come at 9:15?
19:40 egonw yes, perhaps...
19:40 egonw will try to be at bmc then
19:41 samuell Ok
20:21 samuell joined #bioclipse
20:28 egonw going offline
20:29 egonw bye
20:29 egonw cu tomorrow
20:32 samuell cu
20:38 samuell Going offline too now, will take train to Uppsala tonight.
21:56 sneumann joined #bioclipse

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