Camelia, the Perl 6 bug

IRC log for #cdk, 2011-09-16

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All times shown according to UTC.

Time Nick Message
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08:37 maclean morning
08:43 egonw hi mac
08:43 egonw hi maclean
08:43 maclean hi egon. ('mac'  is not one of my recommended names :)
08:43 maclean Unless, perhaps, if you are American.
08:44 egonw tab complete #fail
08:45 maclean egonw: oh! names tab-complete!
08:46 maclean presumably only on people online.
08:48 egonw yes
08:52 maclean huh. on "git -am" ing a patch, I get : fatal: sha1 information is lacking or useless (src/main/org/openscience/cdk​/silent/AdductFormula.java).
08:52 maclean A patch for the silent module, that is.
08:53 egonw well, silent has been approved, but not signed off
08:53 egonw so I have not applied it yet
08:53 egonw or you trying to sign it off now?
08:53 egonw or are you trying to 'git-am' SMSD patches?
08:54 egonw did I mess up? and have the SMSD rebased on master + silent?
08:54 maclean Sorry, I should have describe the path I took :)
08:54 maclean I checked out the branch I had called "silent" with  dd0161dfefe5368ae8f5dc0553e5cbe7f3b84523 on it
08:55 maclean "Implemented the silent module as a nonotify replacement,..."
08:55 maclean and then tried to apply 0001-Removed-notifyChanged-calls.patch
08:55 maclean So, yes, I'm trying to sign-off on the new patches you made in response to the suggestions.
08:59 maclean Huh. "patch -p1 < patch_file" works better.
09:17 maclean Heh. "git commit -C HEAD --amend --signoff"
09:18 maclean Right, done.
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09:28 maclean How weird : "Jag kan verkligen säga att jag aldrig har läst så mycket användbar information om Blogger: Some Stuff - Post a Comment. Jag vill uttrycka min tacksamhet till webbansvarig för pele.farmbio.uu.se."
09:32 egonw where is that?
09:32 egonw thanx for signing off the silent patch!
09:33 maclean egonw : no problem. The swedish text is a spam comment on my blog. Weirdly, it mentions pele...
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13:23 Topic for #cdk is now The Chemistry Development Kit (http://cdk.sf.net) | JUnit CDK 1.2.7: 15690, 76 fails + 15 errors (0.58%) | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News Feed: http://friendfeed.com/rooms​/chemistry-development-kit
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14:26 egonw maclean: ping
14:26 CIA-38 cdk: Egon Willighagen cdk-1.4.x * r78fb9c8 / (88 files in 6 dirs):
14:26 CIA-38 cdk: Implemented the silent module as a nonotify replacement, copied from the data module, with tests copied from test-nonotify.
14:26 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/EB7sQQ
14:26 CIA-38 cdk: Egon Willighagen cdk-1.4.x * r822189e / (21 files):
14:26 CIA-38 cdk: Removed notifyChanged() calls
14:26 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/qtoP4g
14:26 CIA-38 cdk: Egon Willighagen cdk-1.4.x * r496f242 / (6 files):
14:26 CIA-38 cdk: Removed add/removeListener() calls
14:26 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/_qiGFg
14:27 egonw maclean: the silent patch was in fact for cdk-1.4.x :)
14:27 egonw not for master, but applied fine here
14:28 egonw you can also play with these 'am' options: -3 and --ignore-whitespace
14:28 egonw particulaly the first helps me with getting patches apply nicely
14:38 CIA-38 cdk: Egon Willighagen master * r78fb9c8 / (88 files in 6 dirs):
14:38 CIA-38 cdk: Implemented the silent module as a nonotify replacement, copied from the data module, with tests copied from test-nonotify.
14:38 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/EB7sQQ
14:38 CIA-38 cdk: Egon Willighagen master * r822189e / (21 files):
14:38 CIA-38 cdk: Removed notifyChanged() calls
14:38 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/qtoP4g
14:38 CIA-38 cdk: Egon Willighagen master * r496f242 / (6 files):
14:38 CIA-38 cdk: Removed add/removeListener() calls
14:38 CIA-38 cdk: Signed-off-by: maclean <gilleain.torrance@gmail.com> - http://git.io/_qiGFg
14:38 CIA-38 cdk: Egon Willighagen master * r932b63e / (88 files in 6 dirs): Merge branch 'cdk-1.4.x' - http://git.io/JqDLWw
14:43 maclean egonw : pong, sorry, was AFK.
14:43 egonw np :)
14:43 egonw it was just informative anyway
14:44 maclean I tried -3, actually, it didn't seem to work. Possibly because I was using master, not 1.4
14:45 egonw yeah, could be... dunno
14:45 maclean Is silent going to become default at some point?
14:45 maclean As in, DefaultChemObjectBuilder.
14:46 egonw Rajarshi suggested the same
14:46 egonw one thing that must be fixed first then, is to make *all* modules implementation independent
14:46 egonw I have been working part-time on that for a few years now...
14:46 egonw lot of work
14:46 egonw but I'd be happy with it, yes
14:47 maclean What's involved?
14:47 egonw using the interfaces instead of implementations all over the place
14:47 maclean Ah, right, yes.
14:47 egonw one pratical thing you can do is:
14:47 egonw remove a dep on cdk-data.jar in src/META-INF for some module
14:47 egonw and try to compile that module :)
14:48 maclean So converting method calls from public AtomContainer foo(Atom atom); to public IAtomContainer foo(Atom atom, IChemObjectBuilder builder).
14:48 maclean Hmmm. Or just taking the builder from whatever object was passed in, I suppose.
14:49 egonw yes, on second
14:49 egonw so this will do indeed:
14:49 egonw public IAtomContainer foo(IAtom atom)
14:49 egonw this in fact explains why we have .getBuilder() :)
14:50 maclean Ye-es. I'm not sure why, but I don't like this approach so much.
14:50 maclean ...but I can't put my finger on why,
14:50 maclean Oh, and is it this : https://github.com/egonw/cdk/​tree/137-separateListenerAPI
14:50 egonw :)
14:50 egonw honestly... I'm not 100% confortable with it either, but just cannot think of something better
14:50 egonw yeah, that's part of the story too, indeed
14:51 egonw will try to iron that out for master soon
14:51 maclean I mean, there is the very faint possibility that you might want to do "myObj.foo(new DebugAtom(), SilentChemObjectBuilder.getInstance())"
14:52 maclean But I can't see much reason why anyone would mix the implementations like that.
14:52 egonw true, that is currently not really supported
14:52 egonw except that people can write their own implementation anyway
14:52 egonw (I once in fact worked on the impl that used a DB as backend)
14:52 egonw just for fun
14:53 egonw but I can be weird about these things :)
14:53 maclean I started an AnimatingChemObject impl, but didn't get far.
14:54 egonw that's the good thing about the new IChemObjectBuilder API
14:54 egonw you do not have the implement all classes
14:54 maclean True, I found the copy/paste of the old approach was problematic.
14:56 maclean Also, there was Asad's GraphAtomContainer class
14:58 CIA-38 cdk: maclean master * ra1894f2 / (2 files in 2 dirs):
14:58 CIA-38 cdk: Convenience method for getting an atom container directly from a formula string
14:58 CIA-38 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://git.io/jTlyRw
15:07 egonw maclean++
15:07 egonw for the isomorphism patch
15:08 egonw ... signing off
15:08 maclean n/p. I forget to check up on these things, but I'm getting better.
15:09 maclean finding out about "git commit -C HEAD" makes the whole process a bit smoother.
15:09 egonw yeah, I saw you mention that... I have to read up on that :)
15:09 egonw sounds useful
15:10 maclean It just re-uses the commit message, so avoiding going to $editor.
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15:12 maclean I was amazed to see that Jmol has had so few bug reports and patches on its tracker. Unless you can delete closed ones?
15:13 egonw a lot happens just via the ML
15:14 maclean Yeah, like Random person : "Why doesn't Jmol do X?"... 5 mins later ... Bob Hanson : "Now it does".
15:14 egonw indeed :)
15:18 egonw I'm soon to relocate to the bus home
15:20 maclean Ah, ok. Good luck with the traffic.
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16:09 egonw_ maclean: did you also notice that we passed the 400 closed patch reports?
16:10 maclean Heh. Yes, in a way.
16:10 egonw_ I was quite impressed and surprised when I saw that earlier this afternoon
16:10 maclean I was browsing through them all, 100 per page (with 4 pages), so it vaguely impinged on my brain.
16:10 maclean The oldest one is only in like 2008.
16:11 maclean So that's easily 100 a year.
16:12 egonw_ I see the earliest in 2006
16:12 maclean Oh, ok.
16:12 egonw_ but, you're quite right
16:12 egonw_ the 10th or so is from 2008
16:13 maclean Admittedly, quite a few were shk3's for JCP that got moved.
16:14 * maclean is reading the amazing amount of whining on a site that moved their plugin management system
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16:15 egonw__ [09/16/11 18:12] * egonw_ is opening one by Stefan
16:15 egonw__ [09/16/11 18:12] <egonw_> to see what was commented
16:16 egonw__ first one closed as out of date
16:17 egonw__ yeah, don't you wish SF had a good API
16:17 maclean oh my yes.
16:18 maclean like the prev/next buttons could have _1-10_, _11-20, etc
16:18 maclean Oh, sorry. API, I thought you meant UI.
16:19 maclean Yes, a good API would be nice. There is some 'undocumented' one though.
16:19 egonw__ hehehe
16:19 maclean https://sourceforge.net/app​s/trac/sourceforge/wiki/API
16:19 maclean "unmaintained, read-only "API" for public project data"
16:19 egonw__ I'm trying to count the patches submitted by shk3
16:19 egonw__ and see how many have been closed as Out of Date
16:20 egonw__ 76 patches by stefan
16:20 egonw__ but cannot sort or filter by 'Resultion' it seems :(
16:21 egonw__ I'd guess close to have Out of Date
16:21 egonw__ rest is Fixed, etc...
16:35 maclean gtg, bye. hav nice weekend.
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