Camelia, the Perl 6 bug

IRC log for #cdk, 2011-03-23

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All times shown according to UTC.

Time Nick Message
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10:38 egonw_ moin all.... I got three new small patches lined up, which needs reviewing for 1.4.x ... anyone?
10:44 egonw_ is now known as egonw
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10:49 CIA-59 cdk: jonalv 268-m-loggerdebug * r52691c3 / (102 files in 30 dirs):
10:49 CIA-59 cdk: Switched from + to , in logger.debug() calls
10:49 CIA-59 cdk: Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://bit.ly/hkWd3c
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11:02 maclean hi
11:02 zarah hello maclean, you fantastic person you
11:05 egonw hi maclean
11:05 egonw [2011-03-23 11:39] <egonw_> moin all.... I got three new small patches lined up, which needs reviewing for 1.4.x ... anyone?
11:06 maclean saw that.
11:06 egonw maclean: otherwise... was wondering about the PDB patch state...
11:06 maclean well, I'm doing some command-line git stuff today, so I should do that as well.
11:07 maclean getting SMSD-CMD and SMSD-GUI to build independently of netbeans
11:09 egonw ah, crap...
11:09 egonw someone approved a crappy patch by me:
11:09 egonw test method *without* @Test annotation!
11:10 egonw ah...
11:10 maclean heh. oops.
11:10 egonw Ant?
11:10 egonw and Groovy Ant?
11:10 maclean what about ant?
11:10 egonw the latter is nice of yo don't like XML
11:10 maclean Yes, yes, obviously I will use ant - I have been programming in java for 10 years or so! :)
11:11 egonw https://gist.github.com/882951
11:11 maclean Actually that is quite nice.
11:11 maclean I don't mind XML so much though.
11:12 egonw and this ant.javac() does add a depedency...
11:14 maclean What is the moldbvalidator for? (I mean - I read the README...)
11:14 egonw well, basically...
11:14 egonw blame, blame, blame....
11:14 egonw think of it as:
11:14 egonw cdk blam
11:14 egonw cdk blame
11:15 egonw cdk blame some.sdf
11:15 maclean Ah, right.
11:15 maclean Did I tell you about the ghost hydrogens from the MDLV2000Reader?
11:16 egonw we did talk about ghost hydrogens...
11:16 egonw but from the MDLV2000Reader...
11:16 maclean I found them with the AtomContainerPrinter.
11:16 egonw please tell me (again?)
11:16 maclean Well, the ACP prints a string like "CCC C0:C1,C1:C2"
11:17 maclean which is the atom vertex symbols, and the bonds
11:17 maclean But I was getting things like "CCC H-1:C0,C0:C1..."
11:18 maclean Where "H-1" means that there is a hydrogen bonded to carbon zero, but it wasn't found in the atom list.
11:18 egonw mmmm...
11:18 egonw go on, go on
11:18 maclean So, the bond has a reference to an atom that isn't in the atom list.
11:19 maclean The molfiles are fairly standard, and there are no hydrogens in them, so I reckon its a bug in the reader.
11:19 maclean I mean to step through the debugger, with checkpoints where bonds are added.
11:20 CIA-59 cdk: Egon Willighagen cdk-1.4.x * rdf302b3 / src/test/org/openscience/cdk/atom​type/CDKAtomTypeMatcherTest.java : Added missing @Test annotation (idiot) - http://bit.ly/hZfL6x
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13:48 egonw argh... stupid SF :(
13:50 maclean Dammit. Stupid me!
13:51 maclean Just uploaded a signed-off patch to the wrong page...
13:51 egonw hahaha
13:51 egonw well, I just filed earlier a patch in the feature request tracker :)
13:52 maclean D'oh. It's a patchy comedy of errors.
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14:16 maclean heheh. omnigraffle++ : rotate with mouse (rotates text also) : select all : set rotate 0º - bingo!
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15:36 jkerssem Hi
15:36 zarah hello jkerssem, you fantastic person you
15:36 maclean hi
15:36 zarah hi maclean
15:36 jkerssem hey maclean;
15:36 maclean hej
15:36 jkerssem are you perchance git-savvy?
15:36 maclean heh, perhaps.
15:37 jkerssem Ok, lets see how far we get :)
15:37 maclean Ok.
15:37 jkerssem I'm trying to sign-off Egons Contructs-typo-fix patch
15:37 maclean Right.
15:37 jkerssem to do that, I need to apply it
15:37 jkerssem that fails..
15:37 maclean Ah.
15:38 jkerssem I pulled origin/cdk-1.4.x
15:38 jkerssem made a new branch
15:38 jkerssem and tried "git apply thePatch"
15:38 jkerssem it complains it cant find a piece-of-text in MDLV2000Reader
15:38 maclean Hmmm.
15:39 jkerssem which, upon inspection, had an insert compared to the patch
15:39 jkerssem this insert is touches the first context line for the patch
15:39 maclean Well, firstly, I find that the whole process only works when you use "git am", not "git apply".
15:39 jkerssem but not the patched line itself
15:39 jkerssem ah
15:39 jkerssem git am complained about the same..
15:39 maclean Secondly, from what you are saying, it seems like his patch no longer works.
15:39 jkerssem and told me to "resolve it"
15:40 maclean Yes, to resolve a problem you usually have to edit the file.
15:40 jkerssem I think Egon based his patch not on the github/cdk branch but
15:40 jkerssem on his own egonw/cdk
15:40 maclean It will have bits like : >>>>>>> and <<<<<<
15:40 maclean Right, possibly. This kind of thing happens.
15:41 jkerssem hmm, lemme check for the >>>> things..
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15:41 maclean I think that, so long as the signed off patch does the same thing, it's ok to fix this.
15:42 jkerssem Hi Egon!
15:42 egonw hej!
15:42 egonw what's up?
15:42 jkerssem maclean and I were just discussing your patch :)
15:42 egonw cool
15:42 jkerssem ^^
15:42 egonw did I do something stupid in my patch?
15:43 jkerssem the typoFix patch doesn't apply to my clean github/cdk/1.4.x branch
15:43 maclean You can also do things like "git apply --check aPatch" to see if it applies.
15:43 jkerssem it complains it cant find a match for the MDLV2000Reader
15:43 egonw with: git am -3 --ignore-whitespace ?
15:44 jkerssem I didn't try that one yet
15:44 jkerssem but looking at the diff
15:44 egonw it helps me
15:44 egonw sometimes with patches from Rajarshi
15:44 jkerssem from looking at the files, the GH/cdk branch had an insert
15:44 jkerssem where your patch's context assumes a "}"
15:45 jkerssem so only the first context line changed
15:45 jkerssem what does the "-3" do in your command?
15:45 egonw ok, just complain in the patch report
15:45 egonw 3-way merge
15:45 jkerssem aha
15:47 jkerssem cool, that did it..
15:47 jkerssem I don't know if it was the -3 or the --ignore-whitespace option
15:47 jkerssem but suddenly "git am" didn't complain anymore...
15:49 egonw :)
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15:49 egonw_ jkerssem++
15:50 jkerssem cool, even the tree-diff against the previous commit looks good!
15:50 jkerssem (Eclipse Egit has at least _some_ things that function :-) )
15:51 jkerssem (but I applied the patch from terminal)
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15:52 egonw__ sorry for my sloppy connection... but it's free, so can't complain :)
15:53 jkerssem heh :)
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15:53 egonw__ jkerssem: btw, are you aware that the CDK is also used in Leiden?
15:54 egonw__ have you met the people there?
15:54 jkerssem so, any special considerations I should take when making the patch?
15:54 egonw__ "making the patch"?
15:54 jkerssem Leiden? I've been there for the Netherlands Metabolomics Consortium
15:54 jkerssem but not anymore
15:54 egonw__ oh, have you? nice!
15:54 jkerssem "making the patch" --> amending the previous commit and formatting it to a patch file
15:54 egonw__ no, just;
15:55 egonw__ git commit --amend --signoff
15:55 egonw__ git format-patch -1
15:55 egonw__ (did you meet with Miguel and Julio, the two CDK users there?)
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15:55 egonw__ users/developers
15:56 jkerssem I only met Thomas Hankemeier in Leiden, to talk about how my project could fit with the NMC
15:56 jkerssem wasn't really productive sadly
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15:57 jkerssem So I didn't meet Miguel or Julie
15:57 jkerssem *Julio
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16:00 jkerssem oh joy, How do I upload the signed-off patch to the tracker?
16:00 maclean There's an "add files" button.
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16:01 jkerssem not for me :-S
16:01 maclean It doesn't look much like a button (in safari), but it's there.
16:01 maclean Ah - logged in?
16:01 jkerssem yup
16:01 maclean Hmmm.
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16:01 jkerssem there IS an "add a comment" thing
16:01 jkerssem "button"
16:01 jkerssem but the corresponding place for "Attached Files" is empty
16:01 jkerssem I think I may lack some permissions...
16:01 maclean Oh.
16:02 jkerssem Because I can add files for the bug-tracker
16:02 maclean Weird.
16:02 egonw_ oh... hang on... let me check
16:02 jkerssem no, wait, I can't add for the bug-tracker either
16:04 egonw_ ok, please refresh the page and check
16:05 jkerssem hmm, still only an "add a comment" 'button', nothing comparable under "Attached File (1)"
16:07 egonw_ ok, next iter... try again please
16:08 jkerssem wewt! my hero!
16:08 jkerssem egonw_++
16:09 jkerssem (whatever that ++ does...)
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16:09 egonw_ as in: i++
16:09 egonw_ i = i + 1
16:09 egonw_ egonw = egonw +§
16:09 egonw_ egonw = egonw + 1
16:09 egonw_ @karma jkerssem
16:09 zarah jkerssem has a karma of 2
16:09 egonw_ jkerssem++
16:09 jkerssem @karme egonw
16:09 egonw_ @karma jkerssem
16:09 zarah jkerssem has a karma of 3
16:09 jkerssem @karma egonw
16:09 zarah egonw has a karma of 206
16:09 maclean hah. wow.
16:09 jkerssem ah!
16:09 egonw_ @karma egonw_
16:10 zarah egonw_ has a karma of 4
16:10 jkerssem I expected something like that
16:10 jkerssem but had no idea it was actually monitored
16:10 jkerssem (no feedback or anything like that...)
16:10 egonw_ no, it's not a game
16:10 jkerssem I know
16:10 egonw_ at least, masak doesn't want it to be
16:10 egonw_ the rest of us loves the game .)
16:11 jkerssem karma is actually something that should be representative
16:11 zarah is actually something that should be representative has a karma of 0
16:11 egonw_ hahahahahaha
16:11 egonw_ zarah++
16:11 jkerssem wow, that would set a new record for nick-length :-D
16:11 jkerssem @karma zarah
16:11 zarah zarah has a karma of 130
16:12 jkerssem but poor egonw / egonw_ / egonw__
16:12 jkerssem you have distributed karma...
16:12 jkerssem @karma egonw__
16:12 zarah egonw__ has a karma of 0
16:12 jkerssem @karma egonw_
16:12 zarah egonw_ has a karma of 4
16:12 jkerssem @karma egonw
16:12 zarah egonw has a karma of 206
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16:16 jkerssem oh man, that connection is really bad...
16:16 egonw yes
16:16 egonw they
16:16 egonw they'll be upgrading the wireless routers soon, I was told
16:16 egonw making it faster... but hopefully, particularly more stable
16:17 egonw speed is quite good already
16:17 jkerssem they = swedish Hi hotspots ?
16:17 egonw particularly, since I'm driging 120km in the opposite direction :)
16:17 egonw driVing
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16:17 jkerssem opposite direction of what?
16:18 egonw and 120km/h
16:18 egonw where the bits need to go :)
16:18 jkerssem ah of course :)
16:18 jkerssem ah well, the bits won't be blue-shifted that much at those speeds...
16:18 jkerssem so don't be blue ;-)
16:19 egonw :)
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16:19 jkerssem and there you go again :-)
16:20 egonw no, that was just my ghost
16:21 jkerssem well, that ghost was you a few minutes ago..
16:21 egonw true
16:21 egonw I'm on a rotating security system
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16:21 egonw I'm changing nicks all the time so that others can't read what I see here in the chat
16:21 egonw see -> say
16:23 jkerssem If that's really the case, I think you can do better than appending a few underscores ;-)
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16:33 egonw_ jkerssem: btw, if you approved and signed off a patch, please mark it as 'approved' in the Resolution
16:33 jkerssem ok, will do!
16:34 jkerssem (see, that's the things I mean when "any special considerations"
16:34 jkerssem )
16:34 egonw_ ah :)
16:34 egonw_ you can update the 'Group' field too
16:35 jkerssem would that be "resolution:accepted" and "group:accepted"?
16:35 jkerssem and then once you push it, it will be "status: closed"?
16:36 egonw_ yes
16:36 egonw_ the system is not ideal
16:36 jkerssem as they say in dramatic texts all over the world: "it is done"
16:37 egonw_ tack, tack
16:41 jkerssem "tack, tack"? as in the sound staple-guns make?
16:42 egonw_ zweeds voor bedankt
16:45 egonw_ ok, going offline for a while...
16:46 jkerssem aha!
16:46 jkerssem ok, bye bye!
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