Perl 6 - the future is here, just unevenly distributed

IRC log for #cdk, 2014-01-07

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All times shown according to UTC.

Time Nick Message
06:07 egonw joined #cdk
06:15 slyrus hey egonw
06:16 egonw hi
06:16 egonw I was just replying to your question about silent
06:16 egonw check your email
06:16 slyrus oh, thanks!
06:17 slyrus seems unfortunate to duplicate the classes. couldn't we somehow register listeners or something?
06:18 slyrus or extend the non-silent classes overriding methods as appropriate (or vice-versa)?
06:18 egonw I tried the latter...
06:19 egonw but not possible, because Java does not have multiple extending
06:19 egonw so, you cannot extend both Atom and SilentElement
06:19 egonw which made that set up impossible :(
06:19 egonw but, this is still on our mind...
06:19 egonw and duplication is not that bad...
06:21 egonw OK, got to head to work
06:21 egonw ttl
06:25 slyrus ok, thanks!
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07:27 slyrus egonw: any further thoughts on IUPAC name generation? I see you started something a long time ago, but it looks abandoned. OPSIN is quite handy, now i just need the inverse :)
07:28 egonw yeah, that's one big component missing...
07:28 egonw the framework I set up should work...
07:29 egonw it's just writing the hundreds of rules...
07:30 slyrus where can I find the most current version of your framework?
07:31 egonw well, current does not really apply...
07:32 egonw I have not touched it in prob >10 years
07:32 slyrus least old? :)
07:32 egonw the last version in the CDK, I guess...
07:32 egonw checking...
07:33 egonw the last  version is the one removed in commit a327db3357c1c04b4cbf6cdd12a898083e78a3be
07:34 egonw try:
07:36 egonw git revert a327db3357c1c04b4cbf6cdd12a898083e78a3be
07:36 egonw then you have a copy in the least old code
07:40 egonw biggest problem seems to be that the Fragment class no longer exists...
07:41 konditorn joined #cdk
07:41 egonw slyrus: for that, try: git revert 6a71d6348be0f5d014b65bc6118fd6395319b894
07:48 egonw quite a bit of code to update to newer APIs...
07:50 slyrus ok, thanks!
07:50 slyrus remind me again... do we have any standards for the codebase regarding spaces/tabs? Do we bother regularizing files that don't conform?
07:51 egonw max 120 chars per line
07:51 egonw 4 spaces indent
07:51 egonw we only bother if we fix something, and do the reformatting in a *separate* patch with no code changes
07:51 slyrus and files that use tabs for indentation? Do we just let them sit, or replace the tabs with prejudice
07:51 slyrus ok, thanks.
07:52 egonw better not to touch what you do not plan to change
07:52 slyrus sounds good.
07:52 egonw because it only makes looking up the code history harder
07:52 egonw now, looking at my code...
07:53 egonw there is a lot of room for improvement...
07:53 egonw as said, it was just a hack...
07:53 egonw but there may now be critical mass in the number of people who like to play and work with this bit of code
07:53 egonw I got one fix left to do, and will then push into my GH repos
07:58 egonw which is a harder one...
08:04 egonw ok, more later
08:04 egonw changing trains
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08:32 slyrus where do we keep the mapping between java files and the jars they belong in?
09:04 slyrus or, put another, how do I make sure that the iupac.generator stuff gets added to an appropriate jar?
09:04 slyrus put another way, that is.
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15:36 egonw_ slyrus: ping
15:37 egonw_ slyrus: https://github.com/egonw/cdk/compare/master...491-m-iupacGen
15:52 commitbot joined #cdk
15:52 commitbot [cdk] egonw pushed 1 new commit to master: http://git.io/_zykuA
15:52 commitbot cdk/master a58e340 John May: Check the correct atom is a hydrogen....
15:52 commitbot left #cdk
16:04 slyrus morning egonw
16:04 egonw_ hi slyrus
16:05 egonw_ that branch restores the IUPAC generator hack (it's nothing much more than some 4-5 rules...)
16:05 slyrus yeah, I tried that last night, but I couldn't get the classes to compile (not errors, just no attempted compilation)
16:05 egonw_ correct...
16:05 egonw_ I have not done that yet...
16:05 slyrus do I need to somehow update some manifest or something?
16:05 egonw_ it's in a module "experimental" which is currently not compiled
16:05 egonw_ yes
16:05 egonw_ you can add it to dist-all...
16:05 egonw_ oh, wait...
16:05 egonw_ let me just commit that
16:06 slyrus where does the mapping between module and java source file happen?
16:06 egonw_ class JavaDoc, @cdk.module tag
16:06 slyrus don't tell me it's in the comments?
16:06 egonw_ you can also change that from experimental to extra
16:06 egonw_ no, in the JavaDoc...
16:06 egonw_ so it shows up in the JavaDoc HTML
16:07 egonw_ it's extracted using JavaDoc technology
16:07 slyrus you call it javadoc, i call it comments, but OK, we're both kinda right :)
16:07 egonw_ I can set this up properly, but not in the next hour...
16:07 slyrus no worries
16:08 egonw_ I would prefer it as @Annotation but never figured out how to get that to show up nicely in the JavaDoc
16:08 egonw_ if you have a solution for that...
16:09 slyrus no, just some unproductive language-hating griping :)
16:09 slyrus what happens to classes with no @cdk.module tag? not compiled?
16:11 egonw_ they are..
16:11 egonw_ the end up in the extra module
16:12 slyrus oh, and here I was trying to use extra as the example module to understand the module system. I couldn't figure out how things with no module were ending up there. d'oh!
16:14 egonw_ also, in src/META-INF dependencies are defined...
16:15 slyrus right, but I couldn't find the module mapping. was looking in there without finding it.
16:15 slyrus is the jmol.javafiles file used?
16:16 egonw_ no, no longer
16:16 egonw_ file me a bug report about that, please
16:19 slyrus what's the appropriate bug tracker these days?
16:23 egonw_ still SF
16:23 egonw_ ok, catching a train now...
16:23 egonw_ ttl!
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17:07 egonw_ slyrus: pull request received
17:10 slyrus ok. it still doesn't work, as I get: Java exception 'java.util.MissingResourceException: Can't find bundle for base name org/openscience/cdk/iupac/generator/data/IUPACNames, locale en_US'.
17:11 slyrus a step in the right direction, hopefully.
17:11 egonw_ I would say so...
17:11 egonw_ and the message is kind of correct
17:11 egonw_ we do not have localized names for that Locale
17:12 egonw_ we do have en
17:12 egonw_ we do have "en"
17:12 egonw_ I would expect it to use that one...
17:12 egonw_ try setting the Locale to just "en"
17:15 slyrus we have _de and _nl. I'm not seeing _en. or is that the default?
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17:21 egonw_ yeah, the default
17:21 egonw_ maybe that's the reason
17:22 egonw_ remember, this stuff is so old, I think it even predates some of the Locale changes in later Java versions
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20:55 slyrus any suggestions on getting started with eclipse (or other IDEs) and CDK? Surely there's a better way than just using the shell to run ant to compile the whole kit-and-caboodle every time I make a simple change.
21:00 egonw I use Eclipse
21:04 slyrus can I do anything with this build-eclipse.xml file?
21:04 egonw no need
21:04 egonw just open the folder...
21:04 egonw the .project file should be enough for Eclipse to pick up things properly
21:07 slyrus sorry to be dense, but how do I do that? does this have anything to do with nbproject/project.xml?
21:07 egonw oh, sorry...
21:07 egonw got Eclipse open?
21:07 slyrus yes
21:07 egonw see the Package Explorer on the left?
21:07 slyrus yes
21:08 egonw right click on the white background and select Import
21:08 egonw then, General -> Existing Projcets into Workspace
21:08 egonw (Next)
21:08 slyrus ok
21:08 egonw set the root directory to cdk/
21:08 egonw that should do it
21:09 egonw that is, it should then show up in that dialog under "Projects:"
21:09 slyrus awesome!
21:09 slyrus that would have taken me days to figure out ;)
21:09 egonw this is exactly what this channel is about :)
21:09 egonw we used it a lot for the CDK for this purpose...
21:09 egonw not enough active developers at this moment...
21:10 egonw and Rajarshi can no longer join, as IRC is banned at his workplace
21:10 egonw and John is not so much of a online guy, but a great developer otherwise :)
21:10 egonw (and Chris is just too way up in the academic hierarchy to have time for that kind of thing)
21:10 slyrus no IRC? How do they get anything done?!?
21:10 egonw for #bioclipse it's still used a lot
21:11 egonw yeah, good question :)
21:11 slyrus people were talking on the phone too much, so we banned phones
21:11 slyrus (actually, that might not be a bad idea)
21:11 egonw though mostly on their internal (swedish) channel
21:11 slyrus whole lotta warnings. guess I can ignore those for now.
21:11 egonw the warnings... yes :)
21:11 egonw yeah, very many...
21:12 egonw there is still a lot of code to clean up...
21:13 slyrus and the best way to get up and running with a quick program that can exercise the CDK? (by exercise I mean call CDK functions, of course)
21:14 egonw for me? Groovy
21:14 slyrus well, yeah, abcl for me... but if I want something inside of eclipse?
21:14 slyrus new file? new project?
21:14 egonw good question...
21:15 egonw I don't that kind of thing in Eclipse...
21:15 egonw new file would do
21:15 egonw but I suggest to indeed do it in a separate project
21:17 slyrus and add some jars to the new project somehow?
21:24 egonw right click on the project in the Package Explorer
21:24 egonw and select...
21:24 egonw ... build path -> configure build path
21:25 egonw and then the Libraries tab
21:28 * egonw is going offline...
21:28 egonw I'll be back tomorrow

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