2009-09-08.log

--- Day changed Tue Sep 08 2009
kanzure"STN on the web" looks pretty close (accesses CASREACT) except it doesn't seem to work with ezproxy00:03
kanzurehm: http://www.lib.utexas.edu/chem/sfs1.html00:05
kanzurebroken links?00:06
kanzureah here we go: https://scifinder-cas-org.ezproxy.lib.utexas.edu/scifinder/login.jsf?TYPE=33554433&REALMOID=06-b7b15cf0-642b-1005-963a-830c809fff21&GUID=&SMAUTHREASON=0&METHOD=GET&SMAGENTNAME=-SM-JY4LbS2p%2bgz765P800x5OOaEwqPCbTkVdKHqXjnYiBDMW75oNochBjvKgTBKfbcN&TARGET=-SM-http%3a%2f%2fscifinder.cas.org%2fscifinder%2f00:06
kanzure"This milestone came quickly, since it was only 9 months ago that CAS registered its 40 millionth substance.  In contrast, it took 33 years for CAS to register the 10 millionth compound in 1990."00:07
kanzuregah: http://www.lib.utexas.edu/chem/scifinder/register.html00:09
kanzurehttps://scifinder-cas-org.ezproxy.lib.utexas.edu/registration/index.html?corpKey=A65E4AAB-86F3-50AB-5475-3D89FD84DD8C00:10
genehackercas react?00:10
genehackerwhat's this?00:10
genehackerugh registration00:11
kanzure"To complete your SciFinder registration, you must click the link provided below. By clicking the link, you agree to all of the following terms and conditions:00:11
kanzure* I will not share my username and password with any other person. * I will search only for myself and not for others or other organizations. * I will not use any automated program or script for extracting or downloading CAS data, or any other systematic retrieval of data.00:11
kanzure * I may retain a maximum of 5,00 Records at any given time for personal use or to share within a Project team for the duration oof the Project. * My organization's SciFinder License and the CAS Information Use Policies (http://www.cas.org/legal/infopolicy.html) apply to my use of SciFinder. * I will contact my SciFinder Key Contact if I have questions.00:11
kanzurewtf is this bullshit?00:11
genehackeras if 00:12
genehackereast coast code00:12
kanzure"4)  I will use my search results in the ordinary course of academic research and acknowledge that I may store search results in electronic form for the duration of research projects, provided that at any one time, I store no more than 5,000 records. I may share search results in a limited, reasonable way with other University students or faculty working on the same project. I will delete stored records when I no longer need them for the relevant research project, or after the completion of my degree program, whichever occurs first. If I need to use search results beyond what is described here, I will contact my University Key Contact to discuss and to obtain CAS permission. I ACKNOWLEDGE THAT I AM NOT PERMITTED TO DISTRIBUTE ANY CAS DATA OR SCIFINDER, FOR COMMERCIAL GAIN OR OTHERWISE, OUTSIDE THE UNIVERSITY OR TO THIRD PARTIES."00:13
kanzurethese guys are brutal00:13
kanzurewhy is 5k the magic number?00:14
kanzurehm this is the american chemical society?00:14
kanzureapparently there's a "chemical abstracts exchange" file format called CXF00:15
genehackerat least it doesn't say "unauthorized reproduction is illegal" on every page00:19
genehackerhttp://blog.makezine.com/archive/2009/09/claims_of_pnuematic_processor_full.html00:27
* katsmeow-afk is intrigued by http://ci.nii.ac.jp/naid/110002809091/en00:43
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fennhttp://fennetic.net/irc/Peter%20F.%20Hamilton%20-%20Misspent%20youth.pdf05:17
fenngeez it was 6 months between the time that microfluidic processor was published and the popular media noticed06:06
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fenndamn, now i want a pet armadillo08:02
* dira thinks of green snake with red eyes as his favorite pet08:03
fennhah "In some parts of South America, they are kept as pets — pets which are occasionally eaten."08:03
kanzurethis is pretty fun to play with: http://www.daylight.com/download/contrib/pydaylight.html08:12
kanzurefound here: http://www.daylight.com/download/contrib/index.html08:13
kanzurehm: http://www.daylight.com/download/contrib/transform.tar.gz08:13
kanzure"SMILES was originally developed as a proprietary specification by Daylight Chemical Information Systems. Since the introduction of SMILES in the late 1980's, it has become widely accepted as a defacto standard for exchange of molecular structures"08:27
kanzurehttp://www.opensmiles.org/spec/open-smiles-1-intro.html08:28
kanzureaha: http://frowns.sourceforge.net/08:28
kanzureexample: http://frowns.sourceforge.net/examples/example3.py08:29
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genehackerwhy an armadillo?08:57
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fennapparently hydrogen isn't an atom according to smiles/frowns?09:57
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fennhuh. "Be aware that while GraphViz is opensourced it is not free for commercial applications and any such use must be cleared with AT&T."10:12
fennnevermind i think that's wrong10:13
fennhttp://adl.serveftp.org/lab/fenn/pngs/frowns_graphviz.png10:21
fennmeh: http://adl.serveftp.org/lab/fenn/pngs/frowns_graphviz2.png10:35
fenni guess graphviz doesn't do double or triple bonds :)10:35
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CIA-32skdb: fenn * r cd50243 /import_tools/SMILES_graphviz.py: mucking around with frowns and graphviz10:43
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fennIUPAC to graphviz would be cooler10:51
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fennkalzium is pretty impressive10:58
fennhmm11:05
* fenn conects 6 bonds to a hydrogen atom11:05
fenn"scheme"->iconic is pretty funny11:15
fennhttp://fennetic.net/irc/kalzium_iconic.png11:16
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fennsomehow i find this interesting, it's recommendations on drawing 2D chemical structures http://old.iupac.org/reports/provisional/abstract07/brecher_prs2.pdf11:51
fennit seems like a lot of these rules would apply to instruction generation as well11:52
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kanzureliposuction yields induced pluripotent stem cells better than skin12:29
kanzurefenn: should the retrosynthesis code go into skdb or not?12:30
kanzuredunno if it's package-worthy since it's not really hardware12:30
kanzureideally the thingy that reads the retrosynthesis output would generate hardware and thus belong as an skdb package12:31
fennbleh?12:39
fennopenbabel supports a crapload of formats12:40
kanzurethere's also bluebolesik12:41
kanzurehttp://www.blueobelisk.org/12:42
fennbodr: "Common repository of chemical and physical facts"12:42
fennseems to be what kalzium uses (they dont use the package though? wtf)12:43
fennopenbabel is blueobelisk12:49
fennwell, something like that12:50
fennopenbable makes use of it somehow12:50
kanzurefenn if you find a database of SMARTS I'd really like to see it12:53
kanzureblueobelisk is probably just a social group to be honest12:53
fennwell, i liked what i saw12:53
fennwhat is special about SMARTS?12:53
kanzurenothing, only that people seem to use it12:54
fennand they don't seem to use SMILES?12:54
kanzureit describes chemical reactions/transformations12:54
fennwhat are you saying?12:54
kanzureSMILES and SMARTS are compatible12:54
fennoh it's a reaction language12:54
kanzureSMARTS is an addition to SMILES 12:55
kanzureat most I can find only 11 smarts12:55
fennit's a fingerprint system?12:55
fenndo you even know wtf it is?12:55
kanzureit's not for fingerprinting12:56
kanzurethis is chemistry12:57
kanzurebasically it's a string grammar rule12:57
fennright it looks sorta like a regex12:57
fennfingerprinting is something like searching for a particular functional group12:57
fenn... i guess12:58
fennanyway, i dont care, go away..12:58
kanzureoops sorry, SMIRKS is the reaction string grammar12:59
kanzurethere's a button on this page that says "Reacting carbon" that goes to an online demo:12:59
kanzurehttp://www.daylight.com/dayhtml_tutorials/languages/smirks/index.html12:59
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fennwhy do i get KeyError: 'all_bricks' on line 347 of paths.py?13:05
fennkanzure: *poke*13:07
kanzurehm13:07
kanzureI'm looking, I'm looking13:07
kanzuredid you get this before? this hasn't happened to me13:07
kanzurenot sure if I've used "clear" before though13:07
fennit's because of your function partial stuff, obviously13:08
kanzuredoes add_key's "keyword" have "all_bricks" ?13:08
kanzures/keyword/keywords/13:08
kanzureum did either of us ever test this?13:09
fennclear was broken since the beginning a4c0919bb2dc0f2a169b370ce2312c52809c902e13:09
kanzureright, functools was my attempt at fixing the wacky issues involved with using globals and trying to pass things around13:10
* kanzure tests functools13:10
fennkeywords is {}13:10
kanzurein add_key?13:10
fennin clear13:11
CIA-32skdb: kanzure * r 58f85d4 /gui/gui.py: fix functools.partial (forgot a parameter)13:12
kanzuretry that while I go fetch the foods13:13
fennthat didnt do squat13:14
* fenn reads about **kew13:22
fennbtw it works when i include all_bricks=123 in the argument list for clear13:23
fennclear(event=None, all_bricks=123):13:23
fenndef ^13:23
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kanzurefenn: functools.partial and add_key works when you have all_bricks in the argument list?13:30
fennwhy did we need to use functools again? something about gui.py?13:38
CIA-32skdb: fenn * r 189983b /paths.py: move from globals halfway to OO13:41
kanzurefunctools was so that we could eventually migrate away from using globals13:42
kanzurethe problem was that add_key had to take a function object13:42
kanzureand a function object doesn't have parameters13:42
kanzuredef blah: pass13:42
kanzuremy_func = blah13:42
kanzureor: my_func = functools.partial(blah, some_parameter_here)13:42
fennbut what function in particular needed an argument?13:42
kanzure'def blah' should have had an example of a named argument I guess13:42
kanzurefenn: clear13:42
fennbut clear gets overwritten in paths.py13:43
kanzureno that's where clear was defined I thought13:43
fennit's also defined in gui.py13:43
kanzureisn't it the same thing?13:43
kanzureoh in gui it's just display.EraseAll13:43
fennyeah13:44
kanzureyeah overwriting it in paths.py is fine13:44
kanzurethat's clear for a gui, not clear for the paths.py demo13:44
kanzurepaths.py obviously has a few more things worth clearing13:44
fenndef bar(a=7, b=9, c=None): print c,b,a13:46
fennfoo = {'a':4, 'b':5, 'c':6}13:47
fennbar(**foo)13:47
fennprints 6 5 413:47
fennjust FYI13:47
fennbar(*foo) prints b c a13:48
fennpart of the confusion was due to the fact that i can't get the traceback when i press 'c'13:54
fennso i was doing demo->clear instead, which didn't use the partial13:54
kanzurewxpython is totally lame13:54
kanzurewhy would it hide the traceback?13:54
kanzureit's not multithreaded..13:54
kanzureso it has access to it somewhere13:55
fennit's something to do with the try: except ValueError:13:57
fennduh. it's not "except ValueError:" it's just "except:"14:00
fenns/except:/except KeyError:/14:03
fenni guess that would still swallow some errors14:03
fennjust get rid of the whole try/except statement14:04
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kanzureuse except KeyError, k:14:20
CIA-32skdb: fenn * r f6a4d93 / (gui/gui.py paths.py): move App from paths.py to gui.py, fix show_interfaces14:20
fenndid you actually try that?14:22
fennKeyError, k:14:22
kanzureit puts the exception into "k"14:23
kanzureer, that's just how python wroks I thought14:23
kanzure*works14:23
kanzureso then just go print k or something14:23
kanzureor is it k.message?14:23
fenni dont know and pydoc doesn't help14:26
CIA-32skdb: kanzure * r 3d052f0 / (5 files in 3 dirs): move dependency code into core14:27
kanzureyou can now delete the "dep" folder btw14:27
fennlooks like git removed it automatically14:28
kanzureyay for git14:28
kanzurewire exploring code: http://pastebin.com/f5aeaf87514:29
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fennwhat are you going to do with that?14:34
kanzurealready implemented it in BoundingBox in geom/geom.py14:34
kanzure(just cleaning up some uncommitted files)14:34
fennhey could you try to keep import statements at the top of the file?14:35
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kanzurefenn: ok.14:36
kanzuremy bad :)14:36
kanzurethere were four near BoundingBox IIRC14:36
fennif [x, y, z] is not [None, None, None] and x is not [] and y is not [] and z is not [] and shape is None:14:36
fennwtf is that14:36
kanzurebrainfart14:37
kanzurehow do I make that better?14:37
kanzureI don't want x, y, or z to be [] or None, and I need shape to be None14:37
fennfirst of all, i thought you were doing two points14:38
kanzurei am14:38
fennno, you have x = [min, max] etc14:38
kanzureright..14:38
kanzurepoint1 = x min, y min, z min14:39
kanzurepoint2 = x max, y max, z max14:39
kanzureI count only two14:39
fenndo you often get this error with add_valid_lego? ValueError: invalid null reference in method 'TopoDS_Shape___eq__', argument 2 of type 'TopoDS_Shape const &'14:40
kanzureno never14:40
kanzurebut I got that somewhere else the other day14:40
kanzureand even pasted it in here14:41
kanzureso if you want to search the logs to see my fix ..14:41
fennkanzure: why not just __init__(point1, point2)14:41
kanzurewhat about shape?14:41
fennwhat about shape?14:41
kanzurelook at the __init__14:42
fennhey why don't you just use OCC bounding box instead of compute_from_edges14:42
kanzurebecause I don't know about it14:43
kanzurealso is it slow?14:43
fennhttp://adl.serveftp.org/lab/opencascade/doc/ReferenceDocumentation/FoundationClasses/html/classBnd__Box.html14:44
kanzurewell. great.14:44
kanzureblah14:44
fenner, that's not what you want14:44
* fenn looks at http://www.opencascade.org/org/forum/thread_13902/14:47
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CIA-32skdb: fenn * r 7742635 /gui/gui.py: forgot import14:54
CIA-32skdb: kanzure * r 474e599 /import_tools/readme: now you know what this crap is14:56
fennhttp://adl.serveftp.org/lab/opencascade/doc/ReferenceDocumentation/ModelingAlgorithms/html/classBRepBndLib.html14:59
ybit2got my welder in today: http://www.millerwelds.com/products/stick/thunderbolt_xl_ac_dc/14:59
fennkanzure: so should i fix this?15:01
kanzuredon't start now15:02
kanzureit's almost 153015:02
fennharumph15:02
kanzurethat's a new one15:02
katsmeow-afkybit , first thing you should do is open it up and remove the main diodes which are wired up with 14awg, and put in some serious hardware on real heatsinks, then wire the fan to a thermostat15:03
katsmeow-afkmy Miller had 4 small diodes on 2 5x3 inch aluminum plates, they relied on the surge rating of the diodes15:04
fennkanzure: did you not happen to notice that test_part_mating locks up consistently?15:05
fennkanzure: anyway, it's hardly a unit test15:05
kanzuretest_part_mating is in which file?15:05
fennin test_geom.py15:06
kanzuretest_geom?15:06
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kanzureworks for me15:06
kanzureran 1 test in 3.775s15:06
kanzure(most of that was the crappy STEPImporter textpuking)15:06
fennconnecting 2x2 round brick's stud  to 2x2 round brick's anti stud brick1[6] to brick2[1])15:06
fennthis makes me think it's doing the same thing that paths.py does when it starts off with a round brick15:07
kanzurehave you noticed it sucks when it starts with a round brick?15:07
kanzurepaths.py, I mean15:07
fennyes15:07
kanzureany clues?15:07
fenni thought i might have two interfaces in the same spot or something15:08
fennbut i think i checked and that wsn't the case15:08
kanzureok so still an open problem15:08
kanzurehey why the hell don't we have a bug tracker?15:08
fennbecause they're more trouble than worth half the time15:08
kanzureis it lame to just keep a file with a list of bugs?15:09
fennno15:09
CIA-32skdb: kanzure * r 7882750 /doc/todo: update the todo to represent recent progress15:09
ybit2thank you katsmeow-afk, you always provide helpful info15:11
ybit2..most times ;)15:11
katsmeow-afki won't force you to do it15:11
kanzurefenn: it crashes for me too15:12
kanzurewhen it does the roundbrick15:12
fennthis is annoying.. bpython is crashing on me a lot now15:18
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kanzuredid you update it?15:20
kanzureis it crashing only on this round brick problem or when doing normal stuff?15:20
CIA-32skdb: kanzure * r 2dc6439 /readme: update readme to reflect dependency resolution engine changes15:21
fennno i mean bpython actually crashes15:25
fennthe round brick thing just sits there twiddling its thumbs15:25
fennwhat does this mean? "doesn't support rectangular prisms at the moment"15:25
kanzureI was wrong15:25
kanzureyou explained to me why I was wrong15:25
kanzureit was a silly thing for me to think anyway15:25
CIA-32skdb: kanzure * r 61e35be /doc/todo: fix mismatched apostrophe15:28
fennok i implemented the OCC bounding box finder and it seems to do the same thing (not having a functional unit test kinda sucks)15:28
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kanzurefenn: ok15:50
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CIA-32skdb: fenn * r 717abce /geom/geom.py: fix bounding box clusterfuck. now uses OCC Bnd_Box methods which don't rely on edges defining the extents (for example like you'd get in a nurbs patch15:56
CIA-32skdb: fenn * r 43e63f4 / (doc/todo import_tools/readme readme): Merge branch 'master' of ssh://adl.serveftp.org/var/www/skdb15:56
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fennshould BoundingBox use the OCC Bnd_Box methods like IsOut?16:01
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ybithttp://hackerspaces.org/wiki/HackerSoundScapes17:00
xp_prgwhat is the best tool/program for molecular visualization and animation?17:16
xp_prgis it pymol?17:17
fennflash, definitely17:22
ybitscrew flash, silverlight ftw :)17:22
fennum, yeah, that's what i meant17:22
fennstill getting used to flash not being the ultimate evil17:23
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xp_prgfenn I mean an already made program/tool17:32
xp_prglike if I have a pdb etc...17:32
* katsmeow-afk shudders17:55
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genehackerpython doesn't happen to have any handy uncertainty libraries now does it?18:45
kanzurewhat do you mean? like statistics?19:08
Phreedomuncertainity isn't usually handy :P19:12
kanzureit is when you're planning for reliability or failure analysis19:33
kanzureer just something I've recently become more obsessed with19:34
kanzurethere's this paper that I just forwarded to a few lists about failure propagation analysis in hardware designs19:34
kanzurefenn: do you know how to conveniently convert from SLiP to YAML?19:38
kanzureon adl:~/lab/roomba-to-yaml/slippy_0.2/ I have a copy of SLiP19:38
kanzureand in the parent directory there's roomba.slip19:38
genehackerfailure propagation analysis?19:41
genehackeryou should ask my statistics teacher about nuclear plant failure analysis then19:41
kanzureI wouldn't imagine that to be very discrete, would it?19:42
kanzureWhat's in a nuclear power plant anyway besides the reactor?19:43
kanzurecontrol systems I guess19:43
kanzuresteam turbines? are we doing that?19:43
kanzurereaxys is awesome, they provide XML output for its search results19:54
kanzurenow if onyl I can grab their actual database19:54
kanzureheh reactions with ID=96669 19:54
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CIA-32skdb: kanzure * r 8e925af /doc/todo: parametric modeling added to todo20:15
kanzureblah20:15
CIA-32skdb: kanzure * r 20d68e2 /import_tools/ (yaml2outline.pl ysh.pl): perl tools to play with yaml, like yaml2outline.pl20:15
CIA-32skdb: kanzure * r 4d26a7c /geom/geom.py: Merge branch 'master' of ssh://bryan@adl.serveftp.org/var/www/skdb20:15
katsmeow-afki need a file to dl that's bigger than a gigabyte20:43
katsmeow-afkcontents don't matter20:43
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ybitkatsmeow-afk: http://download.wikimedia.org/backup-index.html or http://thepiratebay.org/torrent/3505908/2001_A_Space_Odyssey_DVDRip_XviD21:07
ybithttp://wiki.dbpedia.org/Downloads33#h81-221:08
katsmeow-afkthatnks, gmta, i am doing http://download.wikipedia.org/enwiki/latest/enwiki-latest-pages-articles.xml.bz2 atm21:10
katsmeow-afkit's small enough, yet big enough, i wanna proove a certain lib crashes on files over ~500megbytes, and proove a mod will let it dl any size files21:12
katsmeow-afkin case you were wondering21:13
katsmeow-afkplus it doing ~70 page faults/sec21:14
ybitwhat library/21:14
katsmeow-afki don't wanna say, they'll blame it on me21:14
ybitalright21:14
* katsmeow-afk goes to get clearance to let it out in the wild21:15
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CIA-32skdb: kanzure * r 0b1fa52 /import_tools/del_repo/repo_to_yaml.py: code to convert from dot repo to dot yaml (xml2yaml)21:34
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CIA-32skdb: kanzure * r 0ca6adf /import_tools/readme: update readme to reflect new import tool21:55
ybitmy phone had been turned off for a few days because it wasn't able to charge22:03
ybitturned it on this afternoon and there's a ddos attacked from twitter.com/kanzure skdb messages. google voice wasn't able to reach me for minutes :P22:04
ybits/attacked/attack22:04
katsmeow-afkheh22:05
ybitkanzure: iirc, the occ build for debian fails miserably?22:05
kanzureno otherwise how would we have the dot deb?22:06
dirayou phone uses Google voice? how is that?22:08
kanzurehttp://adl.serveftp.org/lab/opencascade/debs/22:11
ybitdira: i'm using an older phone temporarily, it's a pita to use the keys and it's quicker to just copy and paste a number from the web to the google voice interface. so anyway, from the google voice interface i was attempting to call a business, and the process is that g.v. calls me first, but it was unable to reach me because the phone was unable to process so many requests at once :)22:11
ybitdid you build the debs kanzure or are these the ones that are in Lenny?22:12
kanzurethey are from squeeze22:12
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ybitoh, katsmeow-afk, do you buy your welding rods online or are they just as cheap in the store?22:15
* ybit was planning on visiting http://www.valleyairsupply.com/ tomorrow (a local company)22:15
ybitfenn: you do some welding as well iirc22:16
ybitwe can cast metal at work and that makes me happy22:17
katsmeow-afkin the store, i make 3 compete for my busines22:17
katsmeow-afki buy 50lbs at a time too, drives the price down some22:17
ybit50lbs == ~$?22:17
katsmeow-afkit changes a lot,, and i don't remember last time22:18
ybitanyone worked with capacitance detectors?22:20
katsmeow-afk$125? ,,,, $130?22:20
katsmeow-afki get some discount22:20
ybiti might go with 25lbs. then, that's a little more than i'm willing to spend atm22:21
kanzurefenn: I'm not convinced OCC is doing it right. test_geom's test_boundingbox fails (it didn't fail before you changed it to OCC)22:21
kanzure    self.assertTrue([box.x_max, box.y_max, box.z_max] == [len_x, len_y, len_z])22:21
kanzurefrankly that should be a very easy test to pass22:21
kanzurerun as: python test_geom.py TestGeom.test_boundingbox22:22
kanzurealso in case any one is interested, here's the results of my xml2yaml stuff: http://adl.serveftp.org/lab/roomba-to-yaml/roomba.yaml22:22
genehackercoolant pumps kanzure22:34
genehackerif a coolant pump fails22:34
genehackerwhat's being cooled tends to overheat22:34
genehackeralso there is a federally mandated nuclear power plant failure rate22:43
genehackerright now it's something like one meltdown per 1 million years22:43
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parolanghttp://science.slashdot.org/comments.pl?sid=1361651&threshold=-1&commentsort=3&mode=thread&cid=2936009722:53
parolangYou know, once I learned about hydrocarbons on Titan, I wondered about the same thing :)22:53
genehackershort chain hydrocarbons mind you23:02
genehackerin a thick atmosphere that saps away heat faster than the vacuum of space23:03
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kanzuremeeting notes from ADL today: http://adl.serveftp.org/dokuwiki/2009-09-0823:29
kanzure(they are not particularly verbose)23:29
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