IRC logs of #shogun for Tuesday, 2016-02-23

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--- Log opened Tue Feb 23 00:00:08 2016
@drwikingshogun-buildbot: force build --branch=develop 'bsd1 - libshogun'00:46
shogun-buildbotbuild #2766 forced00:46
shogun-buildbotI'll give a shout when the build finishes00:46
shogun-buildbotbuild #2766 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/276600:53
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shogun-notifier-shogun: Viktor Gal :develop * 7f5310d / src/shogun/io/SerializableJsonFile.cpp: https://github.com/shogun-toolbox/shogun/commit/7f5310df956e14a3127d655ed49f0075f8b88c7605:28
shogun-notifier-shogun: Fix JSON serialization with JSON-C v0.12 or newer05:28
shogun-buildbotbuild #2767 of bsd1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/276705:35
shogun-buildbotbuild #1131 of FCRH - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/FCRH%20-%20libshogun/builds/113105:37
shogun-buildbotbuild #116 of FC22 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/FC22%20-%20libshogun/builds/11605:37
@drwiking:)05:37
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shogun-buildbotbuild #578 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/578  blamelist: Viktor Gal <viktor.gal@maeth.com>08:57
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shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * ace057f / doc/sphinx/ (15 files): https://github.com/shogun-toolbox/shogun/commit/ace057f4365d1ba9d4b70ed08e18683c58b2250515:26
shogun-notifier-shogun: Merged prototype from karlnapf/shogun_manual15:26
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * a9951f5 / doc/sphinx/TODO: https://github.com/shogun-toolbox/shogun/commit/a9951f5f6ecb01577256e98007a776c1c37abf9e15:26
shogun-notifier-shogun: added some notes15:26
shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * 9686aac / / (49 files): https://github.com/shogun-toolbox/shogun/commit/9686aace28d9f188414997739eb7f047744b427815:26
shogun-notifier-shogun: Create some sandbox for automatically built examples15:26
shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * 50fb2ba / / (14 files): https://github.com/shogun-toolbox/shogun/commit/50fb2ba6bad5a0702f063666eb568b65e11da43e15:26
shogun-notifier-shogun: Store generated examples in the build directory15:26
shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * dd2c1a5 / doc/CMakeLists.txt,doc/sphinx/source/conf.py,doc/sphinx/extensions/sgexample.py: https://github.com/shogun-toolbox/shogun/commit/dd2c1a545fb7e3825b2f816fe54ad61cc73a3fa915:26
shogun-notifier-shogun: Pass paths to sgexample by parameter15:26
shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * b435913 / doc/sphinx/CMakeLists.txt: https://github.com/shogun-toolbox/shogun/commit/b435913be7a8e20f6422dc6fdebcee11b13a478115:26
shogun-notifier-shogun: Add missed sphinx cmakelists15:26
shogun-notifier-shogun: - Put different languages' CMakeLists into targets15:26
shogun-notifier-shogun: Sergey Lisitsyn :feature/sphinxdoc * ca5a439 / doc/sphinx/Makefile,doc/sphinx/make.bat: https://github.com/shogun-toolbox/shogun/commit/ca5a439be01971a6eaa837f532de6669fbf1b8fe15:26
shogun-notifier-shogun: Remove no longer needed autogenerated make files of sphinx15:26
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * c195e9d / doc/sphinx/source/conf.py: https://github.com/shogun-toolbox/shogun/commit/c195e9d8f92a6f727afe05caceeca4cb7a79d7c115:26
shogun-notifier-shogun: change to pngmath due to its availability to define custom latex operators, and define a argmax and argmin15:26
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 7a6240a / / (4 files): https://github.com/shogun-toolbox/shogun/commit/7a6240a7990d1f81e7cebd2b96349c759deb1c2c15:26
shogun-notifier-shogun: remove a few obsolete files15:26
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * cfaa74a / doc/sphinx/source/examples/classifier/knn.rst: https://github.com/shogun-toolbox/shogun/commit/cfaa74ae9668d7a2c1a441c0c9945c0896f5b9c915:26
shogun-notifier-shogun: use custom latex operator15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * df35a3d / doc/sphinx/source/index.rst: https://github.com/shogun-toolbox/shogun/commit/df35a3d67b8c2165d299386049744c29cb9d8bd115:27
shogun-notifier-shogun: put some initial structure in main file15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 7c9b5e6 / doc/sphinx/TODO: https://github.com/shogun-toolbox/shogun/commit/7c9b5e6ad168bde8a7145fd831b5663250fb0f3215:27
shogun-notifier-shogun: remove old file15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * de3bea6 / doc/sphinx/source/ (3 files): https://github.com/shogun-toolbox/shogun/commit/de3bea687df63ae5afc4e0ef3698fb71de2e0c6915:27
shogun-notifier-shogun: added bibtex references draft15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 5eb00b4 / doc/sphinx/source/index.rst: https://github.com/shogun-toolbox/shogun/commit/5eb00b4b0ff539ebd6ec574ddf8eeae885a6ac8e15:27
shogun-notifier-shogun: remove unnecessary entries at start15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 59e1407 / doc/sphinx/source/examples/classifier/knn.rst: https://github.com/shogun-toolbox/shogun/commit/59e14072b39642e87478c8a06cdb6867415857c515:27
shogun-notifier-shogun: put doxygen docs in own folder and re-factor cmake build to distinguish between cookbook and doxygen15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * e1a8e0c / doc/cookbook/README.md: https://github.com/shogun-toolbox/shogun/commit/e1a8e0cbc47f3434d4567ad23e4dc10095656ae015:27
shogun-notifier-shogun: update links due to folder name change15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * f85b384 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/f85b384eba5b2d4c09d729cff07d7bea356c615815:27
shogun-notifier-shogun: install pyparsing to make meta examples work on travis15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 48bc95c / / (5 files): https://github.com/shogun-toolbox/shogun/commit/48bc95c366fa3e1ef2e84bb7b18796772c69310815:27
shogun-notifier-shogun: add seperate option for meta examples, disable when requirements not found, and make doc build still work when disabled15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * 8a1aa34 / CMakeLists.txt,doc/cookbook/CMakeLists.txt,cmake/FindSphinx.cmake: https://github.com/shogun-toolbox/shogun/commit/8a1aa340b19a8b7460d57ca440cc975f457c435f15:27
shogun-notifier-shogun: include optional sphinx dependency in cmake build15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * f49ea25 / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/f49ea25058ace56501c4fce602f48d08b4fbee5815:27
shogun-notifier-shogun: attempt to install sphinx and ply to build meta examples and cookbook15:27
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * f88910e / .travis.yml: https://github.com/shogun-toolbox/shogun/commit/f88910e77595fa005c402fe3abdfff4d63351d9415:27
shogun-notifier-shogun: put in develop version15:27
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travis-ciit's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: https://travis-ci.org/shogun-toolbox/shogun/builds/11121882316:17
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@lambdaylisitsyn: hey17:57
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shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * a5053a7 / configs/Dockerfile: https://github.com/shogun-toolbox/shogun/commit/a5053a7a002e0a7cf19582a95b252947f6057bcd23:04
shogun-notifier-shogun: add meta-example and cookbook dependencies23:04
lisitsynHeikoS: hey23:07
@HeikoSlisitsyn: jojo23:07
lisitsynsoo got some time now23:07
@HeikoSlisitsyn: the new docker stuff that drwiking did is really cool23:07
@HeikoSlisitsyn: cool23:07
@HeikoSjust adding the cookbook to travis23:07
@HeikoSthen you can think about the web deploy23:08
lisitsynHeikoS: what do you want to add?23:08
@HeikoSbut let drwiking know23:08
@HeikoSlisitsyn: see the email23:08
lisitsyna sec23:08
lisitsynHeikoS: ok I see23:09
shogun-notifier-shogun: Heiko Strathmann :feature/sphinxdoc * d42e721 / configs/Dockerfile: https://github.com/shogun-toolbox/shogun/commit/d42e7212bbf53d0e27aa41da4cc5b74fbca6ee6523:09
shogun-notifier-shogun: add sphinx bibtex extension23:09
lisitsynHeikoS: I think we should make it simpler than with api23:09
@HeikoSlisitsyn: what do you have in mind23:09
lisitsynscp23:09
lisitsyn:D23:09
lisitsynrsync23:09
lisitsynjust have to know how to pass a secret23:10
@HeikoSlisitsyn: one thing we have to think about23:10
@HeikoShow long the html stays around23:10
@HeikoSand how we handle different git revisions23:10
@HeikoSsecond is easy: with the git hash in url23:10
@HeikoSfirst is more tricky, after a while the html needs to be deleted23:10
lisitsynHeikoS: we could have an rsync share23:10
lisitsynand cron that removes old ones23:10
@HeikoSlisitsyn: you know how to set this up?23:10
@HeikoSlisitsyn: yeah I thoguth that23:11
@HeikoSlisitsyn: key is that it is easily maintainable23:11
lisitsynyes it is mostly easy but23:11
@HeikoSby people other than you ;)23:11
lisitsynI don't know how to pass a key to travis23:11
lisitsynchecking23:11
@HeikoSlisitsyn: cool23:11
lisitsynHeikoS: uhmm I need sudo somewhere23:13
@HeikoSlisitsyn: dont have that?23:13
lisitsyndo you?23:13
lisitsynhedonismbot doesnt work23:13
lisitsynHeikoS: well I can setup something on some other machine23:15
@HeikoSlisitsyn: I never log into these things23:16
@HeikoSbut I think I do23:16
@HeikoSwhats the hostname?23:16
lisitsynHeikoS: hedonismbot.shogun-toolbox.org23:17
@HeikoSlisitsyn: think my publickey is not known23:17
@HeikoSor I forgot my username ;)23:17
@HeikoSlisitsyn: btew23:17
@HeikoSbtw23:17
@HeikoSjust creating a docker image for shogun developing23:18
@HeikoSthat might be handy for our gsoc students23:18
@HeikoSif having build problems23:18
@HeikoSthey just runt the same docker image that we use in travis23:18
@HeikoSpretty awesome23:18
lisitsynHeikoS: yes23:18
@HeikoSlisitsyn: I will document this soon I guess23:18
lisitsynit is pretty cool23:18
@HeikoSlisitsyn: we need a nightly binary build as well23:18
lisitsynHeikoS: like a modern way to do things :)23:18
@HeikoSand one for the 5.0 release23:19
@HeikoSlisitsyn: I mean this could  solve all this installation shit23:19
@HeikoSthen we just do a debian package23:19
@HeikoSand the docker23:19
@HeikoSand reduce things we have to maintain23:19
@HeikoSwell osx should work natively23:19
@HeikoSand windows as well23:19
lisitsynHeikoS: but how does it solve installation?23:20
@HeikoSlisitsyn: well we can ship an image with an installed shogun23:20
@HeikoSas a first step23:20
lisitsynah23:20
lisitsynyes but package would be better for sure23:21
@HeikoSagreed23:21
@HeikoSthats why we have the gsoc project23:21
@HeikoSbut still cool23:21
@HeikoSand also good for developing23:21
@HeikoSlisitsyn: Ill stay a bit in case you have news23:22
@HeikoSbut make it quick ;)23:22
lisitsynHeikoS: well we can do it together hah23:23
lisitsynlet me setup rsync first23:23
@HeikoSokok23:24
@HeikoSill stay with you to keep you motivated ;)23:24
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lisitsynHeikoS: ok rsync would work I think23:43
@HeikoSlisitsyn: details!23:44
lisitsynHeikoS: I am yet to get to know how to pass an ssh key to travis23:44
Fod_Hello everyone. I am using Shogun to detect if a file is malware or not. I do a dynamic analysis (execute the binary) and extract the instructions traces,23:44
Fod_I turn them into a matrix representing a Markov chain, where each node is an instruction trace (example: mov) and each edge is the probability of moving from one instruction to other.23:44
Fod_Therefore, for each trace I have a matrix and not a vector. I need to use a Gaussian kernel, but I do not know how I can use this matrix as a feature instead of a vector.23:44
lisitsynHeikoS: but we will just put an rsync call in the travis job23:44
Fod_Should I use MKL ?. (sorry for my English, someone speaks Spanish?). Thank you.23:44
@HeikoSFod_: hi there, no spanish here23:44
lisitsynwell fernando, but he is not here now23:45
@HeikoSFod_: just reshape your matrix23:45
@HeikoSto a giant vector23:45
@HeikoSwhich interface are you using?23:45
@HeikoSlisitsyn: ok23:45
@HeikoSlet me push the new docker image and see whether the cookbook works then23:45
Fod_modular23:45
@HeikoSjust building the image locally23:45
Fod_It is the only way? MKL?23:45
@HeikoSFod_: no need for MKL23:46
@HeikoSFod_: just take your matrix, transform it into a vector, and pass these vectors to shogun23:46
Fod_mmm ok, no matter the size?23:47
Fod_my matrix is 300x30023:47
@HeikoSthe vector will be 300*300 elements in size23:48
@HeikoSthere might be better kernels than the gaussian for this problem, but this is a good way to start23:48
@HeikoSFod_: cool application btw23:48
@HeikoSIt would be great to have this documented if it works23:48
@HeikoSwe could put a notebook onto our webpage23:48
lisitsynHeikoS: woah there is deploy keys in github23:48
@HeikoShttp://www.shogun-toolbox.org/page/documentation/notebook23:49
@HeikoSlisitsyn: where?23:49
lisitsynHeikoS: just in settings of repo23:49
Fod_what kernel you suggest?23:49
@HeikoSFod_: start with linear23:49
lisitsynthis should work23:49
@HeikoSand use a primal SVM23:49
@HeikoSLiblinear23:49
@HeikoSlisitsyn:23:50
Fod_if I work I pass the code to put it as an example. Thanks a lot!!! :)23:51
@HeikoSFod_: thanks!23:52
lisitsynHeikoS: ok I've added some key23:52
lisitsynuhmm how does it help haha23:53
lisitsynI need private key anyway23:53
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@HeikoSlisitsyn: is that a blocker?23:54
lisitsynHeikoS: well I just need to understand how can we pass an ssh key to travis23:55
lisitsynHeikoS: do you get how it works then?23:55
lisitsynHeikoS: just to let you know23:56
lisitsynin travis job we do make doc stuff23:56
lisitsynthen rsync generated_html_directory some_machine:/shogun/$(git revision)23:56
lisitsynso its updated23:56
lisitsynsupereasy23:57
@HeikoSwhere is the command?23:57
@HeikoSin travis?23:57
@HeikoSor in cmake?23:57
lisitsynHeikoS: trravis23:57
@HeikoSdid you push that change already?23:58
lisitsynHeikoS: no23:58
lisitsynI need some working prototype first23:58
@HeikoSlisitsyn: I see23:58
@HeikoSyou mean the html output23:58
lisitsynyes23:58
@HeikoSI am working on it23:58
@HeikoSdocker hub does not update my repo for some reason23:58
@HeikoSlisitsyn: and the webserver?23:58
lisitsynHeikoS: we have our dockerfile not in the root of repository23:58
@HeikoSis running anyways?23:58
@HeikoSlisitsyn: what do you mean?23:59
lisitsynHeikoS: ok two threads we have:D23:59
-!- Netsplit *.net <-> *.split quits: @lambday, shogun-buildbot23:59
-!- Netsplit *.net <-> *.split quits: @HeikoS, lisitsyn, sonne|work, @drwiking, shogun-notifier-, @ChanServ, lupinix, @sonney2k, rcurtin23:59
--- Log closed Wed Feb 24 00:00:09 2016
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