March 2016 - Pharo-users - lists.pharo.org

Re: [Pharo-users] Call about Numerical Methods in Pharo :)

by stepharo

Le 3/3/16 06:25, HernÃ¡n Morales Durand a Ã©crit : > Hi Stef, > > For bioinformatics research it would be **really** nice to have: > > - Tree creation algorithms: UPGMA, WPGMA. > - MCMC methods: Metropolis-adjusted Langevin algorithm (MALA and > SMMALA), Metropolis-coupled MCMC (MC3) would enable Bayesian > inferences and to work with evolution of genes. I cannot tell how > important is to have such algorithms implemented in Smalltalk. > - Mahalanobis distance for analyzing bacterial plasmids. > - Random Forest is used a lot for gene expression, protein-protein > interaction predictions, genome-wide association studies, etc . For > the argument "let's use FFI for it" please remember many of these > methods are extended, like enriched random forest, for research with > specialized data. Yes we need random forest for our untangler too. > > There are implementations of naive Bayes classifier in > NaturalSmalltalk (which could be adapted to SciPharo) > http://smalltalkhub.com/#!/~hernan/NaturalSmalltalk > <http://smalltalkhub.com/#%21/%7Ehernan/NaturalSmalltalk> Thanks! First we should clean and move forward SciPharo > > As a side note I found an interesting history report of SciPy. > From the slide 9 onwards: > > http://sssslide.com/www.slideshare.net/shoheihido/sci-pyhistory Yes this is really interesting. I was wondering what is the NumPy Array exactly page 34 Do you think that this is something like WordArray a kind of Array with typed elements? > > Presentation shows SciPy history (credited contributors with pictures, > very nice!). > As you can se they even have a Foundation NumFOCUS for raising money. > > HernÃ¡n > > 2016-03-02 10:17 GMT-03:00 stepharo <stepharo(a)free.fr > <mailto:stepharo@free.fr>>: > > Hi guys > > I met Didier Besset and we had a great hacking session and > discussions with Serge Stinckwich. > Didier would like to help Pharo and the numerical part of it. > ***Big thanks*** Didier. > > We would like to do several things: > > - Work on "Hows to" > The numerical methods in Pharo is good but the gap between > us and the math is too large :) > so the idea is to have a series of "how to ..." > - histomgram (simple, based on distribution) > > - Improve the SciPharo/NumPha (previously SciSmalltalk) library > This morning we started to implement a > ComponentPrincipalDecomposition by combining two of the > objects available in SciPharo. > Then we started to enhance the distributions to make sure > that we can plug other distribution for having > controlled random number. > > - Do a public call to know what is missing for you: this is > this mail :) > Didier would like to work on concrete cases. I love that attitude > So tell us :) > > Hernan ?? > Alex: ?? pvalue? better distribution? > Vincent: covariance? CPA? > Philippe: times series > Serge R frames? > Sami: Better random number and various distributions? > > - Organise a two day lectures with practices on concrete case > in September with a recording session. > Either at IRD Bondy or Lille. > > - Make sure that the Numerical Method book will get on lulu :) > with a better cover and title :) > > > Stef > > >

March 5, 2016

Re: [Pharo-users] Using the new OSProcess still no Stdout string

by john pfersich

Well, I have to take back the comment on command:. I have this code snippet that gets output from a command: | p d | p := (PipeableOSProcess command: 'netstat -a | grep LISTEN | grep 27017'). p keepInitialStdOutOpen: true. d := Delay forMilliseconds: 500. d wait. [Transcript show: (p next: 300); flush. p isComplete] whileFalse: [d wait]. Transcript show: 'Error output'; cr; show: (p errorUpToEnd). p closeOutput. The netstat takes forever on a Mac, which is why the delays are so long. The On Friday, March 4, 2016, john pfersich <jpfersich(a)gmail.com> wrote: > You want to use waitForCommand: instead of command:, like > > Transcript show: (PipeableOSProcess waitForCommand: 'whoami') output > > command: doesn't wait for output and is useful only for commands that > don't return anything. It's kind of useless for anything that returns > values. I haven't tried this on Pharo 5, I've gotten it to work on Pharo 4. > > > > On Friday, March 4, 2016, Dimitris Chloupis <kilon.alios(a)gmail.com > <javascript:_e(%7B%7D,'cvml','kilon.alios(a)gmail.com');>> wrote: > >> I once reported a bug for OSProcess on MacOS >> >> >> https://pharo.fogbugz.com/f/cases/16944/OSProcess-stdout-is-not-returned-ba… >> >> Still experience the same problem, is this suppose to be fixed with new >> OSProcess ? >> >> >>

March 5, 2016

Re: [Pharo-users] Using the new OSProcess still no Stdout string

by john pfersich

I just loaded the latest image and vm using curl get.pharo.org/alpha+vmLatest | bash and OSProcess and CommandShell seem to work OK. On Friday, March 4, 2016, john pfersich <jpfersich(a)gmail.com> wrote: > You want to use waitForCommand: instead of command:, like > > Transcript show: (PipeableOSProcess waitForCommand: 'whoami') output > > command: doesn't wait for output and is useful only for commands that > don't return anything. It's kind of useless for anything that returns > values. I haven't tried this on Pharo 5, I've gotten it to work on Pharo 4. > > > > On Friday, March 4, 2016, Dimitris Chloupis <kilon.alios(a)gmail.com > <javascript:_e(%7B%7D,'cvml','kilon.alios(a)gmail.com');>> wrote: > >> I once reported a bug for OSProcess on MacOS >> >> >> https://pharo.fogbugz.com/f/cases/16944/OSProcess-stdout-is-not-returned-ba… >> >> Still experience the same problem, is this suppose to be fixed with new >> OSProcess ? >> >> >>

March 5, 2016

Re: [Pharo-users] Call about Numerical Methods in Pharo :)

by stepharo

Thanks for this great list!!! Alex what would be cool is to sketch a test with some data some that like that it is a good incentive for didier. :) > Hi ! > >> - Do a public call to know what is missing for you: this is this mail :) >> Didier would like to work on concrete cases. I love that attitude >> So tell us :) > This is an excellent initiative! > I personally need the following: > - Shapiro-Wilk test to check for data normality > - Kruskal-Wallis to analyze differences in median values between samples > - Bonferroni-Dunn to support multiple comparison and controlling the group error rate > - Mann-Whitney U test is a nonparametric statistical test that operates over two samples of the same size. > > Cheers, > Alexandre >

March 5, 2016

(no subject)

by john pfersich

I tried to execute curl get.pharo.org/alpha+vm | bash I executed it 8 times and it terminated after downloading the image. I finally tried curl get.pharo.org/alpha+vmLatest | bash and it worked the first time. Is there a problem with the alpha+vm script? Trying to test OSSubprocess.

March 5, 2016

Re: [Pharo-users] Using the new OSProcess still no Stdout string

by john pfersich

You want to use waitForCommand: instead of command:, like Transcript show: (PipeableOSProcess waitForCommand: 'whoami') output command: doesn't wait for output and is useful only for commands that don't return anything. It's kind of useless for anything that returns values. I haven't tried this on Pharo 5, I've gotten it to work on Pharo 4. On Friday, March 4, 2016, Dimitris Chloupis <kilon.alios(a)gmail.com> wrote: > I once reported a bug for OSProcess on MacOS > > > https://pharo.fogbugz.com/f/cases/16944/OSProcess-stdout-is-not-returned-ba… > > Still experience the same problem, is this suppose to be fixed with new > OSProcess ? > > >

March 5, 2016

Re: [Pharo-users] PharoLauncher eventual slowdown

by Ben Coman

On Sat, Mar 5, 2016 at 1:59 AM, Nicolai Hess <nicolaihess(a)gmail.com> wrote: > > > 2016-03-04 17:15 GMT+01:00 Ben Coman <btc(a)openinworld.com>: >> >> Hi Peter, I see you had this problem 12 months ago. >> >> http://lists.pharo.org/pipermail/pharo-users_lists.pharo.org/2015-February/… >> >> What you can try is in development mode, closing the PharoLauncher >> window, nil out class variables and garbage collect, then check what >> instances remain of PharoLauncher classes. >> >> cheers -ben > > > > I use pharo launcer a lot (on windows) and I did not see any slow down. > But I don't use it for anything else then launching the images. > Do you notice the slow down by launching images or do you use the > PharoLauncher image for anything else? I think it was more when I was helping with PharoLauncher development and would close down/open it a lot. Since I've been mostly only using it I haven't noticed the problem. Or the root of that particular issue was fixed. cheers -ben > >> >> >> On Fri, Mar 4, 2016 at 6:42 PM, Peter UhnÃ¡k <i.uhnak(a)gmail.com> wrote: >> > Yeah I saw that when he was in Prague (incidentally that's where my >> > launcher >> > slowdown started :)). >> > >> > I've removed write access and will report back in couple of days. :) >> > >> > Thanks, >> > Peter >> > >> > On Fri, Mar 4, 2016 at 11:24 AM, Damien Cassou <damien.cassou(a)inria.fr> >> > wrote: >> >> >> >> Hi Peter, >> >> >> >> Peter UhnÃ¡k <i.uhnak(a)gmail.com> writes: >> >> > I've been using Pharo Launcher for quite a while and problem that I >> >> > am >> >> > constantly encountering is that launching of it becomes slower and >> >> > slower. >> >> >> >> StÃ©phane, in CC, reported the same months ago on OS X. I don't know if >> >> StÃ©phane still experiences the problem. Could you please try to remove >> >> write access to the .image and .changes files? >> >> >> >> -- >> >> Damien Cassou >> >> http://damiencassou.seasidehosting.st >> >> >> >> "Success is the ability to go from one failure to another without >> >> losing enthusiasm." --Winston Churchill >> > >> > >> >

March 5, 2016

Re: [Pharo-users] Understanding Slang for building a compiler to C++

by Dimitris Chloupis

Thanks guys for the pointers, Clement I dont care about the VM my goal is not something like Slang but rather something that I will take a small piece of code in pharo lets say a few classes and convert it to C++ code that is human readable. But Esteban recommended to take a look at Slang anyway for what I want to create. My priority here is readable C++ code, rather than keeping the code as close to Pharo as possible. I know that compromises will have to be made, so no GC, static types etc. So I am looking into creating something that can take pharo code then the user adds annotations or extra syntax like types, pointers, manual memory managment, templates etc and then my compiler takes that and turns it to readable C++. I think this approach would be much easier for me to do instead of doing the hard work of trying to map Pharo to C++ which most likely is not possible since C++ even lacks simple reflection and of course will have to implement my own VM and my own GC . Essentially my goal is writing C++ with Pharo syntax or close to Pharo syntax. So people like me that want to take Pharo code and port it to C++ can do it easier than a manual rewrite. On Fri, Mar 4, 2016 at 10:36 PM Bernardo Ezequiel Contreras < vonbecmann(a)gmail.com> wrote: > Hi Dimitris, > Pavel has extracted the code generator in this project > > http://smalltalkhub.com/#!/~PavelKrivanek/CCodeGenerator > > On Fri, Mar 4, 2016 at 9:06 AM, Dimitris Chloupis <kilon.alios(a)gmail.com> > wrote: > >> Hey pharo experts I am interesting into studying how Slang works for >> making a compiler that takes pharo code and turns it to C++ code, my >> questions is where to find Slang , how to extract the code that compiles >> Slang to C and study it as an example for making my own compiler for C++. >> > > > > -- > Bernardo E.C. > > Sent from a cheap desktop computer in South America. >

March 4, 2016

Re: [Pharo-users] Making STON exportation lighter

by Mariano Martinez Peck

Not sure which is the reason of making it lighter, but you may also want to use a compressing stream so that the resulting stream is much smaller. On Thu, Mar 3, 2016 at 2:03 PM, Cyril Ferlicot <cyril.ferlicot(a)gmail.com> wrote: > HI, > > There is a method in the class side of Object to override. This method > return all the instVar name that need to be serialized. You can > override it to store only the text. > > For example: > > Text class >>stonAllInstVarNames > "Override to encode my instances using a custom set of instance > variables or to define their order." > > ^ self allInstVarNames \ #runs > > On Thu, Mar 3, 2016 at 5:55 PM, Offray Vladimir Luna CÃ¡rdenas > <offray.luna(a)mutabit.com> wrote: > > Hi, > > > > I'm using STON as my notebook storage file format for grafoscopio[1]. One > > example of such notebooks is at [2], but they grow large easily. That's > > because STON serialize a lot of information of each node. A snipped of > such > > info is something like [3], showed at the end of this mail. I remember > that > > someone told me about a way to store only the #string part of the Text > node, > > without any #runs or #values information in STON. How can this be done? > > > > Thanks, > > > > Offray > > > > Extra links and info: > > > > [1] http://mutabit.com/grafoscopio/index.en.html > > [2] > > > http://mutabit.com/repos.fossil/grafoscopio/doc/tip/Docs/Es/Tutoriales/tuto… > > > > =[3][STON code sniped]======= > > > > GrafoscopioNode { > > #header : > 'LecciÃ³n > > 1: Bienvenida', > > #headers : > > OrderedCollection [ ], > > #key : '', > > #body : Text { > > #string : > > '\"Hola!, Soy el profesor Stef. Debes querer que te ayude a aprender > > \rPharo. AsÃ que vamos a la primera lecciÃ³n: aprender a ejecutar cÃ³digo. > > \rPara ello hay varias opciones:\r - OpciÃ³n 1: Selecciona el texto > debajo, > > o coloca el cursor luego del punto, dale clic derecho y selecciona \'do > it > > (d)\'\r - OpciÃ³n 2: Haz click en el botÃ³n con el Ãcono de play que > aparece > > justo cerca a la esquina superior\r derecha de este > > panel\"\n\nPharoTutorial openPharoZenWorkspace \"no se qpoeadÃ±l > > aldskfjlasdf\"\r', > > #runs : > > RunArray { > > > > #runs : [ > > > > 421, > > > > 2, > > > > 13, > > > > 1, > > > > 21, > > > > 1, > > > > 1, > > > > 26, > > > > 1, > > > > 1, > > > > 1 > > > ], > > > > #values : [ > > > > [ > > > > TextColor { > > > > #color : Color { > > > > #rgb : 451328430, > > > > #alpha : 255 > > > > } > > > > }, > > > > TextFontChange { > > > > #fontNumber : 1 > > > > } > > > > ], > > > > [ > > > > TextColor { > > > > #color : Color { > > > > #rgb : 0, > > > > #cachedDepth : 32, > > > > #cachedBitPattern : Bitmap [ > > > > 4278190080 > > > > ], > > > > #alpha : 255 > > > > } > > > > }, > > > > @18 > > > > ], > > > > [ > > > > TextColor { > > > > #color : Color { > > > > #rgb : 512, > > > > #alpha : 255 > > > > } > > > > }, > > > > RubTextClassLink { > > > > #className : #PharoTutorial > > > > }, > > > > RubTextClassLink { > > > > #className : #PharoTutorial > > > > }, > > > > RubTextClassLink { > > > > #className : #PharoTutorial > > > > }, > > > > RubTextClassLink { > > > > #className : #PharoTutorial > > > > > > > > ================== > > > > > > -- > Cheers > Cyril Ferlicot > > -- Mariano http://marianopeck.wordpress.com

March 4, 2016

Re: [Pharo-users] Understanding Slang for building a compiler to C++

by Bernardo Ezequiel Contreras

Hi Dimitris, Pavel has extracted the code generator in this project http://smalltalkhub.com/#!/~PavelKrivanek/CCodeGenerator On Fri, Mar 4, 2016 at 9:06 AM, Dimitris Chloupis <kilon.alios(a)gmail.com> wrote: > Hey pharo experts I am interesting into studying how Slang works for > making a compiler that takes pharo code and turns it to C++ code, my > questions is where to find Slang , how to extract the code that compiles > Slang to C and study it as an example for making my own compiler for C++. > -- Bernardo E.C. Sent from a cheap desktop computer in South America.

March 4, 2016