- Pharo-users - lists.pharo.org

Re: [Pharo-users] [Pharo-dev] Little how to

by Damien Cassou

stepharo <stepharo(a)free.fr> writes: > Now I would love to get your ideas and their solution. getting a photo from an email address through gravatar: email := 'damien(a)cassou.me'. url := 'http://www.gravatar.com/avatar/', (MD5 hashMessage: email trimBoth asLowercase) hex, '.jpg'. (ZnEasy getJpeg: url) asMorph openInHand -- Damien Cassou http://damiencassou.seasidehosting.st "Success is the ability to go from one failure to another without losing enthusiasm." --Winston Churchill

March 3, 2016

Re: [Pharo-users] Little how to

by Sven Van Caekenberghe

> On 03 Mar 2016, at 09:23, stepharo <stepharo(a)free.fr> wrote: > > Hi guys > > for the mooc I would like have a list of how to that students should look in the system and implement. > The idea is to show to the participants that Pharo is open and that they can find information. > For example, > - extracting a sprite from a png file > - access a time service of the web Time is soo simple that there is no real need for a true web service and such a service would be trivial anyway (yet I did not find any public/free ones). Here is one way to do it: | stream unixTime | stream := nil. [ "RFC 868 TCP protocol https://en.wikipedia.org/wiki/Time_Protocol " stream := ZdcSocketStream openConnectionToHostNamed: 'time.nist.gov' port: 37. unixTime := (stream next: 4) asInteger ] ensure: [ stream ifNotNil: [ [ stream close ] on: Error do: [] ] ]. DateAndTime fromUnixTime: unixTime. The real stuff is SNTP though http://en.wikipedia.org/wiki/Network_Time_Protocol http://tools.ietf.org/html/rfc2030 which is implemented in ZTimestamp and which can do much more: ZTimestampSNTPClient new remoteClock. Sven > Now I would love to get your ideas and their solution. > > Stef > > >

March 3, 2016

CollectionValueHolder ValueAdded ValueRemoved

by Peter UhnÃ¡k

This is something that was discussed some time ago but never resolved. To summarize: When working with CollectionValueHolder one can only see whether the collection as a whole changed and not how, e.g. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ col := OrderedCollection new asValueHolder. col add: 1. col add: 2. col add: 3. col add: 4. col whenChangedDo: [ :c :changedValue | 1halt. ]. "col = #(1 2 3 4)" col add: 4. "whenChangedDo: c = col, changedValue = 4" col remove: 4. "whenChangedDo: c = col, changedValue = 4" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In the last two cases the changedValue is the same so I can't tell from the block if the value was added or removed. My proposition: * introduce (at least) two more Announcements: ValueAdded and ValueRemoved * add messages #whenAddedDo:/#whenChangedDo: * maybe add #when:do: so it can be used as an announcable object (valueHolder when: ValueSomething do: [ :ann | ... ]) The ValueAdded/ValueRemoved would be fired when an item is added, resp. removed. Thierry also proposed to add an index (I'd make it optional). ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ col whenAddedDo: [ :col :addedValue :optionalIndex | "here we know for sure that value was added" ]. col whenRemovedDo: [ :col :addedValue :optionalIndex | "here we know for sure that value was removed" ] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finally Thierry mentioned a way to handle situations where values are replaced (either single one or multiple ones). As this is edge use-case and the current behavior is pretty much random I wouldn't address the replacement unless a defined use case emerges. Any thoughts, Peter

March 3, 2016

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

by Serge Stinckwich

On Thu, Mar 3, 2016 at 10:43 AM, Blondeau Vincent <vincent.blondeau(a)worldline.com> wrote: > Hi, > > That's a very good idea. > For now, I use a Pharo-R binding to make the statistics, but it is better if it is directly in the image. > > For my part, it should be nice to have: > - Principal Component Analysis > - Time series I already a very simple time series class. What kind of operations you want to do on time series ? > - Correlation with several variables (Correlation matrix) + significance tests (pearson, spearman...) > - Standard statistical tests: normality, variance, mean, distribution > - And the more important is to have nice tools to visualize the data (Box plot, histogram, scatterplots, PCA ones) with a simple API for standard things but that we can customize. The best is that we are able to draw regression lines on them. But I think that is more a Roassal part. You have to ask Alex to the viz :-) Please join the SciSmalltalk ml in order to express your needs ;-) -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

March 3, 2016

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

by Blondeau Vincent

Hi, That's a very good idea. For now, I use a Pharo-R binding to make the statistics, but it is better if it is directly in the image. For my part, it should be nice to have: - Principal Component Analysis - Time series - Correlation with several variables (Correlation matrix) + significance tests (pearson, spearman...) - Standard statistical tests: normality, variance, mean, distribution - And the more important is to have nice tools to visualize the data (Box plot, histogram, scatterplots, PCA ones) with a simple API for standard things but that we can customize. The best is that we are able to draw regression lines on them. But I think that is more a Roassal part. Thanks for the initiative, Cheers, Vincent > -----Message d'origine----- > De : Pharo-users [mailto:pharo-users-bounces@lists.pharo.org] De la part de > stepharo > EnvoyÃ© : mercredi 2 mars 2016 14:17 > Ã : Pharo Development List; Any question about pharo is welcome; Didier > Besset; Souissi Sami > Objet : [Pharo-users] Call about Numerical Methods in Pharo :) > > 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 > !!!************************************************************************************* "Ce message et les piÃ¨ces jointes sont confidentiels et rÃ©servÃ©s Ã l'usage exclusif de ses destinataires. Il peut Ã©galement Ãªtre protÃ©gÃ© par le secret professionnel. Si vous recevez ce message par erreur, merci d'en avertir immÃ©diatement l'expÃ©diteur et de le dÃ©truire. L'intÃ©gritÃ© du message ne pouvant Ãªtre assurÃ©e sur Internet, la responsabilitÃ© de Worldline ne pourra Ãªtre recherchÃ©e quant au contenu de ce message. Bien que les meilleurs efforts soient faits pour maintenir cette transmission exempte de tout virus, l'expÃ©diteur ne donne aucune garantie Ã cet Ã©gard et sa responsabilitÃ© ne saurait Ãªtre recherchÃ©e pour tout dommage rÃ©sultant d'un virus transmis. This e-mail and the documents attached are confidential and intended solely for the addressee; it may also be privileged. If you receive this e-mail in error, please notify the sender immediately and destroy it. As its integrity cannot be secured on the Internet, the Worldline liability cannot be triggered for the message content. Although the sender endeavours to maintain a computer virus-free network, the sender does not warrant that this transmission is virus-free and will not be liable for any damages resulting from any virus transmitted.!!!"

March 3, 2016

Lost class migrating from 3.0 to 4.0

by Hilaire

I am migrating a web application from 3.0 to 4.0. I noted one class can't get load! It is however present in the Squeaksource repo. The class is a WAComponent, it is the entry point of the application with all the initializations. All the libraries dependencies are satisfied. I don't see reason why the class can't be load, and there is no such warning. Trying to load by hand this sole class does not work either. Did any of you meet such problem with Pharo 4.0 Hilaire -- Dr. Geo http://drgeo.eu

March 3, 2016

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

by stepharo

>> Then we started to enhance the distributions to make sure that we >> can plug other distribution for having >> controlled random number. > Ok, did you commit the code ? No I lost my internet connection at home ;( Ask the company to check. > >> - 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 :) > Thank you Stef for pushing ! > Can we move this discussion of the SciSmalltalk mailing-list ?

March 3, 2016

Little how to

by stepharo

Hi guys for the mooc I would like have a list of how to that students should look in the system and implement. The idea is to show to the participants that Pharo is open and that they can find information. For example, - extracting a sprite from a png file - access a time service of the web Now I would love to get your ideas and their solution. Stef

March 3, 2016

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

by Serge Stinckwich

On Thu, Mar 3, 2016 at 6:25 AM, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: > 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. Can you add enhancement issues in the SciSmalltalk issue tracker : https://github.com/SergeStinckwich/SciSmalltalk/issues in order to keep them in mind ? We are trying to create a pure Smalltalk library, so we try to avoid FFI as much as possible :-) > There are implementations of naive Bayes classifier in NaturalSmalltalk > (which could be adapted to SciPharo) > http://smalltalkhub.com/#!/~hernan/NaturalSmalltalk Great, if we can move them to SciSmalltalk. > 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 > > Presentation shows SciPy history (credited contributors with pictures, very > nice!). > As you can se they even have a Foundation NumFOCUS for raising money. For sure, money always help ;-) The only problem at the moment is that the Pharo community is much smaller at the moment than the Python one. Thank you for your help. -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

March 3, 2016

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

by Serge Stinckwich

On Wed, Mar 2, 2016 at 11:39 PM, Alexandre Bergel <alexandre.bergel(a)me.com> wrote: > 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. Great list ! At the moment, there is only Kolmogorov-Smirnov test implemented. Can you create issues in the SciSmalltalk issue tracker in order to keep track of your needs ? The issue tracker is here: https://github.com/SergeStinckwich/SciSmalltalk/issues You can also join the SciSmalltalk mailing-list: https://groups.google.com/forum/#!forum/scismalltalk Thank you Alex. -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

March 3, 2016