September 2016 - Pharo-users

Re: [Pharo-users] PhyloclassTalk Demo Video

by HernÃ¡n Morales Durand

2016-09-29 5:22 GMT-03:00 Serge Stinckwich <serge.stinckwich(a)gmail.com>: > On Thu, Sep 29, 2016 at 10:02 AM, HernÃ¡n Morales Durand > <hernan.morales(a)gmail.com> wrote: > > Hi Serge, > > > > 2016-09-29 4:05 GMT-03:00 Serge Stinckwich <serge.stinckwich(a)gmail.com>: > >> > >> Hi HernÃ¡n, > >> > >> very impressive demo ! > >> > > > > Thanks! > > > >> > >> We are working on similar tools in the context of epidemiological > >> modelling: > >> https://github.com/UMMISCO/kendrick > >> > >> I see the nice table views. > >> Did you build something specific or reuse existing stuff ? Can you > >> edit tables from UI ? > > > > > > I built several support packages. From helpers like SpecUIAddOns and > > StringExtensions to a Query Builder and a Project Framework (the Project > UI > > is based on the work of Peter Uhnak IIRC). The GenBank Browser could be > > generalized to a XML node editor. > > > > For editing tables it was never a requirement for the app. > > Ok I will have a look later. > > >> Territories looks interesting. We might be interesting to use such > >> information for building spatial epidemiology simulation evolving many > >> countries. Looks at Ebola modelling we have done here: > >> > >> https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/ > EpidemiologicalModels/0301-EpidemiologicalModels.html > >> > > > > It looks really interesting! > > > > For Territorial I am analyzing now what we could get from Bioregions. > > Integration of repositories is not so straightforward, so I plan also to > > finish my Code Generator to automate generation of classes and methods > when > > importing CSV's and XML's, a good test case could be the Unicode's CLDR. > > In PhyloclasTalk for most analysis we start always from the reported DNA > > sequences, for example if we would have to analyze Ebola we would start > from > > here > > https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/ > Database/nph-select.cgi > > and then apply NER to curate the locations or other features of > isolates. If > > you execute the query for Zaire ebolavirus, the PhyloclassTalk GenBank > > Browser could be adapted to load the CSV (which seems pretty curated) or > > accession list, and then use the Classifier directly. > > I see you define routes in your code, good starting point to add the > feature > > :) > > Routes ? yes, because usually when you are doing an epidemiological > modeling, you want to know how the countries are connected and what > the rates of propagation between these countries. Some people are > using flights routes also (they are available freely on Internet). > > We are not working at the level of virus DNA sequences, we are just > modelling propagation of diseases. > But integrating both would be amazing in the long term. > > I think that Territorial is not MIT, all Kendrick code is MIT and I'm > bit reluctant to mix licences. > This is the only drawback for me at the moment. > > I changed the Territorial license to MIT some days after the announce: http://forum.world.st/ANN-Territorial-Re-Licensing-td4914705.html Regards, HernÃ¡n > Regards, > -- > Serge Stinckwich > UCBN & UMI UMMISCO 209 (IRD/UPMC) > Every DSL ends up being Smalltalk > http://www.doesnotunderstand.org/ > >

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by Denis Kudriashov

2016-09-29 16:51 GMT+02:00 stepharo <stepharo(a)free.fr>: > Hi denis > > Yes. XStream supports it: >> >> (1 to: 1000) reading transforming: [:in :out | | each | each := in get. >> out put: each -1; put: each; put: each + 1] >> > > But you probably wants different: > > (1 to: 1000) reading collecting: [:each | {each -1. each. each + 1} ] > > > My point is can we control the next action so that we can take any > collection > and turn it in a stream. Transforming is main approach to do this. And it is quite simple

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by stepharo

Tx guille I will read it. Le 29/9/16 Ã 11:47, Guille Polito a Ã©crit : > Hi Stef, > > I have some experiments I did last year in here > > http://www.smalltalkhub.com/#!/~Guille/ReactiveExtensions > > They allow you to do something like you want. > > It is based on the ideas in > > https://gist.github.com/staltz/868e7e9bc2a7b8c1f754 > http://www.introtorx.com/ > > These guys model a stream with different transformations (such as > select:, collect: flatCollect: and so on...) as a chain of observers > where each transformation observes the one before, transforms the > result and notifies its observers with the modified value. > > - The funny side is that with these they can manage polymorphically > both collections as streams, and normal streams (that may never end). > Also they do nice things with concurrency and retry operations fairly > easily. > - The odd part is DEBUGGING this. > * You may have tons of elements into your collection => Then you > may block all incoming events as soon as you debug one. > * You have to debug chains of observer/observed pairs, with the > boilerplate code that comes to it. Maybe a domain specific debugger > would be need for this... > > Guille > > Guille > > -------- Original Message -------- >> Hi >> >> I was looking at how we can turn a collection into a stream. >> >> I played with >> >> g := Generator on: [ :gen | >> | current | >> current := 0. >> [ gen yield: (current := current + 1) ] repeat ]. >> g next. >> >> and now imagine that we have >> >> (1 to: 1000) collect: [:each | {each -1 . each . each + 1}]. >> >> I was wondering how we could turn it into a stream >> >> (1 to: 1000) asStream collect: [:each | {each -1 . each . each + 1}]. >> >> and what would be the asStream method. >> >> for index based I can see that next >> >> next is something like >> >> next >> >> ^ self at: (current := current + 1) >> >> and collect: could be rewritten to use a generator. >> >> Now does anybody play with this already? >> >> Does xtream provide a way to do something in the same vein? >> >> We can have a stream of blocks. >> >> Stef >> >> >> >> >> >> >> >> >> > >

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by Damien Pollet

It's in http://smalltalkhub.com/#!/~cdlm/Experiments Not sure if it's Transducers or Reducers. Most probably the latter is the ported code from VW, I recall having success running some examples, but the tests probably will not (I recall trying to rewrite them using BabyMock2 but it's either failed or unfinished). On 29 September 2016 at 16:50, stepharo <stepharo(a)free.fr> wrote: > I would love to see this package and a little documentation on it. > > Stef > > Le 29/9/16 Ã 15:02, Damien Pollet a Ã©crit : > > Same with transducers/reducers, except they work by pushing values through > the pipeline instead of pulling them. The library I started porting from VW > last year had a dual API, one more like the original Clojure transducers, > and one more like Xtreams. > > One nice point of going collectionâstream & filtersâresult is that the > final step is explicit, so you can pick what kind of result you build > (could be a collection or a single aggregated value). > > On 29 September 2016 at 12:40, Denis Kudriashov <dionisiydk(a)gmail.com> > wrote: > >> >> 2016-09-29 12:39 GMT+02:00 Denis Kudriashov <dionisiydk(a)gmail.com>: >> >>> and collect: could be rewritten to use a generator. >>>> >>>> Now does anybody play with this already? >>>> >>>> Does xtream provide a way to do something in the same vein? >>>> >>> >>> Yes. XStream supports it: >>> >>> (1 to: 1000) reading transforming: [:in :out | | each | each := in get. >>> out put: each -1; put: each; put: each + 1] >>> >> >> But you probably wants different: >> >> (1 to: 1000) reading collecting: [:each | {each -1. each. each + 1} ] >> > > >

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by stepharo

Hi denis > Yes. XStream supports it: > > (1 to: 1000) reading transforming: [:in :out | | each | each := in > get. out put: each -1; put: each; put: each + 1] > > > But you probably wants different: > > (1 to: 1000) reading collecting: [:each | {each -1. each. each + 1} ] My point is can we control the next action so that we can take any collection and turn it in a stream. Stef

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by stepharo

I would love to see this package and a little documentation on it. Stef Le 29/9/16 Ã 15:02, Damien Pollet a Ã©crit : > Same with transducers/reducers, except they work by pushing values > through the pipeline instead of pulling them. The library I started > porting from VW last year had a dual API, one more like the original > Clojure transducers, and one more like Xtreams. > > One nice point of going collectionâstream & filtersâresult is that the > final step is explicit, so you can pick what kind of result you build > (could be a collection or a single aggregated value). > > On 29 September 2016 at 12:40, Denis Kudriashov <dionisiydk(a)gmail.com > <mailto:dionisiydk@gmail.com>> wrote: > > > 2016-09-29 12:39 GMT+02:00 Denis Kudriashov <dionisiydk(a)gmail.com > <mailto:dionisiydk@gmail.com>>: > > and collect: could be rewritten to use a generator. > > Now does anybody play with this already? > > Does xtream provide a way to do something in the same vein? > > > Yes. XStream supports it: > > (1 to: 1000) reading transforming: [:in :out | | each | each > := in get. out put: each -1; put: each; put: each + 1] > > > But you probably wants different: > > (1 to: 1000) reading collecting: [:each | {each -1. each. each + 1} ] > >

Sept. 29, 2016

Re: [Pharo-users] PhyloclassTalk Demo Video

by stepharo

Hi hernan it is really excellent. I suggest that you add a title and a end slide with you name and email :) so that people can contact you. Stef Le 29/9/16 Ã 08:38, HernÃ¡n Morales Durand a Ã©crit : > > I want to share with you a video I did just yesterday (no audio yet) > of the PhyloclassTalk application: > > https://youtu.be/1iPbDHbjbLU > > As some of you may know, I work in a research institute, so the > workflow is very specific to phylogeography and bioinformatics. But I > hope you may find it useful as a showcase for Pharo, or to grab some > ideas. It took some years to get here. > > It also uses code many of you wrote, so you can say Hi! if you > recognize your source there :) > > Here is the web site for documentation and details: > http://phyloclasstalk.github.io/ > > I would love to read your recommendations, or comments. > > Cheers, > > HernÃ¡n > >

Sept. 29, 2016

Re: [Pharo-users] PhyloclassTalk Demo Video

by Alexandre Bergel

Hi HernÃ¡n, Impressive work! Very cool demo! Object Profile will advertise your work Alexandre > On Sep 29, 2016, at 2:38 AM, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: > > > I want to share with you a video I did just yesterday (no audio yet) of the PhyloclassTalk application: > > https://youtu.be/1iPbDHbjbLU <https://youtu.be/1iPbDHbjbLU> > > As some of you may know, I work in a research institute, so the workflow is very specific to phylogeography and bioinformatics. But I hope you may find it useful as a showcase for Pharo, or to grab some ideas. It took some years to get here. > > It also uses code many of you wrote, so you can say Hi! if you recognize your source there :) > > Here is the web site for documentation and details: http://phyloclasstalk.github.io/ <http://phyloclasstalk.github.io/> > > I would love to read your recommendations, or comments. > > Cheers, > > HernÃ¡n > >

Sept. 29, 2016

Re: [Pharo-users] Speeding-up >>#instVarNamed: in Pharo-5.0 and beyond?

by Holger Freyther

> On 29 Sep 2016, at 12:28, Denis Kudriashov <dionisiydk(a)gmail.com> wrote: > > Cool. > > What the percentage of speedup? Random micro benchmark... | m | m := Morph new. [ | var | var := m instVarNamed: #submorphs ] bench From: 983,066 per second To: 1,302,098 per second

Sept. 29, 2016

Re: [Pharo-users] turning a collection (interval for example) into a stream

by Damien Pollet

Same with transducers/reducers, except they work by pushing values through the pipeline instead of pulling them. The library I started porting from VW last year had a dual API, one more like the original Clojure transducers, and one more like Xtreams. One nice point of going collectionâstream & filtersâresult is that the final step is explicit, so you can pick what kind of result you build (could be a collection or a single aggregated value). On 29 September 2016 at 12:40, Denis Kudriashov <dionisiydk(a)gmail.com> wrote: > > 2016-09-29 12:39 GMT+02:00 Denis Kudriashov <dionisiydk(a)gmail.com>: > >> and collect: could be rewritten to use a generator. >>> >>> Now does anybody play with this already? >>> >>> Does xtream provide a way to do something in the same vein? >>> >> >> Yes. XStream supports it: >> >> (1 to: 1000) reading transforming: [:in :out | | each | each := in get. >> out put: each -1; put: each; put: each + 1] >> > > But you probably wants different: > > (1 to: 1000) reading collecting: [:each | {each -1. each. each + 1} ] >

Sept. 29, 2016