- Pharo-users - lists.pharo.org

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

by Holger Freyther

> On 29 Sep 2016, at 10:25, Marcus Denker <marcus.denker(a)inria.fr> wrote: > > > > Slice committed: > > https://pharo.fogbugz.com/f/cases/19155/speedup-instVarNamed > > Marcus that was quick! I had locally modified to use 1 to: specLayout size do: [] and then use specLayout at: directly. It seemed to make a small difference as well So I was "lucky" to pick PointerLayout as class to put the method in? classLayout will always be an instance of PointerLayout (or its subclasses)? thank you holger PS: It luckily speeds up instVarNamed:put: as well :)

Sept. 29, 2016

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

by Marcus Denker

> On 29 Sep 2016, at 10:08, Marcus Denker <marcus.denker(a)inria.fr> wrote: > > >> On 28 Sep 2016, at 23:41, Holger Freyther <holger(a)freyther.de> wrote: >> >> Hi, >> >> Magritte and my TagLengthValue (TLV) both use >>#instVarNamed:/>>#instVarNamed:put: to read and write from an object. I was just running >>#bench on my SMPP library and noticed that besides Spur Pharo5 is slower than Pharo3. >> > > Yes! I will add it. > Slice committed: https://pharo.fogbugz.com/f/cases/19155/speedup-instVarNamed <https://pharo.fogbugz.com/f/cases/19155/speedup-instVarNamed> Marcus

Sept. 29, 2016

Re: [Pharo-users] PhyloclassTalk Demo Video

by Serge Stinckwich

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/Epidemiolog… >> > > 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. 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] Speeding-up >>#instVarNamed: in Pharo-5.0 and beyond?

by Marcus Denker

> On 28 Sep 2016, at 23:41, Holger Freyther <holger(a)freyther.de> wrote: > > Hi, > > Magritte and my TagLengthValue (TLV) both use >>#instVarNamed:/>>#instVarNamed:put: to read and write from an object. I was just running >>#bench on my SMPP library and noticed that besides Spur Pharo5 is slower than Pharo3. > > > I added this to PointerLayout: > >>> # instVarIndexFor: aString ifAbsent: aBlockClosure > | idx | > idx := 1. > slotScope do: [:each | > each isVisible ifTrue: [ > each name = aString ifTrue: [^idx]. > idx := idx +1]]. > ^aBlockClosure value > > and modified ClassDescription/TClassDescription to use it: > > "protocol: instance variables" > instVarIndexFor: instVarName ifAbsent: aBlock > "Answer the index of the named instance variable." > > | index | > index := self classLayout instVarIndexFor: instVarName ifAbsent: [0]. > index = 0 ifTrue: > [^self superclass == nil > ifTrue: [aBlock value] > ifFalse: [self superclass instVarIndexFor: instVarName ifAbsent: aBlock]]. > ^self superclass == nil > ifTrue: [index] > ifFalse: [index + self superclass instSize] > > > The speed-up comes from filtering allSlots to allVisibleSlots (and creating an Array), then collecting the slot names and finally searching the name. Does it make sense to integrate such speed-ups? > > Yes! I will add it. Marcus

Sept. 29, 2016

Re: [Pharo-users] PhyloclassTalk Demo Video

by HernÃ¡n Morales Durand

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. > 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 :) Best regards, HernÃ¡n Regards, > > On Thu, Sep 29, 2016 at 7:38 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 > > > > 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 > > > > > > > > -- > Serge Stinckwich > UCBN & UMI UMMISCO 209 (IRD/UPMC) > Every DSL ends up being Smalltalk > http://www.doesnotunderstand.org/ > >

Sept. 29, 2016

Re: [Pharo-users] PhyloclassTalk Demo Video

by Serge Stinckwich

Hi HernÃ¡n, very impressive demo ! 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 ? 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/Epidemiolog… Regards, On Thu, Sep 29, 2016 at 7:38 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 > > 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 > > -- Serge Stinckwich UCBN & UMI UMMISCO 209 (IRD/UPMC) Every DSL ends up being Smalltalk http://www.doesnotunderstand.org/

Sept. 29, 2016

Re: [Pharo-users] double dispatch example

by Peter H. Meadows

On 13 September 2016 at 11:33, stepharo <stepharo(a)free.fr> wrote: > Hi > > If you happen to know a double dispatch situation in Pharo, I'm interested > since I'm revisiting my lecture. > There is a good example in http://www.lulu.com/shop/andres-valloud/fundamentals-of-smalltalk-programmi… He uses it in an implementation of Game Of Life. > > Stef > >

Sept. 29, 2016

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

by Bernardo Ezequiel Contreras

cheap hack. if you replace this line index := self classLayout instVarIndexFor: instVarName ifAbsent: [0]. with index := self classLayout instVarIndexFor: instVarName ifAbsent: 0. in instVarIndexFor: instVarName ifAbsent: aBlock it will be faster because it won't create a closure, but no one will approve that use. to cheap :) On Wed, Sep 28, 2016 at 6:41 PM, Holger Freyther <holger(a)freyther.de> wrote: > Hi, > > Magritte and my TagLengthValue (TLV) both use >>#instVarNamed:/>>#instVarNamed:put: > to read and write from an object. I was just running >>#bench on my SMPP > library and noticed that besides Spur Pharo5 is slower than Pharo3. > > > I added this to PointerLayout: > > >># instVarIndexFor: aString ifAbsent: aBlockClosure > | idx | > idx := 1. > slotScope do: [:each | > each isVisible ifTrue: [ > each name = aString ifTrue: [^idx]. > idx := idx +1]]. > ^aBlockClosure value > > and modified ClassDescription/TClassDescription to use it: > > "protocol: instance variables" > instVarIndexFor: instVarName ifAbsent: aBlock > "Answer the index of the named instance variable." > > | index | > index := self classLayout instVarIndexFor: instVarName ifAbsent: > [0]. > index = 0 ifTrue: > [^self superclass == nil > ifTrue: [aBlock value] > ifFalse: [self superclass instVarIndexFor: > instVarName ifAbsent: aBlock]]. > ^self superclass == nil > ifTrue: [index] > ifFalse: [index + self superclass instSize] > > > The speed-up comes from filtering allSlots to allVisibleSlots (and > creating an Array), then collecting the slot names and finally searching > the name. Does it make sense to integrate such speed-ups? > > > cheers > holger > > > -- Bernardo E.C. Sent from a cheap desktop computer in South America.

Sept. 29, 2016

PhyloclassTalk Demo Video

by HernÃ¡n Morales Durand

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] Subscript Out Of Bounds: 1 when commiting from Versionner

by HernÃ¡n Morales Durand

If I understood right I think only 18927 should be back ported. Hope it gets integrated soon, seems to me a showstopper for Metacello + Versionner. HernÃ¡n 2016-09-28 12:47 GMT-03:00 stepharo <stepharo(a)free.fr>: > so do you think that we should back port these two big fixes? at least > 18927 I think > > Le 28/9/16 Ã 13:48, HernÃ¡n Morales Durand a Ã©crit : > > May be this issue : https://pharo.fogbugz.com/f/ > cases/18684/Versionner-Error-while-commiting-a- > configuration-for-the-first-time > > And here for the fix : https://pharo.fogbugz.com/f/ > cases/18927/Komitter-throws-up-if-it-has-committed-everything > > HernÃ¡n > > > 2016-09-28 1:29 GMT-03:00 stepharo <stepharo(a)free.fr>: > >> Yes it was fix in pharo 60 and we should port it back but I forgot the >> issue number >> >> >> >> Le 27/9/16 Ã 21:00, HernÃ¡n Morales Durand a Ã©crit : >> >> When commiting with Versionner in Pharo 5.0 I always have to manually >>> override this method >>> >>> KomitStagingArea>>remotes >>> | result | >>> >>> result := self packages first remotes. >>> self packages allButFirst do: [ :each | >>> result := result intersection: each remotes ]. >>> >>> ^ result collect: [ :each | each koRemote ] >>> >>> to >>> >>> KomitStagingArea>>remotes >>> >>> self packages isEmpty >>> ifFalse: [ >>> | result | >>> result := self packages first remotes. >>> self packages allButFirst do: [ :each | >>> result := result intersection: each remotes ]. >>> ^ result collect: [ :each | each koRemote ] ]. >>> ^ Array empty. >>> >>> Screenshot attached. >>> Is this known issue or was this reported before? >>> >>> Hernan >>> >>> >> >> > >

Sept. 29, 2016