March 2015 - Pharo-users - lists.pharo.org

Re: [Pharo-users] Fwd: Re: [ANN] BioSmalltalk

by HernÃ¡n Morales Durand

Hi Offray, For a biologist without interest in bioinformatics at all, it would be hard to "sell" him any Bio* library. They could be better with workflow systems like Galaxy, MyExperiment, or the Integrated Genome Viewer, etc. biology is an extremely diversified field, but actually Smalltalk is the perfect environment for biologists! To me, a demonstration of the power of BioSmalltalk is the realease of PhyloclassTalk which I *know* couldn't be possible with Python, Java, Perl, for a single developer in a short period of time. No matter how many books and marketing they try to sell, the capability of exploring and debugging objects in a live environment is unbeatable. But BioSmalltalk needs desperately other developers. I am open to explain the internals and boring details to anyone. In the past I tried to talk with pythonists but that was like talking to a wall, the feeling I perceived was the environment was so different that they seemed to be scared. Scared of everything they learnt was not worth it. But the power is there for everyone, you can inspect a DNA sequence, query for its properties in a new Inspector, send it to a server and return its alignment, re-format and serialize, all like using an exploratory data analysis with observational transformations. I also tried to BioSmalltalk gets accepted to the Open Bionformatics Foundation (actually I only requested a page in their wiki for project visibility & promotion), but **precisely** at the time of my request, they occurred to implement a new whole policy of project acceptance (but of course BioRuby, BioJava, BioPerl and BioPython were all in so they were excluded) and I would have to pay international conference calls to talk with them(?) about.... I don't know. So, the status is the same, but with more objects :). I have added classes for parsing the Taxonomy Of Life, taxdb, EBI and file formats. I hope to have the chance to work with the cools project people is releasing in this community. Cheers, HernÃ¡n 2015-03-18 23:06 GMT-03:00 Offray Vladimir Luna CÃ¡rdenas <offray(a)riseup.net> : > > > > -------- Mensaje reenviado -------- > Asunto: Re: [Pharo-users] [ANN] BioSmalltalk > Fecha: Wed, 18 Mar 2015 20:53:05 -0500 > De: Offray Vladimir Luna CÃ¡rdenas <offray(a)riseup.net> > Para: pharo-users(a)lists.gforge.inria.fr > > Hi, > > I just found this old mail. I know that BioSmalltalk is well and > advancing and I have a friend who works on biocomputing. I Saw the > Google Code page of the project, but as a not-programmer I found > difficult to understand what is the "selling point" of Biosmalltalk for > a biologist... > > Anyway I'm just curious about which new experience brings Smalltalk to > old fields. In my own case, making my notebook for data narratives and > visualization has been very enriching and even if there are external > tools in other ecosystems to work on it (pandas, Jupyter, LaTeX), the > integration with them inside a moldable and modifiable tool is hard to > beat. > > Cheers, > > Offray > > El 15/03/12 a las 07:32, HernÃ¡n Morales Durand escribiÃ³: > >> Dear all, >> >> It's been two years since I've started to work in bioinformatics with >> Smalltalk. It has been a difficult decision because the quality and >> amount of bioinformatics libraries is absolutely amazing, but I've >> received a lot of support from the main researchers at the Institute >> of Genetics where I'm working in Argentina. >> >> Now the initial step for a BioSmalltalk release is done. I hope the >> FOSS community receive this pre-release as the basis for future >> enhacements for bioinformatics with any Smalltalk flavor. Although in >> the short-term it is unlikely for a BioSmalltalk to reach the users, >> maturity and competitive level of major Bio* toolkits (BioPerl, >> BioPython, BioRuby or BioJava), it could take too many years more if I >> continue this work alone. However, BioSmalltalk was not conceived to >> replace or defeat any other similar packages, but to provide to the >> bioinformatics community the features of a pure object system. So feel >> free to spread the word for all bioinformaticians, newcomers, >> developers, or life scientists, for helping in any way and discovering >> why Smalltalk is such a special environment. >> >> This release was implemented in Pharo 1.3 custom Core, but cross >> Smalltalk portability was a priority. I'm working now to release >> versions for GemStone, Squeak and VisualWorks is there is enough >> interest. Everybody is welcome to contribute. >> >> You may download a pre-compiled release from the project page: >> http://code.google.com/p/biosmalltalk/ >> >> Best regards, >> >> HernÃ¡n >> >> >> > > > >

March 19, 2015

Get OS uptime

by Julien Delplanque

Hi everyone, I can't find out how to get the uptime of the OS from pharo. I tried: (FileLocator root / 'proc' / 'uptime') readStream contents. and (FileSystem disk root / 'proc' / 'uptime') readStream contents. but all what I get is an empty string ''. I don't know if there are messages in some specific classes to do this (in OSProcess for example?). Thanks in advance. Julien

March 19, 2015

Logic in Pharo ?

by Alain Busser

Hello, I am currently working on mechanical means to solve Aristotle's syllogisms. My project is here: https://github.com/AlainBusser/LogicGame (programmed in CoffeeScript for a webApp). When I will present it (in a little more than two months) I plan to solve the same syllogisms with a software tool which must be free, of course. I am thinking about a lightweighted Prolog. Does this exist on Pharo? Or anything which would be similar (computing in a boolean algebra, something like alt-ergo etc)... and, if it runs on Raspbian it will be even better ;-) Alain

March 19, 2015

Fwd: Re: [ANN] BioSmalltalk

by Offray Vladimir Luna CÃ¡rdenas

-------- Mensaje reenviado -------- Asunto: Re: [Pharo-users] [ANN] BioSmalltalk Fecha: Wed, 18 Mar 2015 20:53:05 -0500 De: Offray Vladimir Luna CÃ¡rdenas <offray(a)riseup.net> Para: pharo-users(a)lists.gforge.inria.fr Hi, I just found this old mail. I know that BioSmalltalk is well and advancing and I have a friend who works on biocomputing. I Saw the Google Code page of the project, but as a not-programmer I found difficult to understand what is the "selling point" of Biosmalltalk for a biologist... Anyway I'm just curious about which new experience brings Smalltalk to old fields. In my own case, making my notebook for data narratives and visualization has been very enriching and even if there are external tools in other ecosystems to work on it (pandas, Jupyter, LaTeX), the integration with them inside a moldable and modifiable tool is hard to beat. Cheers, Offray El 15/03/12 a las 07:32, HernÃ¡n Morales Durand escribiÃ³: > Dear all, > > It's been two years since I've started to work in bioinformatics with > Smalltalk. It has been a difficult decision because the quality and > amount of bioinformatics libraries is absolutely amazing, but I've > received a lot of support from the main researchers at the Institute > of Genetics where I'm working in Argentina. > > Now the initial step for a BioSmalltalk release is done. I hope the > FOSS community receive this pre-release as the basis for future > enhacements for bioinformatics with any Smalltalk flavor. Although in > the short-term it is unlikely for a BioSmalltalk to reach the users, > maturity and competitive level of major Bio* toolkits (BioPerl, > BioPython, BioRuby or BioJava), it could take too many years more if I > continue this work alone. However, BioSmalltalk was not conceived to > replace or defeat any other similar packages, but to provide to the > bioinformatics community the features of a pure object system. So feel > free to spread the word for all bioinformaticians, newcomers, > developers, or life scientists, for helping in any way and discovering > why Smalltalk is such a special environment. > > This release was implemented in Pharo 1.3 custom Core, but cross > Smalltalk portability was a priority. I'm working now to release > versions for GemStone, Squeak and VisualWorks is there is enough > interest. Everybody is welcome to contribute. > > You may download a pre-compiled release from the project page: > http://code.google.com/p/biosmalltalk/ > > Best regards, > > HernÃ¡n > >

March 19, 2015

Re: [Pharo-users] when iterating over a collection how to determine the current objects index

by Johan Fabry

Actually, using keysAndValuesDo: makes a lot of sense to me and seems to be a nice and clean way to resolve this discussion. I really like that itâs nicely polymorphic if we consider the keys of a sequenced collection to be the indexes. I just like this kind of simplicity â¦ > On Mar 18, 2015, at 18:55, Sean P. DeNigris <sean(a)clipperadams.com> wrote: > > Lastly, apparently e.g. Dolphin has removed it completely in favor of #keysAndValuesDo: in response to a change in the ANSI standard. From http://forum.world.st/doWithIndex-tp3374968p3374975.html <http://forum.world.st/doWithIndex-tp3374968p3374975.html> : >> #doWithIndex: was in an early ANSI draft, presumably >> proposed by one of IBM's representatives but I can't really remember, and we >> had it in the version of Dolphin current at the time. Later it was removed >> from the standard and replaced with #keysAndValuesDo:, which makes sense >> since a sequenced collection can legimitately represent a "keyed collection" >> with integer keys. Therefore there is no need for a second enumerator that >> does the same thing but with key and value reversed. > ---> Save our in-boxes! http://emailcharter.org <--- Johan Fabry - http://pleiad.cl/~jfabry PLEIAD lab - Computer Science Department (DCC) - University of Chile

March 19, 2015

deprecation warning in code critic

by Peter UhnÃ¡k

Hi, is there a deprecation warning option in the code critic? Thanks, Peter

March 18, 2015

Re: [Pharo-users] when iterating over a collection how to determine the current objects index

by Nicolai Hess

2015-03-18 22:55 GMT+01:00 Sean P. DeNigris <sean(a)clipperadams.com>: > e.g. someObject mongoDo: [ ... ]. > > withIndexDo: obeys the principle of least astonishment to me. > > Except the difference between this case and the other examples is that > "withIndex + Do:" reverses the argument order (:e :i). > No, the argument order is perfectly right :) aCollection withIndexDo: == "for each collection element 'e' with index 'i' do: [:e :i | ....]" > > But more importantly, GNU and other Smalltalks have #doWithIndex:. I donât > think that the payoff here is enough to diverge from the rest of the world. > > Lastly, apparently e.g. Dolphin has removed it completely in favor of > #keysAndValuesDo: in response to a change in the ANSI standard. From > http://forum.world.st/doWithIndex-tp3374968p3374975.html : > > #doWithIndex: was in an early ANSI draft, presumably > proposed by one of IBM's representatives but I can't really remember, and > we > had it in the version of Dolphin current at the time. Later it was removed > from the standard and replaced with #keysAndValuesDo:, which makes sense > since a sequenced collection can legimitately represent a "keyed > collection" > with integer keys. Therefore there is no need for a second enumerator that > does the same thing but with key and value reversed. > > > Cheers, > Sean > > ------------------------------ > View this message in context: Re: when iterating over a collection how to > determine the current objects index > <http://forum.world.st/when-iterating-over-a-collection-how-to-determine-the…> > Sent from the Pharo Smalltalk Users mailing list archive > <http://forum.world.st/Pharo-Smalltalk-Users-f1310670.html> at Nabble.com. >

March 18, 2015

Re: [Pharo-users] Pharo and Pi

by kilon alios

I agree with Stef that Pharo needs code that is easy to understand , because code that is easy to understand is far more likely to be maintained. There is little value to boosted performance if you come face to face with show stopper bugs that never get fixed because none dares touch them. Also I am still not convinced that NB is as fast as people claim to be unless I see a very detailed performance test suite that compares NB vs other FFIs side by side. So far it seems to me that people are easily convinced that NB is fast because its based on Assembly code but that is debatable since C is perfectly capable to generate heavily optimized machine code. The one thing that makes NB cool for me is that it can generate machine code on the fly the only downside is that is uses Assembly, which is very verbose and too low level. If NB used C type of syntax for Pharo I think it would be ideal . It would allow you to write C code using Pharo syntax and without a need for a compiler or compiling / linking. In any case none stops anyone from moving NB forward as a third party library. I know I wont be one to do so ;)

March 18, 2015

Re: [Pharo-users] Running startup scripts after the UI has finished

by Peter UhnÃ¡k

After a lot of experimenting and unsuccessful attempts to use both defer: and addDeferredStartupAction: (because I'm probably using it wrong) I ended up with [ myCode ] fork This has not only the wanted behavior of executing after the UI has rendered, but also doesn't freeze the UI when loading external packages. In fact the loader itself seems much responsive. Peter On Tue, Mar 10, 2015 at 6:45 PM, Esteban Lorenzano <estebanlm(a)gmail.com> wrote: > Smalltalk addDeferredStartupAction: aBlock. > > aBlock will be executed after startup, as the comment says: > > "Add the monadic or nulladic block to the list of actions that we will be > performed immediately after the startup is totally executed.â > > and > > World defer: aBlock > > aBlock will be executed in the next UI rendering cycle, as the comment > DOES NOT says (because is missing) ;) > > So I think the first one, or the two combined will give you the solution. > > cheers, > Esteban > > > On 10 Mar 2015, at 18:36, Peter UhnÃ¡k <i.uhnak(a)gmail.com> wrote: > > > > Hi, > > > > is it possible to execute startup scripts after the UI has finished > rendering / the image has loaded? > > > > I have install startup script that executes when I create the image, > however since it starts executing very early the UI is frozen and I don't > get any progress bar so I don't know what's happening (since I'm > downloading Roassal and other libraries it can take quite a while.) > > > > Thanks, > > Peter > > >

March 18, 2015

Re: [Pharo-users] when iterating over a collection how to determine the current objects index

by Sean P. DeNigris

> e.g. someObject mongoDo: [ ... ]. > > withIndexDo: obeys the principle of least astonishment to me. > Except the difference between this case and the other examples is that "withIndex + Do:" reverses the argument order (:e :i). But more importantly, GNU and other Smalltalks have #doWithIndex:. I donât think that the payoff here is enough to diverge from the rest of the world. Lastly, apparently e.g. Dolphin has removed it completely in favor of #keysAndValuesDo: in response to a change in the ANSI standard. From http://forum.world.st/doWithIndex-tp3374968p3374975.html : > #doWithIndex: was in an early ANSI draft, presumably > proposed by one of IBM's representatives but I can't really remember, and we > had it in the version of Dolphin current at the time. Later it was removed > from the standard and replaced with #keysAndValuesDo:, which makes sense > since a sequenced collection can legimitately represent a "keyed collection" > with integer keys. Therefore there is no need for a second enumerator that > does the same thing but with key and value reversed. ----- Cheers, Sean -- View this message in context: http://forum.world.st/when-iterating-over-a-collection-how-to-determine-the… Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

March 18, 2015