- Pharo-users - lists.pharo.org

Re: [Pharo-users] Pharo and Pi

by itlists＠schrievkrom.de

I found the NB approach as a fresh breeth of air - beside all the problems (I am/was not aware of). Marten -- Marten Feldtmann

March 19, 2015

Get OS uptime

by Torsten Bergmann

Julien Delplanque wrote: >I can't find out how to get the uptime of the OS from pharo (FileSystem disk root / 'proc' / 'uptime') asFileReference readStreamDo: [:s | s upToEnd asString ] or if you load the "OSUnix" project in Pharo 4 from the config browser it is even easier: UnixSystem upTime bye T.

March 19, 2015

Re: [Pharo-users] deprecation warning in code critic

by Peter UhnÃ¡k

Thank you for the explanation, makes more sense now. :) Peter On Thu, Mar 19, 2015 at 7:46 AM, Marcus Denker <marcus.denker(a)inria.fr> wrote: > > > On 19 Mar 2015, at 00:01, Peter UhnÃ¡k <i.uhnak(a)gmail.com> wrote: > > > > Hi, > > > > is there a deprecation warning option in the code critic? > > > > only for calls to globals. As code critic analysis statically and does > not even try to do call graph interference (which is hard). > > What people sometimes do is to provide specific rules when the deprecrate. > > Marcus > > >

March 19, 2015

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

by Peter UhnÃ¡k

> > keysAndValuesDo: > +1 this is also what Dictionary use. Peter

March 19, 2015

Re: [Pharo-users] deprecation warning in code critic

by Marcus Denker

> On 19 Mar 2015, at 00:01, Peter UhnÃ¡k <i.uhnak(a)gmail.com> wrote: > > Hi, > > is there a deprecation warning option in the code critic? > only for calls to globals. As code critic analysis statically and does not even try to do call graph interference (which is hard). What people sometimes do is to provide specific rules when the deprecrate. Marcus

March 19, 2015

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