July 2013 - Pharo-users - lists.pharo.org

Re: [Pharo-users] [ANN] BioSmalltalk published in Bioinformatics Journal

by HernÃ¡n Morales Durand

Doru, I can access the article through the "Full Text (PDF)" link at the right box titled "This Article". Maybe you have the right columns collapsed? There is an arrow button "Show all columns" if you cannot see the link. Let me know. HernÃ¡n 2013/7/16 Tudor Girba <tudor(a)tudorgirba.com> > Congratulations! > > Is the paper available somewhere? > > Cheers, > Doru > > > On Jul 16, 2013, at 8:33 AM, HernÃ¡n Morales Durand < > hernan.morales(a)gmail.com> wrote: > > > Dear Smalltalkers, > > > > I am proud to announce that Bioinformatics Journal has accepted and > > published my article "BioSmalltalk: A pure object system and library for > bioinformatics". > > > > Bioinformatics is the leading journal in the Bioinformatics field, and > publishes the highest quality scientific papers and review articles of > interest to academic and industrial researchers. > > > > > http://bioinformatics.oxfordjournals.org/content/early/2013/07/09/bioinform… > > > > I want to thank you, all the nice people who write regularly and helped > > me in these lists over last three years. And feel free to join the Bio* > > lists, there is always new cool things to do! > > > > Best regards, > > > > http://code.google.com/p/biosmalltalk/ > > > > HernÃ¡n Morales > > Institute of Veterinary Genetics. > > National Scientific and Technical Research Council (CONICET). > > La Plata (1900), Buenos Aires, Argentina. > > Telephone: +54 (0221) 421-1799. > > Internal: 422 > > Fax: 425-7980 or 421-1799. > > > > > > > > -- > www.tudorgirba.com > > "In a world where everything is moving ever faster, > one might have better chances to win by moving slower." > > > > >

July 16, 2013

Re: [Pharo-users] [ANN] BioSmalltalk published in Bioinformatics Journal

by Tudor Girba

Congratulations! Is the paper available somewhere? Cheers, Doru On Jul 16, 2013, at 8:33 AM, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: > Dear Smalltalkers, > > I am proud to announce that Bioinformatics Journal has accepted and > published my article "BioSmalltalk: A pure object system and library for bioinformatics". > > Bioinformatics is the leading journal in the Bioinformatics field, and publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. > > http://bioinformatics.oxfordjournals.org/content/early/2013/07/09/bioinform… > > I want to thank you, all the nice people who write regularly and helped > me in these lists over last three years. And feel free to join the Bio* > lists, there is always new cool things to do! > > Best regards, > > http://code.google.com/p/biosmalltalk/ > > HernÃ¡n Morales > Institute of Veterinary Genetics. > National Scientific and Technical Research Council (CONICET). > La Plata (1900), Buenos Aires, Argentina. > Telephone: +54 (0221) 421-1799. > Internal: 422 > Fax: 425-7980 or 421-1799. > > > -- www.tudorgirba.com "In a world where everything is moving ever faster, one might have better chances to win by moving slower."

July 16, 2013

Re: [Pharo-users] Generate Bytecodes manually

by Udo Schneider

On 16.07.13 17:15, Marcus Denker wrote: > No. A decompiler has to be very specific for the code generated by the compiler. I thought so. > For Pharo3, we even opted to not support decompilation at allâ¦ (IR -> AST). We will instead save a higher-level representation that has much > more information (e.g. names of variables). For deployment, people can strip the names, giving them the same "obfuscation" the decompiler > provides now. Sounds reasonable - so if I generate IR (-> BC) from non-Smalltalk sources ... is there any recommended way to make the non-Smalltalk-source visible in browsers? Up to now I would simply generate IR/BC directly which would mean that a class would have a method but w/o the source. Or do I miss a crucial piece here? Udo

July 16, 2013

[ANN} Pharo Consultants

by Sven Van Caekenberghe

Dear Fellow Pharoers, We are happy to announce a new initiative, a listing of Pharo Consultants, http://consultants.pharo.org If you are able and willing to provide professional Pharo Consultancy services and would like to be listed as such, please send the necessary info to board(a)pharo.org so that we can include you. This is a listing of individuals. Apart from your knowledge of and involvement with Pharo itself, the only requirement is that you are either a paying Pharo Association (http://association.pharo.org) member or related to one of the members of the Pharo Consortium (http://consortium.pharo.org) The recorded information is minimal, but includes a link to a website. The order of the listing itself is randomised each time it is generated. Your email address will be obfuscated a bit to limit spam. As a Pharo Consultant, you can advertise that fact using a nice URL, http://consultants.pharo.org#seandenigris Cool, right ? Please provide your info in one of the following forms. Smalltalk expression: PharoConsultant new name: 'Sven Van Caekenberghe'; location: 'Hasselt, Belgium'; email: 'sven(a)stfx.eu'; website: 'http://stfx.eu'; languages: 'Dutch (native), English, French, German'; industryExperienceSince: 1990; smalltalkExperienceSince: 1993; pharoExperienceSince: 2010; areasOfExpertise: 'Web Services & Applications, Servers, Networking, Protocols'; yourself STON: PharoConsultant { #name : 'Sven Van Caekenberghe', #email : 'sven(a)stfx.eu', #website : 'http://stfx.eu', #location : 'Hasselt, Belgium', #languages : 'Dutch (native), English, French, German', #areasOfExpertise : 'Web Services & Applications, Servers, Networking, Protocols', #industryExperienceSince : 1990, #pharoExperienceSince : 2010, #smalltalkExperienceSince : 1993 } Regards, Sven, on behalf of the Pharo Board. PS: The Pharo Contributors page will get an overhaul soon too.

July 16, 2013

Re: [Pharo-users] Generate Bytecodes manually

by Marcus Denker

On Jul 16, 2013, at 5:10 PM, Udo Schneider <udo.schneider(a)homeaddress.de> wrote: > > > On 16.07.13 16:39, Marcus Denker wrote: >> In 3.0 we have two nice additions: >> >> 1) you can easily create CompiledMethods from RB ASTs > Looks nice but isn't usable for me as I don't have an AST. > >> 2) For low level stuff there is IRBuilder. IR is a bytecode-level representation >> (CFG) that abstracts away from the details yet is very close. > Now we're talking!!! This looks exactly like what I need. > > Just a theoretical question: Can every sequence of bytecodes be decompiled to a Smalltalk method? I doubt it but wanted to ask nevertheless. > No. A decompiler has to be very specific for the code generated by the compiler. For Pharo3, we even opted to not support decompilation at allâ¦ (IR -> AST). We will instead save a higher-level representation that has much more information (e.g. names of variables). For deployment, people can strip the names, giving them the same "obfuscation" the decompiler provides now. BC-> IR decompilation always works. Marcus

July 16, 2013

Re: [Pharo-users] SerialPlugin

by Friedrich Dominicus

Bernat Romagosa <tibabenfortlapalanca(a)gmail.com> writes: > Hi Friedrich, > > My machine is already a 32 bits one... here's the output of ldd: > > Â Â Â Â linux-gate.so.1 => Â (0xb7782000) > Â Â Â Â libm.so.6 => /lib/i386-linux-gnu/i686/cmov/libm.so.6 > (0xb7746000) > Â Â Â Â libdl.so.2 => /lib/i386-linux-gnu/i686/cmov/libdl.so.2 > (0xb7742000) > Â Â Â Â libpthread.so.0 => > /lib/i386-linux-gnu/i686/cmov/libpthread.so.0 (0xb7728000) > Â Â Â Â libc.so.6 => /lib/i386-linux-gnu/i686/cmov/libc.so.6 > (0xb75c5000) > Â Â Â Â /lib/ld-linux.so.2 (0xb7783000) > > Thanks! :) Well that looks fine to me. Sorry that I could not help Regards Friedrich

July 16, 2013

Re: [Pharo-users] Generate Bytecodes manually

by Udo Schneider

On 16.07.13 16:39, Marcus Denker wrote: > In 3.0 we have two nice additions: > > 1) you can easily create CompiledMethods from RB ASTs Looks nice but isn't usable for me as I don't have an AST. > 2) For low level stuff there is IRBuilder. IR is a bytecode-level representation > (CFG) that abstracts away from the details yet is very close. Now we're talking!!! This looks exactly like what I need. Just a theoretical question: Can every sequence of bytecodes be decompiled to a Smalltalk method? I doubt it but wanted to ask nevertheless. Best Regards, Udo

July 16, 2013

Re: [Pharo-users] Generate Bytecodes manually

by Marcus Denker

On Jul 16, 2013, at 4:10 PM, Udo Schneider <udo.schneider(a)homeaddress.de> wrote: > All, > > is there a supported interface to generate methods (incl. their bytecodes) manually? > In 3.0 we have two nice additions: 1) you can easily create CompiledMethods from RB ASTs | cm methodNode | methodNode := RBMethodNode selector: #test body: (RBReturnNode value: (RBLiteralNode value: 1)) asSequenceNode. methodNode doSemanticAnalysis. cm := methodNode generate. cm valueWithReceiver: nil arguments: #() 2) For low level stuff there is IRBuilder. IR is a bytecode-level representation (CFG) that abstracts away from the details yet is very close. | cm | cm := IRBuilder buildMethod: [ : builder | builder pushLiteral: 3; pushDup; send: #=; returnTop]. cm valueWithReceiver: nil arguments: #()

July 16, 2013

Generate Bytecodes manually

by Udo Schneider

All, is there a supported interface to generate methods (incl. their bytecodes) manually? Best Regards, Udo

July 16, 2013

Re: [Pharo-users] 3.0 almost green

by Sven Van Caekenberghe

On 16 Jul 2013, at 12:51, Marcus Denker <marcus.denker(a)inria.fr> wrote: >> very nice, 3.0 is almost green :) >> >> https://ci.inria.fr/pharo/job/Pharo-3.0-Update-Step-2-Validation/lastComple… >> >> - some strange unknown processes only under mac and win > > I vote for changing the test to just check for number of process <15 or something like that. I have to defend my test ;-) No seriously: ReleaseTest is there to guard quality (but #testMethodsWithUnboundGlobals is skipped). They all pass in my 3.0 image that I have been developing in for some days now. So that is really nice. Ideally, we should not weaken the rules, but try to understand why it behaves so strangely. Maybe some bright soul can rewrite the test so that is less brittle. Sven

July 16, 2013