- Pharo-users - lists.pharo.org

Aida 6.5 loading in Pharo 2.0!
by phil＠highoctane.be Feb. 27, 2013

Feb. 27, 2013

I loaded the 'Aida (janko.43)' from the Configuration browser. Then: (ConfigurationOfAida project version: '6.5') load. SwazooAida start. And I got the demo working on http://localhost:8888 Hey, cool.

4 4

TWM in 2.0
by Sean P. DeNigris Feb. 26, 2013

Feb. 26, 2013

Anyone using it? I loaded it with: Gofer it squeaksource: 'TilingWindowManager'; package: 'TWM'; load. And all tests passed; which surprised me because I figured all the keymapping changes would've broken it. I poked around though, and the few things that I tried seemed to work fine. Also, I looked at the Metacello configuration and it looks like it's been split up into sub-packages, but I see a keymapping one, and no symbolic versions for Pharo 2.0, so I guess I'll stick with gofer for now... Thanks, Sean -- View this message in context: http://forum.world.st/TWM-in-2-0-tp4672131.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

2 1

Pharo 2 and old shortcuts
by Norbert Hartl Feb. 26, 2013

Feb. 26, 2013

For a new project I started to use pharo 2.0. But I find it really cumbersome to use the new keyboard shortcuts. As long as I use 1.4 in parallel I don't want to switch to the new ones. I've found a setting in Settings named "use historical shortcuts" but it is not effective in most places. Is there a way change that? Norbert

7 25

zinc streaming post
by Camillo Bruni Feb. 26, 2013

Feb. 26, 2013

we're having our weekly git hacking session and are working on the http protocol. The smart git protocol simply runs over http, nothing too fancy once you found the documentation (which is the hardest part). Now we want to post a request and wanted to directly stream it to the server, but we only figure out on how to do it using an intermediate string. The code looks something like this: requestContents := self createGitRequestEntity. client := ZnClient new url: 'https://github.com/pharo-project/phar-core'; entity: (requestContents); post. Now I would like to do something like this. postStream := ZnClient new url: 'https://github.com/pharo-project/phar-core'; postStream. self writeGitRequestOn: postStream How can I do that in Zn? I already skimmed the documentation but it only shows the example of files, where we copy over from a fully existing source. best cami

3 3

Morphic View UI and Pharo Tabbed Pane IDE on Pharo 2.0
by S Krish Feb. 26, 2013

Feb. 26, 2013

HI, Just started to use Pharo 2.0 and find it nice overall. The package loading time, is something I need to recheck, profile and see, but feel there is a lag. Few other minor issues, nothing major so far. Smooth integration of the work I had done in 1.4: Pharo Morphic View and Pharo Tabbed Pane IDE. Try it out and let me know: http://skrishnamachari.wordpress.com/2013/02/26/pharo-2-0-morphic-view-and-… Will come back on the Pharo Tablet like interface that I have talked of earlier as also the integrated Brett Taylor like dynamic UI construction...

2 1

[JOB][Research] 16 month Postdoc "Architectural Design Exploration"
by Marcus Denker Feb. 25, 2013

Feb. 25, 2013

Architectural Design Exploration ================================ About Inria and the job ----------------------- Inria, with its academic, institutional and industrial partners, is commited to major research and innovation projects in the field of computational sciences. The institute disseminates across France thanks to its eight research centres. The Inria Lille - Nord Europe research centre, inaugurated in 2008, employs 357 people, including 250 scientists, in its seventeen research teams. Recognised for its significant contribution to the social and economic development of the Nord - Pas-de-Calais region, the Inria Lille - Nord Europe research centre promotes a policy of close cooperation with major businesses and small enterprises. By encouraging synergies between researchers and industrial partners, Inria contributes to the transfer of skills and expertise in computational technologies and provides access to top-level European and international research in order to support innovation and businesses, particularly in the region of Lille. Whether designing innovative software for business or logistics, modelling living cells or fusion plasma, or developing medical simulators or interfaces to facilitate human-computer interaction, our research opens up new possibilities that can revolutionise common practice and contribute to a better understanding of the natural phenomena which surround us. The postdoc is hosted by Team-Project RMoD. The goal of RMoD is to support remodularization of object-oriented applications. This objective is tackled from two complementary perspectives: reengineering and modularity constructs for programming languages. In the reengineering perspective we will propose new analyses to understand and restructure existing large applications (specialized package metrics, adapted visualizations, layer identification) on top of Moose [Duca08a], [Bhat12b]. http://rmod.lille.inria.fr/web/ Mission -------- Changes in the architecture may occur during the entire lifecycle of a system. Some of them might only affect local parts of a system, while others have more systemic impact. In general, we distinguish three types of approaches for handling change systematically, listed in an order of increasing severity: - Refactoring. They correspond to improvements and concern only certain components and connectors. They do not alter the offered functionality of the system. - Renovating. Sometimes, parts of the architecture are in such a bad condition that refactoring cannot work anymore. In such contexts, renovating the architecture â by restoring its fundamental principles or refreshing essential components â may be the better choice. Renovating also deals with only parts of the system. - Re-architecting. When an architecture is subject to significant changes, refactoring or renovating may not suffice. This might be the case if for example the technology platform is to be replaced by a new one, if there is a large change in business scope, or if the architecture is in such a bad shape that errors keep emerging. In such cases, re-architecting is required. The re-architecting process usually analyzes the existing architecture (e.g., using a SWOT analysis) and results in a new architecture by: a) reusing those components worthwhile to keep, b) modifying some of the existing components (refactoring) and c) re-building the rest of the components (renovating).[Ieee13] Because software engineers do not have a full understanding of the complete source code, each kind of changes may solve some problems (e.g. reduce some cycle between package), while creating new problems (e.g. creating new cycles). In this situation it would be profitable to have a tool that allows to test a possible new configuration (refactored, renovated or re-architectured) of the source code to see if the abstract property one wishes to improve, first actually improved, and second, did not improve at the expense of another equally important one. For this several alternatives new configurations have to be considered. In the RMoD team, we developed Orion [Lava10b], a tool that uses models as abstract representations of the program and enables the definition of several possible alternative versions of this program. Each version differentiates from the others by a set of refactoring operations. Currently, once an adequate version is selected, the user has to manually perform the operations on the code. Job offer description ---------------------- In this postdoc, we would like to enhance Orion in order to automatically generate code or modify the existing one once a version is chosen. Thus, it would be possible to study various alternatives of possible refactoring or restructuring of an existing program, using metrics [Abde12a], [Mord12b] or some other means [Hema12] to check the improvement in the "quality" of the code, and then ask the tool to perform the changes of the selected final solution onto the source code. The used metamodel enables a representation where code details are abstracted. A new metamodel for example AST metamodel, representing code will be introduced and the links between the two models will have to be maintained. Skills and profile -------------------- The candidate should : - hold a PhD degree in Computer Science - be fluent in English (French is an advantage but not required) - be knowledgeable in the domains of Software Engineering, maintenance, code analysis - have good programming skills in Smalltalk or be able to acquire them in a short amount of time Benefits --------- - Possibility of French courses - Help for housing - Participation for transportation - Scientific Resident card and help for husband/wife visa Additional information ----------------------- - Duration : 16 months - Salary: 2 620,84 â¬ gross/month - Monthly salary after taxes : around 2 138â¬ (medical insurance included). - Before applying, please contact the scientist advisor: nicolas.anquetil(a)inria.fr - For the first selections, please apply before March 2013, 22nd Security and defense procedure ------------------------------- In the interests of protecting its scientific and technological assets, Inria is a restricted-access establishment. Consequently, it follows special regulations for welcoming any person who wishes to work with the institute. The final acceptance of each candidate thus depends on applying this security and defense procedure. More information: http://rmod.lille.inria.fr/web/pier/blog/2013-02-22-2

1 0

Does a Stepper Widget exist for Pharo?
by MartinW Feb. 24, 2013

Feb. 24, 2013

I am looking for a Stepper Widget - 2 buttons placed directly above each other, that will increase/decrease a numerical value. Does something like this exist for Pharo? If not, how would i start to build one? There are so many different Button classes in the image :) See attached image of a Stepper: <http://forum.world.st/file/n4671822/Stepper.png> -- View this message in context: http://forum.world.st/Does-a-Stepper-Widget-exist-for-Pharo-tp4671822.html Sent from the Pharo Smalltalk Users mailing list archive at Nabble.com.

3 2

[JOB][Research] Postdoc position: IDEs
by Marcus Denker Feb. 24, 2013

Feb. 24, 2013

Infrastructure for new generation IDEs ===================================== About Inria and the job ----------------------- Inria, with its academic, institutional and industrial partners, is commited to major research and innovation projects in the field of computational sciences. The institute disseminates across France thanks to its eight research centres. The Inria Lille - Nord Europe research centre, inaugurated in 2008, employs 357 people, including 250 scientists, in its seventeen research teams. Recognised for its significant contribution to the social and economic development of the Nord - Pas-de-Calais region, the Inria Lille - Nord Europe research centre promotes a policy of close cooperation with major businesses and small enterprises. By encouraging synergies between researchers and industrial partners, Inria contributes to the transfer of skills and expertise in computational technologies and provides access to top-level European and international research in order to support innovation and businesses, particularly in the region of Lille. Whether designing innovative software for business or logistics, modelling living cells or fusion plasma, or developing medical simulators or interfaces to facilitate human-computer interaction, our research opens up new possibilities that can revolutionise common practice and contribute to a better understanding of the natural phenomena which surround us. The goal of the RMoD research team at Inria Lille is to support re-modularization of object-oriented applications. This objective is tackled from two complementary perspectives: reengineering and modularity constructs for programming languages. For more information on RMOD, see http://rmod.lille.inria.fr Mission ------- The objectives will be to reconsider and develop a new infrastructure to build new and modern IDEs. The goal of this postdoc is to help the RMOD team rethinking the infrastructure of Pharo from the point of view of its user interface and interaction foundation as well as code navigation. The following topics will be analysed and rethought : - Alternate models of event handling - Decomposing responsibilities of event handler and dispatchers. - Alternative ways to navigate code - Queries to access code elements - Smart handling of coding contexts - Management of window plague - Support for contextual refactorings and automated code transformation. Skills and profile ------------------ - English - Pharo: http://www.pharo.org - User interface design, Vector graphics - IDE design and user interactions Benefits --------- - Possibility of French courses - Help for housing - Participation for transportation - Scientific Resident card and help for husband/wife visa Additional information ----------------------- - Duration : 16 months - Salary: 2 620,84 â¬ gross/month - Monthly salary after taxes : around 2 138 â¬ (medical insurance included) - For the first selections, please apply before March 2013, 22nd. - Before applying, please contact the scientist advisor: stephane.ducasse(a)inria.fr - More information: http://rmod.lille.inria.fr/web/pier/blog/2013-02-22 Security and defense procedure ------------------------------ In the interests of protecting its scientific and technological assets, Inria is a restricted-access establishment. Consequently, it follows special regulations for welcoming any person who wishes to work with the institute. The final acceptance of each candidate thus depends on applying this security and defense procedure.

1 0

NB crash boom
by DeNigris Sean Feb. 24, 2013

Feb. 24, 2013

Why is this simple experiment crashing the vm? It seemed like such a small change from the getenv example that I was sure it would succeed. Mac 10.8.2 with lastest nbcog vm... run: str "self run: 'open http://www.google.com'." <primitive: #primitiveNativeCall module: #NativeBoostPlugin error: errorCode > ^ self nbCall: #( int system (String str) ) module: NativeBoost CLibrary Thanks, Sean

4 4

PhyloclassTalk (was: Re: [squeak-dev] [ANN] BioSqueak 0.4)
by HernÃ¡n Morales Durand Feb. 23, 2013

Feb. 23, 2013

Hello Hannes, Sorry for the late response, I have been working intensively in an application using BioSmalltalk. Here is a post with some screenshots: http://biosmalltalk.blogspot.com.ar/2013/02/phyloclasstalk-preview.html as I've said, it is developed in Pharo but most subsystems work in Squeak too. I cross-post to the Pharo users list in case someone is interested. El 16/02/2013 16:00, H. Hirzel escribiÃ³: > Hello HernÃ¡n > > Thank you for your elaboration on the topic of BioSqueak. > > On 2/1/13, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: >> >> Hello Hannes, >> Thanks for the feedback! Some answers then between the lines: >> >> El 01/02/2013 11:35, H. Hirzel escribiÃ³: >>> Hello HernÃ¡n >>> >>> This is interesting. >>> http://biosmalltalk.blogspot.com/ >>> >>> I understand that you have constructed an internal domain specific >>> language (a DSL, a query language) for dealing with genetic data in >>> Smalltalk >>> >>> search := BioNCBIWWWBlastClient new nucleotide query: >>> 'CCCTCAAACAT...TTTGAGGAG'; >>> hitListSize: 150; >>> filterLowComplexity; >>> expectValue: 10; >>> wordSize: 11; >>> blastn; >>> blastPlainService; >>> alignmentViewFlatQueryAnchored; >>> formatTypeXML; >>> fetch. >>> search outputToFile: 'blast-query-result.xml' contents: search result. >>> >>> Is there a description of this DSL? >> >> Is not a DSL in the traditional sense, i.e., using ANTLR, Lex or Yacc, >> but a "DSL" which is embedded thus inheriting the syntax and execution >> semantics of Smalltalk. > > Yes, I understand, the regular thing in Smalltalk as every Smalltalk > domain model could be considered a DSL to a certain extent/ > > Lukas Renggli has a useful classification on DSLs in his PhD dissertation on > 'Dynamic Language Embedding'' > http://scg.unibe.ch/archive/phd/renggli-phd.pdf > Chapter 2 > > According to that you probably have an Internal DSL (chapter 2.1), right? > Yes, it would fit into the Internal DSL category. I didn't knew about that classification, thanks for sharing. > >> To clarify: I've not built a DSL specification for the QBlast API, >> although I'm willing to develop DSLs for bioinformatics APIs in a >> Smalltalk language workbench (anyone?). > > OK > >> Currently the messages for performing alignments at the NCBI are based >> in the API specification, >> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html . > > The unary >> sends are the result of a plan to reduce parametrization and to >> replicate or customize Blast settings through a UI. This is because >> geneticists experiment changing Blast parameters over time and I want my >> system not to be tied to textual parameters. >> > > >> > The data is kept in XML files and >> > all is read into the image to be queried. It seems that you don't have >> > a problem with the image size? >> >> Yes I had problems with image size and performance, a lot indeed. > >> Actually working with XML DOM with alignments of 5000 or more hits >> Squeak (and Pharo of course) started to show slowliness. So I cannot >> keep all XML nodes in memory. To overcome this problem I've tried the >> SAX (push) parser and the XMLPullParser (which is a StAX parser). Then >> my idea was to reduce the tree by specifying only the XML nodes which >> I'm interested for. After reducing the nodes, I wrote custom XML tree >> classes with a specific API to query blast XML results, taken form the >> DTD specification. AFAIK this is known as a XML digester, which is >> somewhat "evolved" in Java >> (http://commons.apache.org/digester/xmlrules.html) > > I understand that you took > http://www.squeaksource.com/XMLSupport/ > (the XML support repo for Pharo, for Squeak XML support is in > the trunk image) > and modified it. > >> I have built a >> dynamic query builder in Morphic for querying the XML providing the >> possibility of persist and update the filters. Unfortunately for Squeak >> users I'm using the Polymorph API, which I think is not available in >> Squeak. > > A screen shot would be appreciated... :-) > Ok, the blog post includes some screenshots. >> We worked using the XML push/pull parsers for reading genomes and they >> worked acceptably. But it is impossible to keep nodes for 3 GBytes of >> XML at least for now in Squeak/Pharo. > > According to my experience keeping XML structures in the image is > inefficient in terms of memory usage. More efficient ways are needed > and XML is then only for reading/writing to external files. > Exactly, XML is not good at all for big data. >> More and critical problems arise when trying to work with microarray >> data (big data) in Smalltalk which is not document-oriented. I had to >> switch to "solutions" like SQL, or HDF5 using Pytables with >> well-designed scheme for our input. The advantages are that supports >> indexing and reading data in blocks, besides tools like Vitables or >> HDFView to navigate the data. Until someone provides some bits in this >> field, there is little opportunity for using Smalltalk. > > But what I understand is that people keep DNA data in memory for speed > reasons and use C++ or Perl programs to deal with it. > It really depends of the type of analysis, I've seen most starter bioinformaticians prefer Python over Perl because of the nicer syntax and more complete library support. I don't know big data projects using C++ with raw DNA data. Compression with indexing, and specialized file formats are used these days, splitting data in clusters where needed. I would love to see some Smalltalkers working on dataspaces too. See these presentations: http://www.slideshare.net/mndoci/presentations >>> I would welcome a short writeup with a general introduction to what >>> you are doing in http://biosmalltalk.blogspot.com/. > > >> >> We have submitted a paper recently and we are waiting for the review >> results. On the other side we are preparing another paper for a >> phylogenetics decision support system which includes text-mining and a >> rule engine. I will try to write an entry in the next week with >> screenshots. > > Any news on this? > No news so far, still in the reviewing process. Best regards, HernÃ¡n > Kind regards > Hannes > > >> Best regards, >> >> HernÃ¡n >> >>> Kind regards >>> >>> Hannes Hirzel >>> >>> On 2/1/13, HernÃ¡n Morales Durand <hernan.morales(a)gmail.com> wrote: >>>> Hi, >>>> >>>> Few days ago I created a port of BioSmalltalk for Squeak too. >>>> BioSmalltalk is a library for doing Bioinformatics with Smalltalk. This >>>> port is labelled "BioSqueak" and I expect to release a version for >>>> Windows sometime soon. You can find it in: >>>> >>>> http://code.google.com/p/biosmalltalk/downloads/list >>>> >>>> I'm very interested in feedback. >>>> Thanks for reading. >>>> >>>> HernÃ¡n >>>> >>>> -- >>>> HernÃ¡n Morales >>>> Institute of Veterinary Genetics (IGEVET) >>>> http://igevet.fcv.unlp.edu.ar >>>> 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. >>>> >>>> >>> >>> >> >> >> > >

1 0