- Pharo-users - lists.pharo.org

The Grapher charting engine

by Alexandre Bergel

Dear all, As many of you know, Grapher is a Ã¼ber-cool charting engine, part of Roassal. For people who do not know what Grapher is, here is a (compelling we hope) example: Which is obtained by the following script: -=-=-=-=-=-=-=-=-=-=-=-=-=-=-= | b colors points ds pts dec lb | b := RTGrapher new. colors := Array with: Color red with: Color blue. points := OrderedCollection new. colors do: [ :c | ds := RTStackedDataSet new. pts := ((1 to: 100) collect: [ :i | 50 atRandom - 25 ]) cumsum. points add: pts. ds points: pts. dec := RTDevVarDecorator new. dec moveBehind; desviation: 0.5; color: (c alpha: 0.3); points: pts. ds connectUsing: (RTLine new color: (c alpha: 0.5); width: 1 ). b add: ds. b addDecorator: dec. ]. b axisX; axisY. b build. lb := RTLegendBuilder new. lb view: b view. colors doWithIndex: [ :c :i | lb addColor: c text: 'Series ', i printString ]. lb build. b view @ RTZoomableView. b view -=-=-=-=-=-=-=-=-=-=-=-=-=-=-= In our grand vision of making Roassal the best visualizing engine of the Universe (we also know to be modest time to time, but not today :-), Grapher will play a very important role. We would like to stabilize Grapher and make it sure it happily fits everybody needs. You can help on it: - When you are tempted to look at the dark side of the planet (this is where R, JFreeChart, gnuplot, D3 and all their friends live), let us know. We will make sure to make you are happy again. - Share your wishlist with us. We already have a long todo list, but your opinion does matter and will take it seriously - we are open to contributions, which could be financial, bug fixe, enhancement, or simply encouragement. I am very happy to be surrounded by very smart engineers. Your encouragement are making them happy :-) Cheers, Alexandre, in the name of the Object Profile Team NB: sorry for the cross-list posting, but this email is very important for us, and for you we hope. -- _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: Alexandre Bergel http://www.bergel.eu ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.

March 20, 2015

Re: [Pharo-users] Confusing ZeroDivide

by Nicolai Hess

2015-03-20 16:56 GMT+01:00 webwarrior <reg(a)webwarrior.ws>: > Why this: > > [ 1/0 ] on: ZeroDivide do: [:ex | ex resume: 1 ]. > > returns 1, but this: > > [ 1.0/0 ] on: ZeroDivide do: [:ex | ex resume: 1 ]. > > hangs (causes infinite loop) ? > ------------------------------ > View this message in context: Confusing ZeroDivide > <http://forum.world.st/Confusing-ZeroDivide-tp4813627.html> > Sent from the Pharo Smalltalk Users mailing list archive > <http://forum.world.st/Pharo-Smalltalk-Users-f1310670.html> at Nabble.com. > It is a bug. and now it has a bug entry: 15187 <https://pharo.fogbugz.com/default.asp?15187> Endless loop on catching ZeroDivide for floats

March 20, 2015

Re: [Pharo-users] A Pillar language package for Atom editor?

by HernÃ¡n Morales Durand

Ok, alternatively, is someone generating Pillar chapters in Windows? My problem is GT-InspectorExtensions-Pillar highlights the syntax but not properly (see attachment). Could I be using a wrong syntax? I also figured out a command line to execute pdflatex passing a modified PFTE.tex, but latex errors are cryptic (and I don't want to follow there). HernÃ¡n 2015-03-17 17:57 GMT-03:00 HernÃ¡n Morales Durand <hernan.morales(a)gmail.com>: > Is this working? > How to preview a .pier file? > > https://github.com/pillar-markup/language-pillar > > Cheers, > > HernÃ¡n > >

March 20, 2015

Re: [Pharo-users] Users of Versionner?

by Juan Ignacio Vaccarezza

I use it for my rockola project. Im learning all the configuration stuff, very useful tool On Fri, Mar 20, 2015 at 2:01 AM, HernÃ¡n Morales Durand < hernan.morales(a)gmail.com> wrote: > Same here. > > > 2015-03-18 14:01 GMT-03:00 stepharo <stepharo(a)free.fr>: > > I use it but I often code by hand the configurations ;) >> >> Le 18/3/15 09:46, Stephan Eggermont a Ã©crit : >> >> Who is actually using Versionner to maintain configurations? >>> Especially configurations that are used in other configurations? >>> >>> Stephan >>> >>> >>> >>> >>> >> >> >

March 20, 2015

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

by HernÃ¡n Morales Durand

https://github.com/hernanmd/BioSmalltalk/issues HernÃ¡n 2015-03-20 14:38 GMT-03:00 stepharo <stepharo(a)free.fr>: > How do you manage your bugs now? > > Le 20/3/15 05:46, HernÃ¡n Morales Durand a Ã©crit : > > Ok, done > > > http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through… > > Cheers, > > HernÃ¡n > > 2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm(a)gmail.com>: > >> >> On 19 Mar 2015, at 13:34, HernÃ¡n Morales Durand < >> hernan.morales(a)gmail.com> wrote: >> >> Hi Stef, >> >> 2015-03-19 9:00 GMT-03:00 stepharo <stepharo(a)free.fr>: >> >>> Hernan >>> >>> The pharo board could send a mail to the open bio informatic foundation. >>> >> >> That would be really nice! >> >> >>> Are you member of their foundation? >>> >> >> Yes, I have became member by Sep 27/2011. >> >> >>> BTW I imagine that you will have to migrate >>> https://code.google.com/p/biosmalltalk/ >>> to github? >>> >>> >> Will do it then tomorrow. >> >> >> (thatâs because Google is closing his code site and they suggest to use >> github or bitbucket instead, not a requirement from our side :P) >> >> cheers, >> Esteban >> >> Thank you >> >> HernÃ¡n >> >> Stef >>> >>> Le 19/3/15 07:39, HernÃ¡n Morales Durand a Ã©crit : >>> >>> 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 20, 2015

Re: [Pharo-users] Roassal2, navigate in your view with scrollbars

by Alexandre Bergel

Really cool video! Thanks Pierre Alexandre > On Mar 20, 2015, at 2:02 PM, Pierre CHANSON <chans.pierre(a)gmail.com> wrote: > > Hi all, > > new version of smooth scrollbars and pads is available, it allows you to navigate with scalability in the view, check this out: > > https://vimeo.com/122758568 > > try out: > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > | b | > b := RTMondrian new. > b shape rectangle > withBorder; > width: [ :cls | cls numberOfVariables * 5]; > height: #numberOfMethods; > linearFillColor: #numberOfLinesOfCode within: RTObject withAllSubclasses. > b nodes: RTObject withAllSubclasses. > b edges connectFrom: #superclass. > b layout tree. > b build. > > b view @ RTDoubleScrollBar > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > More examples in RTScrollBarBuilderExamples > > <scroll1.png> > <scroll2.png> > â > > Cheers, > > Pierre > > -- _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: Alexandre Bergel http://www.bergel.eu ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.

March 20, 2015

Re: [Pharo-users] Pharo-Launcher Windows 8.1

by kilon alios

there is also an options in settings that downloads and install sources for you automagically. This is the right place to report issues and if you are 100% sure its a bug you can report it also in the pharo fogbuz On Fri, Mar 20, 2015 at 7:04 PM, Sebastian Heidbrink <sheidev(a)yahoo.de> wrote: > Hi, > > I recently mentioned issues with the installation of the pharo-launcher on > Windows 8.1 > > Turned out I just needed to download the PharoV30.sources file and place > into the installation folder. > > Now everything seems fine. > > Is this also a topic for the pharo bug list, or is there another place > where I can mention this? > > Sebastian > >

March 20, 2015

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

by stepharo

How do you manage your bugs now? Le 20/3/15 05:46, HernÃ¡n Morales Durand a Ã©crit : > Ok, done > > http://biosmalltalk.blogspot.com/2015/03/biosmalltalk-now-available-through… > > Cheers, > > HernÃ¡n > > 2015-03-19 9:37 GMT-03:00 Esteban Lorenzano <estebanlm(a)gmail.com > <mailto:estebanlm@gmail.com>>: > > >> On 19 Mar 2015, at 13:34, HernÃ¡n Morales Durand >> <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote: >> >> Hi Stef, >> >> 2015-03-19 9:00 GMT-03:00 stepharo <stepharo(a)free.fr >> <mailto:stepharo@free.fr>>: >> >> Hernan >> >> The pharo board could send a mail to the open bio informatic >> foundation. >> >> >> That would be really nice! >> >> Are you member of their foundation? >> >> >> Yes, I have became member by Sep 27/2011. >> >> BTW I imagine that you will have to migrate >> https://code.google.com/p/biosmalltalk/ >> to github? >> >> >> Will do it then tomorrow. > > (thatâs because Google is closing his code site and they suggest > to use github or bitbucket instead, not a requirement from our > side :P) > > cheers, > Esteban > >> Thank you >> >> HernÃ¡n >> >> Stef >> >> Le 19/3/15 07:39, HernÃ¡n Morales Durand a Ã©crit : >>> 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 <mailto:offray@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 >>> <mailto:offray@riseup.net>> >>> Para: pharo-users(a)lists.gforge.inria.fr >>> <mailto:pharo-users@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 20, 2015

Re: [Pharo-users] New random generator

by stepharo

Le 20/3/15 12:29, Werner Kassens a Ã©crit : > On 03/20/2015 09:32 AM, stepharo wrote: >> Now I saw that the postload invoke this method but >> DhbMaximumLikelihoodHistogramFit does not exist. >> So the postload should be removed. > > Hi Stephane, hi Serge, > this postload was made by someone as a kind of improvised depreciation > (DhbMaximumLikelihoodHistogramFit does exist). but it certainly is not > necessary anymore. i can update the config accordingly, if thats ok > with you. i would keep the #alias... method nevertheless so that the > older versions still work. and i noticed that you did not change the > stable version for pharo3 to the new version, but i could not find any > incompatibilities in the new rngs with 3.0. i guess i could change the > stable version for 3.0 too, is that correct? I did not change it because I did not test it on 30. > werner > > >

March 20, 2015

Pharo-Launcher Windows 8.1

by Sebastian Heidbrink

Hi, I recently mentioned issues with the installation of the pharo-launcher on Windows 8.1 Turned out I just needed to download the PharoV30.sources file and place into the installation folder. Now everything seems fine. Is this also a topic for the pharo bug list, or is there another place where I can mention this? Sebastian

March 20, 2015