Preview of Microdown, simplified syntax for documentation in Pharo 9

Exciting times are coming in the next Pharo 9 release. Have you heard about Pillar? It is a markup syntax with tools to write and generate documentation, books and slides. The new Pharo 9 release will allow to format documentation with a simplified version of Pillar, called Microdown This is how Microdown looks like with System Browser class comments:...

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lunes, noviembre 02, 2020 Hernán Leave a comment markup, microdown, pharo, pillar, syntax

nCoV-2019 basic analysis with Pharo

I pushed two Pharo scripts which may help someone to do a basic analysis of the novel virus: One script is a one-liner to download the reference genome form NCBI and the other one downloads the publicly available sequenced genomes, reports some basic statistics, filter out genomes which are not complete, and align the sequences with MAFFT. You can access the repository code here: https://github.c...

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Pharo Script of the Day: Super easy meme generation

Couldn't resist sharing this one:ZnClient new logToTranscript; url: 'https://api.imgflip.com/'; addPath: 'caption_image'; formAt: 'template_id' put: '95158268'; formAt: 'username' put: '...'; formAt: 'password' put: '...'; formAt: 'text0' put: 'Just Zinc'; formAt: 'text1' put: 'HTTP Components'; accept: 'application/json'; contentReader:...

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Pharo Script of the Day: DesignInfo

Hi there. Not so much of a script today. Continuing a little bit on the SLOC subject, yesterday I kind of resurrected on GitHub a package called DesignInfo. This package is based purely on Morphic (so it is possible even to run it without Roassal or Moose) and takes every package in a Pharo image, and count the lines of code (LOC, as provided by RPackage),...

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Pharo Script of the Day: One-liner identity matrix

Check how easy is to create an identity matrix in Pharo, in just one line: require matrix size from user and print the output: (Array2D identity: (UIManager default request: 'Enter size of the matrix:') asInteger) asStri...

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Pharo Script of the Day: Mass image format conversion from PNG to JPEG

You might find useful the following code to convert a whole directory of image in PNG format to JPEG: (FileSystem disk workingDirectory filesMatching: '*.png') do: [ : pngFile | pngFile asFileReference binaryReadStreamDo: [ : stream | PluginBasedJPEGReadWriter putForm: (PNGReadWriter formFromStream: stream) onFileNamed: pngFile withoutExtension , 'jpg' ] ] displayingProgress: 'Converting...

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Pharo Script of the Day: Text analysis using tf-idf

Today's snippet takes a natural language text as input (a.k.a. the Corpus) where each line is considered a different document, and outputs a matrix of term documents with word mappings and frequencies for the given documents. This is also known as tf-idf, a distance metric widely used in information retrieval and provides the relevance or weight of terms in a document. Why is not this just simple...

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Pharo Script of the Day: Count lines of code

Lines of code, LOC, SLOC, ELOC... one the simplest and metrics around, and we could find the method with the most LOC in the image with just one line of code (tested in Pharo 6.1): SystemNavigation default allMethods collect: [ : m | m -> m linesOfCode ] into: (SortedCollection sortBlock: [ : a : b | a value < b value ]) For more advanced software engineering queries have a look to the cool...

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Pharo Script of the Day: SPARQL access to DBPedia

Let's face it, how many times you could have a mix of Natalie Portman with Smalltalk code? :) If you install a little SPARQL wrapper library in Pharo, you could for example access the Natalie's movie list querying DBPedia by writing something like the following code in the SPARQL query language: DBPediaSearch new setJsonFormat; timeout: 5000; ...

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Pharo Script of the Day: Visualize SVG paths using Roassal

Let's suppose we want to render a SVG shape described in a SVG Path. As SVG is basically XML you can grab (read: parse) the figure coordinates from the SVG path description attribute. For this we can use the XML DOM parser, Roassal and pass just the coordinates found in the "d" attribute of the "path" node, to build more complex shapes, like the following...

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Pharo Script of the Day: Unzip, the Smalltalk way

Hi everybody. Today a simple but useful script to uncompress a ZIP file in the current image directory. Notice the #ensure: send, Smalltalk provides an very elegant way to evaluate a termination block: | zipArchive fileRef | zipArchive := ZipArchive new. fileRef := 'myFile.zip' asFileReference. [ zipArchive readFrom: fileRef fullName; extractAllTo: FileSystem workingDirectory ] ensure: [ zipArchive...

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Pharo Script of the Day: Massive uncontrolled send and log of unary messages

Want to play and break your VM today? Try this useless saturday script just for fun: | outStream | outStream := FileStream newFileNamed: 'unary_sends.txt'. Smalltalk allClasses reject: [ : cls | (cls basicCategory = #'Kernel-Processes') or: [ cls = HashedCollection ] ] thenDo: [ : cls | cls class methodDictionary select: [: sel | sel selector isUnary ] thenCollect: [ : cm | | result...

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Pharo Script of the Day: A quiz game script to test your Collection wisdom

I want to play a game :) The following script implements an "Is this Sequenceable?" kind of quiz. You are presented with a series of inspectors with method sources in the image, without its class name. And by looking only the source code you have to guess if the method belongs to a SequenceableCollection hierarchy or not. If you miss, you can see the class and its class hierarchy. At the end of the...

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Pharo Script of the Day: Find your IP address

I' back :) Today let's update the PSotD blog with a script to find your IP address using Zinc HTTP Components. Credits also to Sven Van Caekenberghe which helped me to figure out why Zn was getting a 403ZnClient new systemPolicy; beOneShot; url: 'http://ifconfig.me/ip'; accept: ZnMimeType textPlain; headerAt: 'User-Agent' put: 'curl/7.54.0'; timeout: 6000; ge...

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Pharo Script of the Day: Generate random strings

Today's script is just a one-liner to generate 10 random Strings: (Generator on: [ : g | 10 timesRepeat: [ g yield: UUID new asString36 ] ]) upToEn...

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Pharo Script of the Day: Colorizing nucleotides

Some days ago I experimented a bit to colorize a random DNA sequence given an alphabet and the desired sequence size, with a little help of BioSmalltalk. This is what I've got: | text attributes | text := ((BioSequence forAlphabet: BioDNAAlphabet) randomLength: 6000) sequence asText. attributes := Array new: text size. 1 to: text size do: [ : index...

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Pharo Script of the Day: One minute frequency image saver

You can save the image every 60 seconds (or any other frequency) to avoid loss changes to the image with the following script:[ [ true ] whileTrue: [ (Delay forSeconds: 60) wait. Smalltalk snapshot: true andQuit: false ] ] forkAt: Processor userInterruptPriority named: 'Image Saver '.You can use the Process Browser under the World menu to terminate or pause the proce...

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Pharo Script of the Day: Create a directory tree at once

Suppose you want to create a directory tree at once. Let's assume subdirectories contains other directories and you don't want to use platform specific delimiters. We can do it in Pharo using the almighty #inject:into: and the FileSystem API. | rootPath | rootPath := Path / FileSystem disk store currentDisk / 'App1'. #( #('Resources') #('Doc') #('Projects') #('Tools') #('Tools' 'AppTool1') ...

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Pharo Script of the Day: Execute command in a MSYS2 MinGW64 context

For this to work first ensure you have the MSYS2 bin directory added to the PATH environment variable. Just run the following from command line and add "c:\msys64\usr\bin\" to the end of the PATH variable: systempropertiesadvanced We will use ProcessWrapper, although with limited features, it works perfectly for simple tasks. And now you can run all those complex bash shell commands from Pharo :)...

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Pharo Script of the Day: k-shingles implementation

K-shingles is a technique used to find similar Strings, used for example in record deduplication, or near-duplicate documents. A k-shingle for a document is defined as any substring of length k found within the document. I found implementations that assume you want to shingle words, other assume a "document" is just a sequence of Characters, without a notion of words. For convenience, I will cover...

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Pharo Script of the Day: Smalltalk Russian Roulette

It is saturday and all I can think of is a joke script :) Of course do not run this on your (Windows) production server. ((Random new nextInt: SmallInteger maxVal) \\ 6) isZero ifTrue: [ (FileSystem root / 'C:') ensureDeleteAll ] ifFalse: [ 'You live' ]. If it just happen you ever try the script, you will have to add some exception handlers due to hidden or protected folders like "C:\Documents...

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Pharo Script of the Day: A save,quit & deploy GUI trick

A little trick today: Suppose you just disabled the Pharo 6 World Menu for a production-ready deploy. Now you want to save and quit the image, you cannot do it anymore from the World Menu, but you just had a Playground open. You can close the Playground and save the image using the following: WorldState desktopMenuPragmaKeyword: 'noMenu'. GTPlayground allInstances anyOne window close. [ SmalltalkImage...

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Pharo Script of the Day: Proto proto image preprocessing in Pharo

Smalltalk is so cool! Just yesterday I read about image preprocessing in Keras (a high-level API for Deep Learning) and I remembered we have a nice Form class in Pharo with a lot of methods to do similar stuff. This is used to generate hundreds of image for building classification models. Big disclaimer: This could be done a lot better, specially regarding...

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Pharo Script of the Day: Poor's man test runner: Run package tests in Pharo from a script

Ever wondered how to run tests in your package without using the Test Runner UI? You just need to provide the prefix of the package with tests and this piece of code will show you how to do it: | pkgPrefix pkgSuite result | pkgPrefix := ''. pkgSuite := TestSuite named: 'MyApplication Tests'. (RPackage organizer packageNames select: [ : pkgName | pkgName beginsWith: pkgPrefix ] thenCollect: [...

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Pharo Script of the Day: Open a line-numbered text editor

This is the matching code in Pharo 6.x for the Bash one-liner to view a file with line numbers:cat -n /path/to/file | less The simplest way to open an viewer in Pharo is to inspect the contents of the file:'/path/to/file' asFileReference contents.However you wouldn't see the line numbers by default. If for some reason you also want to avoid the inspector/explorer tool, you may use the following snippet:StandardWindow...

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Pharo Script of the Day: Hash password with PBKDF2 using ApplicationSecurity

Any application accepting passwords from users must use password hashing, which pays off in the event of a website breach by limiting the damage. The basic idea is that you do not store the passwords but a "one-way" derived token, then make it difficult enough (in terms of money and time) to reverse the stored token and get the original password. We say "difficult" because if you have pre computed...

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Pharo Script of the Day: Configure R <-> Pharo Smalltalk with RProjectConnector

RProjectConnector is a package to access the R programming language in Pharo. The following script shows how to install and configure it in a clean image, using OSWindows to automatically get the R path installation:Install OS-WindowsMetacello new baseline: 'OSWindows'; repository: 'github://astares/Pharo-OS-Windows/src'; load. Install RProjectConnectorGofer it smalltalkhubUser: 'VincentBlondeau'...

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Pharo Script of the Day: Migrate FileReferences from Linux/MacOS to Windows

A very simple porting script today: If you move a Pharo image from MacOS/GNU Linux to Windows you could experiment issues with FileReferences file system not automatically converted. In that case, you can evaluate this code to update to the Windows platform and prevent annoying exceptions when accessing file references: | winFS | winFS := FileSystem allInstances detect: [ :fs | fs store isKindOf:...

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Pharo Script of the Day: Prefix all class names in a package

The following Pharo script takes a String with the first letters of a package as input (pkgPrefix) and a two-letter String used to prefix all its classes. It creates then a refactoring environment for such packages and renames all its classes with the provided newClassPrefix: | pkgPrefix newClassPrefix env model | pkgPrefix := ''. newClassPrefix := 'NP'. env := RBBrowserEnvironment new forPackageNames:...

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Pharo Script of the Day: Replay cookies with Zinc HTTP components

For this one we will use a browser plug-in called CookieBro. It will allow us to import existing cookies from a web browser session into Pharo Smalltalk just using the Zinc HTTP Components, which are by default installed in the image, and NeoJSON. Let's assume then we have exported the cookies in a "cookiebro-cookies.json" file, the script translates the cookie's JSON format into a name–value pair...

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Pharo Script of the Day: Sort a column in a CSV file

Hi there. Today I wanted to translate to Pharo Smalltalk the code in a Bash one-liner to sort a column in a CSV file:cat myfile.txt | cut -d \; -f 2 | sortFor replicating this one, you will need the NeoCSV package (doc), and just use the power of SortedCollection:SortedCollection streamContents: [ : out | 'myfile.txt' asFileReference readStreamDo: [ : in | (NeoCSVReader on: (ZnBufferedReadStream...

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Pharo Script of the Day: Parsing Gene Ontology terms

Today a script from the Bioinformatics world, accessing an EBI REST service called QuickGO, to retrieve Gene Ontology information. For the first script I use the NeoJSON library, and return a Pharo dictionary which we can inspect interactively through the Inspector:(NeoJSONReader on: (ZnClient new accept: ZnMimeType applicationJson; url: 'http://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO:0005623,GO:0017071,GO:0030680'; ...

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Pharo Script of the Day: Rename instance variables programmatically

Today I am starting a series of posts sharing some short (I hope) Pharo scripts which can be useful for others in the community. I have published some of them in the mailing list, so it is also an attempt to resurrect them from the oblivion. The first script goal is to programmatically rename an instance variable in MyClass from oldName to newName (tested in Pharo 6.1):(RBRenameInstanceVariableRefactoring ...

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SpecUIAddOns release

I released yesterday SpecUIAddOns, a MIT library providing additional SPEC widgets not included in Pharo Smalltalk by default. If you have any suggestions for how this package could be improved, please get in touch or suggest an improvement using the GitHub issues page. Installation, screenshot and usage instructions are provided in the GitHub pag...

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PI Announcement

Today I just released PI, a MIT-pip-like command line program for Pharo Smalltalk. PI stands for Pharo Install. It is written in bash and tested successfully under Windows (MSYS) and GNU/Linux. Currently supports listing and searching pacakges both in SmalltalkHub and GitHub, Pharo image installation, installing packages from SmalltalkHub, and more features comming. Everything is available through...

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Iliad version 0.9.6 released

Lately I have been playing with the Iliad Web Framework, and decided to publish some updates which I want to share with you:A new web site based in GitHub pages, with install instructions, screenshots and links to pre-loaded images and documentation. Updated Iliad to load in Pharo 6.0 Added an Iliad Control Panel, based in the Seaside one, which allows to create/inspect/remove web server adapters,...

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Territorial: A new package for Geographical Information Retrieval for Smalltalk

Territorial is a Smalltalk library for Geographical Information Retrieval (GIR) in geopolitical objects. It was originally designed for a Phylogeographic Information Retrieval system based in BioSmalltalk. There will be no scripts in this post, everything is explained in the Territorial User Manual (PDF). The Territorial library has two locations: SmalltalkHub is where I will commit latest changes....

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Detecting system platform in Smalltalk

This is a short post describing how to detect the system platform (Operating System) where your virtual-machine is running. You can use the following expressions in several major Smalltalk flavors: Pharo " Pharo >= 4 " Smalltalk os isWin32. Smalltalk os isMacOS. Smalltalk os isMacOSX. Smalltalk os isUnix. " Pharo 3 " OSPlatform current isWindows. " Pharo 2 " OSPlatform isWin32. VisualWorks >=...

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Visualize commit history in Pharo

Overview This is another GraphViz post for Pharo Smalltalk. A few days ago I committed a working version of GraphBuilder. It was mostly coded by Lukas Renggli and I updated the package to work with the current Pharo images and added minor features (like displaying commit date in the nodes). Installation and Usage To install the package, open the Catalog...

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New ISO 3166-1 implementation for Pharo Smalltalk

Introduction If your application lists any of Yugoslavia, Czechoslovakia, South Yemen, USSR, Serbia and Montenegro countries then you have an obsolescence problem. The same as if it doesn't known about South Sudan, Jersey or East Timor. Geopolitical map has changed, countries around the world have dissolved, merged and new ones were created. As of August 2015, ISO web site lists 249 official countries....

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