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pandocOptions: -N --template=mytemplate.tex --variable fontsize=12pt --variable version=1.3.8 --latex-engine=xelatex --toc --bibliography bibliography.bib date: 20 April 2017 title: Grafoscopio User Manual

author: Offray Vladimir Luna Cárdenas

Important information to start with

A small presentation

This manual documents the basics of Grafoscopio, a tool I'm cocreating1 to make reproducible research and literate computing, which allow authors to intertwine prose, code, data and visualizations into storytelling, and readers and coauthors can verify, collaborate on and extend the document claims and artifacts. The context for that cocreation is my PhD in Design and Creation in the University of Caldas (Manizales, Colombia) and in our local hackerspace HackBo (Bogotá, Colombia), but we are making something that moves beyond and between frontiers and our hope is to potenciate that.

This document started as a draft for a simple README file, following the recomendations given in the Jornal of Open Source Software (JOSS), but I entered in some kind of "writing frenzy", and when I stoped, I had 40+ pages of documentation that became this manual, which is a way to introduce Grafoscopio to a wider English speaking/reading audience.

I think there is a lot happening beyond the usual places and languages, here in the Global South: in garages, hackerspaces, makerspaces, favelas, barrios, streets, in Portuguese, Spanish, Hindi and away of indexed journals and their narratives. Away of universities, research centers, software fabrics and "publication scores". JOSS is an interesting enactive hack/critic to hegemonic ways of seeing knowledge and its validation, that visibilizes other creations and artifacts beyond the paper, by given them a paper facade and we need more hacks like this, to make visible non-hegemonic knowledge practices, places, artifacts, cultures and languages.

Grafoscopio is an artifact to bridge, explore and communicate ideas and practices to and from a broader and more diverse group of people and to amplify their voices with digital technology. I hope you find the tools and ideas presented here interesting and they become a bridge to alternatives that resonate with you.

Acknowledgements

I'm the main author of Grafoscopio and its companion packages (Dataviz, Pubiblio) and, as Nadia Egbal [-@floss-few-authors-2016], Benjamin Mako Hill [-@when-floss-isnt-better-2013] and others have pointed, the majority of the Free Libre Open Source Software is created and mantained mainly by one or two individuals, and in that sense Grafoscopio, follows the rule and not the exception. Despite of that, I think that Grafoscopio has been cocreated in a pretty particular sense: our hackathons and workshops have given to me a strong sense of priority and flow, and that requires a lot of commitment and openess from most of the participants. Also, I have received support from family, friends and tech communities in several ways: long coffe talks, code snippets, proactive workshop documentation and note taking, jokes, critic & challenges, travel help, proof reading blog entries, and even small and flexible loans (and is really a bless having them coming from family and not from banks). In that sense each creation requires a lot of people to see the light and I have been lucky enough to count with all of them.

Here is a (probably incomplete)misref list of people that helped me to make Grafoscopio possible:

Philippe Back, Claudia Baez, Carlos Barreneche, Alexandre Bergel, Luis Alejandro Bernal, Andrés Calderón, Hilda Cárdenas, Fernando Castro Toro, Sebastian Castro Toro, Ben Coman, Jose David Cuartas, Stephan Eggermont, Johan Fabry, Yanneth Gil, Tudor Girba, Nicolai Hess, Diddier H., Camilo Hurtado, Luis Linares, Divian Luna, Miltón Mamani, Rafael Medina, Iván Pulido, David Salvador, and Peter Uhnák.

Also, several places and communities were an active part in this project: HackBo hackerspace, mutabiT, Pharo, Moose and Agile Visualization communities, HiTeC Lab of the Los Libertadores University and Object Profile.

To all of them, my sincere thanks.

misref: If I made and error on omission in your name, please use the community contact forms explained at "Community Guidelines" section to let me know.

Reading conventions

This document follows the following conventions:

Document and software versions

As convention, this manual has the same version of the software it documents. So the version number you see on bottom left side of each page, corresponds also to the Grafoscopio version. Sometimes the manual is extended or corrected, while referring to the same version of the software, so an alphanumeric smaller identifier is added next, in square brackets. Version plus revision identify without ambiguity this manual2, which is useful for changing digital artifacts to report bugs, fixes or just to know at which point of their history you are located.

Because we follow a rolling release model for Grafoscopio and its related packages and projects it is possible that the software and the documentation get out of sync. Update them to their latest versions using the Update menu from the docking bar, as will be explained later.

Grafoscopio is packaged with other companion software, that is installed automatically with it. This is the info about this software bundle (taken from the present ConfigurationOfGrafoscopio source code):

version138: spec
	<version: '1.3.8' imports: #('1.1-baseline' )>

	spec for: #'common' do: [
		spec blessing: #'stable'.
		spec description: 'version 1.3.8'.
		spec author: 'OffrayLuna'.
		spec timestamp: '2017-04-06T18:56'.
		spec 
			project: 'Ston' with: #stable;
			project: 'Roassal2' with: #stable;
			"project: 'OSProcess' with: #stable;" 
			project: 'WebBrowser' with: #stable;
			"project: 'Pubiblio' with: #stable;"
			project: 'Dataviz' with: '2.2.3'.
		spec 
			package: #Grafoscopio with: 'Grafoscopio-OffrayLuna.271';
			package: 'Spec-Glamour' with: 'Spec-Glamour-johanfabry.2' ].

On commons, copyright and copyfarleft

Grafoscopio is covered with the same MIT license as Pharo. This document is covered by the P2P license. Both are pretty liberal licenses that grant you a plethora of rights to use, modify and make profit of Grafoscopio and its documentation, under certains conditions, but I think that documentation and software do not need to have the same license, or offer the same rights even in the case of Grafoscopio, where interactive documentation is closer to being a form of software.

I think that a deeper discusion on licences and the protection and expansion of knowledge as a commons is needed and this licenses difference reflect that. You can see a full copy of both licenses, MIT and P2P, included in the "Licenses" section of this document.

Grafoscopio for what and for whom?

This tool and you

Grafoscopio is a moldable tool for literate computing and reproducible research, developed on Pharo live coding and computing integrated environment, in the context of a PhD research in a hacker space of the Global South (HackBo in Bogotá, Colombia), that is being actively used, developed and documented. We will expand on the points of the previous definition.

misref: IDE: Integrated software Development Environment

Grafoscopio and its companion package, Dataviz, are intended to be used by learners and researchers in several fields: academia, journalism, activism, hacktivism and for anyone interested in open reproducible research and data storytelling backed by data and agile visualizations [@bergel_agile_2016]. This document assumes that you are such person. We will introduce the general features of Grafoscopio and point to several external and internal resources to complete your panoramic view of the ecosystem that let you deep your knowledge.

We included introductory resources to learn Pharo and data visualization, processing and storage related technologies (see the Help menu), and the Grafoscopio web page (see figure ref{fig:web-page-en}) shows several examples of how to use them for specific projects: Panama Papers as reproducible research; open community innovation in access to medicine information; Twitter data selfies; specific domain visualizations for medicine information; open, garage and citizen science and research. This whole manual was also created using Grafoscopio and is also an example of the type of documents you can create with this tool. We hope to inspire you to create and publish your own projects.

This document, by not trying to be comprenhensive, is a first invitation to know the Grafoscopio environment and to deep your knowledge with the use of it and other related resources. You will see that, despite of being a manual, it includes pretty practical examples and invitations. That is because I think that learning something new is more like reading a map that reading a manual: you make first a panoramic view of where you are and where you want to be, and take a practical approach to making your tasks and reaching your destination.

No prior knowledge of programming is supposed to follow this manual.

Detail for the Grafoscopio [English web page][grafoscopio-en]. {#fig:web-page-en}

Important note > A prototype pointing to future possibilites

Despite of being pretty usable, you will see that Grafoscopio is not totally finished, and this shows in a few spots of the Graphical User Interface (GUI) that "point to the future", towards funtionality still to be implemented. It's an unusual approach, but I think that is important to convey some sense of possibility, and work to be done in the GUI, instead of a fully polished "product" or a GUI that hides what is not ready. This conviction comes from the hackathons and workshops where we worked and evolved Grafoscopio, while the workshop was happening(!), thanks to the dynamic, moldable and continuous nature of the Pharo live coding environment. Blurring the distinction between interactive documents authors and software developers, means to put the whole environment at their dispossal, and to show the community that they can be part of this future possibilities, and that is why we take this unusual approach to GUI.

Where the GUI is more a remainder for the future, I will point that using the TBD remark (for To Be Done).

Place in the ecosystem

Similar tools

Grafoscopio is similar to other tools and has been inspired by many of them, while is trying to bring also new possibilities, by combining different ideas, diverging from others, puting "parallel" ideas into dialog and, hopefully, bringing new ones. Here we talk about the similarities and differences with other tools.

Technologies behind

Grafoscopio tries to become a simple, understandable, moldable, versatile and flexible tool thanks to the power of Pharo environment and ecosystem and the combination with mature external and internal frameworks and tools. It uses:

Despite of trying to provide a friendly, cohesive and empowering user experience (UX) by integrating default external minimalist and/or self-contained tools into the data exploration and document publishing workflow, other external tools could be integrated (Git, more data bases, including NoSQL, other exporters and light markup languages and so on).

Installation instructions

If you want to install Grafoscopio on Pharo 5, there are two ways of doing: via the Pharo catalog or via running a script from the playground. Both suppose that you have already installed and running Pharo for your platform (Windows, Gnu/Linux or Mac) from its download page, and will be explained below, from the easiest one to the far easy ones. Also both of them use the Monticello package manager, so dependencies are managed automatically for you, making the procedures really short, even for the script based one.

Different install procedures suit different tastes and needs and bring alternatives, so, if one doesn't work for you or your need/taste, you can try others, or just leave it like that, if your chosen method worked.

Install from the Pharo catalog

To install Grafoscopio, from Internet in Pharo 5, follow this steps:

  1. Open the spotter (Shift + Enter) and start to write the first letters of "Grafoscopio" (without the quotes). The spoter will show that it is available in the projects Catalog as shown in the figure ref{fig:install-screen1}.
![ Install screen 1 Finding Grafoscopio in the projects Catalog. ](../../../Imagenes/Install/spotter-grafos-first-launch.png){#fig:install-screen1}
  1. Click with the mouse or move with the keyboard to select the "Grafoscopio" package showed. A install question as the following will be shown (see figure ref{fig:install-screen2} ). Select "Yes" to start the installation process.
![ Install screen 2 Install question. ](../../../Imagenes/Install/install-question.png){#fig:install-screen2 width="50%"}
  1. While the installation is running, some progress bars with package names are going to be showed (see figure ref{fig:install-screen3}):
![ Install screen 3 Installation progress bars. ](../../../Imagenes/Install/progress-bar.png){#fig:install-screen3}
  1. When the installation ends we will see two indicators (as shown in figure ref{fig:install-screen4}):
    • Messages in the lower left corner telling that installation is complete and documentation is installed.
    • A tool bar in the upper side of the Pharo window, called the docking bar.
![ Install screen 4 Installation ended. ](../../../Imagenes/Install/install-ended.png){#fig:install-screen4}
  1. Once we have Grafoscopio installed, we save modifications to our computing environment, by making click in any clean part of the GUI (not occupied by any window) to deploy the World Menu. There we choose Save, to save the system with the same name, or Save as to save it with a new one (see figure ref{fig:install-screen5}).
![ Install screen 5 Saving changes via the World Menu. ](../../../Imagenes/Install/save-menu.png){#fig:install-screen5 width="50%"}

Install from a script

There are two ways of running scripts in the Pharo environment: one by importing them from Internet and the other by writing them manually.

If you want to run a Pharo script from its web address, open the spotter (Shift + Enter) and paste the address and then press Enter to open the interactive playground and finally press the Do it and go green play button or its shorcut (Ctrl + Shift + g). (An empty playground and its play button are showed in figure ref{fig:empty-playground})

Empty *playground* and its play button. {#fig:empty-playground}

For example, if you want to run the first part of the install script, open the spotter and paste this address http://ws.stfx.eu/BMWZPUY38BSF. You will see a screenshot similar to figure ref{fig:install-script-part1}, showing the web address you have pasted and the first lines of the script below, marked in grey.

Loading the install configuration package. {#fig:install-script-part1}

Press Enter or select with the mouse the area with the grey background. You will see the interactive playground with the script loaded. We will see more details about the playground later. For the moment press the play button or the shorcut (Ctrl + Shift + g). You will see that the playground has been executed. An executed playground contains a new column with details of the object resulting from that execution, as shown in figure ref{fig:executed-playground}.

Executed playground. {#fig:executed-playground}

Now repeat the procedure, opening the spotter, pasting this url http://ws.stfx.eu/CZ87ZZ2SXCEM and executing the second part of the installation script (showed in figure ref{fig:install-script-part2}).

Loading Grafoscopio. {#fig:install-script-part2}

You will see the progress bars and the ending of the installation process, as described in the steps 4 to 5 of the previous section.

Is usual to run the previous two steps in a single playground, by executing parts of it. Here we are going to show you how to do it, with the same installation example we have done so far. Open a playground (Ctrl + o + w) and write this (or paste the URL of this playground, in the spotter, as before):

"Start by loading the configuration of Grafoscopio"
  Gofer new
    url: 'http://smalltalkhub.com/mc/Pharo/MetaRepoForPharo50/main';
    package: 'ConfigurationOfGrafoscopio';
  load.

"After that load Grafoscopio"
ConfigurationOfGrafoscopio load.

Now select with the mouse the first 5 lines of the script and make click with the mouse secondary button. A contextual menu will be show near to the selection, as shown in the figure ref{fig:playground-partial-execution}. Choose from that menu the Do it and go option (or press the Ctrl + g keyboard combination). Only the selected part of the script will be executed.

Selecting the script part that will be executed and deploying the contextual menu. {#fig:playground-partial-execution}

Executing the second part of the script. {#fig:playground-partial-execution2}

Now select the second part of the script, the last two lines, as shown in figure ref{fig:playground-partial-execution2} and repeat the previous procedure. You will see the progress bars and the ending of the installation process, as described in the steps 4 to 5 of the previous section.

Using Grafoscopio

This section will show you how to use Grafoscopio from the GUI.

The spotter

One of the first elements of the Pharo GUI that is an excellent companion for Grafoscopio is the spotter, provided by the GT Toolkit. It is a quick finder and laucher of system functionality and behaviour, allowing you to launch and execute scripts, browse the system, and find code, among other uses. Spotter and playgrounds (using before to install Grafoscopio) are a good entry points to deep in the system. We will use them progressively and you will learn more on how to use them, as you use the interactive documentation provided with Grafoscopio and the Dataviz package.

To launch the spotter press Shift + Enter in Pharo. You will see something like the figure ref{fig:spotter}:

The spotter. {#fig:spotter}

You can learn more about the spotter in the Pharo MOOC4, particularly in lesson 9 of Week 3 (video 1, video 2).

The docking bar

The docking bar is a fixed point in the graphical interface for quick access to certain functionalities, located at the top side of the Pharo main window see figure ref{fig:docking-bar}.

The docking bar. {#fig:docking-bar}

The docking bar is divided in three menus that are explained below.

Launch menu

This menu allows the creation of new notebooks and the opening of recent ones. Also it allows to launch playgrounds for writing scripts and code snippets and Transcripts to see logs of the system. Figure ref{fig:launch-menu} shows the Launch menu.

The launch menu. {#fig:launch-menu width="50%"}

This are the options in the Update menu:

Update menu

This menu updates functionality, documentation and settings for Grafoscopio. Grafoscopio has a rolling release model, so continuous updates in functionality and documentation, come after the version packaged with the default installation. The updates frequency increases with our Data Week hackathon-workshop, seminars, and other community events, so is good to go the update menu regularly. Figure ref{fig:update-menu} shows the Update menu.

The update menu. {#fig:update-menu width="50%"}

This are the options in the Update menu:

Help menu

The Help menu contains mostly references to interactive notebooks that teach or exemplify how to use Grafoscopio or the core technologies behind (Pharo tutorial, Roassal, STON, etc). They are installed with Grafoscopio in native format and some are in PDF, like this manual. Figure ref{fig:help-menu} shows the Help menu.

The help menu. {#fig:help-menu width="50%"}

We have followed a local first approach for the Grafoscopio development, which implies that most of the documentation is writen for the local context first and in Spanish. The Grafoscopio Manual is the first English "formal" document (besides blog post and constant communication with the international Pharo communities that are in English). Because the GUI is in English now (it was in Spanish at the begining), we indicate when a Help document is in Spanish. In the future we would like to have multilingual documentation, with a bigger team and community to work on this issues. And of course you're already invited to be part of it.

This are the options in the Help menu:

The notebook GUI

The notebook GUI is composed of tree main parts (as showed in figure ref{fig:new-notebook}):

  1. The top bar
  2. The document tree
  3. The node details

Each of these sections will be detailed below.

Creating a new notebook

To create a new notebook you have several options:

You will see a window like the shown in figure ref{fig:new-notebook}.

A new Grafoscopio notebook. {#fig:new-notebook}

Next section will explain the functionality of the notebook GUI.

The top bar

The top bar groups funtionality to save, export and edit the document tree and associate it to related assets, that form projects.

This is the detailed information.

The notebook menu

Allows the creation new notebooks and their exportation to external formats. Figure ref{fig:notebook-menu}, shows this menu, when the notebook button is clicked.

The notebook menu. {#fig:notebook-menu}

These are the options of this menu:

See the "Exporting" section for details about exporting and the pandoc prerrequisites to make it work.

The project menu (TBD)

A project is a Grafoscopio notebook with the related files to produce particular outputs from it, including data files, HTML and LaTeX templates or other notebooks. A project tracks the historical changes on such files, allows collaboration between collective authors, exploring or unifying work variations (what is called branching and merging) and let the profreaders or audience made suggestions (via ticketing). Projects can be published on the web, providing reproducibility and increasing transparency to research claims.

Project functionality is provided in Grafoscopio thanks to the Fossil SCM (SCM stands for Software Configuration Manager and sometimes is called Distributed Control Version System or DVCS), a simple and self-contained software for asynchronous collaboration with a pretty small footprint (~2 Mb in size for all its functionality), available for major platforms, and providing truly distributed project management features (source file management, wiki, ticketing). Fossil is similar to Git or GitHub, but it is simpler that the former and does not hide functionality under closed source code software or promotes centralization, like the later5.

Despite of not being integrated yet, several projects have been done using the Grafoscopio + Fossil combination. For example, Grafoscopio uses Fossil as backend for its documentation and reporting issues and uses the Fossil JSON Application Programming Interface (API) to query documention and update it to the last versions.

The toolbar

The toolbar provides a series of icons to access frequently used functionality, organized by groups. In the future this functionality will be accessible also via keyboard shorcuts. Figure ref{fig:toolbar} shows the toolbar.

The toolbar. {#fig:toolbar}

Here is a more detailed explanation of the icons functionality in the toolbar.

Notebook saving and node cut, copy & paste
Node addition, deletion and movement

This operations edit the document tree. You are invited to experiment with them in the new notebook already created, to make more sense of this operations.

Switching node body, visiting links, updating content and adding tags

There are two kinds of nodes in Grafoscopio now: text nodes and code nodes. This could change in the future, providing special nodes as particular handlers and viewers for particular content (images, audio, video, and so on). But with the simple combination of this two kinds of nodes, complete and complex interactive documents can be created already, and complemented with the dynamic and inmersive Pharo ecosystem. Text nodes are writen in pandoc's markdown, with support to embedding images, bibliographic references and all the features provided by this simple, mature and extensible markup language. Code nodes are interactive playgrounds of Pharo code, allowing to dive into different objects, and integrated with the Roassal agile visualization toolkit.

The document tree

The document tree is the place where the whole document is shown and provides a uniform metaphor to organize the work. It is at the left of the Grafosocopio Notebook GUI. This part will introduce the document tree and some vocabulary to be used with it.

The tree metaphor provides sequence and hierarchy to the document and its parts and is composed by nodes. Nodes have tree kinds of possible basic relationships: parent, child and sibling, which are represented visually for the indentation level of the nodes. We'll use this visual metaphor to introduce this relationships. The nodes indented inmediately at the right of other are called the children of the node at the left, and, converserly, the node at the left is said to be the parent of the nodes at the right. Nodes at the same indentation level are siblings, sharing the same parent. If a node has children, it will show an arrow head at the left. if the arrow is pointing right, the node is collapsed meaning is not showing its children. If the arrow is pointing down, the node is expanded, meaning that is shown them. (see figure below).

Finally, If a node A is parent of a node B, which is parent of a node C, then A is said to be an ancestor of C and C is said to be a sucessor of A.

Node details

As we said, documents are composed by nodes organized in trees. The node has tree parts: header, body and links. We will explain the detailed composition of a node below.

Node header

The node header is a short text (one line) that summarizes the purpose or content of the node. The header is shown in two places, in the document tree (for navigation) and at the top of the node details, as a text field, for edition. Once the node header has been edited a color mark will be shown near the upper right corner of the text field box. This is known as a dirty marker. To update the header in the document tree press Ctrl + s ( in Windows or Linux) or Cmd + s (Mac).

Node body

The node body contains more extense information for the node and can take several lines of text or code. Node body is located inmediatly below the node header text input. Node body is saved automatically with each keystroke, and takes advantage of the build in persistance for all Pharo objects (called image persistance), but if you want to update the notebook contents to the file system you will need to save the notebook explicitely, by pressing the save button in the top bar or chosing the save option in the Notebook menu.

Node links

Node links store links to web references. Sometimes when you're making quick outlines, you need to organice external web references and have an easy way to visit them. That's the primary functionality for node links. If a node contains a valid link URL in the node links, you can visit them, by pressing the blue arrow icon , which will open the default web browser in such link. The node links behave in a similar way to headers and the modificacions are saved explicitly by pressing Ctrl + s (Gnu/Linux, Windows) or Cmd + s (Mac).

In the future node links will behave in smarter ways, storing, for example, the history of shared playgrounds for code nodes, paths to the file system to export subtrees of a document. Web browsing is just the begining.

More on code nodes

Code nodes are at the core experience of the interactive documentation, exploratory computing, reproducible research and literate computing. Code nodes are full Pharo interactive playgrounds embedded inside the Grafoscopio notebook, with full functionality, including interactive inspectors, to dive into the objects, including graphical capabilities. We use extensively code nodes in our Data Week workshops, in conjunction with the integrated Monticello DVCS, to share code in agile fashion and prototype ideas quickly. Here is a more detailed view of how to use code nodes.

Executing

Once a node has been defined as code (by pressing the button), you will see a playground page inside the node body, with custom buttons for its functionality, as seen in figure ref{fig:code-node-emty}.

An empty code node. {#fig:code-node-emty}

This code node is a fully functional Pharo playground. You can write Pharo code there and execute it totally or partially, as we have seen already on the Grafoscopio script installing method. If you used the Pharo catalog method, take a short look on how to execute playgrounds partially or totally and the keyboard shorcuts.

Just to remember and practice, create a new code node and write this: 

b := RTMondrian new.
b shape label.
b nodes: (1 to: 100).
b edges connectFrom: [ :i | i // 2 ].
b layout cluster.
b

Then press the green play button (or its shorcut Ctrl + g) and you will see something like the figure ref{fig:code-node-executed}:

Executed code node. {#fig:code-node-executed}

What we have done is a small visualization (taken from the Agile Visualization quick start) that connects each number from 1 to 100 with the floor of its half (so, the numbers 18 and 19 are connected to 9, for example), and we put this visualization as an interactive code node of our notebook. You can find more examples of interactive notebooks in the Help menu and create your own on several topics.

Sharing

To share a code node, click the "publish" button in the playground page , that is just at the right of the play button. A question window will be open asking to confirm your publication (see figure ref{fig:playground-publish-question}).

Publishing confirmation question. {#fig:playground-publish-question width="50%"}

Once you accept to share your playround contents, a notification popup will be shown, telling the web address (URL) of your published playground and will be automatically copied to the system's clipboard (see figure ref{fig:notification-published}), so it can be easily pasted in mails and other messages.

Publishing notification in the bottom left corner of the Pharo window. {#fig:notification-published}

Playground publications hosting services is generously provided by Sven Van Caekenberghe (also, he is the author of the superb STON format and NeoJSON importers, used in Grafoscopio and the Dataviz companion package). It is something like a pastebin for Pharo code and a pretty convenient way of sharing small snippets of functionality in Grafoscopio. We use it continuously on our Data Week hackathon/workshops.

Importing

The previous topic show you how to share code nodes from the notebook to the web. This one shows how to import them from the web to your notebooks. For this, the only thing you need to do is to paste the web URL for published playground in the node links section and press enter. The node will become a playground with the contents imported from the web.

We use this feature extensively for our workshops/hackathons and in fact was inspired by them. Usually we have a set of etherpads to write quick notes collaboratively in real time by the event participants and we put there the links of the shared playgrounds, to be imported in Grafoscopio notebooks.

In the future the node links could show the history of the shared playgrounds and its transformations.

Diving on results

Code nodes are fully functional playgrounds, as we have said. So you can use the full functionality of them to dive into the objects resulting from a code execution. By executing the playground, you not only see the results, but also a customized inspector (provided by the GT-Tools) that allows to see the attributes of the object or query them.

Several customized tabs are shown according to the execution in the playground and can be extended and adapted further.

Some of the most used tabs are:

For example, click on any number in the last visualization we have been using in our code node. A new tab will be open, showing more details of that number. Then click on the Meta tab and select SmallInteger. You will see something like the figure ref{fig:code-node-inspector}.

Diving on code node results using the playground inspector. {#fig:code-node-inspector}

To know more about playgrounds and how they can be used and extended vistit the GT-Tools page.

Extending the markup: %keywords

Grafoscopio traverses the notebook's document tree to export it to Pandoc's markdown. Once it is in this format you can customize the output using the rich Pandoc options, adding templates, changing bibliographic citation styles, using metadata and fine tuning the result to get the PDF or HTML you want or need.

But sometimes, you want more control while writing and exporting the document. That's the role of %keywords, that let you extend the writing and exporting syntax to suit your needs as an author. They are programmed entirely on Pharo, and you can see how they are coded and use them as templates of your own special keywords (a topic we will cover in specialized notebooks) and in the future a full Grafoscopio document API and a DSL will be provided to create even easier customizations of Grafoscopio behavior and markup.

A %keyword tells Grafoscopio how to process the document while exporting and is usually located in the node's header, as the first word of it. Sometimes the %keyword also appears in the node's body, as we will see. Everytime Grafoscopio finds a %keyword in a node will process that node accordingly to a set of predefined rules.

In this part of the document, we will show you how to use the %keywords already present. You're invited to explore the Grafoscopio native version of this manual (in the Help > Manual docking bar menu) to see examples of how they are used in this very document.

Exporting: markdown, HTML, LaTeX and PDF

Grafoscopio provides exportation capabilies to Pandoc's markdown and use Pandoc to export to HTML, LaTeX and PDF6. To export a document, choose the appropiate option from the Notebook menu. Exporting to markdown will save the document in the same location as the current notebook, but with .markdown extension, instead of .ston and exporting as PDF, LaTeX or HTML will run the proper Pandoc command on this document for such conversion and will add the .pdf, .tex or .html respective file extension (provided that Pandoc is installed on your system at the usual location, if is not, Grafoscopio will send you an error message). If you want to export a document with a different name, you wil need first to save the native document with such new name.

You can also use Pandoc directly over the markdown file to create beautiful documents for the printing and the web, with templates and customized control over a lot of variables (see the Pandoc website for more information). For example, the PDF version of this document was created in this way, from a single Grafoscopio notebook, using the command:

pandoc -N --template=mytemplate.tex --variable fontsize=12pt --variable 
version=1.3.5 --latex-engine=xelatex --toc --bibliography bibliography.bib
manual.markdown -o manual.pdf
*Important note ** > *Bibliographic support: Zotero and BibTeX

Grafoscopio has preliminar support for reading and generating BibTeX files and to connect with public Zotero collections. In fact, the bibliography file for this manual was done by reading a Zotero collection and creating the respective bibliography.bib from there. This allows to work collaboratively on research, sharing bibliographic references, making annotations and customizing their integration into the final exported document. Open this manual from the Help > Manual docking bar menu and open the Bibliography node to see an example of how this is done for this document.

You can browse the proper folder in the fossil repository to see the manual and companion files in different formats.

Examples

There is a dedicated complementary package, called Dataviz, with examples, that was build with educative purposes, for a recurrent local workshop called the Data Week, where we invite a diverse community in gender, professions, educational and life backgrounds. The Dataviz package is automatically installed when you install Grafoscopio, and you can find more information about it in the [Dataviz intro][dataviz-intro] repository page. Also we have a Spanish introductory tutorial, that is directed towards beginers.

The notebooks for such examples are available in the Help menu of the docking bar, or you can open them by executing this code form the playground:

"This opens the Spanish tutorial"
GrafoscopioNotebook new openTutorial 

"This opens the introductory notebook to the Dataviz package"
GrafoscopioDocumentation openDatavizIntro

API documentation

Because Grafoscopio inhabits a full live coding environment, it follows the custom of making the API documentation available inside a dynamic environment, instead in some static web page. To open the Grafoscopio package inside the system browser, and see the messages organized by protocols execute:

"Browser the notebook API"
GrafoscopioNotebook browse.

"Browse the document tree API"
GrafoscopioNode browse.

Tests

The core functionality of Grafoscopio document tree model is tested. If you want to see and run the tests, just open the tests package by executing:

GrafoscopioNodeTest browse

From there, you can use the extensive test environment provided by Pharo. For a short introduction to how to run test on this environment, I recommend to watch the Coding a Little Domain Specific Language video , from the Pharo MOOC.

Known bugs

There is a non critical but annoying bug that presents from time to time when you are using the notebook GUI.

Some times, when you click the document tree a window popup with an error message, titled "MessageNotUnderstood: receiver of "selectedMorphList" is nil", as shown in figure ref{fig:bug}.

The know bug message. {#fig:bug}

If that is the case, you still can continue your writing in the current document, clicking on other notebook nodes and editing them, but if the message presents again (usually when selecting the same node that originated it the first time), you can save the notebook and reopen it again from the Launch > Recent notebooks... docking bar menu.

We are going to hunt and squeeze that bug out of existance. Resistance is futile. To help us with this or other bugs please look at the Community Guidelines to know how to contribute to the project.

Community Guidelines

Seek support

Grafoscopio has a small and new born community. You can reach it by following the contact links in the Grafoscopio page in Spanish or in English.

Also you can discuss issues related with Grafoscopio in the Pharo users community mailing list. We are in such list and try to be active participants there and bridge the local Spanish community with the international one.

Report issues or problems

To report issues or problems with the software and/or its documentation please visit our ticket section Fossil repository. Before creating a new ticket, please be sure to visit the current tickets, to see if your issue/problem has been not reported already.

When you are filling out the issues form, take into account to include the software version where you found this problem. If you are reporting an issue with documentation, add the document version, usually found in the lower left side of the page, including the document revision in the square brackets.

Contribute to the project

As we said, Grafoscopio wants to help in blurring the distinction between software developer and interactive document author, so we are pretty open to several ways of contribution: from bug reports, as explained above, to the creation of interactive documentation, domain specific languages (DSLs) and visualizations, or software functionality.

Contributions usually take part on our recurrent Data Week hackathon/workshop and there you will learn how to use and adapt the software, starting by the basics, creating DSLs and crafting visualizations and integrating them into interactive notebooks. You will also learn how to use Fossil and how to commit to our shared repositories for code and for documents and issues. Besides this manual, we are creating also a tutorial (in Spanish) with all these themes covered, as memories for us and others to remember and learn from. The idea, as was said before, is to have multilingual documentation with a local first approach.

If you don't have the chance to assist to one of our face to face learning workshops and hackathons or to use the resulting notebooks, but still want and already know who to contribute, you can also ask for permisions in the respositories using any of the contact methods listed above. We are a small, new born and friendly community with low traffic mail communication and can discuss about contributions on an individual case by case approach, so your words, bugfix and suggestions will be listened and taking into account and integrated when and where they make sense.

Welcome again to our community :-).

Licenses

Grafoscopio, Dataviz and Pubiblio Software License

The Grafoscopio, and its companion packages Dataviz and Publibio, are software covered under MIT License

Copyright (c) 2014-2017 Offray Vladimir Luna Cárdenas

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Documention License

THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS COPYFARLEFT PUBLIC LICENSE (“LICENSE”). THE WORK IS PROTECTED BY COPYRIGHT AND ALL OTHER APPLICABLE LAWS. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED. BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED IN THIS LICENSE, YOU AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN AS CONSIDERATION FOR ACCEPTING THE TERMS AND CONDITIONS OF THIS LICENSE AND FOR AGREEING TO BE BOUND BY THE TERMS AND CONDITIONS OF THIS LICENSE.

THE GRAFOSCOPIO MANUAL, THE DATAVIZ NOTEBOOK, AND THEIR DERIVATED FILES LOCATED IN THIS REPOSITORY, ARE COVERED BY THIS DOCUMENTATION LICENSE.

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Bibliography

  1. ^ See the acknowledgements to look for other people that make Grafoscopio possible. Hopefuly this form of cocreation is just the beginning and will become more plural and potent in the future.
  2. ^ For the curious, that code corresponds to the cryptographic hash of the source markdown file used to produce the PDF or HTML version of this document (you will learn more about them in the "Exporting" section of this manual). You can use this hash to locate the exact version of such file in its timeline.
  3. ^ The idea of the "document is a program" is a paraphrasis of "the book is a program", stated in the Pollen documentation, which is a short phrase to express a powerful idea about burring the disctinction between the document and the program, that is present in several programs, like TeXmacs, Leo, Org Mode, and, of course, Grafoscopio.
  4. ^ MOOC stands for Massive Online Open Courseware. The Pharo MOOC is excellent and a really good entry point for programmers wating to learn more about Pharo and live coding. It also provides good complementary information if you come for other disciplines and endeavors and want to complement your reproducible research, modelling, data storytelling and visualization, with solid foundations of the Pharo environment, but it presumes familiary with programming. For an introductory book to object oriented programming, using the Pharo environment, look for the upcomming release of Learning Object-OrientedProgramming, Design and TDDwith Pharo (vol I) @oop-pharo-2017.
  5. ^ There are several alternatives to GitHub that provide a sleek and friendly web user interface (WUI), without complicated overheat, following the same spirit of Fossil, but based on git. Checkout Gogs, for a self hosted and easy to install git based source code management system.
  6. ^ Exporting to PDF, requires the proper instalation of a LaTeX engine, like pdflatex, luatex, xelatex or context. Explanation about how to install them for each specific platfom (Windows, Gnu/Linux and/or Mac) goes beyond the objectives of this manual and is available online. Please consult the published documentation for your particular platform. In the future we hope to provide integration with external package managers, like Nix (for Gnu/Linux and Mac) or Chocolatey (for Windows) to help with external tools and frameworks installations, in case you don't want to make them by yourself.
  7. ^ a b c d Misreference
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