OrderedCollection [
GrafoscopioNode {
#header : '%metadata ',
#body : '| metadata version pandocOptions |
version := \'1.3.8\'.
pandocOptions := \'-N --template=mytemplate.tex --variable fontsize=12pt --variable version=\',version,\' --latex-engine=xelatex --toc --bibliography bibliography.bib\'.
metadata :=
{
\'title\' -> \'Grafoscopio User Manual\'.
\'author\' -> \'Offray Vladimir Luna Cárdenas\'.
\'date\' -> Date today.
\'pandocOptions\' -> pandocOptions
} asDictionary.',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : GrafoscopioNode {
#header : 'Arbol principal',
#body : '',
#children : @1,
#level : 0,
#nodesInPreorder : OrderedCollection [
@4,
@2,
GrafoscopioNode {
#header : 'Important information to start with',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'A small presentation',
#body : 'This manual documents the basics of [Grafoscopio][grafoscopio-en], a tool
I\'m cocreating[^cocreation] 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][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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%footnote cocreation',
#body : '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.',
#children : OrderedCollection [ ],
#parent : @8,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @6,
#level : 2,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'Acknowledgements',
#body : '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)[^incomplete-thanks] list of people that
helped me to make Grafoscopio possible:
%embed people
Also, several places and communities were an active part in this project:
[HackBo][hackbo] hackerspace, [mutabiT][mutabit], [Pharo][pharo-community],
[Moose][moose-community] and [Agile Visualization][agileviz] communities,
[HiTeC Lab][hitec-lab] of the Los Libertadores University and [Object Profile][object-profile].
To all of them, my sincere thanks.
[^incomplete-thanks]:
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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%embed people',
#body : '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,
Serge Stinckwich,
and
Peter Uhnák.',
#children : OrderedCollection [ ],
#parent : @14,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @6,
#level : 2,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'Reading conventions',
#body : 'This document follows the following conventions:
- *Italics* is used for emphasis and for Grafoscopio/Pharo special terms. For example:
"Write this in the *playground*".
- **Bold** is for strong emphasis notes and reminders, like in "**Important note**".
- `Verbatim` is for representing code snippets and commands, keys and file names.
For example: "Open the file named `manual.ston`".
- Code lines are in verbatim and numered, which makes easier to point to specific
parts and to know when a code block splits across sucessive pages.
- `Ctrl` and `Cmd` represent the "Control" and "Command" keys, respectively.
The former is avaible on Windows and Gnu/Linux platforms and the last one
is available on Mac platform.
When we use that key in combination with other that needs to be pressed at
the same time, we use `+` and the other key, so `Ctrl + s` represent the
simultaneos pressing of the keys `Ctrl` and `s`.
Keyboard shorcuts that contain `Ctrl` on Windows and Gnu/Linux, can be
replaced by `Cmd` on Mac and to ease reading we don\'t repeat each shorcut
on each platform.
Sometimes we will put the keyboard shortcut in parenthesis, just after the action it
referst to, like in "Open the spotter (`Shift` + `Enter`)".
- When we refer to menus and submenus in the Graphical User Interface (GUI), we will
use `>` as an indicator of the menus hirarchy.
For example, writing `Update > Grafoscopio`, means to choose the `Update` menu
and then the `Grafoscopio` submenu in it.
- The PDF and HTML versions of this document include clickable links and words, that
are shown in blue, for example the following words are a clickable link to the
[Grafoscopio web page][grafoscopio-en].
- Bibiographic references use the usual convention of being cited between parenthesis,
like in: "(author year)".
',
#children : OrderedCollection [ ],
#parent : @6,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Document and software versions',
#body : '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 manual[^cryptohash], 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][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):
',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%output This software bundle versions',
#body : '(ConfigurationOfGrafoscopio>>#version138:) sourceCode',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @23,
#level : 3,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%footnote cryptohash',
#body : 'For the curious, that code corresponds to the [cryptographic hash][cryptohash] 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][manual-source-timeline].',
#children : OrderedCollection [ ],
#parent : @23,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @6,
#level : 2,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'On commons, copyright and copyfarleft',
#body : '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.',
#children : OrderedCollection [ ],
#parent : @6,
#level : 2,
#links : OrderedCollection [
''
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
''
]
},
@8,
@10,
@14,
@16,
@20,
@23,
@25,
@28,
@32,
GrafoscopioNode {
#header : 'Grafoscopio for what and for whom?',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'This tool and you',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%idea For what',
#body : 'Grafoscopio is a moldable tool for literate computing and reproducible
research, developed on [Pharo][pharo] live coding and computing integrated environment,
in the context of a PhD research in a hacker space of the Global South ([HackBo][hackbo]
in Bogotá, Colombia), that is being actively used, developed and documented.
We will expand on the points of the previous definition.
- Being moldable [@moldable-debugger-2014] means that is easy to adapt the tool to several problems,
which follows the opposite popular path of trying to force several problems into a predefined tool.
Tools change us. So we need to change them back to express our concerns and to help us
in dealing with complex issues and problems in a flexible way.
- Literate computing [@literate-computing-2015] is a way of intertwining prose, code, data
and visualizations to make data based storytelling, experimentation, exploration and
documentation in diverse broad fields like academia, journalism, research and (h)ac(k)tivism.
Grafoscopio allows the creation of literate computing structured interactive notebooks, that
take the form of a tree-like programmable document.
- Research claims and findings and supporting data and visualizations can be integrated in
interactive notebooks with historic traceability, allowing reproducible research.
- Because of the continuity and uniformity of the Pharo environment [@pbe-2016], Grafoscopio blurs
the distinction between code, data, document, application and IDE [^ide] and tries to blur
also the distinction between interactive documents authors and software developers.
- From the particular context where is being developed (HackBo hackerspace and a PhD research on
Design and Creation), Grafoscopio is concived as a empowering simple and self contained *pocket
infrastructure* (that work off-line/on-line from USB thumb drives and/or low resources machines
[@luna-grafoscopio-2014]), wich states a critical approach to exclusionary ideas about data, coding,
research, and their practicioners, places, and supporting tools and infrastructures.
In the [Grafoscopio web page][grafoscopio-en], we showcase several projects aligned with such
critical approach and the idea that technology is mostly not neutral, wich is also reflected in some parts
of this text and in the fact that we\'re opinionated about technology and its uses.
I hope you find our technology and themes choices empowering and reavealing of alternatives.
[^ide]: IDE: Integrated software Development Environment
',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%invisible What is Grafoscopio? Alternative definitions',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'From the web site',
#body : 'Grafoscopio is a moldable tool for interactive documentation, exploratory computing, agile data visualization,
and reproducible research, that is being used in several fields: citizen, garage & open science, (h)ac(k)tivism, open & community innovation, domain specific visualization and data journalism, and has a lot of other potential uses.
Grafoscopio is covered by a Free Libre Open Source Software license (MIT) and it has an associated hackathon/workshop, called the Data Week, oriented to citizen concerns, which are related and mediated by data and visualization. There we learn, adapt and feedback this tool.
Grafoscopio is and integrates simple and self-cointained "pocket infractures", that can be execute On/Off-line, from a USB thumb drive, a rasperry-Pi alike computer, a modest server or any hardware in between and beyond. ',
#children : OrderedCollection [ ],
#parent : @42,
#level : 3,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'From the JOSS article',
#body : '[Literate computing] [@perez&granger-2015] is a way of intertwining prose, code data and visualizations
to make data based storytelling, experimentation, exploration and documentation in diverse broad fields like academia, journalism, research and (h)ac(k)tivism.
Grafoscopio is moldable tool [@girba_scg:_2014] for literate computing
and reproducible research, and
agile data visualizations [@bergel-2015],
in a tree-like interactive document metaphor,
developed on the [Pharo][pharo] live coding and computing integrated environment.
Because of the continuity and uniformity of this environment, Grafoscopio blurs
the distinction between code, data, document, application and IDE and tries to
blur the distinction between interactive documents authors and software developers
[@luna-2017].
Grafoscopio has been developed in the context of a PhD research in a hackerspace of
the Global South ([HackBo][hackbo] in Bogotá, Colombia) and from this particular context was
concived as a empowering, simple, flexible and self contained *pocket infrastructure*
(that works off-line/on-line from USB thumb drives and/or low resources machines [@luna2014]).
',
#children : OrderedCollection [ ],
#parent : @42,
#level : 3,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'From GSoC',
#body : 'Literate computing is a way of mixing text, code, data and visualizations for making data based storytelling, experimentation, exploration and documentation in diverse broad fields like academia, journalism, research and activism, or Pharo specific themes (for Roasall, Polymath etc). Grafoscopio is a tool that brings literate computing to the Pharo environment by allowing the creation of structured interactive notebooks in a tree-like programmable document metaphor.',
#children : OrderedCollection [ ],
#parent : @42,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @40,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @38,
#level : 3,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%idea from whom',
#body : '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][grafoscopio-en] (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]. ](../../../Imagenes/grafoscopio-webpage-en.png){#fig:web-page-en}',
#children : OrderedCollection [ ],
#parent : @38,
#level : 3,
#links : OrderedCollection [
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]
},
GrafoscopioNode {
#header : '%idea TBD',
#body : '**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][dataweek] 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).',
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]
}
],
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#level : 2,
#links : OrderedCollection [
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]
},
GrafoscopioNode {
#header : 'Place in the ecosystem',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Similar tools',
#body : '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.
- Like [Jupyter][jupyter], or [Zeppling][zeppling], [Beaker][beaker]
or [nteract][nteract], Grafoscopio provides interactive notebook functionality,
but it is focused only on Pharo code right now, instead of being a
"language neutral" notebook (but this could be a feature for the future)
and is able to use Pharo bindings to integrate and communicate with other data
languages, like [R][r-lang], [SQL][sql] or [J][j-lang].
Grafoscopio is a multiplatform (Mac, Windows, Gnu/Linux) desktop
application (like nteract, or Electron Beaker), instead of a web one
(like Jupyter, Zepelling or Beaker), providing a simple, extensible,
powerful, self-contained and portable environment for interactive computing,
(as said it can run from a USB thumb drive, modest computers
and anything in between and beyond).
- Grafoscopio organizes documents in a tree like metaphor, also called the *outline*, or the
notebook, that is interactive and programmable, like [Org Mode][org-mode], [Leo Editor][leo],
[TeXmacs][texmacs] or [Pollen][pollen] and share with them the idea that the
"document is the program"[^book-program] (or a programable container
of small chunks of programs and scripts).
Also, the document author, can define custom tags that can be used to traverse the
document tree and produce multiple customized views and outputs from a single document.
A single notebook can contain short or book size interactive documents
(this full manual is in a single Grafoscopio notebook).
- Like [Jupyter Lab][jupyterlab], Grafoscopio environment supports needs beyond the notebook.
Grafoscopio achieves this by leveraging the advantange of the extensible Pharo computing
environment and ecosystem, where it inhabits, with powerful tools for several computing taks, beyond
and complementary to interactive documentation and reproducible research: GUI bulding, data processing
and visualization, unit testing, code repositories and source management, among others.
It could be said that Jupyter Lab and Grafoscopio followed opposite paths, the first started in the Jupyter notebook,
and is trying to become and IDE, and the second started in the Pharo live coding IDE and it bringing interactive
notebooks functionality. In some sense, one is already in the future of what the other can be.
- Grafoscopio uses the [Roassal agile visualization engine][roassal], to build interactive
visualizations and export them to the web.
Roassal provides similar functionality to other visualization engines and toolkits like [D3.js][d3js],
[RaphaelJS][raphaeljs], [Processing][processing] or [Flare][flare], but, by being part of the Pharo
live coding environment, it invites to a more explorative and dynamic building of visualizations in
an agile way.
- At the moment, notebook sharing, collaboration and publishing in print (PDF) and web (HTML) formats
is supported, but in the future we hope to provide advanced interactive notebook publishing
features in a distributed p2p fashion (see next section for the techologies that enable this).
',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%footnote book-program',
#body : '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.',
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},
GrafoscopioNode {
#header : 'Technologies behind',
#body : 'Grafoscopio tries to become a simple, understandable, moldable,
versatile and flexible tool thanks to the power of [Pharo][pharo]
environment and ecosystem and the combination with mature external
and internal frameworks and tools. It uses:
- Internal tools and frameworks:
- [GT Tools][gt-tools] and [Spec][spec] for embeddable code playgrounds, GUI and interactive
notebook nodes.
- [Roassal][roassal] for data visualization.
- [STON][ston] for a light data storage and a human friendly notebooks format.
- [NeoJSON][neojson] for interacting with structured hierarchical [JSON][json] data.
- [Citezen][citezen]: for reading and exporting bibliographies to the [BibTeX][bibtex] format.
- [Fuel][fuel]: For medium data storage and objects serialization.
- [UDBC][udbc]: For connection and management of external data bases.
- External tools and frameworks:
- [Fossil SCM][fossil] for collaboration, publication and traceability of the documents history
(including this very manual).
- [Pandoc][pandoc] for exporting to printing (PDF) and web (HTML) formats.
- [SQLite][sqlite] for storage and management of tabular data, for the `Dataviz` companion package.
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][git],
more data bases, including [NoSQL][nosql], other exporters and
[light markup languages][light-markup-languages] and so on).
',
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GrafoscopioNode {
#header : 'Installation instructions',
#body : '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][pharo-download],
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.
',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Install from the Pharo catalog',
#body : '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}.
{#fig:install-screen1}
2. 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.
{#fig:install-screen2 width="50%"}
3. While the installation is running, some progress bars with package names are going to be showed
(see figure \\ref{fig:install-screen3}):
{#fig:install-screen3}
4. 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.
{#fig:install-screen4}
5. 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}).
{#fig:install-screen5 width="50%"}',
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''
]
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GrafoscopioNode {
#header : 'Install from a script',
#body : '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})
{#fig:empty-playground}',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%idea in two steps',
#body : '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.
{#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}.
{#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}).
{#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.',
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''
]
},
GrafoscopioNode {
#header : '%idea In one step',
#body : '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](http://ws.stfx.eu/D6DDTUAMWIOK), in the spotter, as before):
%embed Grafoscopio single quick install script
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.
{#fig:playground-partial-execution}
{#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.',
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GrafoscopioNode {
#header : '%embed Grafoscopio single quick install script',
#body : '"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.
',
#tags : 'código',
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GrafoscopioNode {
#header : '%invisible',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Instaliing the Grafoscopio configuration',
#body : '"Start by loading the configuration of Grafoscopio"
Gofer new
url: \'http://smalltalkhub.com/mc/Pharo/MetaRepoForPharo50/main\';
package: \'ConfigurationOfGrafoscopio\';
load.
',
#tags : 'código',
#children : OrderedCollection [ ],
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#level : 4,
#links : OrderedCollection [
'',
'http://ws.stfx.eu/BMWZPUY38BSF'
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},
GrafoscopioNode {
#header : 'Load Grafoscopio',
#body : '"After that load Grafoscopio"
ConfigurationOfGrafoscopio load.
',
#tags : 'código',
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#parent : @91,
#level : 4,
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'http://ws.stfx.eu/CZ87ZZ2SXCEM'
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GrafoscopioNode {
#header : 'Using Grafoscopio',
#body : 'This section will show you how to use Grafoscopio from the GUI.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'The spotter',
#body : 'One of the first elements of the Pharo GUI that is an excellent companion
for Grafoscopio is the [spotter][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}:
{#fig:spotter}
You can learn more about the spotter in the [Pharo MOOC][mooc] [^mooc],
particularly in lesson 9 of Week 3 ([video 1][mooc-spotter1], [video 2][mooc-spotter2]).',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%footnote mooc',
#body : '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] (beta version [here][oop-pharo-2017]).',
#children : OrderedCollection [ ],
#parent : @104,
#level : 3,
#links : OrderedCollection [
''
]
}
],
#parent : @102,
#level : 2,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'The docking bar',
#body : '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}.
{#fig:docking-bar}
The docking bar is divided in three menus that are explained below.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Launch menu',
#body : '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.
{#fig:launch-menu width="50%"}
This are the options in the Update menu:
- `New notebook`: Creates a new notebook.
- `Notebook from file...`: opens a pre-existing notebook from a local file.
- `Notebook from internet...`: opens a notebook from an URL and creates a local copy in the
temporal folder.
- `Recent notebooks...`: lists the notebooks that have been recently opened and/or saved.
- `Example notebooks...`: (**TBD**) Lists a set of example notebooks (may be integrated in the
`Help ̀ menu).
- `Roassal visualizations gallery...`: Opens a visualization browser grouped by categories. Useful
as starting point and inspirations for some projects.
- `Playground`: Opens an interactive coding scripting environment, with single "pages".
Playgrounds are also embeddable inside Grafoscopio notebooks.
- `Transcript`: opens an output window to see log of events or see print messages.',
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GrafoscopioNode {
#header : 'Update menu',
#body : 'This menu updates functionality, documentation and settings for Grafoscopio.
Grafoscopio has a [rolling release][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][dataweek] 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.
{#fig:update-menu width="50%"}
This are the options in the Update menu:
- `Grafoscopio`: Updates Grafoscopio to the latest development version from the repository.
- `Documentation`: Updates companion documentation, that comes as native notebooks or in
exported formats (PDF now and HTML in the future).
- `Dataviz Package`: Updates the Dataviz companion package, which contains Domain Specific
Languages and Visualizations that are introduced as Grafoscopio notebooks.
A companion notebook about this package is available on the Help menu, for more detailed
information.
- `Notebooks places`: Updates some globally shared references for notebooks, so they can be
adapted to personal preferences.
This is useful for workshops, so participants can still store some notebooks in their preferred
locations, while sharing relative routes. Examples of this functionality can be found in the Dataviz
package notebooks documentation.
- `All the system`: Updates all of the above, except for the "Notebooks places", without going for
any individual menu.',
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},
GrafoscopioNode {
#header : 'Help menu',
#body : '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.
{#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:
- `Tutorial (Spanish)`: Opens a tutorial used for the [Data Week][dataweek] hackathon/workshop, that
advances in increasding difficulty, covering the Pharo introductory tutorial (Prof. Steph),
some simple scripts, reading of structured data (in JSON), building of a first package (Cinemania),
HTML templating and programatic generation (via Mustache) and basic web publishing (via Teapot).
(For a more detailed view of the contents, you\'re welcomed to explore the tutorial by yourself).
- `Manual`: Opens this manual as a Grafoscopio native document.
- `Manual (PDF)`: Opens this manual, exported as PDF.
- `Dev\'s notes`: Opens a notebook with notes from the developer. Useful to know what is happening
with the development process and where is going and is complementary to other development
infrastructures, like code, docs and issues repositories (provided by SmalltalkHub and Fossil).
- `About Grafoscopio`: Opens the "About" window, showing contributors and the software version.
',
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#header : 'The notebook GUI',
#body : '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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Creating a new notebook',
#body : 'To create a new notebook you have several options:
- Choose `Launch > New notebook`, from the *docking bar*.
- Open a *playground* (`Ctrl + o + w`) and write `GrafoscopioNotebook new openDefault`.
You will see a window like the shown in figure \\ref{fig:new-notebook}.
{#fig:new-notebook}
Next section will explain the functionality of the notebook GUI.',
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},
GrafoscopioNode {
#header : 'The top bar',
#body : '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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'The notebook menu',
#body : '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.
{#fig:notebook-menu}
These are the options of this menu:
- `Save`: Saves the notebook to the filesystem. If no filename has been provided, asks for one.
- `Save as...`: Saves the notebook to the filesyste under a new name.
- `Export as markdown`: Exports the current notebook to [Pandoc\'s markdown][markdown].
- `Export as html`: Exports the current notebook to HTML format.
- `Export as pdf`: Exports the current notebook to HTML format.
- `See html`: (**TBD**) Shows the exported HTML document.
- `See pdf`: (**TBD**) Shows the exported PDF document.
See the "Exporting" section for details about exporting and the pandoc prerrequisites to make it work.',
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GrafoscopioNode {
#header : 'The project menu (TBD)',
#body : '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][fossil] (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][git] or [GitHub][github], but it is simpler that the former and does not hide
functionality under closed source code software or promotes centralization, like the later[^github-alternatives].
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.
',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%footnote github-alternatives',
#body : '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][gogs], for a self hosted and easy to install git
based source code management system.',
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#level : 5,
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]
}
],
#parent : @127,
#level : 4,
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},
GrafoscopioNode {
#header : 'The toolbar',
#body : '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.
{#fig:toolbar}
Here is a more detailed explanation of the icons functionality in the toolbar.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Notebook saving and node cut, copy & paste',
#body : ' - : Saves the current notebook.
- : Cuts the current node of the document tree.
- : Copies the current node of the document tree to the
clipboard.
- : Pastes the current node of the document tree from the
clipboard.',
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},
GrafoscopioNode {
#header : 'Node addition, deletion and movement',
#body : '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.
- : Adds a new node to the tree after the
currently selected one.
- : Removes the currently selected node.
- : Moves the currently selected node one place upward,
unless is the first node.
- : Moves the currently selected node one place
downward, unless is the last node.
- : Promotes the currently selected node one place, to
the same level of its parent.
- : Demotes the currently selected node one place, making
it child of the previous slibing.',
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},
GrafoscopioNode {
#header : 'Switching node body, visiting links, updating content and adding tags',
#body : '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.
- : switches a node from text to code and viceversa.
Because literate computing, weaves code and text, emphasizing narrative and storytelling
supported by data, the default nodes are textual ones.
- : visits a node link, opening it in the web browser,
if it is not empty (see node details for more information about node links).
- : updates node body acording to the node last link, which
is useful for published playgrounds.
In the future this icon will sync body contents with different type of links, including those pointing to
[etherpads][etherpad] or local and remote files.
-  :
the add/remove tags icons will be used to define custom tags to mark nodes (**TBD**).
Custom tags can be used to define node traversal paths to create different outputs from a single
notebook (in a similar way to `%keywords` as is explained after).',
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},
GrafoscopioNode {
#header : 'The document tree',
#body : '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.',
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GrafoscopioNode {
#header : 'Node details',
#body : '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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Node header',
#body : '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).
',
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},
GrafoscopioNode {
#header : 'Node body',
#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`.',
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},
GrafoscopioNode {
#header : 'Node links',
#body : '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.',
#children : OrderedCollection [ ],
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'',
'',
'',
'',
'',
'',
'http://mutabit.com'
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#level : 3,
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'',
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},
GrafoscopioNode {
#header : 'More on code nodes',
#body : '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][dataweek] 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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Executing',
#body : '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}.
{#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:
%embed connecting numbers
Then press the green play button 
(or its shorcut `Ctrl + g`) and you will see something like the figure \\ref{fig:code-node-executed}:
{#fig:code-node-executed}
What we have done is a small visualization (taken from the
[Agile Visualization quick start][agileviz-quickstart]) that connects each number from 1 to 100 with
the [floor][floor-function] 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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%embed connecting numbers',
#body : 'b := RTMondrian new.
b shape label.
b nodes: (1 to: 100).
b edges connectFrom: [ :i | i // 2 ].
b layout cluster.
b',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @168,
#level : 5,
#links : OrderedCollection [
''
]
}
],
#parent : @166,
#level : 4,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
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'',
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''
]
},
GrafoscopioNode {
#header : 'Sharing',
#body : '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}).
{#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.
{#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][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.',
#children : OrderedCollection [ ],
#parent : @166,
#level : 4,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Importing',
#body : '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][etherpad] 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.
',
#children : OrderedCollection [ ],
#parent : @166,
#level : 4,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Diving on results',
#body : '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:
- `Raw`: Shows the attributes of the object resulting from the
playgrounds execution.
Those attributes are also objects, so you can dive into them.
Once you have selected an object, a faceted browsing will start
opening a new set of tabs zooming into this particular object.
The lower panel of the raw view, can be used to send messages to
the main object, or the objects that compose it.
- `Meta`: Shows the objects hierarchy starting with the one resulting
from the playgrounds execution and ascending in the containing classes.
Is pretty useful to have a quick overview of which is the vocabulary of the
object, wich messages can be send and how they\'re organized (protocols)
and implemented.
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}.
{#fig:code-node-inspector}
To know more about playgrounds and how they can be used and extended
vistit the [GT-Tools page][gt-tools].',
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#parent : @166,
#level : 4,
#links : OrderedCollection [
'',
'',
'',
'',
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]
}
],
#parent : @122,
#level : 3,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Extending the markup: `%keywords`',
#body : '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.',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%idea %invisible',
#body : ' - `%invisible`: Use it to mark a node that you don\'t want to become part of the exported document.
This applies to that node and its children. ',
#children : OrderedCollection [ ],
#parent : @184,
#level : 4,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%idea %idea',
#body : ' - `%idea`: Use it when you don\'t want the header of the node to become part of the exported result.
Is useful to split long text that are part of a single section into a set of main ideas.',
#children : OrderedCollection [ ],
#parent : @184,
#level : 4,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%idea %embed',
#body : ' - `%embed`: Use it to change the way that children nodes are included in the exported result.
If you do not use this keyword, all non-invisible children nodes will be added secuencially after the parent.
If you use this keyword, all non-invisible children nodes that start with `%embed` will be added in the
order they where called in the parent\'s body.',
#children : OrderedCollection [ ],
#parent : @184,
#level : 4,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%idea %footnote',
#body : ' - `%footnote`: Use it to create a children node that contains footnotes invoked in the parents body.
The header of the footnote should be the same that is referenced in the parent. So if the parents body
includes a `[^my-ID]` markup reference to a footnode, the children node should have this header:
`%footnode my-ID`.
Useful for long footnotes, (wich are usual in academic writing) or just to have a more organized document tree.',
#children : OrderedCollection [ ],
#parent : @184,
#level : 4,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%idea %output',
#body : ' - \'%output\': Use it if you want to include the textual output of a code node execution in the exported
markdown file.',
#children : OrderedCollection [ ],
#parent : @184,
#level : 4,
#links : OrderedCollection [
''
]
}
],
#parent : @122,
#level : 3,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Exporting: markdown, HTML, \\LaTeX and PDF',
#body : 'Grafoscopio provides exportation capabilies to [Pandoc\'s markdown][markdown]
and use Pandoc to export to HTML, [LaTeX][latex] and PDF[^latex-engine].
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][pandoc] 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
~~~
%embed Bibliographic support: Zotero and BibTeX
You can browse the [proper folder in the fossil repository][manual-tip] to see
the manual and companion files in different formats.',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%footnote latex-engine',
#body : '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][nix] (for Gnu/Linux and Mac) or [Chocolatey][chocolatey] (for Windows) to
help with external tools and frameworks installations, in case you don\'t want to
make them by yourself.',
#children : OrderedCollection [ ],
#parent : @202,
#level : 4,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : '%embed Bibliographic support: Zotero and BibTeX',
#body : '**Important note ** `>` *Bibliographic support: Zotero and BibTeX* |
Grafoscopio has preliminar support for reading and generating [BibTeX][bibtex] files
and to connect with public [Zotero][zotero] collections.
In fact, the bibliography file for this manual was done by reading a [Zotero collection][zotero-manual]
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.',
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#level : 4,
#links : OrderedCollection [
''
]
}
],
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#level : 3,
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GrafoscopioNode {
#header : 'Examples',
#body : '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*:
',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Opening tutorial',
#body : '"This opens the Spanish tutorial"
GrafoscopioNotebook new openTutorial ',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @213,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Opening Dataviz documentation',
#body : '"This opens the introductory notebook to the Dataviz package"
GrafoscopioDocumentation openDatavizIntro',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @213,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
'',
''
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
'',
'',
''
]
},
@215,
@218,
GrafoscopioNode {
#header : 'API documentation',
#body : '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:
',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Opening the code browser for Grafoscopio',
#body : '"Browser the notebook API"
GrafoscopioNotebook browse.
"Browse the document tree API"
GrafoscopioNode browse.',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @222,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
''
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
'',
'',
'',
''
]
},
@224,
GrafoscopioNode {
#header : 'Tests',
#body : '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:
%embed Opening the tests package
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 ][mooc-w3-14],
from the [Pharo MOOC][mooc].',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%embed Opening the tests package',
#body : 'GrafoscopioNodeTest browse',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @228,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
''
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
'',
'',
'',
'',
'',
''
]
},
@230,
GrafoscopioNode {
#header : 'Known bugs',
#body : '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}.
{#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.',
#children : OrderedCollection [ ],
#parent : @4,
#level : 1,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'Community Guidelines',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Seek support',
#body : 'Grafoscopio has a small and new born community.
You can reach it by following the contact links
in the Grafoscopio page in
[Spanish](http://mutabit.com/grafoscopio/)
or in [English](http://mutabit.com/grafoscopio/index.en.html).
Also you can discuss issues related with Grafoscopio in the
[Pharo users community](http://pharo.org/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.',
#children : OrderedCollection [ ],
#parent : @237,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Report issues or problems',
#body : 'To report issues or problems with the software and/or its documentation
please visit our [ticket section][grafoscopio-tickets] Fossil repository.
Before creating a new ticket, please be sure to visit the
[current tickets][grafoscopio-tickets-current], 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.',
#children : OrderedCollection [ ],
#parent : @237,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Contribute to the project',
#body : '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][dataweek]
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][grafoscopio-sthub] and for
[documents and issues][grafoscopio-fossil].
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 :-).',
#children : OrderedCollection [ ],
#parent : @237,
#level : 2,
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
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''
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
'',
'',
'',
'',
'',
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''
]
},
@239,
@242,
@245,
GrafoscopioNode {
#header : '%idea external links',
#body : '[agileviz]: http://agilevisualization.com/
[agileviz-quickstart]: https://dl.dropboxusercontent.com/u/31543901/AgileVisualization/QuickStart/0101-QuickStart.html
[beaker]: http://beakernotebook.com/
[bibtex]: https://en.wikipedia.org/wiki/BibTeX
[chocolatey]: https://chocolatey.org/
[citezen]: http://people.untyped.org/damien.pollet/software/citezen/
[cryptohash]: https://en.wikipedia.org/wiki/Cryptographic_hash_function
[d3js]: https://d3js.org/
[dataweek]: http://mutabit.com/dataweek/
[etherpad]: https://en.wikipedia.org/wiki/Etherpad
[flare]: http://flare.prefuse.org/
[floor-function]: https://en.wikipedia.org/wiki/Floor_and_ceiling_functions
[fuel]: http://rmod.inria.fr/web/software/Fuel
[fossil]: http://fossil-scm.org/
[hitec-lab]: http://www.hiteclab.co.nr/
[joss]: http://joss.theoj.org/
[grafoscopio-en]: http://mutabit.com/grafoscopio/index.en.html
[grafoscopio-fossil]: http://mutabit.com/repos.fossil/grafoscopio/
[grafoscopio-tickets]: http://mutabit.com/repos.fossil/grafoscopio/ticket
[grafoscopio-tickets-current]: http://mutabit.com/repos.fossil/grafoscopio/rptview?rn=1
[grafoscopio-sthub]: http://smalltalkhub.com/#!/~Offray/Grafoscopio
[git]: https://en.wikipedia.org/wiki/Git
[github]: https://en.wikipedia.org/wiki/GitHub
[gogs]: https://gogs.io/
[gt-tools]: http://gtoolkit.org/
[hackbo]: http://hackbo.co/
[j-lang]: https://en.wikipedia.org/wiki/J_(programming_language)
[json]: http://en.wikipedia.org/wiki/JavaScript_Object_Notation
[jupyter]: http://jupyter.org/
[jupyterlab]: http://jupyterlab.github.io/jupyterlab/
[latex]: https://en.wikipedia.org/wiki/LaTeX
[leo]: http://leoeditor.com
[light-markup-languages]: https://en.wikipedia.org/wiki/Light_markup_language
[manual-tip]: http://mutabit.com/repos.fossil/grafoscopio/dir?tip&name=Docs/En/Books/Manual
[manual-source-timeline]: http://mutabit.com/repos.fossil/grafoscopio/finfo?name=Docs/En/Books/Manual/manual.markdown
[markdown]: http://pandoc.org/MANUAL.html#pandocs-markdown
[mooc]: https://siemenbaader.github.io/PharoMooc-website/
[mooc-spotter1]: http://rmod-pharo-mooc.lille.inria.fr/MOOC/Videos/W3/C019-Videos-Spotter1-BrowsingAClassWithSpotter-V2-HD_720p_4Mbs.m4v
[mooc-spotter2]: http://rmod-pharo-mooc.lille.inria.fr/MOOC/Videos/W3/C019-Videos-Spotter2-Categories-V2-HD_720p_4Mbs.m4v
[mooc-w3-14]: http://amara.org/en/videos/04UWGMwnrdXz/info/rmod-pharo-mooclilleinriafrc019-videos-redo-dsl-hd_720p_4mbsm4v/
[moose-community]: http://moosetechnology.org/#twitter
[mutabit]: http://mutabit.com/
[neojson]: https://ci.inria.fr/pharo-contribution/job/EnterprisePharoBook/lastSuccessfulBuild/artifact/book-result/NeoJSON/NeoJSON.html
[nix]: http://nixos.org/nix/
[nosql]: https://en.wikipedia.org/wiki/NoSQL
[nteract]: https://nteract.io/
[object-profile]: http://objectprofile.com/
[oop-pharo-2017]: https://ci.inria.fr/pharo-contribution/view/Books/job/LearningObjectOrientedProgramming/98/artifact/book.pdf
[org-mode]: http://orgmode.org/
[pastebin]: https://en.wikipedia.org/wiki/Pastebin
[pandoc]: http://pandoc.org/
[pharo]: http://pharo.org/
[pharo-download]: http://pharo.org/download
[pharo-community]: http://pharo.org/community
[pollen]: http://docs.racket-lang.org/pollen/
[processing]: https://processing.org/
[raphaeljs]: https://dmitrybaranovskiy.github.io/raphael/
[r-lang]: https://en.wikipedia.org/wiki/R_(programming_language)
[roassal]: http://agilevisualization.com/
[rolling-release]: https://en.wikipedia.org/wiki/Rolling_release
[spec]: http://files.pharo.org/books/spec-tutorial/
[spotter]: http://gtoolkit.org/#spotter
[sql]: https://en.wikipedia.org/wiki/SQL
[sqlite]: http://sqlite.org/
[ston]: https://github.com/svenvc/ston/blob/master/ston-paper.md
[texmacs]: http://texmacs.org/
[udbc]: http://www.smalltalkhub.com/#!/~TorstenBergmann/UDBC
[zeppling]: http://zeppelin-project.org/
[zotero]: https://www.zotero.org/
[zotero-manual]: https://www.zotero.org/groups/diseo_y_creacion_phd_msc_universidad_de_caldas/items/collectionKey/PHGTCZVT',
#children : OrderedCollection [ ],
#parent : @4,
#level : 1,
#links : OrderedCollection [
''
]
},
GrafoscopioNode {
#header : 'Licenses',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Grafoscopio, Dataviz and Pubiblio Software License',
#body : '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.',
#children : OrderedCollection [ ],
#parent : @252,
#level : 2,
#nodesInPreorder : OrderedCollection [
@254
],
#links : OrderedCollection [
'',
'',
'http://vistonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'http://visonte.org',
'../../Licenses/grafoscopio-mit.md'
]
},
GrafoscopioNode {
#header : 'Documention License',
#body : '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](../Books/Manual/manual.ston),
THE [DATAVIZ NOTEBOOK](../../../Packages/Dataviz/dataviz.ston),
AND THEIR DERIVATED FILES LOCATED IN THIS REPOSITORY,
ARE COVERED BY THIS DOCUMENTATION LICENSE.',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Definitions',
#body : 'a. **“Adaptation”** means a work based upon the Work, or upon the Work and other pre-existing works,
such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary
or artistic work, or phonogram or performance and includes cinematographic adaptations or any other
form in which the Work may be recast, transformed, or adapted including in any form recognizably derived
from the original, except that a work that constitutes a Collection will not be considered an Adaptation for
the purpose of this License. For the avoidance of doubt, where the Work is a musical work, performance or
phonogram, the synchronization of the Work in timed-relation with a moving image (“synching”) will be
considered an Adaptation for the purpose of this License.
b. **“Collection”** means a collection of literary or artistic works, such as encyclopedias and anthologies, or
performances, phonograms or broadcasts, or other works or subject matter other than works listed in Section
1(f) below, which, by reason of the selection and arrangement of their contents, constitute intellectual creations,
in which the Work is included in its entirety in unmodified form along with one or more other contributions, each
constituting separate and independent works in themselves, which together are assembled into a collective whole.
A work that constitutes a Collection will not be considered an Adaptation (as defined above) for the purposes of this License.
c. **“Distribute”** means to make available to the public the original and copies of the Work or Adaptation, as appropriate,
through sale, gift or any other transfer of possession or ownership.
d. **“Licensor”** means the individual, individuals, entity or entities that offer(s) the Work under the terms of this License.
e. **“Original Author”** means, in the case of a literary or artistic work, the individual, individuals, entity or entities who
created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance
the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform
literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being the person or legal entity
who first fixes the sounds of a performance or other sounds; and, (iii) in the case of broadcasts, the organization that transmits
the broadcast.
f. **“Work”** means the literary and/or artistic work offered under the terms of this License including without limitation any production
in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book,
pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a
choreographic work or entertainment in dumb show; a musical composition with or without words; a cinematographic work to which
are assimilated works expressed by a process analogous to cinematography; a work of drawing, painting, architecture, sculpture, engraving
or lithography; a photographic work to which are assimilated works expressed by a process analogous to photography; a work of applied art;
an illustration, map, plan, sketch or three-dimensional work relative to geography, topography, architecture or science; a performance; a
broadcast; a phonogram; a compilation of data to the extent it is protected as a copyrightable work; or a work performed by a variety or
circus performer to the extent it is not otherwise considered a literary or artistic work.
g. **“You”** means an individual or entity exercising rights under this License who has not previously violated the terms of this License with
respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation.
h. **“Publicly Perform”** means to perform public recitations of the Work and to communicate to the public those public recitations, by any
means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way
that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the
public by any means or process and the communication to the public of the performances of the Work, including by public digital performance;
to broadcast and rebroadcast the Work by any means including signs, sounds or images.
i. **“Reproduce”** means to make copies of the Work by any means including without limitation by sound or visual recordings and the right
of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic
medium.',
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#level : 3,
#links : OrderedCollection [
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Fair dealing rights',
#body : 'Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or
rights arising from limitations or exceptions that are provided for in connection with the copyright
protection under copyright law or other applicable laws.',
#children : OrderedCollection [ ],
#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
''
]
},
GrafoscopioNode {
#header : 'License Grant',
#body : 'Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide,
royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to
exercise the rights in the Work as stated below:
a. to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce
the Work as incorporated in the Collections;
b. to create and Reproduce Adaptations provided that any such Adaptation, including any translation
in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes
were made to the original Work. For example, a translation could be marked
“The original work was translated from English to Spanish,” or a modification could indicate
“The original work has been modified.”;
c. to Distribute and Publicly Perform the Work including as incorporated in Collections; and,
d. to Distribute and Publicly Perform Adaptations. The above rights may be exercised in all media and formats whether
now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary
to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby
reserved, including but not limited to the rights set forth in Section 4(f).',
#children : OrderedCollection [ ],
#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
''
]
},
GrafoscopioNode {
#header : 'Restrictions',
#body : 'The license granted in Section 3 above is expressly made subject to and limited by the following restrictions:
a. You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI)
for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of
this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense
the Work. You must keep intact all notices that refer to this License and to the disclaimer of warranties with every copy of the Work You Distribute or
Publicly Perform. When You Distribute or Publicly Perform the Work, You may not impose any effective technological measures on the Work that restrict the
ability of a recipient of the Work from You to exercise the rights granted to that recipient under the terms of the License. This Section 4(a) applies to the
Work as incorporated in a Collection, but this does not require the Collection apart from the Work itself to be made subject to the terms of this License. If
You create a Collection, upon notice from any Licensor You must, to the extent practicable, remove from the Collection any credit as required by Section
4(d), as requested. If You create an Adaptation, upon notice from any Licensor You must, to the extent practicable, remove from the Adaptation any credit
as required by Section 4(d), as requested.
b. Subject to the exception in Section 4(c), you may not exercise any of the rights granted to You in Section 3 above in any manner that is primarily intended
for or directed toward commercial advantage or private monetary compensation. The exchange of the Work for other copyrighted works by means of
digital file-sharing or otherwise shall not be considered to be intended for or directed toward commercial advantage or private monetary compensation,
provided there is no payment of any monetary compensation in connection with the exchange of copyrighted works.
c. **You may exercise the rights granted in Section 3 for commercial purposes only if**:
i. **You are a worker-owned business or worker-owned collective; and**
ii. **all financial gain, surplus, profits and benefits produced by the business or collective are distributed among the worker-owners**
d. Any use by a business that is privately owned and managed, and that seeks to generate profit from the labor of employees paid by salary or other wages, is
not permitted under this license.
e. If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4(a), keep
intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or
pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing
entity, journal) for attribution (“Attribution Parties”) in Licensor’s copyright notice, terms of service or by other reasonable means, the name of such party
or parties; (ii) the title of the Work if supplied; (iii) to the extent reasonably practicable, the URI, if any, that Licensor specifies to be associated with the
Work, unless such URI does not refer to the copyright notice or licensing information for the Work; and, (iv) consistent with Section 3(b), in the case of an
Adaptation, a credit identifying the use of the Work in the Adaptation (e.g., “French translation of the Work by Original Author,” or “Screenplay based on
original Work by Original Author”). The credit required by this Section 4(d) may be implemented in any reasonable manner; provided, however, that in the
case of a Adaptation or Collection, at a minimum such credit will appear, if a credit for all contributing authors of the Adaptation or Collection appears, then
as part of these credits and in a manner at least as prominent as the credits for the other contributing authors. For the avoidance of doubt, You may only
use the credit required by this Section for the purpose of attribution in the manner set out above and, by exercising Your rights under this License, You may
not implicitly or explicitly assert or imply any connection with, sponsorship or endorsement by the Original Author, Licensor and/or Attribution Parties, as
appropriate, of You or Your use of the Work, without the separate, express prior written permission of the Original Author, Licensor and/or Attribution
Parties.
f. For the avoidance of doubt:
i. Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing
scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License;
ii. Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing
scheme can be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License if
Your exercise of such rights is for a purpose or use which is otherwise than noncommercial as permitted under Section 4(b) and otherwise waives the right
to collect royalties through any statutory or compulsory licensing scheme; and,
iii.Voluntary License Schemes. The Licensor reserves the right to collect royalties, whether individually or, in the event that the Licensor is a member of a
collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License that is
for a purpose or use which is otherwise than noncommercial as permitted under Section 4(b).
g. Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform
the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to
the Work which would be prejudicial to the Original Author’s honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any
exercise of the right granted in Section 3(b) of this License (the right to make Adaptations) would be deemed to be a distortion, mutilation, modification or
other derogatory action prejudicial to the Original Author’s honor and reputation, the Licensor will waive or not assert, as appropriate, this Section, to the
fullest extent permitted by the applicable national law, to enable You to reasonably exercise Your right under Section 3(b) of this License (right to make
Adaptations) but not otherwise.',
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#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
''
]
},
GrafoscopioNode {
#header : 'Representations, Warranties and Disclaimer',
#body : 'UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR
WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF
TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE
PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO
SUCH EXCLUSION MAY NOT APPLY TO YOU. ',
#children : OrderedCollection [ ],
#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Limitation on liability',
#body : 'EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL,
INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN
ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. ',
#children : OrderedCollection [ ],
#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Termination',
#body : 'a. This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who
have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities
remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License.
b. Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding
the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that
any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and
this License will continue in full force and effect unless terminated as stated above.
',
#children : OrderedCollection [ ],
#parent : @258,
#level : 3,
#links : OrderedCollection [
'',
'',
'',
''
]
},
GrafoscopioNode {
#header : 'Miscellaneous',
#body : 'a. Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and
conditions as the license granted to You under this License.
b. Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and
conditions as the license granted to You under this License.
c. If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the
terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to
make such provision valid and enforceable.
d. No term or provision of this License shall be deemed waived and no breach consented to unless such waiver or consent shall be in writing and signed by
the party to be charged with such waiver or consent.
e. This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or
representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any
communication from You. This License may not be modified without the mutual written agreement of the Licensor and You.
f. The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the
Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO
Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take
effect in the relevant jurisdiction in which the License terms are sought to be enforced according to the corresponding provisions of the implementation of
those treaty provisions in the applicable national law. If the standard suite of rights granted under applicable copyright law includes additional rights not
granted under this License, such additional rights are deemed to be included in the License; this License is not intended to restrict the license of any rights
under applicable law.',
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#parent : @258,
#level : 3,
#links : OrderedCollection [
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]
}
],
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@263,
@266,
@269,
@272,
@275,
@278,
@281
],
#links : OrderedCollection [
'',
'',
'',
'',
'',
'',
'',
'',
'../../Licenses/documents-p2p-ismb.md'
]
}
],
#parent : @4,
#level : 1,
#links : OrderedCollection [
'',
''
]
},
@254,
@258,
@260,
@263,
@266,
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@272,
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@278,
@281,
GrafoscopioNode {
#header : 'Bibliography',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : '%invisible ',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Quering Zotero collection and exporting as BibTeX',
#body : '"This script updates the bibliography for this document with the latest
available online. Useful if you\'re adding new bibliographic references"
| bibTeXData bibFile bibliography tempStream |
bibTeXData := (ZoteroLibrary new groupID: \'204755\') subcollectionAsBibTeX: \'PHGTCZVT\'.
tempStream := \'\' writeStream.
bibliography := CZBibParser parse: bibTeXData.
bibliography entries do: [ :entry |
\tentry fields second key = \'shorttitle\'
\t\tifTrue: [entry key: entry fields second value ].
\ttempStream nextPutAll: (BibBibRenderer new render: entry) contents].
bibFile := FileLocator home asFileReference / \'Programas\' / \'Grafoscopio\' / \'Repo\' / \'Docs\' / \'En\' / \'Books\' / \'Manual\' / \'bibliography.bib\'.
bibFile exists
\tifTrue: [ bibFile delete ]
\tifFalse: [ bibFile ensureCreateFile ].
bibFile writeStreamDo: [ :stream | stream nextPutAll: tempStream contents ].
bibFile
',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @289,
#level : 3,
#links : OrderedCollection [
'',
'http://ws.stfx.eu/4138G3OYJZ9I'
]
},
GrafoscopioNode {
#header : 'Problems with Pandoc and bibliography',
#body : 'This note is here, to provide context, but it should be moved to the developers notebook.
While running the PDF conversion command:
~~~
pandoc -N --template=mytemplate.tex --variable fontsize=12pt --variable version=1.3.4 --latex-engine=xelatex --toc --bibliography bibliography.bib manual.markdown -o manual.pdf
~~~
I got this error:
~~~
pandoc-citeproc: "stdin" (line 8, column 2):
unexpected "m"
expecting "c", "C", "p", "P", "s" or "S"
CallStack (from HasCallStack):
error, called at src/Text/CSL/Input/Bibtex.hs:113:32 in pandoc-citeproc-0.10.4-Ks7e5k595uURtHUpwsSlk:Text.CSL.Input.Bibtex
pandoc: Error running filter pandoc-citeproc
Filter returned error status 1
~~~
The problem is the way Zotero or Citezen are creating BibTeX entries that contain has a value in the field "Adicional" in the Zotero
library (mi Zotero UI is in Spanish), represented in the exported entry as note: {}.
They should be removed.
May be we should control the fields exported by Citezen, editing or deleting all conflicting fields/characters for pandoc-citeproc. ',
#children : OrderedCollection [ ],
#parent : @289,
#level : 3,
#links : OrderedCollection [
'',
'https://github.com/jgm/pandoc/issues/1034'
]
},
GrafoscopioNode {
#header : 'Old citezen tests',
#body : 'Previously I made some tests with [citezen][citezen] for cleaning the bibliographic references,
but that implementation was abandoned, because it was far too specific.
Now that I\'m implemeting Zotero back end in a more general way, would be nice to retake
the initial citezen experiments.
See/browse children nodes for some details on previos exploration.
[citezen]: (http://people.untyped.org/damien.pollet/software/citezen/)',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Tweet',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Script screenshot zoom',
#body : '',
#children : OrderedCollection [ ],
#parent : @299,
#level : 5,
#links : OrderedCollection [
'',
'https://www.enlightenment.org/ss/e-54454b6c965410.68921158.jpg'
]
}
],
#parent : @297,
#level : 4,
#links : OrderedCollection [
'',
'https://twitter.com/offrayLC/status/524258229875142657'
]
},
GrafoscopioNode {
#header : 'Thread asking for bibtex support',
#body : '',
#children : OrderedCollection [
GrafoscopioNode {
#header : 'Old script',
#body : '| bibFile bibliography bibStream bibOutputer |
bibFile := ((FileLocator documents / \'U/Libertadores/Grafoscopio/Docs/Es/Articulos/Libertadores/\') children
detect: [:each | each basename endsWith: \'bib\' ]).
bibliography := CZBibParser parse: bibFile contents.
bibStream := \'\' writeStream.
(bibliography entries) do: [:bibItem |
\tbibItem fields do: [:some | some key = \'shorttitle\'
\t\tifTrue: [ bibItem key: some value ]].
\tbibOutputer := CZBibTeXDocBuilder new.
\tbibStream nextPutAll:
\t\t\t(bibOutputer entryToBibtexString: bibItem); cr].
bibliography.
bibFile writeStreamDo: [:stream |
stream nextPutAll: bibStream contents withUnixLineEndings ].
bibStream contents.
',
#tags : 'código',
#children : OrderedCollection [ ],
#parent : @305,
#level : 5,
#links : OrderedCollection [
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