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Nearly complete pass through chap 3

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Burkhart Wolff 2020-09-16 14:24:39 +02:00
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examples/technical_report/Isabelle_DOF-Manual/03_GuidedTour.thy
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@ -106,8 +106,8 @@ text\<open>
%ë\prompt{}ë sudo aptitude install texlive-latex-extra texlive-fonts-extra %ë\prompt{}ë sudo aptitude install texlive-latex-extra texlive-fonts-extra
%\<close>} %\<close>}
Please check that this, indeed, installs a version of \<^pdftex> that supports the Please check that this really installs a version of \<^pdftex> that supports the
\<^boxed_latex>\<open>\expanded\<close>. To check your \<^pdftex>-binary, execute \<^boxed_latex>\<open>\expanded\<close>. To check your \<^pdftex>-binary, execute:
\begin{bash} \begin{bash}
ë\prompt{}ë pdftex \\expanded{Success}\\end ë\prompt{}ë pdftex \\expanded{Success}\\end
@ -237,7 +237,7 @@ Usage: isabelle mkroot_DOF [OPTIONS] [DIR]
\<^item> which document template (layout)\index{document template} should be used \<^item> which document template (layout)\index{document template} should be used
(\<^eg>, scrartcl\index{scrartcl}). Some templates (\<^eg>, lncs) require that the users manually (\<^eg>, scrartcl\index{scrartcl}). Some templates (\<^eg>, lncs) require that the users manually
obtains and adds the necessary \<^LaTeX> class file (\<^eg>, \inlinebash|llncs.cls|. obtains and adds the necessary \<^LaTeX> class file (\<^eg>, \inlinebash|llncs.cls|.
This is mostly due to licensing restrictions. This is due to licensing restrictions).
\<close> \<close>
text\<open> text\<open>
If you are happy with the defaults, \ie, using the ontology for writing academic papers If you are happy with the defaults, \ie, using the ontology for writing academic papers
@ -291,14 +291,14 @@ users are:
\<^LaTeX>-packages or to add/modify \<^LaTeX>-commands. \<^LaTeX>-packages or to add/modify \<^LaTeX>-commands.
\<close> \<close>
section*[scholar_onto::example]\<open>Writing Academic Publications in \<^boxed_theory_text>\<open>scholarly_paper\<close>)\<close> section*[scholar_onto::example]\<open>Writing Academic Publications in \<^boxed_theory_text>\<open>scholarly_paper\<close>\<close>
subsection\<open>Papers in freeform-style\<close> subsection\<open>Papers in freeform-style\<close>
text\<open> text\<open>
The ontology \<^boxed_theory_text>\<open>scholarly_paper\<close> The ontology \<^boxed_theory_text>\<open>scholarly_paper\<close>
\<^index>\<open>ontology!scholarly\_paper\<close> is an ontology modeling \<^index>\<open>ontology!scholarly\_paper\<close> is an ontology modeling
academic/scientific papers, with a slight bias to texts in the domain of mathematics and engineering. academic/scientific papers, with a slight bias to texts in the domain of mathematics and engineering.
We explain first the principles of its underlying ontology, and then we present two ''real'' We explain first the principles of its underlying ontology, and then we present two ''real''
example instances of our own. examples from our own publication practice.
\<close> \<close>
text\<open> text\<open>
\<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text, \<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text,
@ -324,8 +324,7 @@ text\<open>
\begin{bash} \begin{bash}
ë\prompt{\isadofdirn}ë ë\prompt{\isadofdirn}ë
isabelle jedit examples/scholarly_paper/2018-cicm-isabelle_dof-applications/\ isabelle jedit -d . examples/scholarly_paper/2020-iFM-CSP/paper.thy
IsaDofApplications.thy
\end{bash} \end{bash}
\<close> \<close>
(* We should discuss if we shouldn't put the iFM paper more in the foreground *) (* We should discuss if we shouldn't put the iFM paper more in the foreground *)
@ -333,8 +332,7 @@ text\<open>
text\<open> You can build the PDF-document at the command line by calling: text\<open> You can build the PDF-document at the command line by calling:
@{boxed_bash [display] @{boxed_bash [display]
\<open>ë\prompt{}ë isabelle build \ \<open>ë\prompt{}ë isabelle build -d . 2020-iFM-csp \<close>}
2018-cicm-isabelle_dof-applications\<close>}
\<close> \<close>
subsection*[sss::technical]\<open>A Bluffers Guide to the \<^verbatim>\<open>scholarly_paper\<close> Ontology\<close> subsection*[sss::technical]\<open>A Bluffers Guide to the \<^verbatim>\<open>scholarly_paper\<close> Ontology\<close>
@ -343,7 +341,7 @@ text\<open> In this section we give a minimal overview of the ontology formalize
text\<open> We start by modeling the usual text-elements of an academic paper: the title and author text\<open> We start by modeling the usual text-elements of an academic paper: the title and author
information, abstract, and text section: information, abstract, and text section:
@{theory_text [display] @{boxed_theory_text [display]
\<open>doc_class title = \<open>doc_class title =
short_title :: "string option" <= "None" short_title :: "string option" <= "None"
@ -374,7 +372,7 @@ the document class definition \<open>author\<close> shown above. It is used to e
``owns'' this \<open>text_section\<close>, an information that can give rise to presentational or even ``owns'' this \<open>text_section\<close>, an information that can give rise to presentational or even
access-control features in a suitably adapted front-end. access-control features in a suitably adapted front-end.
@{theory_text [display] \<open> @{boxed_theory_text [display] \<open>
doc_class text_section = text_element + doc_class text_section = text_element +
main_author :: "author option" <= None main_author :: "author option" <= None
fixme_list :: "string list" <= "[]" fixme_list :: "string list" <= "[]"
@ -408,16 +406,17 @@ paper focussing on its form, not refering in any sense to its content which is o
As mentioned before, we chose the paper~@{cite "taha.ea:philosophers:2020"} for this purpose, As mentioned before, we chose the paper~@{cite "taha.ea:philosophers:2020"} for this purpose,
which is written in the so-called free-form style: Formulas are superficially parsed and which is written in the so-called free-form style: Formulas are superficially parsed and
type-setted, but no deeper type-checking and checking with the underlying logical context type-setted, but no deeper type-checking and checking with the underlying logical context
is undertaken. is undertaken. \<close>
The corpus of the paper beginning looks like this (the setup sequence is described later). \<close> figure*[fig0::figure,spawn_columns=False,relative_width="90",src="''figures/header_CSP_source.png''"]
\<open> A mathematics paper as integrated document source ... \<close>
figure*[fig0::figure,spawn_columns=False,relative_width="95",src="''figures/header_CSP_source.png''"] figure*[fig0B::figure,spawn_columns=False,relative_width="90",src="''figures/header_CSP_pdf.png''"]
\<open> A mathematics paper as a document source ... \<close> \<open> \ldots and as corresponding \<^pdf>-output. \<close>
text\<open>The document build process converts this to the following \<^pdf>-output:\<close>
text\<open>The integrated source of this paper-except is shown in \<^figure>\<open>fig0\<close>, while the
document build process converts this to the corresponding \<^pdf>-output shown in \<^figure>\<open>fig0B\<close>.\<close>
figure*[fig0B::figure,spawn_columns=False,relative_width="95",src="''figures/header_CSP_pdf.png''"]
\<open> \ldots and as its resulting \<^pdf>-output. \<close>
text\<open>Recall that the standard syntax for a text-element in \<^isadof> is text\<open>Recall that the standard syntax for a text-element in \<^isadof> is
\<^theory_text>\<open>text*[<id>::<class_id>,<attrs>]\<open> ... text ...\<close>\<close>, but there are a few built-in abbreviations like \<^theory_text>\<open>text*[<id>::<class_id>,<attrs>]\<open> ... text ...\<close>\<close>, but there are a few built-in abbreviations like
@ -426,10 +425,11 @@ The other text-elements provide the authors and the abstract as specified by the
to the \<^theory_text>\<open>doc_class\<close>es of \<^verbatim>\<open>scholarly_paper\<close>; we say that these text elements are \<^emph>\<open>instances\<close> to the \<^theory_text>\<open>doc_class\<close>es of \<^verbatim>\<open>scholarly_paper\<close>; we say that these text elements are \<^emph>\<open>instances\<close>
\<^bindex>\<open>instance\<close> of the \<^theory_text>\<open>doc_class\<close>es \<^bindex>\<open>doc\_class\<close> of the underlying ontology. \<close> \<^bindex>\<open>instance\<close> of the \<^theory_text>\<open>doc_class\<close>es \<^bindex>\<open>doc\_class\<close> of the underlying ontology. \<close>
text\<open>The paper proceeds by providing instances for introduction, technical sections, examples, \<^etc>. text\<open>\vspace{1,5cm} The paper proceeds by providing instances for introduction, technical sections,
We would like to concentrate on one --- mathematical paper oriented --- detail in the ontology examples, \<^etc>. We would like to concentrate on one --- mathematical paper oriented --- detail in the
\<^verbatim>\<open>scholarly_paper\<close>: ontology \<^verbatim>\<open>scholarly_paper\<close>:
@{theory_text [display]
@{boxed_theory_text [display]
\<open>doc_class technical = text_section + . . . \<open>doc_class technical = text_section + . . .
type_synonym tc = technical (* technical content *) type_synonym tc = technical (* technical content *)
@ -472,7 +472,7 @@ accepts any offered event, wheras \<open>CHAOS\<^sub>S\<^sub>K\<^sub>I\<^sub>P\<
(* alternative *) (* alternative *)
figure*[fig01::figure,spawn_columns=False,relative_width="95",src="''figures/definition-use-CSP.png''"] figure*[fig01::figure,spawn_columns=False,relative_width="95",src="''figures/definition-use-CSP.png''"]
\<open> A screenshot of the integrated source with Definitions ...\<close> \<open> A screenshot of the integrated source with definitions ...\<close>
text\<open>An example for a sequence of (Isabelle-formula-) texts, their ontological declarations as text\<open>An example for a sequence of (Isabelle-formula-) texts, their ontological declarations as
\<open>"definition"\<close>s in terms of the \<^verbatim>\<open>scholarly_paper\<close>-ontology and their type-conform referencing \<open>"definition"\<close>s in terms of the \<^verbatim>\<open>scholarly_paper\<close>-ontology and their type-conform referencing
later is shown in \<^figure>\<open>fig01\<close> in its presentation as the integrated source. later is shown in \<^figure>\<open>fig01\<close> in its presentation as the integrated source.
@ -494,7 +494,9 @@ We refrain ourselves here to briefly describe three freeform antiquotations used
or just \<^verbatim>\<open>\<^theory_text> \<open>...\<close>\<close> if the list of style parameters or just \<^verbatim>\<open>\<^theory_text> \<open>...\<close>\<close> if the list of style parameters
is empty, is empty,
\<^item> the freeform antiquotations for verbatim, emphasized, bold, or footnote text elements. \<^item> the freeform antiquotations for verbatim, emphasized, bold, or footnote text elements.
\<close>
text\<open>
\<^isadof> text-elements such as \<^theory_text>\<open>text*\<close> allow to have such standard term-antiquotations inside their \<^isadof> text-elements such as \<^theory_text>\<open>text*\<close> allow to have such standard term-antiquotations inside their
text, permitting to give the whole text entity a formal, referentiable status with typed meta- text, permitting to give the whole text entity a formal, referentiable status with typed meta-
information attached to it that may be used for presentation issues, search, or other technical information attached to it that may be used for presentation issues, search, or other technical
@ -507,8 +509,7 @@ figure*[fig02::figure,spawn_columns=False,relative_width="95",src="''figures/def
text\<open>The corresponding output of this snippet in the integrated source is shown in\<^figure>\<open>fig02\<close>. \<close> text\<open>The corresponding output of this snippet in the integrated source is shown in\<^figure>\<open>fig02\<close>. \<close>
subsection*[scholar_pide::example]\<open>More Freeform Elements, and Resulting Navigation\<close>
subsection\<open>More Freeform Publication Elements\<close>
(* (*
figure*[fig1::figure,spawn_columns=False,relative_width="95",src="''figures/Dogfood-Intro''"] figure*[fig1::figure,spawn_columns=False,relative_width="95",src="''figures/Dogfood-Intro''"]
\<open> Ouroboros I: This paper from inside \ldots \<close> \<open> Ouroboros I: This paper from inside \ldots \<close>
@ -558,7 +559,7 @@ doc_class figure = text_section +
\<close>} \<close>}
\<close> \<close>
figure*[fig_figures::figure,spawn_columns=False,relative_width="85",src="''figures/Dogfood-figures''"] figure*[fig_figures::figure,spawn_columns=False,relative_width="85",src="''figures/Dogfood-figures''"]
\<open> Ouroboros II: figures \ldots \<close> \<open> Declaring figures in the integrated source \ldots \<close>
text\<open> text\<open>
The document class \<^boxed_theory_text>\<open>figure\<close> (supported by the \<^isadof> command abbreviation The document class \<^boxed_theory_text>\<open>figure\<close> (supported by the \<^isadof> command abbreviation
@ -587,11 +588,11 @@ text\<open>
close_monitor*[this] close_monitor*[this]
\<close>} \<close>}
which signals to \<^isadof> begin and end of the part of the integrated document which signals to \<^isadof> begin and end of the part of the integrated source
in which the text-elements are expected to appear in a fixed ontological ordering. in which the text-elements instances are expected to appear in the textual ordering
defined by \<^theory_text>\<open>article\<close>.
\<close> \<close>
subsection*[scholar_pide::example]\<open>Navigation Support induced by an Ontology\<close>
side_by_side_figure*[exploring::side_by_side_figure,anchor="''fig-Dogfood-II-bgnd1''", side_by_side_figure*[exploring::side_by_side_figure,anchor="''fig-Dogfood-II-bgnd1''",
caption="''Exploring a reference of a text-element.''",relative_width="48", caption="''Exploring a reference of a text-element.''",relative_width="48",
@ -604,7 +605,7 @@ side_by_side_figure*["hyperlinks"::side_by_side_figure,anchor="''fig:Dogfood-IV-
caption="''Hyperlink to class-definition.''",relative_width="48", caption="''Hyperlink to class-definition.''",relative_width="48",
src="''figures/Dogfood-IV-jumpInDocCLass''",anchor2="''fig:Dogfood-V-attribute''", src="''figures/Dogfood-IV-jumpInDocCLass''",anchor2="''fig:Dogfood-V-attribute''",
caption2="''Exploring an attribute.''",relative_width2="47", caption2="''Exploring an attribute.''",relative_width2="47",
src2="''figures/Dogfood-III-bgnd-text_section''"]\<open> Hyperlinks.\<close> src2="''figures/Dogfood-III-bgnd-text_section''"]\<open>Navigation via generated hyperlinks.\<close>
text\<open> text\<open>
From these class definitions, \<^isadof> also automatically generated editing From these class definitions, \<^isadof> also automatically generated editing
support for Isabelle/jedit. In \autoref{fig-Dogfood-II-bgnd1} and support for Isabelle/jedit. In \autoref{fig-Dogfood-II-bgnd1} and
@ -620,11 +621,11 @@ figure*[figDogfoodVIlinkappl::figure,relative_width="80",src="''figures/Dogfood-
\<open> Exploring an attribute (hyperlinked to the class). \<close> \<open> Exploring an attribute (hyperlinked to the class). \<close>
text\<open> text\<open>
An ontological reference application in @{figure "figDogfoodVIlinkappl"}: the An ontological reference application in @{figure "figDogfoodVIlinkappl"}: the
ontology-dependant antiquotation \<^boxed_theory_text>\<open>@ {example ...}\<close> refers to the corresponding ontology-dependant antiquotation \<^boxed_theory_text>\<open>@ {example ...}\<close> refers to the corresponding
text-elements. Hovering allows for inspection, clicking for jumping to the definition. If the text-elements. Hovering allows for inspection, clicking for jumping to the definition. If the
link does not exist or has a non-compatible type, the text is not validated. link does not exist or has a non-compatible type, the text is not validated,\<^ie>, Isabelle/jEdit
\<close> will respond with an error.\<close>
section*[cenelec_onto::example]\<open>Writing Certification Documents (CENELEC\_50128)\<close> section*[cenelec_onto::example]\<open>Writing Certification Documents (CENELEC\_50128)\<close>
subsection\<open>The CENELEC 50128 Example\<close> subsection\<open>The CENELEC 50128 Example\<close>
@ -632,8 +633,8 @@ text\<open>
The ontology ``CENELEC\_50128''\index{ontology!CENELEC\_50128} is a small ontology modeling The ontology ``CENELEC\_50128''\index{ontology!CENELEC\_50128} is a small ontology modeling
documents for a certification following CENELEC 50128~@{cite "boulanger:cenelec-50128:2015"}. documents for a certification following CENELEC 50128~@{cite "boulanger:cenelec-50128:2015"}.
The \<^isadof> distribution contains a small example using the ontology ``CENELEC\_50128'' in The \<^isadof> distribution contains a small example using the ontology ``CENELEC\_50128'' in
the directory \nolinkurl{examples/CENELEC_50128/mini_odo/}. You can inspect/edit the example the directory \nolinkurl{examples/CENELEC_50128/mini_odo/}. You can inspect/edit the
in Isabelle's IDE, by either integrated source example by either
\<^item> starting Isabelle/jedit using your graphical user interface (\<^eg>, by clicking on the \<^item> starting Isabelle/jedit using your graphical user interface (\<^eg>, by clicking on the
Isabelle-Icon provided by the Isabelle installation) and loading the file Isabelle-Icon provided by the Isabelle installation) and loading the file
\nolinkurl{examples/CENELEC_50128/mini_odo/mini_odo.thy}. \nolinkurl{examples/CENELEC_50128/mini_odo/mini_odo.thy}.
@ -644,9 +645,8 @@ text\<open>
isabelle jedit examples/CENELEC_50128/mini_odo/mini_odo.thy isabelle jedit examples/CENELEC_50128/mini_odo/mini_odo.thy
\end{bash} \end{bash}
\<close> \<close>
text\<open> text\<open>\<^noindent> Finally, you
You can build the PDF-document by calling: \<^item> can build the PDF-document by calling:
\begin{bash} \begin{bash}
ë\prompt{}ë isabelle build mini_odo ë\prompt{}ë isabelle build mini_odo
\end{bash} \end{bash}
@ -656,17 +656,18 @@ subsection\<open>Modeling CENELEC 50128\<close>
text\<open> text\<open>
Documents to be provided in formal certifications (such as CENELEC Documents to be provided in formal certifications (such as CENELEC
50128~@{cite "boulanger:cenelec-50128:2015"} or Common Criteria~@{cite "cc:cc-part3:2006"}) can 50128~@{cite "boulanger:cenelec-50128:2015"} or Common Criteria~@{cite "cc:cc-part3:2006"}) can
much profit from the control of ontological consistency: a lot of an evaluators work consists in much profit from the control of ontological consistency: a substantial amount of the work
tracing down the links from requirements over assumptions down to elements of evidence, be it in of evaluators in formal certification processes consists in tracing down the links from
the models, the code, or the tests. In a certification process, traceability becomes a major requirements over assumptions down to elements of evidence, be it in form of semi-formal
documentation, models, code, or tests. In a certification process, traceability becomes a major
concern; and providing mechanisms to ensure complete traceability already at the development of concern; and providing mechanisms to ensure complete traceability already at the development of
the global document will clearly increase speed and reduce risk and cost of a certification the integrated source can in our view increase the speed and reduce the risk certification
process. Making the link-structure machine-checkable, be it between requirements, assumptions, processes. Making the link-structure machine-checkable, be it between requirements, assumptions,
their implementation and their discharge by evidence (be it tests, proofs, or authoritative their implementation and their discharge by evidence (be it tests, proofs, or authoritative
arguments), is therefore natural and has the potential to decrease the cost of developments arguments), has the potential in our view to decrease the cost of software developments
targeting certifications. Continuously checking the links between the formal and the semi-formal targeting certifications. Note that continuously checking the links between the formal and the
parts of such documents is particularly valuable during the (usually collaborative) development semi-formal parts of such documents is particularly valuable during the development,
effort. which is usually a collaborative effort.
As in many other cases, formal certification documents come with an own terminology and pragmatics As in many other cases, formal certification documents come with an own terminology and pragmatics
of what has to be demonstrated and where, and how the trace-ability of requirements through of what has to be demonstrated and where, and how the trace-ability of requirements through
@ -726,7 +727,7 @@ We now can, \<^eg>, write
@{boxed_theory_text [display]\<open> @{boxed_theory_text [display]\<open>
text*[ass123::SRAC]\<open> text*[ass123::SRAC]\<open>
The overall sampling frequence of the odometer subsystem is therefore The overall sampling frequence of the odometer subsystem is therefore
14 khz, which includes sampling, computing a$$nd result communication 14 khz, which includes sampling, computing and result communication
times \ldots times \ldots
\<close> \<close>
\<close>} \<close>}
@ -737,6 +738,8 @@ text*[ass123::SRAC] \<open> The overall sampling frequence of the odometer
subsystem is therefore 14 khz, which includes sampling, computing and subsystem is therefore 14 khz, which includes sampling, computing and
result communication times \ldots \<close> result communication times \ldots \<close>
text\<open>Note that this pdf-output is the result of a specific setup for "SRAC"s.\<close>
subsection*[ontopide::technical]\<open>Editing Support for CENELEC 50128\<close> subsection*[ontopide::technical]\<open>Editing Support for CENELEC 50128\<close>
figure*[figfig3::figure,relative_width="95",src="''figures/antiquotations-PIDE''"] figure*[figfig3::figure,relative_width="95",src="''figures/antiquotations-PIDE''"]
\<open> Standard antiquotations referring to theory elements.\<close> \<open> Standard antiquotations referring to theory elements.\<close>
@ -746,14 +749,14 @@ conformimg to the CENELEC 50128 ontology. The first sample shows standard Isabel
of a document get ``formal content'' and become more robust under change.\<close> of a document get ``formal content'' and become more robust under change.\<close>
figure*[figfig5::figure, relative_width="95", src="''figures/srac-definition''"] figure*[figfig5::figure, relative_width="95", src="''figures/srac-definition''"]
\<open> Defining a SRAC reference \ldots \<close> \<open> Defining a "SRAC" in the integrated source \ldots \<close>
figure*[figfig7::figure, relative_width="95", src="''figures/srac-as-es-application''"] figure*[figfig7::figure, relative_width="95", src="''figures/srac-as-es-application''"]
\<open> Using a SRAC as EC document reference. \<close> \<open> Using a "SRAC" as "EC" document element. \<close>
text\<open> The subsequent sample in @{docitem \<open>figfig5\<close>} shows the definition of an text\<open> The subsequent sample in @{figure \<open>figfig5\<close>} shows the definition of an
\<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which \<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which
has the consequence that a certain calculation must be executed sufficiently fast on an embedded has the consequence that a certain calculation must be executed sufficiently fast on an embedded
device. This condition can not be established inside the formal theory but has to be device. This condition can not be established inside the formal theory but has to be
checked by system integration tests. Now we reference in @{docitem \<open>figfig7\<close>} this checked by system integration tests. Now we reference in @{figure \<open>figfig7\<close>} this
safety-related condition; however, this happens in a context where general \<^emph>\<open>exported constraints\<close> safety-related condition; however, this happens in a context where general \<^emph>\<open>exported constraints\<close>
are listed. \<^isadof>'s checks establish that this is legal in the given ontology. are listed. \<^isadof>'s checks establish that this is legal in the given ontology.
\<close> \<close>
@ -883,6 +886,16 @@ students but just additional material for the internal review process of the exa
*) *)
section*[tech_onto::example]\<open>Writing Technical Reports in \<^boxed_theory_text>\<open>technical_report\<close>\<close>
text\<open>While it is perfectly possible to write documents in the
\<^boxed_theory_text>\<open>technical_report\<close> ontologie in freeform-style (the present manual is mostly an
example for this category), we will briefly explain here the tight-checking-style in which
most Isabelle reference manuals themselves are written. \<close>
subsection\<open>Papers in tight-checking-style\<close>
text\<open>TODO: Write high-level on more text antiquotations and The Isabelle Programming Manual.\<close>
section\<open>Style Guide\<close> section\<open>Style Guide\<close>
text\<open> text\<open>
The document generation process of \<^isadof> is based on Isabelle's document generation framework, The document generation process of \<^isadof> is based on Isabelle's document generation framework,