Isabelle_DOF/README.md

# [Isabelle/DOF](https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF): Document Preparation Setup

Isabelle/DOF is a novel Document Ontology Framework on top of Isabelle.
Isabelle/DOF allows for both conventional typesetting as well as formal
development. The manual for [Isabelle/DOF 1.2.0/Isabelle2021 is available 
online.](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.pdf)

## Pre-requisites

Isabelle/DOF has three major pre-requisites:

* **Isabelle:** Isabelle/DOF requires [Isabelle 2021-1](http://isabelle.in.tum.de/website-Isabelle2021-1/).
  Please download the Isabelle 2021-1 distribution for your operating
  system from the [Isabelle
  website](http://isabelle.in.tum.de/website-Isabelle2021-1/).
* **AFP:** Isabelle/DOF requires two entries from the [Archive of
  Formal Proofs (AFP)](https://www.isa-afp.org/). Please install the 
  AFP following the instructions given at
  <https://www.isa-afp.org/using.html>. For your convenience, we also
  provide a script that only installs the two entries required by
  Isabelle/DOF into the local Isabelle/DOF directory. You can use this 
  script as follows:
  ```console
  foo@bar:~$ isabelle env ./install-afp
  ```  
* **LaTeX:** Isabelle/DOF requires a modern LaTeX installation, i.e., at least 
  [TeX Live 2022](https://www.tug.org/texlive/) with all available updates applied.
  
## Installation

Isabelle/DOF is provided as a Isabelle component. After installing the
pre-requisites the Isabelle/Archive needs to be unpacked and
registered.  Change into the directory you unpacked Isabelle/DOF (this
should be the directory containing this `README.md` file) and execute

```console
foo@bar:~$ isabelle components -u `pwd`
```

The final step for the installation is:

```console
foo@bar:~$ isabelle build -D .
```

This will compile Isabelle/DOF and run the example suite.

## Usage

### Opening an Example

If you want to work with or extend one of the examples, e.g., you can
open it similar to any standard Isabelle theory:

```console
isabelle jedit -d . -l Isabelle_DOF examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
```

This will open an example of a scientific paper using the pre-compiled
session ``Isabelle_DOF``, i.e., you will not be able to edit the
ontology definitions. If you want to edit the ontology definition,
just open the theory file with the default HOL session:

```console
isabelle jedit -d . -l HOL examples/scholarly_paper/2018_cicm/IsaDofApplications.thy
```

While this gives you more flexibility, it might "clutter" your editing
experience, as a lot of internal theories are loaded into Isabelle's
editor.

### Creating a New Project

The DOF-plugin provides an alternative to Isabelle's ``mkroot`` command.
Isabelle projects that use DOF need to be created using

```console
foo@bar:~$ isabelle mkroot_DOF
```

The ``mkroot_DOF`` command takes the same parameter as the standard
``mkroot`` command of Isabelle. Thereafter, the normal Isabelle
command for building documents can be used.

Using the ``-o`` option, different ontology setups can be
selected and using the ``-t`` option, different LaTeX setups 
can be selected. For example,

```console
foo@bar:~$ isabelle mkroot_DOF -o scholarly_paper -t scrartcl
```

creates a setup using the scholarly_paper ontology and the article
class from the KOMA-Script bundle.

The help (option ``-h``) show a list of all supported ontologies and
document templates:

```console
foo@bar:~$ isabelle mkroot_DOF -h

Usage: isabelle mkroot_DOF [OPTIONS] [DIR]

  Options are:
    -h           print this help text and exit
    -n NAME      alternative session name (default: DIR base name)
    -o ONTOLOGY  (default: scholarly_paper)
       Available ontologies:
       * cenelec_50128
       * mathex
       * scholarly_paper
    -t TEMPLATE   (default: scrartcl)
       Available document templates:
       * lncs
       * scrartcl
       * scrreprt
       * scrreprt-modern

  Prepare session root DIR (default: current directory).
```

## Releases

For releases, signed archives including a PDF version of the Isabelle/DOF manual are
are available:

* Isabelle/DOF 1.2.0/Isabelle2021
  * [Isabelle_DOF-1.2.0_Isabelle2021.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.pdf)
  * [Isabelle_DOF-1.2.0_Isabelle2021.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.tar.xz)
  * [Isabelle_DOF-1.2.0_Isabelle2021.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.2.0_Isabelle2021.tar.xz.asc)
* Isabelle/DOF 1.1.0/Isabelle2021
  * [Isabelle_DOF-1.1.0_Isabelle2021.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.pdf)
  * [Isabelle_DOF-1.1.0_Isabelle2021.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.tar.xz)
  * [Isabelle_DOF-1.1.0_Isabelle2021.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2021.tar.xz.asc)
* Isabelle/DOF 1.1.0/Isabelle2020
  * [Isabelle_DOF-1.1.0_Isabelle2020.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.pdf)
  * [Isabelle_DOF-1.1.0_Isabelle2020.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.tar.xz)
  * [Isabelle_DOF-1.1.0_Isabelle2020.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.1.0_Isabelle2020.tar.xz.asc)
* Isabelle/DOF 1.0.0/Isabelle2019
  * [Isabelle_DOF-1.0.0_Isabelle2019.pdf](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.pdf)
  * [Isabelle_DOF-1.0.0_Isabelle2019.tar.xz](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.tar.xz)
  * [Isabelle_DOF-1.0.0_Isabelle2019.tar.xz.asc](https://artifacts.logicalhacking.com/releases/Isabelle_DOF/Isabelle_DOF/Isabelle_DOF-1.0.0_Isabelle2019.tar.xz.asc)

## Team

Main contacts:

* [Achim D. Brucker](http://www.brucker.ch/)
* [Burkhart Wolff](https://www.lri.fr/~wolff/)

### Contributors

* Idir Ait-Sadoune
* Paolo Crisafulli
* Chantal Keller
* Nicolas Méric 

## License

This project is licensed under a 2-clause BSD license.

SPDX-License-Identifier: BSD-2-Clause

## Publications

* Achim D. Brucker, Idir Ait-Sadoune, Paolo Crisafulli, and Burkhart
  Wolff. [Using The Isabelle Ontology Framework: Linking the Formal
  with the Informal](https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf).
  In Conference on Intelligent Computer Mathematics (CICM). Lecture
  Notes in Computer Science (11006), Springer-Verlag, 2018.
  [doi:10.1007/978-3-319-96812-4_3](https://doi.org/10.1007/978-3-319-96812-4_3).

* Achim D. Brucker and Burkhart Wolff. [Isabelle/DOF: Design and
  Implementation](https://www.brucker.ch/bibliography/download/2019/brucker.ea-isabelledof-2019.pdf).
  In Software Engineering and Formal Methods (SEFM). Lecture Notes in
  Computer Science (11724), Springer-Verlag, 2019.
  [doi:10.1007/978-3-030-30446-1_15](https://doi.org/10.1007/978-3-030-30446-1_15).

* Achim D. Brucker, Burkhart Wolff. [Using Ontologies in Formal Developments Targeting Certification](https://www.brucker.ch/bibliography/download/2019/brucker.ea-ontologies-certification-2019.pdf). In 
  Integrated Formal Methods (IFM). Lecture Notes in Computer Science (11918). Springer-Verlag 2019.
  [doi:10.1007/978-3-030-34968-4_4](http://dx.doi.org/10.1007/978-3-030-34968-4_4)  

* Sergio Bezzecchi, Paolo Crisafulli, Charlotte Pichot, and Burkhart Wolff. [Making Agile Development 
  Processes fit for V-style Certification Procedures.](https://hal.archives-ouvertes.fr/hal-01702815/document)
   In ERTS 2018. <https://hal.archives-ouvertes.fr/hal-01702815>

## Upstream Repository

The upstream git repository, i.e., the single source of truth, for this project is hosted
at <https://git.logicalhacking.com/Isabelle_DOF/Isabelle_DOF>.