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Developers documentation

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Introduction

Pamhyr2 is free and open source software (FOSS) graphical user interface (GUI) for 1D hydro-sedimentary modelling of rivers developed in Python (with version 3.8). It use PyQt at version 5 and matplotlib in version 3.4.1 or later for the user insterface (see {{{file(/requirements.txt)}}} for details). The architecture of project code follow the Qt Model/View architecture [fn:qt-arch] (see details in section Architecture). Pamhyr2 packages can be build manually (see section Building packages), but there are automatically build with the gitlab-ci (see the section <a href=”Setup the CI environment”>Setup the CI environment). Documentation files are written with org-mode[fn:org], let see section Documentation files. Finally, to see the contribution rules, see the section How to contribute?.

[fn:qt-arch] Qt Model/View documentation: https://doc.qt.io/qt-5/model-view-programming.html (last access 2023-09-15) [fn:org] The org-mode website: https://orgmode.org/ (last access 2023-09-15)

Architecture

Model

Solver

View

Unit tests

The debug mode

Build the project

Building packages

Linux

Windows

Setup the CI environment

Documentation files

This document and the user documentation are org files. This text file format is formatted so that it can be exported in different formats: PDF (with latex), ODT, HTML, etc. It was originally designed for the GNUEmacs[fn:emacs] text editor, but can be edited with any text editor. Here we take a look at the different features used in these documents.

[fn:org] The org-mode website: https://orgmode.org/ (last access 2023-09-15) [fn:emacs] The GNUEmacs project website: https://gnu.org/s/emacs/ (last access 2023-09-15)

Org-mode

Document structure

Org uses the * character to define a new document section. To add a sub-section, you can add an additional * to the current section[fn:: See document structure documentation: https://orgmode.org/org.html#Headlines (last access 2023-09-15)].

* Top level headline
** Second level
*** Third level
    some text
*** Third level
    more text
* Another top level headline

Format

Org-mode is a markup file, using markup in the text to modify the appearance of a portion of text[fn:: See markup documentation: https://orgmode.org/org.html#Emphasis-and-Monospace (last access 2023-09-15)].

Markup Results
*Bolt* Bolt
/Italic/ Italic
_underline_ underline
==verbatim== verbatim
~code~ code
+strike-through+ strike-through

Source code blocks

You can add some code blocks[fn:: See org-mode documentation for source code: https://orgmode.org/org.html#Working-with-Source-Code (last access 2023-09-15)] in the document.

Here is an example for python source code:

#+CAPTION: Get os type name in Python code
import os

print(f"Document build on system: {os.name}")

If you use GNUEmacs, it is also possible to run the code inside a block and export (or not) the reuslts in the document.

import os

print(f"Document build on system: {os.name}")
Document build on system: posix

Latex

If we export the file to PDF, org-mode use \LaTeX. So we can add some piece of \LaTeX into the document[fn:: See \LaTeX part in documentation: https://orgmode.org/org.html#Embedded-LaTeX (last access 2023-09-15)]. For exemple, we can add math formula like $E=mc^2$ ($E=mc^2$) or \[E=mc^2\]:

\[E=mc^2\]

But we can also add every type of \LaTeX:

# Add latex in line
#+LATEX: <my line of latex>

# Add multiple line of LaTeX
<my latex here>

It is also possible to add specific \LaTeX file header with #+LATEX_HEADER. In this document we use the file {{{file(doc/tools/latex.org)}}} for all \LaTeX headers.

Macro

In this document, we use a few macros[fn:: See marcos documentation https://orgmode.org/org.html#Macro-Replacement (last access 2023-09-15)] to simplify writing. They allow you to define sequences of text to be replaced, so that the macro name is replaced by its value. They are defined in the {{{file(doc/tools/macro.org)}}} file. Once defined, they can be used in the document as follows: {{{<macro-name>}}}. You can also have macros with arguments, in this case: {{{<macro-name>(arg1,...)}}}. Les macros peuvent aussi utiliser du code emacs-lisp.

# Exemple of macro définition

#+MACRO: toto               tata
#+MACRO: add                \(($1 + $2)\)
#+MACRO: emacs-version      (eval (nth 2 (split-string (emacs-version))))

Macro apply:

  • Marco {{{toto}}}: {{{toto}}}
  • Marco {{{add(x,y)}}}: {{{add(x,y)}}}
  • Marco {{{emacs-version}}}: {{{emacs-version}}}

Footnotes

Footnote in org-mode is define with marker =[fn:…]=[fn:: Create footnotes in org-mode documentation https://orgmode.org/org.html#Creating-Footnotes (last access 2023-09-15)]:

The Org website[fn:1] now looks a lot better than it used to.
...
[fn:1] The link is: https://orgmode.org

or:

The Org website[fn:: The link is: https://orgmode.org] now looks
a lot better than it used to.
...

References

The references use the \LaTeX bibtex tools. The bib file is in {{{file(/doc/tools/ref.bib)}}} and use for developers and user documentation. In document, use {{{cite(<name>)}}} to cite a paper.

Export

To export the files, a {{{build.sh}}} script is available in the org files directories. On GNU/Linux system you can build the documentation PDF file with the command ./build.sh. Some org-mode configuration used in documentations files are define in /doc/tools/:

  • {{{file(PamhyrDoc.cls)}}}: The \LaTeX theme
  • {{{file(macro.org)}}}: Available macro
  • {{{file(latex.org)}}}: \LaTeX configutation for documentations files
  • {{{file(setup.el)}}}: GNUEmacs configuration to build documentations
  • {{{file(ref.bib)}}}: Bibtex files for documentations files

How to contribute?

Contribution rules

Translate

Code contribution

{{{biblio}}}