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public

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[submodule "hugo-mus-theme"]
path = hugo-mus-theme
url = https://forge.s1gm4.eu/sortion/hugo-mus-theme.git

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# org-blog
# [blog.samuel.ortion.fr](https://blog.samuel.ortion.fr/)
My Emacs/Org-Mode powered blog
A Hugo powered blog.

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---
title: "{{ replace .Name "-" " " | title }}"
date: {{ .Date }}
draft: true
---

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---
baseURL: 'https://blog.samuel.ortion.fr/'
languageCode: en-us
title: A blog from a juvenile Geekus biologicus
theme: 'mus'
paginate: 10
params:
author: Samuel Ortion
email: samuel@ortion.fr
avatar: /images/me.png
description: ""
# Uncomment if you need this
# images:
# - images/og-featured.png # relative path to "static" directory
# customCSS:
# - css/my.css # relative path to "assets" directory (don't use main.css filename)
# customJS:
# - js/main.js # relative path to "assets" directory
dateFormat: "2006-01-02"
paginationSinglePost: true
style: light-without-switcher
mainSections: [ "posts" ] # which sections should be on index/main page
sectionsWithFullContentOnListPage: [ "notes" ] # for which sections content should be displayed on list pages
readMore: false # show read more button
readNextPosts: 5 # show 5 related posts, 0 by default
disableSummary: false
toc: true # display Table of Contents
tocWordCount: 300 # ...when a post is longer than 300 words
copyCodeButton: true # true by default
rssAsSocialIcon: true
mathjax: true # https://www.mathjax.
languages:
fr:
languagedirection: fr
title: Le blog d'un <i>Geekus biologicus</i> juvénile
weight: 1
en:
title: The blog of a juvenile <i>Geekus biologicus</i>
languagedirection: en
weight: 2
markup:
highlight:
style: nord
goldmark:
renderer:
unsafe: true # enable raw HTML in Markdown
extensions:
passthrough:
delimiters:
block:
- - \[
- \]
- - $$
- $$
inline:
- - \(
- \)
- - $
- $
enable: true
params:
math: true
repo: https://forge.s1gm4.eu/sortion/blog/
# mediaTypes:
# text/gemini:
# suffixes:
# - "gmi"
outputFormats:
# GEMINI:
# name: GEMINI
# isPlainText: true
# isHTML: false
# mediatype: text/gemini
# protocol: "gemini://"
# permalinkable: true
outputs:
home: ["HTML", "RSS", "GEMINI"]
page: ["HTML", "GEMINI"]

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---
title: Analyse Sound on GNU/Linux using Wine
author: Samuel Ortion
date: 2021-03-25
tags: [audio, bat, bird, ultrasound, syrinx, batsound]
lang: en
---
After recording bats, orthoptera or birds, it is often necesserary to see the spectrograms of the sounds, for instance while analysing [Vigie-Chiro Program](http://www.vigienature.fr/fr/chauves-souris) bat records
The software needed to do so are often only for Windows, in the present article, we will learn how to install these softwares (i.e. Kaleidoscope, Syrinx, Batsound 4, 7-zip, Lupas-Rename).
Install Wine
------------
Wine is a software that enable .exe software to run on UNIX systems such as Linux or Mac OS.
### On Debian and derivatives (Ubuntu...)
Enable 32 bit packages (if you haven't already):
```bash
sudo dpkg --add-architecture i386
```
Download and install the repository key:
```bash
wget -nc https://dl.winehq.org/wine-builds/winehq.key
sudo apt-key add winehq.key
```
Add the repository to /etc/apt/sources.list or create a wine.list under /etc/apt/sources.list.d/ with the following content:
```textile
deb https://dl.winehq.org/wine-builds/debian/ buster main
```
Update packages
```bash
sudo apt update
```
Install Wine stable
```bash
sudo apt install --install-recommends winehq-stable
```
### On Fedora, RHEL, and derivatives
Add repository :
```bash
dnf config-manager --add-repo https://dl.winehq.org/wine-builds/fedora/33/winehq.repo
```
Install stable package :
```bash
dnf install winehq-stable
```
Install Kaleidoscope
--------------------
Kaleidoscope is available on both fedora and debian based distros at [wildlife acoustics](https://www.wildlifeacoustics.com/).
Install Syrinx
--------------
As all following softwares, Syrinx is not available for GNU/Linux, we need Wine to execute the `.exe`.
Syrinx-PC is available at [Google Drive](https://drive.google.com/file/d/0B5ZM90wrDzUOM0ZfYlpDR2l1cU0/view).
You will also need the config files available at [Google Drive](https://drive.google.com/file/d/0B5ZM90wrDzUOQnBhRjNVRFM1Rkk/view).
You have almost two options :
You can either right click on the `.exe` installer and select `Open with other application` and `Wine Windows Program Loader`, or either run `wine syrinxalphainst.exe` in Terminal.
### Set up app launcher
You have to create a new file `.local/share/applications/syrinx.desktop`:
```textile
[Desktop Entry]
Type=Application
Encoding=UTF-8
Name=Syrinx
Comment=Acoustic analysis
Exec=/usr/bin/wine /home/<USER>/.wine/drive_c/Program\ Files\ (x86)/syrinx/Syrinx.exe
Icon=/home/<USER>/.wine/drive_c/Program Files (x86)/syrinx/img/vigie-chiro.png
Terminal=false
```
Change `<USER>` by your username. To have the icon, you can download [`vigie-chiro.png`](/images/vigie-chiro.png).
To analyse ultrasound, with a 384 kHz sampling frequency, we have to open `Configs_syrinx/exp384.dsp`; and next Load sound file (`Ctrl+L`). To switch to other sound file in same folder, we can use `alt+arrows`. For more tips, you can view [the video of Charlotte ROEMER (Fr)](https://www.youtube.com/watch?v=BPPSw2FSLxs).
Install and Configure Batsound 4
--------------------------------
The procedure is quite similar with Syrinx-PC installation.
### Set up app launcher
Create a new file `.local/share/applications/batsound.desktop`:
```textile
[Desktop Entry]
Type=Application
Encoding=UTF-8
Name=Batsound
Comment=Acoustic analysis
Exec=/usr/bin/wine /home/<USER>/.wine/drive_c/Program\ Files\ (x86)/Pettersson/Batsound4/BatSound.exe
Icon=/home/<USER>/.wine/drive_c/Program Files (x86)/Pettersson/Batsound4/img/batsound.png
Terminal=false
```
(Do not forget to change `<USER>` to your username.)
To have the icon, you can download [`batsound.png`](/images/batsound.png).
### Configure Batsound to analyse ultrasounds
* Enter the `Sound/Sound Format` menu.
![Entering `Sound/Sound Forma` menu](/images/batsound/enter-sound-format-menu.png)
* Change `Time expansion` value to 10 (according to your recorder settings)
* Keep 44 100 as `Samples per second` value.
* Enter the `Analysis/Spectrogram Settings - Defaults` menu.
![Entering `Spectrogram Setting - Defaults` menu](/images/batsound/spectrogram-settings-default-values.png)
* Change `Max frequency` to `150000`;
* Set `Amplitude color mapping` to `Yellow, Red & Blue`;
* Adapt `Threshold` to sound intensity.
* You can zoom in.
With a *Pipistrellus kuhlii* record, I obtain the following spectrogram with the above settings :
![pipkuh spectro](/images/batsound/pipkuh-spectro-batsound.png)
Install 7-zip
-------------
7-zip is useful in Vigie-Chiro process to compress audio files for faster upload to [https://vigiechiro.herokuapp.com](https://vigiechiro.herokuapp.com).
1. Download `.exe` installer at [https://www.7-zip.org/](https://www.7-zip.org/)
2. Execute `7z1900.exe` with wine.
Install Lupas-Rename
--------------------
Lupas-Rename is used in Vigie-Chiro protocole to batch rename audio file to add protocoles informations such as pass and square.
1. Dowload `.exe` installer at [https://rename.lupasfreeware.org/download.php](https://rename.lupasfreeware.org/download.php)
2. Execute installer with wine
3. Batch rename audio files...
Conclusion
----------
With all these functionnal softwares, you are able to perform Vigie-Chiro protocole and sound analysis on GNU/Linux. I look forward to see your participation at [https://vigiechiro.herokuapp.com](https://vigiechiro.herokuapp.com) !

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---
title: Draw a Plot in C with GNU plotutils
author: Samuel Ortion
date: 2022-06-12
tags: [math]
lang: en
---
## Install plotutils
### Debian
```bash
$ sudo apt-get install plotutils-dev
```
### Fedora
```bash
$ sudo dnf install plotutils-devel
```
## Use PlotUtils to plot a graph
Let us draw the $sin(x)$ function using math library.
```c
#include <stdio.h>
#include <math.h>
#define RANGE 100
// Export data to stdout
void plot(double *x, double *y, size_t len)
{
for (unsigned int i = 0; i < len; i++)
printf("%lf %lf\n", x[i], y[i]);
}
int main(void)
{
int i;
double x[RANGE], y[RANGE];
// Compute sin(x)
for (i = 0; i < RANGE; i++)
{
x[i] = i * 0.1;
y[i] = sin(x[i]);
}
plot(x, y, 100);
return 0;
}
```
```bash
$ gcc -o plot plot.c -lm
$ ./plot # Show data on screen
```
### Use graph utility to plot the data
```bash
$ ./plot | graph -T X -T PNG -L "sin(x)" > output.png
```

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---
title: How to render LaTeX formula in Pelican
date: 2022-06-14
lastmod: 2022-06-14
tags: [math, latex, pelican]
slug: rendering-latex-pelican
author: Samuel Ortion
lang: en
---
Rendering $\LaTeX$ formulas in Pelican is easy.
Firstly import the pelican plugin in the proper python environment:
```bash
pip install pelican-render-math
```
Add `render_math` to PLUGINS list in your `pelicanconf.py` file:
```python
PLUGINS = ['render_math']
```
Then type formula in your blog post markdown documents:
```tex
$$
\frac{1}{2}
$$
```
$$
\frac{1}{2}
$$
And that's it !

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---
title: How to make automatic documentation using Doxygen, breathe and Sphinx
date: 2022-06-15
lastmod: 2022-06-15
tags: documentation
Tags: [C++, Doxygen, Sphinx]
slug: automatized-code-documentation
author: Samuel Ortion
Summary: Doing documentation is required, to allow people to use your project. Here I present a rather easy solution.
lang: en
---
## Introduction
I recently wrote a C++ Library, and I wanted to document how to use it. I searched for a solution to extract the documentation from the code, and I found [Doxygen](https://www.doxygen.org/). It works well, but produces an ugly html output.
So I decided, with advices from the [JeBif](https://jebif.fr/) discord, to use Sphinx, to render the documentation.
Sphinx does not extract documentation from source code, it rather generates the documentation from Markdown or ReStructuredText files, so I still use Doxygen to do this job, and thanks to breathe, we can use its xml output to render documentation using Sphinx.
## Let's go !
### Setting all the stuff up
First of all, Install Doxygen.
```bash
apt-get install doxygen
```
Let us create a dummy example:
```bash
mkdir myawesomelibrary
cd myawesomelibrary
mkdir include
cd include
```
And create a dummy header file:
```c++
// myawesomelibrary/include/cat.hpp
/**
* @brief This is a cat
*/
class Cat {
public:
Cat() {
say("I'm a cat");
}
/**
* @brief the cat is saying meow
*/
void meow()
{
say("meow");
}
/**
* @brief the cat is saying something
*/
void say(const std::string& message)
{
std::cout << message << std::endl;
}
};
```
Let's generate the doxygen cofiguration file:
```bash
cd ..
doxygen -g Doxyfile
```
Then in this file, we have to set the path to the header files source directory, and allow doxygen to look up to source code files recursively. It is also time to set the output directory.
```text
INPUT = "./include"
EXTRACT_ALL = YES
RECURSIVE = YES
OUTPUT_DIRECTORY = "./doc/"
```
We need to tell doxygen to generate the xml output.
```text
GENERATE_XML = YES
```
And, we can disable html and $\LaTeX$ output.
```tex
GENERATE_HTML = NO
GENERATE_LATEX = NO
```
Now let's set up Sphinx
```bash
mkdir doc
cd doc
sudo apt install python-sphinx
sphinx-quickstart
```
In the `conf.py` file, we need to add the following lines:
```python
extensions = ['breathe']
breathe_projects = {'myawesomelibrary': '../xml'}
breathe_default_project = 'myawesomelibrary'
```
Of course we also need to install the `breathe` package.
```bash
pip install breathe
```
We need to tell Sphinx to render the class documentation:
```rst
// in `index.rst`
.. doxygenclass:: Cat
:members:
```
We can use the theme from ReadTheDocs:
```bash
pip install sphinx_rtd_theme
```
```python
# in conf.py
html_theme = 'sphinx_rtd_theme'
```
### Generating the documentation
```bash
cd .. # go back to the root of the project
doxygen Doxyfile
cd doc
make html
```
That's it !
The output is in the `doc/build/html` directory.
Here is the result I got:
![sphinx dummy documentation](/images/sphinx/make_documentation_sphinx.png)

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---
title: Install Gephi on Linux
date: 2022-06-19
lastmod: 2022-06-19
tags: [graph, visualization, linux]
slug: install-gephi-on-linux
author: Samuel Ortion
lang: en
---
Gephi is a software package for graph visualization. Let's install it on Linux.
## Install Gephi
```bash
su - # Switch to root
cd /opt/
wget https://github.com/gephi/gephi/releases/download/v0.9.5/gephi-0.9.5-linux-x64.tar.gz -o
tar -xzf gephi-0.9.5-linux-x64.tar.gz
rm gephi-0.9.5-linux-x64.tar.gz
cd gephi-0.9.5
```
Now you could use it by running `./bin/gephi` in the terminal.
## Setup desktop entry
For an easier access, you could add a desktop entry to your menu.
```text
// /home/$USER/.local/share/applications/gephi.desktop
[Desktop Entry]
Name=Gephi
Comment=Launch Gephi
Path=/opt/gephi-0.9.5/
Exec=/opt/gephi-0.9.5/bin/gephi
Terminal=true
Type=Application
Icon=gephi.jpg
StartupNotify=true
Categories=Development;Education;
Keywords=graph;
```
And download a logo for your application.
```bash
cd /opt/gephi-0.9.5/
wget https://dighumlab.org/wp-content/uploads/2020/03/gephi-tool-icon-200x200-1.jpg -o gephi.jpg
```
That's it !
## References
- [Gephi](https://gephi.org/)

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---
title: How to use virtual environments
date: 2022-06-19
lastmod: 2022-06-19
tags: code
Tags: [python, R, julia]
slug: using-virtual-environments
author: Samuel Ortion
lang: en
status: published
---
To not interfere with your os configuration and keep your project reproducible, you should use a virtual environment as long as possible.
Virtual environment are a way to isolate your project from the rest of the system, and to avoid dependencies conflicts.
## Python Virtualenv
Lets start by installing the virtualenv package.
```bash
sudo apt install python3-venv
```
And now you can create venvs for your project:
```bash
python3 -m venv .venv/myproject
```
It is a good practice not to create a virtualenv with name "venv", but to use a name that reflects the project you are working on, in order to see directly in which venv you are working.
Now you can activate the virtualenv:
```bash
source .venv/myproject/bin/activate
```
And deactivate it when you are done:
```bash
deactivate
```
One other way to create a virtualenv is to use the `virtualenv` command.
Once you installed python packages, you should create a snapshot of your project dependencies using:
```bash
pip freeze > requirements.txt
```
That way, you can allow other people to use your project and installi its dependencies with the following command:
```bash
pip install -r requirements.txt
```
You could also use conda, as a package manager, to create a virtualenv.
## R Virtualenv
R also has its own virtualenv gestionnal system named packrat.
First install packrat with R.
```R
install.packages("packrat")
```
And create your virtual environment with:
```R
packrat::init("myproject")
```
Similarly, you can then install packages:
```R
install.packages("dplyr")
```
And create a snapshot of your dependencies with:
```R
packrat::snapshot()
```
The dependency list is available in `packrat/packrat.lock`.
## Julia Virtualenv
Julia venv is very similar to Python venv.
First, you install the VirtualEnv package:
```bash
julia -e 'using Pkg; Pkg.add("VirtualEnv")'
```
And add `~/.julia/bin` to your path:
```bash
julia -e 'using VirtualEnv; VirtualEnv.comonicon_install_path()'
```
Then you can use `venv` to create a virtualenv for your project:
```bash
venv .venv/myproject
```
And you can activate/deactivate it:
```bash
source .venv/myproject/bin/activate
deactivate
```
That's it !
## References
- [Python venv documentation](https://docs.python.org/3/library/venv.html)
- [Packrat documentation](https://rstudio.github.io/packrat/)
- [Julia venv documentation](https://juliapackages.com/p/virtualenv)

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---
title: How to mount a shared folder between Linux KVM Host and Guests
date: 2022-06-21
lastmod: 2022-06-21
tags: [qemu, kvm, linux]
slug: kvm-shared-folder
author: Samuel Ortion
lang: en
---
Sharing folder between KVM virtual machines and host, may be useful. Here is a way found in fedora forum.
## Quickstart
Change `vm` to your vm hostname.
```bash
sudo mkdir -p /mnt/shared
sudo chmod -R a+rwX /mnt/shared
sudo semanage fcontext -a -t svirt_home_t "/mnt/shared(/.*)?"
sudo restorecon -R /mnt/shared
tee fs.xml << EOF > /dev/null
<filesystem type='mount' accessmode='mapped'>
<source dir='/mnt/shared'/>
<target dir='shared'/>
</filesystem>
EOF
virsh shutdown vm
virsh attach-device vm fs.xml --config
virsh start vm
ssh vm
sudo mkdir -p /mnt/shared
sudo tee -a /etc/fstab << EOF > /dev/null
shared /mnt/shared 9p trans=virtio 0 0
EOF
sudo mount -a
```
## References
- [Virt-manager and shared folder host/guest permission issue?](https://ask.fedoraproject.org/t/virt-manager-and-shared-folder-host-guest-permission-issue/10938/5)

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---
title: Faire tourner Stable Diffusion sur Google Colab
date: 2022-10-01
lastmod: 2022-10-01
tags: [ia, machine learning, python, notebook]
author: Samuel Ortion
slug: run-stable-diffusion-on-colab
---
## Introduction
Stable Diffusion est un modèle de deep learning permettant de générer des images photoréalistes à partir d'un *prompt* texte
J'ai récemment découver ce modèle via [lexica.art](https://lexica.art/), après avoir entendu parler des concurents DALL-E, Imagen et consorts.
Stable Diffusion a l'avantage d'être open source: tout le monde peut l'utiliser, et il fonctionne bien de surcroît.
## Prérequis
J'utilise un compte Google dédié, avec [Google Colab](https://colab.research.google.com/) pour faire tourner Stable Diffusion.
Le modèle devrait pouvoir tourner sur n'importe quelle plateforme Python, pourvu qu'il y ai assez de ressources GPU.
## Comment lancer Stable Diffusion
Sur Colab, importez le notebook [Art_Stable_Diffusion](/upload/stablediff/Art_Stable_Diffusion.ipynb) et lancer le.
Il faudra sans doute modifier le prompt dans le formulaire prévu à cet effet.
Ensuite vous pouvez générer les images et si les résultats vous plaisent, les télécharger ou les téléverser directement sur Drive.
Vous pouvez aussi utiliser le notebook original de Stable Diffusion comme expliqué dans l'[article Geekculture](https://medium.com/geekculture/2022-how-to-run-stable-diffusion-on-google-colab-5dc10804a2d7) en référence.
J'ai juste supprimé des bouts de codes qui ne me servaient pas et ajouté une cellule d'export sur Google Drive, avec édition des métadonnées (auteur, licence et surtout prompt utilisé).
## Résultats
Voici quelques images que j'ai obtenu avec Stable Diffusion:
<img src="/images/stablediff/fox_monet.png" alt="StableDiffusion's prompt: 'a painting of a fox sitting in a field at sunrise in the style of Claude Monet'" title="StableDiffusion's prompt: 'a painting of a fox sitting in a field at sunrise in the style of Claude Monet'">
<img src="/images/stablediff/horse.png" alt="StableDiffusion's prompt: 'A horse riding an astronaut'">
## References
- [Article Tuto Medium Geekculture (en)](https://medium.com/geekculture/2022-how-to-run-stable-diffusion-on-google-colab-5dc10804a2d7)

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---
title: Générer le code LaTeX/chemfig d'une réaction chimique avec Zyme
date: 2022-10-02
lastmod: 2022-10-02
tags: [chimie]
slug: zyme-chemical-scheme-with-chemfig-and-pubchem
author: Samuel Ortion
status: published
---
Durant les trois années de licence bioinformatique, nous avons des cours de biochimie, et ceux ci viennent avec leur lots de structure chimiques à connaître.
En L1, j'avais réalisé un document pdf avec LaTeX/chemfig des [acides aminées protéinogènes](/upload/chemical/acides_aminées_protéinogènes.pdf) en représentation de FISCHER, et j'avais trouvé ça plutôt sympa, bien que ça m'avait pris pas mal de temps à rédiger.
Ajourd'hui, j'améliore ma méthode: fini le code de la structure en chemfig (extension LaTeX) *a la mano*, vive le code généré par du code !
## Zyme
[Zyme](https://framagit.org/BioloGeeks/bioinfo/zyme) est un petit script python basé sur [mol2chemfig](https://pypi.org/project/mol2chemfigPy3/), permettant à partir d'une représentation simplifiée d'une réaction chimique du type:
```text
{Glucose} + ATP -> {Glucose-6-phosphate} + ADP + P_i
```
de générer le code chemfig correspondant, permettant le rendu de la structure chimique en utilisant la base de données [PubChem](https://pubchem.ncbi.nlm.nih.gov/).
Un fois que le fichier `.tex` est générer, il est possible de générer un pdf, ou un svg par exemple.
## Installation
Rendez vous sur le [dépôt git de zyme](https://framagit.org/BioloGeeks/bioinfo/zyme), et suivez les instructions d'installation.
Globalement, il suffit de cloner le dépôt et d'ajouter le dossier `./zyme` au `PATH` de votre système (sous Linux). Je n'ai pas testé sous Windows, mais ça devrait fonctionner (🤞).
## Utilisation
Pour générer le code LaTeX/chemfig d'une réaction chimique, il suffit de lancer la commande `zyme` avec en argument le fichier contenant la réaction chimique, et eventuellement le fichier de sortie.
Exemple:
```bash
zyme.py -i reaction.scheme -o reaction.tex
```
Le fichier `reaction.scheme` contient la réaction chimique au format texte, et le fichier `reaction.tex` contient le code LaTeX/chemfig généré.
### Format du fichier de la réaction chimique
Le fichier de la réaction est un simple fichier texte contenant les réactifs, produits et flêches de la réaction chimique.
Un ';' permet de séparer deux réactions différentes (plusieurs `\schemestart[...]\schemestop` seront générés).
Un mot entre accolades `{}` sera remplacé par le code chemfig de la structure correspondante (en faisant appel à l'API PubChem des formats SMILES).
Exemple, pour le tryacilglycérol:
```text
{triacylglycerol}
```
Donne dans un premier temps:
```tex
\schemestart
\chemfig{--[:60]--[:60]--[:60]--[:60]--[:60]--[:60]--[:60]--[:60]-(=[:300]O%
)-[:60]O--[:60](-[:120]O-[:60](-[:120]-[:60]-[:120]-[:60]-[:120]-[:60]%
-[:120]-[:60]-[:120]-[:60]-[:120]-[:60]-[:120]-[:60]-[:120]-[:60]-[:120])=O%
)--[:300]O-(=[:60]O)-[:300]--[:300]--[:300]--[:300]--[:300]--[:300]--[:300]%
--[:300]--[:300]}
\schemestop
```
Qui peut être compilé en pdf, en donnant:
![triacylglycérol générer avec Zyme, PubChem, LaTeX/chemfig](/images/chemical/triacylglycerol_zyme_chemfig.png)
Zyme accepte d'autres arguments, tel que `+standalone` pour générer un fichier `.tex` compilable directement (instruction `\documentclass[]{standalone}`).
### Générer un `.svg`
Pour générer un fichier `.svg` à partir du fichier `.pdf` généré, il suffit d'utiliser la commande `pdf2svg` (à installer avec votre gestionnaire de paquet préféré).
```bash
pdf2svg reaction.pdf reaction.svg all
```
## Conclusion
Et voilà, j'espère que ce petit outil vous sera utile.
N'hésitez pas à me remonter des bugs ou des suggestions d'améliorations, par exemple sur [le dépôt git de zyme](https://framagit.org/BioloGeeks/bioinfo/zyme/issues).

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---
title: 'Astuce: Copier du texte dans le presse-papier depuis un terminal Linux'
date: 2023-02-05
lastmod: 2023-02-05
tags: [tip]
slug: xclip-clipboard-depuis-terminal
author: Samuel Ortion
---
Il suffit d'installer `xclip`:
```bash
sudo dnf install xclip # sur fedora par exemple
```
Puis, c'est tout simple:
```bash
echo "Coucou !" | xclip -selection c
```
Un exemple d'utilisation: copier une clé publique ssh dans le presse papier depuis le terminal:
```bash
cat ~/.ssh/id_ecdsa.pub | xclip -selection c
```

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---
title: Analyze projects programming languages using github-linguist
date: 2023-03-29
lastmod: 2023-03-29
tags: [code]
slug: github-linguist-for-programming-languages-usage-analysis
author: Samuel Ortion
lang: en
---
github-linguist is a Ruby library and command line tool for detecting the programming languages used in a project. It is used by GitHub to detect the language of a project and to generate language statistics.
We can use it through the command line, in order to analyze the programming languages used in a project.
During my application to bioinformatics master degree, I had to say which programming languages I commend. So here is some quick tips to use `github-linguist` as I learned to do for this purpose.
## Installation
### Requirements
- Ruby, `gem` and `ruby-devel` packages
### Install
```bash
$ gem install github-linguist
```
### Usage
```bash
$ github-linguist
```
For instance on my [blog source code](https://forge.chapril.org/sortion/blog/) I get:
```text
65.80% 945252 Jupyter Notebook
17.12% 245876 CSS
14.37% 206405 HTML
1.29% 18478 Less
0.77% 11019 Python
0.43% 6212 Shell
0.17% 2472 Makefile
0.06% 879 JavaScript
```
Let's use a script to get the result for all my projects:
Let's assume you have a directory with all your projects, say in `~/Documents/Projects/`:
```bash
#!/bin/bash
# linguist.sh
# Usage: ./linguist.sh ~/Documents/Projects/
#
# Recursively search for git repositories in the given directory
# and print the programming languages used in each of them.
# Get the directory to search for git repositories
if [ -z "$1" ]; then
echo "Usage: $0 <directory>"
exit 1
fi
DIR=$1
for REPO in $(find $DIR -name .git -type d); do
echo -e "repo: $REPO"
github-linguist $REPO/
echo -e "\n"
done
```
```bash
$ ./linguist.sh ~/Documents/Projects/
```
This has the disadventage to print the result of each repository, including included dependencies.
Let's assume that a project is a git repository root, and that the other git repositories in subdirectories are dependencies:
```bash
#!/bin/bash
# linguist.sh
# Usage: ./linguist.sh ~/Documents/Projects/
#
# Recursively search for git repositories in the given directory
# and print the programming languages used in each of them.
recurse_directory() {
local directory
directory="$1"
if [[ -d "$directory" ]]; then
if [[ -d "$directory/.git" ]]; then
echo -e "repo: $directory"
github-linguist $directory/
echo -e "\n"
else
for subdirectory in "$directory"/*; do
recurse_directory "$subdirectory"
done
fi
fi
}
local directory
directory="$1"
if [[ -z "$directory" ]]; then
echo "Usage: $0 <directory>"
exit 1
fi
recurse_directory "$directory"
```
### Let's have fun with some statistics
One we have our report for all our projects, we can use some tools to get some statistics.
First, let's transform the output of `linguist.sh` into a CSV file using `awk`:
1. Counting the number of projects using a programming language:
```awk
#!/bin/awk -f
# linguist-count.awk
BEGIN {
OFS = ";"
}
/^[0-9]/ {
languages[$3]++
}
END {
for (language in languages) {
print language, languages[language]
}
}
```
```bash
$ ./linguist.sh ~/Documents/Projects/ | ./linguist-count.awk
```
Now that we have our first data let's use R to plot it:
```r
#!/usr/bin/Rscript
# linguist-count.R
# Usage: ./linguist-count.R <csv>
#
# Plot the number of projects using a programming language.
library(ggplot2)
# Parse the command line arguments
args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 1) {
stop("Usage: ./linguist-count.R <csv>")
}
csv <- args[1]
languages_count_df <- read.csv(file = csv, header = FALSE, sep = ";")
colnames(languages_count_df) <- c("language", "count")
ggplot(data = languages_count_df, aes(x = reorder(language, count), y = count)) +
geom_bar(stat = "identity") +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
labs(x = "Programming language", y = "Number of projects")
ggsave("linguist-project-count.png", width = 10, height = 5)
```
<img src="/images/R/linguist-project-count.png" alt="bar plots of languages I used, according to github-linguist">

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---
title: How to Classify Blood Cells Using Neural Networks
date: 2022-06-18
lastmod: 2022-06-18
tags: [machine learning, biology]
slug: classify-blood-cells-using-neural-networks
author: Samuel Ortion
Summary: Machine Learning is widely used for image recognition. Here, we tried to perform blood cell classification using Convolutional Neural Networks.
lang: en
---
## Introduction
Machine Learning is widely used for image recognition. Here, we tried to perform blood cell classification using Convolutional Neural Networks.
There is a dataset of blood cells that can be used for training and testing [[2, 3]](#ref2).
According to the paper [[1]](#ref1), the model that performed the best is the Regionnal Convolutional Neural Network (R-CNN).
We tried to reproduce their results.
## The dataset
The dataset is a set of images of white blood cells and platelets sorted in 8 classes: immature granulocytes (ig), monocytes, basophils, neutrophils, eosinophils, erythroblasts and platelets.
The dataset contains 17092 images.
## The model
Firstly, we tried to use a classic Convolutional Neural Network (CNN).
## References
<span id="references"></span>
[1] [White blood cells detection and classification based on regional convolutional neural networks](https://www.sciencedirect.com/science/article/abs/pii/S0306987719310680?via%3Dihub) <span id="ref1"></span>
[2] [A dataset of microscopic peripheral blood cell images for development of automatic recognition systems](https://www.sciencedirect.com/science/article/pii/S2352340920303681?via%3Dihub) <span id="ref2"></span>
[3] [The precedent dataset, download page](https://data.mendeley.com/datasets/snkd93bnjr/1)

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@ -0,0 +1,45 @@
#+title: Unixfu
#+date: <2024-01-14 Sun>
#+category: linux
A bin for some useful UNIX command.
* Add two hours
This could be useful for nocmig fan, to ease the hour computation of a bird contact.
#+begin_src bash
hour() {
start=$1
duration=$2
IFS=":" read -r duration_hour duration_minute <<< $duration
date -d "$start $(($duration_hour * 60 + $duration_minute)) minutes" +"%H:%M"
}
hour 17:00 5:43
#+end_src
#+RESULTS:
: 22:43
* WAV creation datetime
Here is a small snippet that demonstrates how to get the creation date-time of a WAV file with =ffprobe=
#+begin_src bash
wav_creation_date() {
wav="$1"
date_key="date"
time_key="creation_time"
for key in $date_key $time_key; do
ffprobe "${wav}" -v quiet -select_streams v:0 -of default=noprint_wrappers=1:nokey=1 -show_entries stream=codec_type=stream_tags=creation_time:format_tags=${key}
done
}
#+end_src
Then, on the WAV file =example.wav=:
#+begin_src bash
echo $(wav_creation_date example.wav)
#+end_src
#+begin_example
2024-01-12 18:56:28
#+end_example

View File

@ -0,0 +1,23 @@
#+title: ortion.fr.eu.org - A journey towards domain self-hosting on a budget
#+status: draft
#+category: self-hosting
#+draft: true
#+date: 2024-02-10
[[https://nic.eu.org]] provides free domain registring, provided once has its own domain name servers.
* Steps
** Contact record
**
** FDN primary zone record
* The bill
- FDN VPN subscription (1€ / month (student));
- <name>.fr.eu.org record (0€)
* References
[[- https://www.domainepublic.net/Creer-et-heberger-un-sous-domaine.html]]
-

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@ -0,0 +1,99 @@
---
title: How to render pseudocode in Hugo with pseudocode.js
slug: pseudocodejs-hugo
pseudocode: true
date: 2024-03-09
---
To render pseudocode in Hugo, you can use the `pseudocode.js` library.
Here is what I did to make this working on my blog.
## Theme configuration
In your theme files, you will first need to add link to the library CDN.
```html
<!-- in themes/<theme>/layouts/partials/pseucodode.html -->
<script>
MathJax = {
tex: {
inlineMath: [['$','$'], ['\\(','\\)']],
displayMath: [['$$','$$'], ['\\[','\\]']],
processEscapes: true,
processEnvironments: true,
}
}
</script>
<script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-chtml-full.js"
integrity="sha256-kbAFUDxdHwlYv01zraGjvjNZayxKtdoiJ38bDTFJtaQ="
crossorigin="anonymous">
</script>
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/pseudocode@latest/build/pseudocode.min.css">
<script src="https://cdn.jsdelivr.net/npm/pseudocode@latest/build/pseudocode.min.js"></script>
```
And render all element with `pseudocode` HTMl class.
```html
<!-- in themes/<theme>layouts/partials/pseudocode-render.html -->
<script>
let pseudocodeElements = document.getElementsByClassName("pseudocode");
for (let element of pseudocodeElements) {
pseudocode.renderElement(element);
}
</script>
```
```html
<!-- in themes/<theme>/layouts/_default/baseof.html -->
<head>
...
{{ if .Param "pseudocode" }}
{{ partialCached "pseudocode" . }}
{{ end }}
</head>
<body>
...
<main>
{{ block "main" . }}{{ end }}
{{ if .Param "pseudocode" }}
{{ partialCached "pseudocode-render" . }}
{{ end }}
<main>
</body>
```
## Writing
Then, in your Markdown article, add the following in your frontmatter:
```yaml
---
pseudocode: true
---
```
And write your pseudocode, using the `algorithmic` $\LaTeX$ syntax.
````markdown
<pre id="hello-world-code" class="pseudocode">
\begin{algorithmic}
\PRINT \texttt{'hello world'}
\end{algorithmic}
</pre>
````
Which willl be rendered as:
<pre id="hello-world-code" class="pseudocode">
\begin{algorithmic}
\PRINT \texttt{'hello world'}
\end{algorithmic}
</pre>
## References
- `pseudocode.js` <https://github.com/SaswatPadhi/pseudocode.js>
- Mathematics in Markdown (Hugo documentation) <https://gohugo.io/content-management/mathematics/>

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---
title: 'Piège Photo Raspberry Pi avec Motion'
slug: 'piege-photo-raspberry-pi-motion'
date: 2022-10-04T22:14:23+02:00
lang: fr
---
Après avoir réalisé un piège photo avec un caméra déclenchée par un détecteur de mouvement infrarouge et Arduino, j'ai eu envie d'essayer de faire le même type de système avec un Raspberry Pi.
L'avantage de Raspberry Pi est que c'est un vrai ordinateur (pas un simple microcontrolleur comme l'ATMega de l'Arduino). De ce fait il a une plus grande capacité de calculs, et on peut se passer du PIR sensor en utilisant de l'analyse d'image pour détecter le mouvement.
J'ai donc utilisé le logiciel [Motion](https://motion-project.github.io/), qui permet de détecter le mouvement dans une vidéo, et de déclencher une action (ici la prise de vue).
## Matériel
- Raspberry Pi;
- Alimentation pour Raspberry Pi;
- Batterie externe USB (optionnel, utile pour obtenir un piège photo autonome);
- Caméra Raspberry Pi (avec sa nâpe de câblage), ou une caméra USB;
- Carte SD (avec assez de stockage pour les photos et l'OS);
- Une boîte (étanche de préférence).

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---
title: 'Piège Photo Arduino'
slug: 'piege-photo-arduino'
date: 2022-09-18T18:15:49+02:00
lang: fr
---
Il y a maintenant quelques années, j'ai eu l'occasion de créer un piège photo basé sur une carte Arduino. Ce projet avait pour but de capturer des photos d'animaux sauvages, et de m'amuser un peu en électronique et programmation.
À l'époque, j'avais réalisé un site web en html, pour présenter le projet; mais je ne retrouve plus le code source... C'est con.
Je vais tout de même essayer de présenter ce vieux projet, à nouveau, en espérant que cela puisse intéresser quelqu'un.
## Principe
Une caméra automatique du commerce se base généralement sur un détecteur de chaleur (capteur infrarouge), et prends des images au moment où celui-ci détecte un mouvement.
Ces détecteur sont similaires aux détecteurs de présence qu'on peut trouver dans des toilettes publiques, par exemple.
Le