+
-
-
-Cell2Fire es un simulador de incendios forestales y de paisajes silvestres basado en una cuadrícula 2D, enfocado en áreas a gran escala y simulaciones rápidas para proporcionar análisis de riesgos espaciales robustos, aprovechando los métodos de cálculo paralelo de c++.
-
-Version actual
-- [W](https://github.com/fire2a/c2f-w) incluye los tres modelos de comportamiento de combustible!
-
-Sabores liberados (*ya no se mantienen, solo para archivo*):
-- [Scott & Burgan](https://github.com/fire2a/C2FSB)
-- [Kitral](https://github.com/fire2a/C2FK)
-- [FBP](https://github.com/fire2a/C2FFBP)
-
-El [original](https://github.com/cell2fire/Cell2Fire/)
-
-# Ejemplos de salida
-
-## Scott & Burgan
-### Zona 60 de Previncat (Instancia Catalana): bosque y propagación de fuego simulada con su correspondiente cicatriz y árbol de propagación de crecimiento.
-
-### Metricas de riesgo: Probabilidad de quema (BP), Centralidad de Intermediación (BC), Valor de Protección Agua Abajo (DPV), y Árbol de Propagación de Crecimiento (GPT).
-
-
-## Kitral
-### El Portillo, simulación con comportamiento de fuego de copa.
-
-
-## Sistema Canadiense de Predicción de Comportamiento de Incendios Forestales
-
-|:-------------|:------------------|
-| Bosque Dogrib, Canada {: width="100%" } | shortest paths propagation {: width="80%" } |
-| Caminos más cortos de propagación e intensidad ROS {: width="100%" } | Burn-Probability {: width="80%" } |
-
-
-# Compilación
-Lanzamientos precompilados, los usuarios normales probablemente no necesitan esta guía.
-
-Verifica los [artefactos de acción del repositorio](https://github.com/fire2a/C2F-W/actions) para la última actualización de las compilaciones automáticas.
-
-## UNIX Overview
-```bash
-# install build-essentials, gcc-12, boost, eigen3 & openmp
-
-cd
-git clone git@github.com:fire2a/C2F-W.git
-
-# go to c++ files
-cd C2F-W/Cell2FireC
-
-# clean & build [select platform makefile]
-make clean [-f custom_makefile]
-make [-f custom_makefile]
-
-```
-### developer setup
-```bash
-# rename binary for the QGIS toolbox plugin
-ext=`python3 -c "import platform;print(f'.{platform.system()}.{platform.machine()}')"`
-cp Cell2Fire Cell2Fire$ext
-
-cd
-git clone git@github.com:fire2a/fire-analytics-qgis-processing-toolbox-plugin.git fire-toolbox
-
-source ~/your/venv/bin/activate
-(venv) $ pip install -r fire-toolbox/fireanalyticstoolbox/requirements.txt
-
-git clone git@github.com:fire2a/fire2a-lib
-cd fire2a-lib
-(venv) $ pip install -e .
-
-# symlink C2F-W repo into C2F directory of the fire2a-toolbox repo
-ln -s C2F-W fire-toolbox/fireanalyticstoolbox/simulator/C2F
-
-cd ~/.local/share/QGIS/QGIS3/profiles/default/python/plugins
-ln -s ~/source/fire-toolbox/fireanalyticstoolbox .
-```
-Next time you start QGIS, look for fire2a-toolbox icon - Tabla de contenidos -
- {: .text-delta } -1. TOC -{:toc} -
, on the Processing Toolbox panel.
-
-## Linux
-[Make](compile_linux.html)
-
-## Macos
-[Make](compile_macos.html)
-
-## Windows
-[Using Visual Studio](compile_windows.html)
diff --git a/docs/fire2a-lib.md b/docs/fire2a-lib.md
deleted file mode 100644
index 6e53a55..0000000
--- a/docs/fire2a-lib.md
+++ /dev/null
@@ -1,100 +0,0 @@
----
-layout: default
-title: Librería de Algoritmos
-nav_order: 3
-has_toc: false
----
-{: .warning}
-Código en Python para línea de comandos; Revisa la versión gráfica amigable: [fire2a toolbox](/docs/qgis-toolbox/README.html)
-# fire2a-lib
-{: .no_toc}
-
-
-
-Esta biblioteca es un paquete de python compuesto por nuestros algoritmos relacionados con incendios, utilidades comunes y herramientas para GIS, optimización, agrupación, etc.
-
-Algúnos casos de uso:
-
-* Quieres mirar/usar/adaptar la implementación del Valor de Protección Aguas Abajo?
-* Nuevamente olvidaste cómo cargar un ráster .tif en un array numpy + un diccionario de propiedades?
-* Necesitas un algoritmo de agrupación de paisajes?
-
-Desarrolladores y académicos son bienvenidos a contribuir!
-
-* [Repositorio]
-* [Documentación API]
-
-## Inicio Rápido
-Sugerimos instalar [QGIS] antes de usar, aunque no todos los módulos dependen de él.
-```bash
-$ pip install git+https://github.com/fire2a/fire2a-lib.git
-$ ipython
-In [1]: from fire2a.- Tabla de contenidos -
- {: .text-delta } -1. TOC -{:toc} --QGIS cookbook -
-{: .no_toc} -
-
-# Getting Help 🚑
-
-Before reaching out, make the sanity test:
-* QGIS is updated (please try switching from LTR to latest)
-* Fire2a toolbox is updated (`Menu : Plugins > Manage and Install Plugins... > Installed > Fire Analytics Processing-Toolbox > Upgrade`)
-* Your Operating System (OS e.g. Linux, Windows, MacOS) is updated
-* No funny formats in `Options > Processing > default raster & vector layers, set to tif & gpkg`
- {: width="50%"}
-* Restart your computer and try again on a fresh QGIS project on a directory that is *not shared* (no OneDrive, GoogleDrive, network drive, etc.) and has no spaces in its name
-
-If the problem persists, follow the next steps to create an issue [here](https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/issues):
-
-1. Look for similar issues beforehand
-
-2. Identify your OS, Fire2a toolbox plugin, and QGIS versions:
- - **Operating System:**
- -- Windows : `press Win key > type About > Windows specifications section : click Copy button`
- -- MacOS : `Apple > TODO`
- -- Linux: `$ uname -a`
- - **Plugin Version:** Navigate to `Plugins > Manage and Install Plugins... > Installed > Fire Analytics Processing-Toolbox > Installed version`.
- {: width="75%" }
- - **QGIS Version:** `Menu :Help > click About` copy at least the first paragraph
-
-3. **Include Relevant Files:**
- - Compress and attach the instance and/or results (make a `.zip` file) you were using when the error occurred.
- - If not already in results, attach the corresponding `algorithmName_log.html` file (`Menu : View > Panels > Log Messages > fire2a`)
-
-Clear and concise descriptions are paramount when submitting a bug report. Please focus on **details about the issue encountered, including your goal and the unexpected behavior you experienced.** Then, provide the **steps to reproduce the issue. Include any error messages or other relevant observations you encountered.**
-
-back to top
-{: style="text-align: right;"}
-
-# - Table of contents -
- {: .text-delta } -1. TOC -{:toc} -
-: [Save All](https://plugins.qgis.org/plugins/SaveAllScript/), choose a location, name a new directory, done! everything gets written to disk, never worry again about temp folders or in memory layers!
-
-
-: [Serval](https://plugins.qgis.org/plugins/Serval/), Modify your rasters as if you were using paint!
-
-
-: [IPyConsole](https://plugins.qgis.org/plugins/IPyConsole/), "No offense, but QGIS python console just sucks." ([sic](https://www.itopen.it/qgis-and-ipython-the-definitive-interactive-console/#comment-140751)) [documentation](http://www.itopen.it/qgis-and-ipython-the-definitive-interactive-console/), [fix to use latest qtconsole](https://github.com/elpaso/qgis-ipythonconsole/compare/master...fdobad:qgis-ipythonconsole:master)
-
-
-: [Plugin Reloader](https://plugins.qgis.org/plugins/plugin_reloader/), If a plugin starts misbehaving easier to reload it than to restart QGIS
-
-
-: [Plugin Builder](https://plugins.qgis.org/plugins/pluginbuilder3), Jumpstart your plugin development!
-
-back to top
-{: style="text-align: right;"}
-
-# Linux 🗽
-## QGIS install
-* On Debian getting the Long Term Release is easy as:
- * Gnome: `Super (or Meta) Key > type 'QGIS' > Click 'Install' on the Software app dialog`
- * Synaptic: search for qgis, click install
- * Terminal: `sudo apt install qgis qgis-plugin-grass`
-* Getting the Latest Release on Debian: add QGIS [apt source](https://qgis.org/en/site/forusers/alldownloads.html#debian-ubuntu)
-* [Other distributions](https://qgis.org/en/site/forusers/alldownloads.html#linux)
-
-
-## Python
-
-{: .warning}
-`sudo pip` is insecure and may break your system!
-
-{: .info}
-expert tl;dr: `-m venv --system-site-packages -r` [requirements.txt], [requirements.dev.txt]
-
-### setup a virtual environment
-Handle separate dependencies but share system packages because installing QGIS brings addional packages through `python3-qgis` that binds c binaries such as GDAL.
-1. Download [requirements.txt] list (2ndary clicking the link and Save Link As...)
-2. Open a terminal
-```bash
-# good practice: a directory to keep all venvs
-mkdir -p ~/pyenv
-# recommended: name this venv qgis
-python3 -m venv --system-site-packages ~/pyenv/qgis
-# activate it
-$ source ~/pyenv/qgis/bin/activate
-# from activated venv, upgrade tools
-(qgis) $ python -m pip install --upgrade pip wheel setuptools
-# install requirements (check where you saved it)
-(qgis) $ pip install -r ~/Downloads/requirements.txt
-# related bug: matplotlib can't find qt backend
-(qgis) $ pip install --upgrade matplotlib
-```
-
-### usage: activate venv, launch qgis
-```bash
-$ source ~/pyenv/qgis/bin/activate
-(qgis) $ qgis
-```
-
-### handy terminal aliases
-```bash
-# appending to .bashrc:
-echo 'alias pyqgis="source ~/pyenv/qgis/bin/activate"'>>~/.bashrc
-echo 'alias myqgis="source ~/pyenv/qgis/bin/activate && qgis"'>>~/.bashrc
-# NOTE: must source bashrc for aliases to work
-$ source ~/.bashrc
-# NOTE: or restart same shell (every time a bash terminal is launched it gets sourced)
-$ bash
-# first alias: to activate venv
-$ pyqgis
-# second alias: to launch with venv activated
-$ myqgis
-```
-
-### activated ~~icon~~ desktop environment launcher
-
-{: .success}
-Avoid `ModuleNotFoundError` when QGIS starts from the default launcher or associated (i.e. Open with) files (e.g., .shp, .gpkg), by activating the venv before starting QGIS
-
-To do this, edit the QGIS ~~icon~~ launcher. Some Desktop Environments (xfce, gnome?) allow editing the launcher by 2ndary clicking on the QGIS icon; then edit the launch command on the displayed menu:
-```bash
-# From
-Exec=qgis %F
-# To
-Exec=bash -c 'source ~/pyenv/qgis/bin/activate && qgis %F'
-
-# It's the same as editing this file
-~/.local/share/applications/org.qgis.qgis.desktop
-
-# If not found on your user's files it's on system launchers, copy it:
-cp /usr/share/applications/org.qgis.qgis.desktop ~/.local/share/applications/.
-# then edit
-```
-### locations
-```bash
-# user plugin directory
-~/.local/share/QGIS/QGIS3/profiles/default/python/plugins/example_plugin
-# processing plugin directory
-/usr/share/qgis/python/plugins/processing
-```
-
-back to top
-{: style="text-align: right;"}
-
-# MacOS 💰
-## QGIS Install
-Download it [here](https://qgis.org/en/site/forusers/download.html#mac) also read the instruction to not get security blocked at startup.
-## Python
-This QGIS version includes its own python, so be careful to use it instead of systems's python
-```zsh
-# optional or pro: be extra careful confirming is the right python
-# these are not the same:
-% ./python3 -c "import sys;print(sys.prefix)"
-% python3 -c "import sys;print(sys.prefix)"
-```
-
-### installing requirements
-1. Download [requirements.txt] list (2ndary clicking the link and Save Link As...)
-2. Open a terminal
-```zsh
-# go to QGIS python location
-% cd /Applications/QGIS.app/Contents/MacOS/bin
-# install into qgis python environment
-% ./python3 -m pip install -r ~/Downloads/requirements.txt
-# matplotlib bug: can't find qt_backend
-% ./python3 -m pip install --upgrade matplotlib
-```
-
-### locations
-```zsh
-# user plugin folder
-~/Library/Application\ Support/QGIS/QGIS3/profiles/default/python/plugins/example_plugin
-# python location
-/Applications/QGIS.app/Contents/MacOS/bin
-```
-
-back to top
-{: style="text-align: right;"}
-
-# Windows 💩™
-## QGIS Install
-A. Web install [link](https://qgis.org/en/site/forusers/download.html#windows), there are 3 flavors:
-- Latest version is recommended
-- LTR works with some issues
-- OSGeo4W Network Installer can be upgraded in place
-
-B. "Terminal" install
-0. Using `winget` cli, if not available, activate it in Microsoft Store
-1. Open a "privileged terminal", e.g. On your keyboard press the 'Win' button > type 'cmd' > 2dary click on the app > Click 'Run as administrator'
-2. Input `winget install -e --id OSGeo.QGIS --scope machine` (`--scope machine` option is recommended to making launcher icons for all users)
-3. Follow on screen instructions (all defaults are ok)
-
-
-## Python
-Windows version of QGIS comes bundled with its own python, a special launcher must be used to access it
-### installing requirements
-1. Download [requirements.txt] list (2ndary clicking the link and Save Link As...)
-2. Activate QGIS python by starting `OSGeo4W Shell` app `Win button > type OSGeo > select & click` to launch a CMD terminal
-3. Type `pip install -r "%USERPROFILE%\Downloads\requirements.txt"` press Enter. (Adjust the path as needed, on Windows 11 you can select the file with the secondary button then click 'Copy path', use 2ndary click to paste into CMD terminal)
-
-{: width="75%" }
-
-If you couldn't understand last 2 steps, try the [last resort](forcing-python-requirements.html) solution.
-
-__All ready!__
-
-__Except__ if you'll be running our _Decision Optimization algorithms, specially on big rasters_; then the next two steps are required to use CPLEX as a MIP solver from within QGIS.
-
-back to top
-{: style="text-align: right;"}
-
-### make it writable
-Recommended for machines with a single user, or to share modifications to the environment to all users (explainer gif after)
-
-Also to integrate a local cplex install with QGIS python environment (see our decision optimization algorithms)
-
-1. Open QGIS install folder, open the `bin` folder
- - probably: `C:\Program Files\QGIS 3.45.6\bin` (adjust version)
- - surely: `Win button > type QGIS > 2ndary click > Open file location > 2ndary click > Open file location > click 'bin' folder`
-2. Select `Python39` (check same version), properties, security, ... full control for user.
-
-{: width="75%" }
-
-Also on the gif, a success install of qtconsole being installed on `Program Files\Qgis` and not on user's `%APPDATA%` path, meaning success in making the python environment writable
-
-### setup CPLEX solver
-
-__At the moment (May 1st 2024, and for the last year), IBM has not released a python >3.10 compatible version. So QGIS<=3.36.0 is required.__
-
-0. Make your QGIS python environment writable by users (see previous section)
-1. Download and install the CPLEX solver from IBM's website (tested with CPLEX_Studio2211)
-2. Open OSGeo4W Shell
-3. Execute changing directory to the CPLEX install location, python folder, then run setup.py with the install argument:
-```batch
-cd ..\IBM\ILOG\CPLEX_Studio2211\python
-python setup.py install
-```
-Now you can just select CPLEX on any decision [optimization](/docs/docs/qgis-toolbox/README.html#deployed-algorithms) algorithm (advanced parameters section, on the dropdown form)
-{: width="75%" }
-
-### making a python environment launcher for developers
-
-To have a location independent launcher that activates the environment in a CMD terminal;
-- for running python scripts using QGIS without the application raised
-- that could be chained into VSCode for development [.vscode\settings.json](https://raw.githubusercontent.com/fire2a/fire2a-lib/main/.vscode/settings.json)
-
-Copy and modify `python-qgis.bat` that comes in QGIS `bin` folder, in these 3 steps (explainer gif after, [sample](https://raw.githubusercontent.com/fire2a/fire2a-lib/main/python-qgis-cmd.bat)):
-
-1. Open QGIS install folder, open the `bin` folder
- - probably: `C:\Program Files\QGIS 3.45.6\bin` (adjust version)
- - surely: `Win button > type QGIS > 2ndary click > Open file location > 2ndary click > Open file location > click 'bin' folder`
-2. Copy and rename `python-qgis.bat` to a location and name of your choosing
-3. Edit the 2nd and last line with:
-```batch
- REM call it from an absolute path
- REM adjust location and version
- call "%PROGRAMFILES%\QGIS 3.45.6\bin\o4w_env.bat" (adjust version)
-
- REM print the prefix as check
- echo python sys says:
- python -c "import sys; print('prefix:', sys.prefix, '\npath:', sys.path)"
- REM leave the terminal running
- cmd.exe /k
-```
-
-{: width="75%" }
-
----
-[QGIS]: https://qgis.org
-[requirements.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/fireanalyticstoolbox/requirements.txt
-[requirements.dev.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/requirements.dev.txt
-[Scott&Burgan-dialog-server]: https://fdobad.github.io/qgis-processingplugin-template/plugins.xml
-[Kitral simulator dialog-server]: https://fdobad.github.io/fire2am-kitral/plugins.xml
-[Processing-Toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
-[toolbox-releases]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/releases
-[toolbox-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
-[kitral-dialog-requirements.txt]: https://raw.githubusercontent.com/fdobad/fire2am-kitral/main/requirements.txt
-[TODO-Cell2Fire-requirements.txt]: https://github.com/fire2a/C2F-W
-
-[toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
-[fetching plugins]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html
-[custom]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html#basic-fa-configuring-additional-plugin-repositories
-[new plugin]: https://docs.qgis.org/3.28/en/docs/training_manual/qgis_plugins/fetching_plugins.html#basic-fa-installing-new-plugins
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diff --git a/docs/qgis-cookbook/img/qgis_windows_activate_venv.gif b/docs/qgis-cookbook/img/qgis_windows_activate_venv.gif
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diff --git a/docs/qgis-dialog/img/win_install_script.gif b/docs/qgis-dialog/img/win_install_script.gif
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diff --git a/docs/qgis-toolbox/README.md b/docs/qgis-toolbox/README.md
deleted file mode 100644
index 6092633..0000000
--- a/docs/qgis-toolbox/README.md
+++ /dev/null
@@ -1,153 +0,0 @@
----
-layout: default
-title: QGIS Fire Analytics Toolbox
-nav_order: 1
-has_children: true
-has_toc : false
----
--Fire Analytics Toolbox -
-{: .no_toc} -
-
-# Resumen
-Nuestra investigación aplicada en incendios como **herramientas gráficas GIS amigables para el usuario**:
-- *Simula* incendios forestales a gran escala usando Cell2Fire++
-- Obtén *métricas* de amenaza y riesgo
-- Usa el *sistema de soporte a la decisión* de ubicación de cortafuegos
-- *Combina* nuestros algoritmos con cualquier otro [QGIS] fácilmente
-
-Sin salir del entorno gráfico de [QGIS], solo instalando nuestro **plugin de algoritmos de procesamiento** *fire2a-toolbox*.
-
-Este tipo de plugins difiere de los plugins regulares -al ser mucho más que un cuadro de diálogo emergente- porque siguen una arquitectura de *pipeline de ciencia de datos*.
-Delimita claramente: entradas, salidas, algoritmos y contextos; logrando una integración perfecta con todos los algoritmos proporcionados en la [caja de herramientas], proporcionando 5 formas de ser ejecutado.
-
-# Alternativas de uso
-1. Tan simple como *llenar un **[cuadro de diálogo]*** (casillas de verificación, menús desplegables, selección de archivos, etc.); siendo las entradas mínimas un ráster de combustible y un escenario climático.
-2. **[Lote de formularios]**: Ejecuta ejecuciones secuenciales configurándolas en estilo de hoja de datos donde cada fila es un formulario (mostrado en columnas), *experimenta fácilmente sensibilidades de parámetros*.
-3. Como parte de un **[flujo de trabajo de modelo] gráfico**: Arrastra y suelta cajas de parámetros y algoritmos, conecta flechas como entradas-salidas entre ellos, en un [personalizado] *GIS-data-science-pipeline*.
-4. Desde una **herramienta de línea de comandos**, ejecuta `qgis_process` [envoltura cli] para llamar a cualquier algoritmo de procesamiento *sin sobrecarga gráfica de QGIS*.
-5. **Script de Python**, trabajando *tanto* [llamándolo] desde la [consola de python] de QGIS *o* como [código independiente]
-
-# Instalación
-[Guía completa aquí](/docs/docs/qgis-cookbook/README.html) o resumen:
-1. [QGIS] versión > 3.28.12 (la versión LTR es en su mayoría compatible pero carece, por ejemplo, de agrupación de resultados de simulación; se recomienda la última versión)
-2. La instalación de fire2a-toolbox casi se puede hacer directamente desde el **[gestor de plugins]** de QGIS *pero*:
- - Las [dependencias][requirements.txt] de Python deben resolverse manualmente
- - El enlace del repositorio/tienda de plugins de fire2a [enlace][toolbox-server] debe agregarse como una fuente de plugins personalizada (*)
-
-**¡Listo!** *El icono de fire2a-toolbox - Tabla de contenidos -
- {: .text-delta } -1. TOC -{:toc} - aparecerá en la lista de algoritmos del Panel de la Caja de Herramientas de Procesamiento*
-
-(*) : Debido a que contiene código binario c++ compilado -para el simulador Cell2Fire, pero el código binario no se puede verificar fácilmente, por lo que el plugin no se permite en el [repositorio/tienda](https://plugins.qgis.org/). Sin embargo, todo nuestro código es de código abierto, su compilación es "reproducible" por una acción automatizada; todo se puede auditar en [fire2a@github](
-
-* **Probadores** deben instalar por archivo `.zip` desde las [versiones][toolbox-releases] de fire2a-toolbox
-* **Desarrolladores** deben clonar nuestros repos ([toolbox-repo], [c2f-repo], [fire2a-lib-repo]), compilar cell2fire, hacer un enlace simbólico y configurar dependencias de python adicionales para contribuir ([tl;dr](/docs/docs/Cell2Fire/README.html#unix-overview))
-
-# Primer ejecución de prueba
-(¡Mira el gif al final!) Obtener o generar un ráster de modelo de combustible puede ser desafiante (próximamente tutorial), por lo que la forma más simple es:
-
-1. Usar el algoritmo de descarga 
para obtener una instancia preparada
-2. Guardar un [proyecto] vacío en la carpeta descargada (donde están los archivos de combustible, elevación y Weather.csv)
-3. Arrastrar y soltar capas desde el inicio del proyecto (Panel de Explorador de archivos) al Panel de Capas
-4. Establecer el mismo SRC a las capas y al proyecto (cualquiera en metros es suficiente)
-5. Abrir el algoritmo del simulador 
, seleccionar el modelo de combustible adecuado (Canadá, Kitral o S&B), seleccionar la capa de combustible en el menú desplegable de combustible, presionar ejecutar.
-
-
-{: width="75%" }
-
-
-Nota: El paso 2 se puede omitir, pero es engorroso seleccionar cada capa desde los exploradores de archivos que usar el menú desplegable para seleccionar entre las capas cargadas actualmente; Además, `Weather.csv` se selecciona automáticamente cuando hay un proyecto guardado.
-
-# Algoritmos desplegados
-
-**Fire Analytics Toolbox**
-
-
-: [(Cell2)Fire Simulator](./algo_simulator.html)
-
-
-: (Simulator) Instances Downloader
-
-**Decision optimization**
-
-
-: [Raster knapsack optimization](./algo_knapsack.html)
-
-
-: Polygon knapsack optimization : Optimiza el problema clásico de la mochila utilizando polígonos con atributos de valores y/o pesos, devuelve una capa de polígonos con los polígonos seleccionados.
-
-
-: Polygon treatment optimization : Usando posibles tratamientos para cada polígono, maximiza el valor cambiado de los polígonos tratados
-
-
-: Raster treatment optimization : Maximiza el valor cambiado del ráster tratado, decidiendo qué tratamiento aplicar a cada píxel (o sin cambios), sujeto a restricciones de presupuesto y área
-
-
-: Raster treatment & teams optimization : Maximiza el valor cambiado del ráster tratado, decidiendo qué tratamiento aplicar por qué equipo a cada píxel (o sin cambios), sujeto a restricciones de presupuesto, área y capacidades del equipo
-
-**Simulator Post Processing (simpp)**
-
-Bundle: Todos los post procesamientos combinados para conveniencia
-
-
-: Ignition Point(s)
-
-
-: (Propagation) Fire Scar(s)
-
-
-: Propagation Digraph
-
-
-: Spatial Statistics, cualquiera de: Hit Rate Of Spread, Flame Length, Byram Fire Line Intensity, Crown Fire Scar, Crown Fire Fuel Consumption Ratio, Surface Burn Fraction
-
-**simpp Risk Metrics**
-
-
-: DownStream Protection Value
-
-
-: Betweenness Centrality
-
-
-: Burn Probability
-
-**Auxiliariares**
-
-Match AII Grid Rasters : Simplifica el uso de gdal translate tres veces, para recortar la extensión, luego redimensionar y reemplazar el geotransform para que coincida con un ráster ascii en otro
-
-
----
-[QGIS]: https://qgis.org
-
-[requirements.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/fireanalyticstoolbox/requirements.txt
-[requirements.dev.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/requirements.dev.txt
-
-[Scott&Burgan-dialog-server]: https://fdobad.github.io/qgis-processingplugin-template/plugins.xml
-[Kitral simulator dialog-server]: https://fdobad.github.io/fire2am-kitral/plugins.xml
-[toolbox-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
-[c2f-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
-[fire2a-lib-repo]: https://www.github.com/fire2a/fire2a-lib
-
-
-[graphical model]: https://docs.qgis.org/latest/en/docs/user_manual/processing/modeler.html
-[toolbox]: https://docs.qgis.org/latest/en/docs/user_manual/processing/toolbox.html
-[form dialog]: https://docs.qgis.org/latest/en/docs/user_manual/processing/toolbox.html#the-algorithm-dialog
-[Batch of forms]: https://docs.qgis.org/latest/en/docs/user_manual/processing/batch.html#processing-batch
-[cli wrapper]: https://docs.qgis.org/latest/en/docs/user_manual/processing/standalone.html
-[python console]: https://docs.qgis.org/latest/en/docs/user_manual/plugins/python_console.html#console
-[calling it]: https://docs.qgis.org/latest/en/docs/user_manual/processing/console.html
-[standalone code]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/script_samples/standalone.py
-[custom]: https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/tree/main/graphical_models
-[plugin manager]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html
-
-[toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
-[toolbox-releases]: https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/releases
-[project]: https://docs.qgis.org/3.28/en/docs/user_manual/introduction/project_files.html
diff --git a/docs/qgis-toolbox/algo_knapsack.md b/docs/qgis-toolbox/algo_knapsack.md
deleted file mode 100644
index e10c4bf..0000000
--- a/docs/qgis-toolbox/algo_knapsack.md
+++ /dev/null
@@ -1,34 +0,0 @@
----
-layout: default
-title: Raster knapsack optimization
-nav_order: 2
-has_children: false
-has_toc : false
-parent: QGIS Fire Analytics Toolbox
----
-## Optimización de la mochila de ráster
-### Introducción
-_Una integración de prueba de concepto de solucionadores de programación matemática para modelar y resolver problemas de optimización con entidades GIS._
-
-Los usuarios pueden crear una nueva capa de ráster que seleccione los píxeles más valiosos en un ráster, de acuerdo con una restricción de capacidad definida por otro ráster -opcional- y una proporción fraccional.
-
-Varios solucionadores pueden ser utilizados (cbc, glpk, cplex_direct, gurobi, ipopt, NEOS, etc.), gracias a que el MIP se modela y resuelve a través de [pyomo](http://www.pyomo.org).
-
-Antes de ejecutar este algoritmo, asegúrese de haber instalado los solucionadores correspondientes que desee utilizar. Consulte la [documentación de pyomo](https://pyomo.readthedocs.io/en/stable/installation.html#conditional-dependencies) para obtener más detalles.
-
-| captura de pantalla |
-| --- |
-|
|
-
-### Descripción detallada
-Al seleccionar una capa de Valores y/o una capa de Pesos, y establecer el límite en la capacidad total, se crea una capa que maximiza la suma de los valores de los píxeles seleccionados.
-
-La restricción de capacidad se establece eligiendo una proporción (entre 0 y 1), que multiplica la suma de todos los pesos (excepto no-data). Por lo tanto, 1 selecciona todos los píxeles que no son no-data en ambas capas.
-
-Este problema de la mochila de ráster es NP-duro, por lo que se utiliza un motor de solución MIP para encontrar "casi" la solución óptima, porque -a menudo- es asintóticamente difícil probar el valor óptimo. Por lo tanto, un margen predeterminado del 0,5% y un límite de tiempo de 5 minutos cortan la ejecución del solucionador. El usuario puede experimentar con estos parámetros para equilibrar entre precisión, velocidad y tamaño de la instancia(*). ¡En Windows, cerrar la ventana de terminal en blanco abortará la ejecución!
-
-Al usar Pyomo, se pueden utilizar varios solucionadores MIP: CBC, GLPK, Gurobi, CPLEX o Ipopt; Si son accesibles a través de la ruta del sistema, de lo contrario, el archivo ejecutable puede ser seleccionado por el usuario.
-
-La instalación de los solucionadores(solvers) es responsabilidad del usuario, aunque la versión de Windows se incluye con binarios no firmados de CBC, por lo que sus usuarios verán una advertencia de "Windows protegió su PC", evite presionar el botón "No ejecutar", siga el enlace "Más información", desplácese y luego presione "Ejecutar de todos modos".
-
-(*): La complejidad puede reducirse en gran medida reescalando y/o redondeando los valores en enteros, o incluso mejor, coarsando la resolución del ráster (ver gdal translate resolution).
diff --git a/docs/qgis-toolbox/algo_simulator.md b/docs/qgis-toolbox/algo_simulator.md
deleted file mode 100644
index 1fa24bc..0000000
--- a/docs/qgis-toolbox/algo_simulator.md
+++ /dev/null
@@ -1,170 +0,0 @@
----
-layout: default
-title: (Cell2)Fire simulator
-nav_order: 1
-has_children: false
-has_toc : false
-parent: QGIS Fire Analytics Toolbox
----
-
-{: .no_toc}
-
-
-# Preparación de datos
-## Rasters
-* Las instancias preparadas están disponibles con el algoritmo "descargador de instancias"
-* Todos los rásteres (y el proyecto) deben estar proyectados en el mismo SRC, en metros cuadrados
-* Usando el ráster de combustible como base, los rásteres deben coincidir:
- - En número de píxeles en ambas direcciones
- - A lo sumo un desplazamiento de un píxel en cada dirección
- - Por lo tanto, el tamaño del píxel debe ser muy cercano [~mm]
-
-| rásteres | propósito | unidades |
-| --- | --- | --- |
-| combustibles | codificar el paisaje | tabla de modelos de combustible |
-| elevación | dem | metros |
-| cbh | altura de la base del dosel es donde está la rama más baja | metros |
-| cbd | densidad a granel del dosel | kg/m3 |
-| ccf | fracción de cobertura del dosel es como un indicador de cobertura de nubes | [0,1] |
-| py | mapa de densidad de probabilidad es para dibujar igniciones | [0,1] |
-
-## Clima
-**Especificación de la tabla Weather.csv:**
-* columnas mínimas: `name,timestamp,wind-speed,wind-direction`
-* filas: por defecto cada fila dura una hora
-* columnas dependientes del modelo de combustible:
-
-Canadá
-: `Scenario,datetime,APCP,TMP,RH,WS,WD,FFMC,DMC,DC,ISI,BUI,FWI`
-
-Kitral
-: `Instance,datetime,WS,WD,TMP,RH`
-
-Scott&Burgan
-: `Scenario,datetime,WS,WD,FireScenario`
-
-* FireScenario fue deprecado por "Live & Dead Fuel Moisture Content Scenario [1=seco..4=húmedo]"
-* No es necesario ser consistente con las marcas de tiempo, pero se debe seguir la isoformat `AAAA-MM-DDTHH:MM:SS`
-* TrabajoEnProgreso: unificar formatos de clima, confiar en los nombres de las columnas en lugar del orden para leerlos
-
-volver_arriba
-{: style="text-align: right;"}
-
-# Rellenando el diálogo
-El diálogo del simulador se divide en cuatro secciones principales: *Paisaje, igniciones, clima y salidas*. Y dos opcionales: configuración de ejecución y opciones avanzadas.
-Aunque intuitivo (por ejemplo, hacer coincidir cada unidad dimensional mostrada entre corchetes), cada sección se comenta a continuación:
-
-## Paisaje
-{: width="85%"}
-* El modelo de combustible de superficie debe coincidir con la codificación del ráster de combustible (ver [tablas de búsqueda])
-* La casilla de verificación de estilo de ráster no solo "pinta" usando el algoritmo 'native:setlayerstyle' según cada [capa de estilo qml], sino que también muestra la clasificación en el panel de capas
-* Habilitar el comportamiento del fuego de copa tiene sentido *incluso sin rásteres de dosel porque hay números estándar fijos* para ellos según la codificación del combustible (solo disponible en el modelo de combustible de Canadá)
-
-volver_arriba
-{: style="text-align: right;"}
-
-## Igniciones
-{: width="85%"}
-* Al simular **una o pocas simulaciones**, obtener una salida detallada es relevante (como **digrafo de propagación y cicatrices de propagación**)
-* Al simular **cientos o miles**, las estadísticas de media y desviación estándar son más importantes que una salida detallada que puede ahogar innecesariamente la computadora (usar **cicatriz final** en lugar de cicatrices de propagación; el digrafo de propagación es la entrada para las medidas de DPV y Centralidad; pero no se podrá cargar en la vista!)
-* Hay 3 formas de generar igniciones:
- 0. Sortear un píxel aleatorio pero quemable **distribuido uniformemente**
- 1. Sortear usando un ráster de **mapa de probabilidad**
- 2. Especificar un **punto** y opcionalmente un radio para especificar un **círculo** desde donde sortear uniformemente
-* Si se pasan varios puntos en la "capa de un solo punto", solo se tomará en consideración el último[?] (ver id de característica (fid) en la tabla de atributos de la capa)
-* Tenga en cuenta que hay una entrada para definir semilla aleatoria, por lo tanto, la misma semilla implica dibujar el mismo punto (o secuencia de puntos)
-
-volver_arriba
-{: style="text-align: right;"}
-
-## Tiempo Atmosférico
-{: width="85%"}
-* El simulador asume **parámetros meteorológicos constantes en la cuadrícula**, pueden cambiar con el tiempo, pero no en el espacio
-* Estos parámetros se pasan al simulador usando un archivo `.csv`
-* En una simulación regular **cada fila dura 1 hora**, cuando las filas terminan, la simulación termina
-* Hay dos opciones:
- 0. Usar solo un `Weather.csv`
- 1. Sortear al azar de un directorio `Weathers/WeatherN.csv : N = 1,2,...` nombrado correlativamente
-* TrabajoEnProgreso: una base de datos meteorológica; mientras tanto, los climas se pueden obtener de *weather.org desde cualquier ubicación desde 1970 hasta la fecha actual*
-
-volver a especificacion del tiempo \| arriba
-{: style="text-align: right;"}
-
-## Configuración de ejecución
-{: width="85%"}
-* Solo baje los hilos de la CPU de la simulación si planea seguir trabajando en otra cosa mientras las simulaciones se ejecutan en segundo plano (para la oficina o la navegación web nunca necesitará más de 2)
-* Llevar un registro de la semilla garantiza la reproducibilidad de todos los números aleatorios generados
-
-volver_arriba
-{: style="text-align: right;}
-
-## Salidas
-Esta sección tiene tres partes principales: opciones, avanzadas y directorios de destino.
-{: width="85%"}
-
-### Opciones
-* Acceda a la selección múltiple haciendo clic en los `...` a la derecha
-{: width="85%}
-* La mayoría de las salidas se adaptan según sean 1 o >1 simulaciones
-* Al simular **una o pocas simulaciones**, una salida detallada es relevante (como **digrafo de propagación y cicatrices de propagación**)
-* Al simular **cientos o miles**, las estadísticas de media y desviación estándar son más importantes que una salida detallada que puede ahogar innecesariamente la computadora (usar **cicatriz final** en lugar de cicatrices de propagación; el digrafo de propagación es la entrada para las medidas de DPV y Centralidad; pero no se podrá cargar en la vista!)
-
-| nombre de la salida | tipo de unidad | descripción |
-|:-------------|:------------------|:------|
-| Cicatrices finales | ráster `0,1` | |
-| Gráfico dirigido de propagación | líneas vectoriales `períodos` | bordes etiquetados con el tiempo del evento de simulación |
-| Tasa de propagación de incendios | ráster float32 `m/m` | multibanda x simulación y bi-banda media y desviación estándar |
-| Cicatrices de propagación de incendios | polígonos | _animar añadiendo la columna_ `=now()+ make_interval(hours:=time)` |
-| Longitud de la llama | ráster float32 `m` | multibanda x simulación y bi-banda media y desviación estándar |
-| Intensidad de la línea de fuego de Byram | ráster float32 `kW/m` | multibanda x simulación y bi-banda media y desviación estándar |
-| Cicatriz de incendio de copa | ráster `0,1` | multibanda x simulación y bi-banda media y desviación estándar |
-
-volver_arriba
-{: style="text-align: right;}
-
-### Opciones Avanzadas
-* - Tabla de contenidos -
- {: .text-delta } -1. TOC -{:toc} -Desplegar el bloque usando el triángulo
a la izquierda de Parámetros Avanzados+Cell2FireW simulator +
+ +{: .warning} +CLI C++ code; Check the graphical user friendly version: [Fire Analytics Toolbox QGIS plugin]({{ site.baseurl }}/qgis-toolbox) + +{: .no_toc} +
+
+
+# Overview
+
+_Originally forked from [Cell2Fire](https://github.com/cell2fire/Cell2Fire), thanks to the work of Cristobal Pais, Jaime Carrasco, David Martell, [David L. Woodruff](https://github.com/DLWoodruff), Andres Weintraub, et al._
+
+Cell2Fire is a 2D-grid-based forest and wildland landscape fire simulator, focused on large scale areas and fast simulations to provide robust risk spatial analytics, harnessing c++ parallel computation methods.
+
+Current Version:
+- [W](https://github.com/fire2a/c2f-w) bundles Spain, Chile and Canada fuel model behaviors!
+- _Want your own local fuel model? [Contact us!](getting-help/#how-to-reach-us)_
+
+Released flavors (*no longer maintained*):
+- [Scott & Burgan](https://github.com/fire2a/C2FSB)
+- [Kitral](https://github.com/fire2a/C2FK)
+- [FBP](https://github.com/fire2a/C2FFBP)
+
+# Output examples
+
+## Scott & Burgan
+### Previncat's Zone 60 (Catalonian Instance): forest and a simulated fire spread with its corresponding scar and growth propagation tree.
+
+### Risk metrics: Burn Probability (BP), Betweenness Centrality (BC), Downstream Protection Value (DPV), and Growth Propagation Tree (GPT).
+
+
+## Kitral
+### El Portillo, simulation with crown fire behavior.
+
+
+## Canadian Forest Fire Behavior Prediction System
+
+|:-------------|:------------------|
+| Dogrib forest, Canada {: width="100%" } | shortest paths propagation {: width="80%" } |
+| Shortest paths propagation and ROS intensity {: width="100%" } | Burn-Probability {: width="80%" } |
+
+# Get Cell2FireW
+## gui
+Most users would want to get the graphical user friendly version: [Fire Analytics Toolbox QGIS plugin](/qgis-toolbox)
+## cli
+Get a ready to use binary (choose your platform), from the [latest release](https://www.github.com/fire2a/C2F-W/releases/latest) page.
+## source
+- Check the [repo's action artifacts](https://github.com/fire2a/C2F-W/actions) for the latest info on automated builds
+- Check the [developer setup guide](https://github.com/fire2a#developer-setup) for a global view
+### Linux [Make](compile_linux.html)
+### Macos [Make](compile_macos.html)
+### Windows [Visual Studio](compile_windows.html)
diff --git a/Gemfile b/site/Gemfile
similarity index 64%
rename from Gemfile
rename to site/Gemfile
index 5fd82f8..0a31a6a 100644
--- a/Gemfile
+++ b/site/Gemfile
@@ -1,9 +1,9 @@
source 'https://rubygems.org'
-gem "jekyll", "~> 4.3.3" # installed by `gem jekyll`
+gem "jekyll", "~> 4.3.4" # installed by `gem jekyll`
# gem "webrick" # required when using Ruby >= 3 and Jekyll <= 4.2.2
-gem "just-the-docs", "0.7.0" # pinned to the current release
+gem "just-the-docs", "0.10.1" # pinned to the current release
# gem "just-the-docs" # always download the latest release
#
diff --git a/Gemfile.lock b/site/Gemfile.lock
similarity index 70%
rename from Gemfile.lock
rename to site/Gemfile.lock
index bd26e79..55c09ff 100644
--- a/Gemfile.lock
+++ b/site/Gemfile.lock
@@ -1,21 +1,24 @@
GEM
remote: https://rubygems.org/
specs:
- addressable (2.8.6)
- public_suffix (>= 2.0.2, < 6.0)
+ addressable (2.8.7)
+ public_suffix (>= 2.0.2, < 7.0)
+ bigdecimal (3.1.9)
colorator (1.1.0)
- concurrent-ruby (1.2.3)
+ concurrent-ruby (1.3.5)
em-websocket (0.5.3)
eventmachine (>= 0.12.9)
http_parser.rb (~> 0)
eventmachine (1.2.7)
- ffi (1.16.3)
+ ffi (1.17.1)
forwardable-extended (2.6.0)
- google-protobuf (3.24.4-x86_64-linux)
+ google-protobuf (4.29.3-x86_64-linux)
+ bigdecimal
+ rake (>= 13)
http_parser.rb (0.8.0)
- i18n (1.14.1)
+ i18n (1.14.7)
concurrent-ruby (~> 1.0)
- jekyll (4.3.3)
+ jekyll (4.3.4)
addressable (~> 2.4)
colorator (~> 1.0)
em-websocket (~> 0.5)
@@ -41,45 +44,45 @@ GEM
jekyll (>= 3.8, < 5.0)
jekyll-watch (2.2.1)
listen (~> 3.0)
- just-the-docs (0.7.0)
+ just-the-docs (0.10.1)
jekyll (>= 3.8.5)
jekyll-include-cache
jekyll-seo-tag (>= 2.0)
rake (>= 12.3.1)
- kramdown (2.4.0)
- rexml
+ kramdown (2.5.1)
+ rexml (>= 3.3.9)
kramdown-parser-gfm (1.1.0)
kramdown (~> 2.0)
liquid (4.0.4)
- listen (3.8.0)
+ listen (3.9.0)
rb-fsevent (~> 0.10, >= 0.10.3)
rb-inotify (~> 0.9, >= 0.9.10)
mercenary (0.4.0)
pathutil (0.16.2)
forwardable-extended (~> 2.6)
- public_suffix (5.0.4)
- rake (13.0.6)
+ public_suffix (6.0.1)
+ rake (13.2.1)
rb-fsevent (0.11.2)
- rb-inotify (0.10.1)
+ rb-inotify (0.11.1)
ffi (~> 1.0)
- rexml (3.2.6)
- rouge (4.2.0)
+ rexml (3.4.0)
+ rouge (4.5.1)
safe_yaml (1.0.5)
- sass-embedded (1.69.5)
- google-protobuf (~> 3.23)
- rake (>= 13.0.0)
+ sass-embedded (1.83.4)
+ google-protobuf (~> 4.29)
+ rake (>= 13)
terminal-table (3.0.2)
unicode-display_width (>= 1.1.1, < 3)
- unicode-display_width (2.5.0)
- webrick (1.8.1)
+ unicode-display_width (2.6.0)
+ webrick (1.9.1)
PLATFORMS
x86_64-linux
DEPENDENCIES
- jekyll (~> 4.3.3)
+ jekyll (~> 4.3.4)
jekyll-avatar (~> 0.8.0)
- just-the-docs (= 0.7.0)
+ just-the-docs (= 0.10.1)
BUNDLED WITH
- 2.3.26
+ 2.3.15
diff --git a/_config.yml b/site/_config.yml
similarity index 85%
rename from _config.yml
rename to site/_config.yml
index 1684f16..143c20a 100644
--- a/_config.yml
+++ b/site/_config.yml
@@ -1,7 +1,7 @@
# https://just-the-docs.github.io/just-the-docs/docs/configuration/
-title: Fire2a Documentación
-description: Documentación para herramientas publicadas del grupo de investigación Fire2a
+title: Fire2a User Documentation
+description: User documentation of tools & software published by Fire2a research group.
theme: just-the-docs
url: "https://fire2a.github.io/docs"
repository: fire2a/docs
@@ -9,14 +9,14 @@ repository: fire2a/docs
# color_scheme: nil
aux_links:
- "View on github": https://github.com/fire2a/documentacion
+ "View on github": https://github.com/fire2a
aux_links_new_tab: true
heading_anchors: true
-logo: "/docs/assets/f2a-icon.png"
-favicon_ico: "/docs/assets/nofire.ico"
+logo: "/assets/f2a-icon.png"
+favicon_ico: "/assets/nofire.ico"
exclude:
# from https://github.com/jekyll/jekyll/blob/master/lib/site_template/_config.yml:
@@ -77,19 +77,19 @@ search:
callouts:
# grey-lt, grey-dk, purple, blue, green, yellow, red
success:
- title: Éxito
+ title: Success
color: green
opacity: 0.3
info:
- title: Información
+ title: Information
color: blue
opacity: 0.3
warning:
- title: Advertencia
+ title: Warning
color: yellow
opacity: 0.3
critical:
- title: Crítico
+ title: Critical
color: red
opacity: 0.3
diff --git a/_includes/footer_custom.html b/site/_includes/footer_custom.html
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rename from _includes/footer_custom.html
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diff --git a/site/algo-lib/api_doc.md b/site/algo-lib/api_doc.md
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+++ b/site/algo-lib/api_doc.md
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+---
+layout: default
+title: API Documentation
+nav_order: 2
+has_toc: false
+parent: Algorithms Library
+---
+
+
diff --git a/site/algo-lib/index.md b/site/algo-lib/index.md
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+++ b/site/algo-lib/index.md
@@ -0,0 +1,26 @@
+---
+layout: default
+title: Algorithms Library
+nav_order: 3
+has_toc: false
+---
+# Algorithms Library
+
+This library is a [Python package] containing fire-related algorithms, decision optimization tools, common utilities, and tools for GIS, clustering, and more.
+
+It supports the integration of [QGIS Fire Analytics Toolbox] with [Cell2FireW simulator].
+
+The target users are developers and researchers who want to reuse these algorithms in their own projects, as well as terminal users looking to gain efficiency by running the algorithms via CLI instead of through the QGIS GUI.
+
+* [Installation & Quickstart](https://github.com/fire2a/fire2a-lib/blob/main/README.md)
+* [API Documentation]
+
+{: .info}
+Everything Everywhere All at Once [https://github.com/fire2a#developer-setup](https://github.com/fire2a#developer-setup)
+
+---
+[python package]: https://pypi.org/project/fire2a-lib
+[QGIS Fire Analytics Toolbox]: /docs/qgis-toolbox/
+[Cell2FireW simulator]: /docs/Cell2Fire/README.html
+[API Documentation]: https://fire2a.github.io/fire2a-lib
+
diff --git a/site/algo-lib/repo_quickstart.md b/site/algo-lib/repo_quickstart.md
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--- /dev/null
+++ b/site/algo-lib/repo_quickstart.md
@@ -0,0 +1,9 @@
+---
+layout: default
+title: Installation & Quickstart
+nav_order: 1
+has_toc: false
+parent: Algorithms Library
+---
+
+
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diff --git a/site/getting-help/index.md b/site/getting-help/index.md
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+---
+layout: default
+title: Getting Help
+nav_order: 6
+has_children: true
+has_toc: false
+---
+# Getting Help 🚑
+## How to reach us
+
+1. Public relations mail (ask to join our mailing list!) or [linkedin](https://www.linkedin.com/company/fire2a).
+2. Chat with us at [discord](https://discord.gg/wSuSFjrt).
+3. Post a Github Issue
+
+## Before getting help checklist
+
+1. Avoid cloud drives and network shared folders
+ - Use QGIS temporary outputs.
+ - Create `C:\local` or `~/local` folder for your work.
+2. Avoid funny characters (` `,`á`,`é`,`í`,`ö`, etc.) in directories, files and names.
+3. Avoid funny formats for rasters and vectors
+ - `Options > Processing > default raster & vector layers` formats set to `tif & gpkg` respectively
+ - Save all input and output layers in these formats.
+4. Update or reinstall -if apply:
+ - Cell2FireW release
+ - Algorithms Library: fire2a-lib package (further see into recreating the virtual environment)
+ - QGIS Fire Analytics Toolbox Plugin.
+5. Update and restart: QGIS, your OS, your computer.
+6. Try again in a new, clean project; if the problem persist, gather these details:
+
+## Help message indispensables
+
+1. [If using] QGIS system info: `Help > About > Copy to clipboard`
+2. Your goal, expectations and unexpected behavior
+3. Clear steps to reproduce the issue (fullscreen video recording is a plus)
+4. Specific logs and error messages (full QGIS processing log is a plus)
+5. [If using] Other QGIS log messages: `View > Panels > Log Messages` (Plugins, Processing, Python, fire2a)
+6. [If using] Cell2FireW simulator, zip the input instance folder and attach it. If possible, the output log file.
+
+## Github Issues
+
+1. [Cell2FireW](https://www.github.com/fire2a/C2F-W/issues)
+2. [QGIS Fire Analytics Toolbox](https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/issues)
+3. [Algorithms Library](https://www.github.com/fire2a/fire2a-lib/issues)
+4. [This very documentation](https://www.github.com/fire2a/docs/issues)
diff --git a/site/index.md b/site/index.md
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+++ b/site/index.md
@@ -0,0 +1,59 @@
+---
+title: Home
+layout: home
+---
+Welcome to Fire2a's research group user documentation, choose your component:
+
+[__QGIS Fire Analytics Toolbox__](qgis-toolbox): Our research as **user friendly graphical tools**: Simulate wildfires, get risk metrics, optimize firebreak location, etc. All from within [QGIS]. **Simple as filling a form**. Also available: drag'n'drop boxes (algorithms) into a *GIS-data-science-pipeline*.
+
+[__Cell2FireW__](Cell2FireW): Forest fire simulator ([Forked]) and improved ([Here]). Supports Canada, Kitral, S&B fuel models , surface and crown fire, deals with weather scenarios, surface and vegetation moisture content; various output metrics. Also enhances in memory management, platform support, etc. **C++ only command line interface.**
+
+[__Algorithms Library__](algo-lib) of common tasks & patterns of GIS. Also showcasing proof of concepts and special algorithms developed such as landscape clustering, firebreak optimization allocation, downstream protection value, etc. **A python package.**
+
+[__QGIS cookbook__](qgis-cookbook): Install & setup guides, python environments, plugins and workflows examples.
+
+[__QGIS management__](qgis-management): Install & setup guides, python environments, plugins and workflows examples.
+
+[__Getting help__](getting-help): How to reach us, before getting help checklist, help message indispensables.
+
+
+# About us
+
+We are a research group that seeks solutions to complex problems arising from the terrestrial ecosystem and its natural and anthropogenic disturbances, such as wildfires.
+
+Currently hosted at [ISCI](https://isci.cl) offices.
+
+Contact us at fire2a@fire2a.com.
+
+Visit our public webpage.
+
+[{: width="40" }](https://www.dii.uchile.cl/~aweintra/)
+[{% avatar caro %}](https://github.com/car0espinoza/)
+[{% avatar fdobad %}](https://github.com/fdobad/)
+[{% avatar felipe %}](https://github.com/FelipedlB/)
+[{% avatar jaime %}](https://github.com/jaimecarrasco/)
+[{% avatar matiasuno %}](https://github.com/matiasuno/)
+[{% avatar matilde %}](https://github.com/matilderivas/)
+[{% avatar rodrigo %}](https://github.com/RodrigoMahalufRecasens/)
+
+[{% avatar bulla %}](https://github.com/antoniochavez18/)
+[{% avatar diego %}](https://github.com/diegoteran99/)
+[{% avatar esteban %}](https://github.com/Sigggma/)
+[{% avatar felipeUlloa %}](https://github.com/fulloaf/)
+[{% avatar fire2a %}](https://github.com/fire2a/)
+[{% avatar lucas %}](https://github.com/lucasmurray97/)
+[{% avatar ramiro %}](https://github.com/R4miro-P/)
+[{% avatar sebastian %}](https://github.com/sebarojasmorales/)
+
+
+
+
+### _About this page_
+It's all [markdown!](markdown_kitchen_sink.html)
+[content license](https://github.com/fire2a/docs/raw/refs/heads/main/LICENSE)
+[just-the-docs-licence](https://github.com/just-the-docs/just-the-docs-template/raw/refs/heads/main/LICENSE)
+
+---
+[QGIS]: https://qgis.org
+[Forked]: https://github.com/cell2fire/Cell2Fire/
+[Here]: https://github.com/fire2a/C2F-W/
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+---
+layout: default
+title: QGIS Cookbook
+nav_order: 4
+has toc: false
+---
+{: .no_toc}
++ Table of contents +
+ {: .text-delta } +1. TOC +{:toc} +
+
+
+# Check a fire2a algorithm's html log from WSL
+_Did you accidentally close the algorithm's dialog window, and at reopening the execution log is gone? We got you covered:_
+- [Open the log messages panel](https://docs.qgis.org/latest/en/docs/user_manual/introduction/general_tools.html#log-messages-panel)
+- Look for the `fire2a` tab
+- Each algorithm execution is timestamped, identified by its name and the location of its log file, copy the location of the log file
+- Open a terminal and navigate to the log file location
+- Start a python [http server](https://docs.python.org/3/library/http.server.html) to visualize the html log file back in windows
+```bash
+cd /tmp/processing_vYybGp/8a8bd04a438641cf8a780de0dbe7eea6/InstanceDirectory/results
+python3 -m http.server
+ Serving HTTP on 0.0.0.0 port 8000 (http://0.0.0.0:8000/) ...
+ 127.0.0.1 - - [24/Jan/2025 22:48:48] "GET / HTTP/1.1" 200 -
+# stop the server with Ctrl+C or closing the terminal
+```
+- Back on Windows, open your favorite web-browser (firefox) and open [http://localhost:8000/](http://localhost:8000/)
+
+---
+[QGIS]: https://qgis.org
+[requirements.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/fireanalyticstoolbox/requirements.txt
+[requirements.dev.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/requirements.dev.txt
+[Scott&Burgan-dialog-server]: https://fdobad.github.io/qgis-processingplugin-template/plugins.xml
+[Kitral simulator dialog-server]: https://fdobad.github.io/fire2am-kitral/plugins.xml
+[Processing-Toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
+[toolbox-releases]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/releases
+[toolbox-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
+[kitral-dialog-requirements.txt]: https://raw.githubusercontent.com/fdobad/fire2am-kitral/main/requirements.txt
+[TODO-Cell2Fire-requirements.txt]: https://github.com/fire2a/C2F-W
+
+[toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
+[fetching plugins]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html
+[custom]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html#basic-fa-configuring-additional-plugin-repositories
+[new plugin]: https://docs.qgis.org/3.28/en/docs/training_manual/qgis_plugins/fetching_plugins.html#basic-fa-installing-new-plugins
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+---
+layout: default
+title: QGIS Management
+nav_order: 5
+has_children: true
+has_toc: false
+---
+## [Install & Setup guide](./install.html)
+__tl;dr:__
+- prefer the latest over the LTR (long term release) of QGIS
+- __Linux__: setup an system aware python virtual environment for QGIS
+- __MacOS__: use the bundled python directly
+- __Windows__:
+ - `WSL` >> `OSGeo4W installer` >> `Standalone` installer
+ - make your python environment writable
+ - use the bundled python directly
+
+## [Plugins guide](./plugins.html)
+__tl;dr:__
+- There are store plugins, custom store plugins, zip releases and manual installations
+- Must have plugins: Save All, Serval, IPyConsole, Plugin Reloader, Plugin Builder
+- Python dependencies are up to the user to install, but our plugin has a built-in dependency installer
diff --git a/site/qgis-management/install.md b/site/qgis-management/install.md
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+---
+layout: default
+title: Install & Setup
+nav_order: 5
+parent: QGIS Management
+has_children: false
+has_toc: false
+---
+{: .no_toc}
++ Table of contents +
+ {: .text-delta } +1. TOC +{:toc} +
+
+# tl;dr:
+- prefer the latest over the LTR (long term release) of QGIS
+- __Linux__: setup an system aware python virtual environment for QGIS
+- __MacOS__: use the bundled python directly
+- __Windows__:
+ - `WSL` >> `OSGeo4W installer` >> `Standalone` installer
+ - make your python environment writable
+ - use the bundled python directly
+
+# LTR vs Latest
+QGIS has two versions: Long Term Release (LTR) and Latest. The LTR may be the most stable version, but lacks new features that the Latest version has. But also [QGIS relase schedule](https://qgis.org/resources/roadmap/#schedule) moves very fast (every 3 or so months), so there's no much point into supporting old versions for long.
+
+At the time of writing we support 3.36.2 and up.
+
+# Linux 🗽
+- Official QGIS [install tutorial](https://qgis.org/download/)
+- Make a system aware python virtual environment for QGIS:
+ ```bash
+ # required
+ sudo apt install python3-venv
+
+ # ~/pyvenv/qgis is just an example
+ python3 -m venv --system-site-packages ~/pyvenv/qgis
+ ```
+- Usage: activate before launching qgis
+ ```bash
+ source ~/pyvenv/qgis/bin/activate
+ qgis
+ ```
+- Customize QGIS's application "icon" launcher for ease of use:
+ ```bash
+ # make a user copy
+ mkdir -p ~/.local/share/applications
+ cp /usr/share/applications/org.qgis.qgis.desktop ~/.local/share/applications/org.qgis.qgisvenv.desktop
+
+ # edit the sections in
+ nano ~/.local/share/applications/org.qgis.qgisvenv.desktop
+ # rename the launcher
+ Name=QGIS Desktop (venv)
+
+ # activate the python environment
+ Exec=bash -c 'source ~/pyvenv/qgis/bin/activate && qgis %F'
+
+ # + make local binaries available (usually user local binaries not in PATH)
+ # do you even have a ~/.local/bin?
+ Exec=bash -c 'export PATH=$HOME/.local/bin:$PATH && source ~/pyvenv/qgis/bin/activate && qgis %F'
+
+ # + all logs for developers
+ Exec=bash -c 'export PATH=$HOME/.local/bin:$PATH && source ~/pyvenv/qgis/bin/activate && qgis %F | tee -a /tmp/qgis.log'
+ Terminal=true
+
+ # if the icon not showing right away
+ update-desktop-database ~/.local/share/applications/
+ ```
+
+back to top
+{: style="text-align: right;"}
+
+# MacOS
+- Official QGIS [install tutorial](https://qgis.org/resources/installation-guide/#mac-os-x--macos)
+
+back to top
+{: style="text-align: right;"}
+
+# Windows
+Our recommendation priorities: Use the linux subsystem for windows (WSL), else the OSGeo4W installer, else the standalone installer.
+
+Some algorithms (DPV) don't parallelize in Windows; the standalone installer doesn't update, so upgrading is slow! Using the bundled python is difficult -it can't even make a virtual environment to isolate different plugins! So WSL FTW!
+
+## Windows Subsystem for Linux (WSL2)
+Official [guide](https://learn.microsoft.com/en-us/windows/wsl/tutorials/gui-apps), nevertheless here are the main steps for setting up Debian with QGIS:
+- Prerequisites: Windows 10 Build 19044+ or Windows 11 (for WSL2 with GUI)
+
+1. Virtualization must be enabled (usually is, but restart to bios or uefi setup and check, else the next step will fail)
+2. Activate the Windows Subsystem for Linux (WSL) additional feature (Start > Search > `Turn Windows features on or off` > checkbox `Windows Subsystem for Linux`, needs restarting)
+3. Install Debian Linux distribution from the Microsoft Store or type in PowerShell
+ ```powershell
+ wsl --install -d Debian
+ ```
+4. Install the graphic drivers for gui apps (Open Debian from the Start menu)
+ ```bash
+ # update and upgrade the system (tip: repeat monthly)
+ sudo apt update && sudo apt upgrade -y
+
+ # install the graphic drivers by allowing firmware packages
+ sudo nano /etc/apt/sources.list
+
+ # add contrib, non-free and non-free-firmware to the end of the lines (3 or 4 lines), like this:
+ deb http://deb.debian.org/debian bookworm main contrib non-free non-free-firmware
+
+ # save and exit the editor: Ctrl+O, Enter, Ctrl+X
+
+ # update and install the drivers
+ sudo apt update && sudo apt install firmware-linux firmware-linux-nonfree -y
+ sudo reboot
+
+ # test the drivers
+ sudo apt install x11-apps
+ xeyes
+ ```
+
+5. Check this [tutorial](https://learn.microsoft.com/en-us/windows/wsl/filesystems?source=recommendations), tl;dr:
+ - _Linux programs should work over linux locations, mixing windows locations is slow_
+ - linux path `/home/+ Table of contents +
+ {: .text-delta } +1. TOC +{:toc} +
+
+# tl;dr:
+- There are store plugins, custom store plugins, zip releases and manual installations
+- Must have plugins: Save All, Serval, IPyConsole, Plugin Reloader, Plugin Builder
+- Python dependencies are up to the user to install, but our plugin has a built-in dependency installer
+
+# Installing
+QGIS provides a plugin ["app store"](https://plugins.qgis.org/) that allows many developers to share their work.
+There are several ways to install plugins, using the plugin manager is the most common way:
+## _Search and install_ [official guide](https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html#lesson-installing-and-managing-plugins)
+## _Install a custom app repository_ [official guide](https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html#follow-along-configuring-additional-plugin-repositories)
+To install our plugin, add fire2a's [plugin store URL][toolbox-server] as a custom plugin source
+- `QGIS menu > Plugins > Manage and Install Plugins > Settings > Add > paste the URL > Ok`
+- On the `Not Installed` tab search `Fire` and install `Fire Analytics Processing-Toolbox`
+- _Why custom? Audit our [binaries](https://github.com/fire2a/C2F-W/actions)_
+
+## _Load a zip release file_
+- For example, download the [latest release](https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/releases/latest) of our plugin.
+- Install it using the `Install from ZIP` in the `Plugin Manager`
+
+## Or skip the plugin manager and _manually place the plugin into the plugins directory_
+Using `fireanalyticstoolbox` as an example:
+### Linux 🗽
+```bash
+# user plugin directory
+~/.local/share/QGIS/QGIS3/profiles/default/python/plugins/fireanalyticstoolbox
+# processing plugin directory
+/usr/share/qgis/python/plugins/processing
+```
+### MacOS
+```zsh
+# QGIS python location
+/Applications/QGIS.app/Contents/MacOS/bin/python3
+# user plugin directory
+~/Library/Application\ Support/QGIS/QGIS3/profiles/default/python/plugins/fireanalyticstoolbox
+```
+### Windows
+```batch
+REM QGIS python location
+C:\OSGeo4W\bin\python-qgis.bat # osgeo4w
+C:\Program Files\QGIS 3.40.2\bin\python-qgis.bat # standalone
+REM user plugin directory
+C:\Users\+ Table of contents +
+ {: .text-delta } +1. TOC +{:toc} +
+: [Save All](https://plugins.qgis.org/plugins/SaveAllScript/), Tired of saving temporary layers? Choose a location & new directory, done! every layer gets written, never worry again about temporary or memory layers!
+
+
+: [Serval](https://plugins.qgis.org/plugins/Serval/), Modify your rasters with your mouse, as if you were using paint!
+
+
+: [IPyConsole](https://plugins.qgis.org/plugins/IPyConsole/), "No offense, but QGIS python console just sucks." ([sic](https://www.itopen.it/qgis-and-ipython-the-definitive-interactive-console/#comment-140751)) [documentation](http://www.itopen.it/qgis-and-ipython-the-definitive-interactive-console/), [fix to use latest qtconsole](https://github.com/elpaso/qgis-ipythonconsole/compare/master...fdobad:qgis-ipythonconsole:master)
+
+
+: [Plugin Reloader](https://plugins.qgis.org/plugins/plugin_reloader/), If a plugin starts misbehaving easier to reload it than to restart QGIS
+
+
+: [Plugin Builder](https://plugins.qgis.org/plugins/pluginbuilder3), Jumpstart your plugin development!
+
+back to top
+{: style="text-align: right;"}
+
+# Python dependencies
+Each plugin may have its own unique combination of python dependencies and the combination of various plugins may create unique conflicting version requirements (further read [dependency hell](https://en.wikipedia.org/wiki/Dependency_hell))
+
+| 
| 
|
+|:--:| :--: |
+| Our plugin has a built-in dependency installer | But it can be disabled |
+
+That's why the installation of these dependencies is up to the user, so they can control their own environment; __Usually this just means installing the requirements of the plugin at last and restarting QGIS.__ (Any other plugin complaining about a dependencies should be disabled for the time being)
+
+
+4 ways to manually install python dependencies, using:
+
+## QGIS python console
+This is the easiest way but ___Can crash QGIS!___ save your work before trying this
+
+Open the [python console](https://docs.qgis.org/latest/en/docs/user_manual/plugins/python_console.html) to use pip directly from the parent terminal using the escape char `!`, for example type:
+```
+>>> !pip install -r /path/to/requirements.txt # to install a list of requirements
+>>> !pip install fire2a-lib # to install a package
+```
+Restart QGIS to see the changes
+
+## OSGeo4W shell (Windows)
+Open the OSGeo4W shell and activate the custom environment, then use pip as usual:
+```batch
+C:\OSGeo4W> cd bin
+C:\OSGeo4W\bin> python-qgis.bat
+>>> exit()
+C:\OSGeo4W\bin> pip install -r /path/to/requirements.txt
+C:\OSGeo4W\bin> pip install fire2a-lib
+```
+Start QGIS after the process ends
+
+## Directly (macOS)
+Use the bundled python directly:
+```zsh
+% /Applications/QGIS.app/Contents/MacOS/bin/python3 -m pip install -r /path/to/requirements.txt # to install a list of requirements
+% /Applications/QGIS.app/Contents/MacOS/bin/python3 -m pip install fire2a-lib # to install a package
+```
+
+## Virtual environment (Linux)
+```bash
+python -m venv --system-site-packages ~/pyvenv/qgis
+source ~/pyvenv/qgis/bin/activate
+pip install -r /path/to/requirements.txt # to install a list of requirements
+pip install fire2a-lib # to install a package
+qgis
+```
+Start QGIS after the process ends
+
+back to top
+{: style="text-align: right;"}
+
+# Install/Update troubleshoot
+## Dissapeared plugin
+Sometimes after an update, the plugin doesn't appear on the Processing Toolbox panel: Reload it by pressing on the checkbox next to its name in the `Installed` section of the `Plugin Manager` or restart QGIS.
+
+
+back to top
+{: style="text-align: right;"}
+
+## Conflicting plugins
+A good practice is to enable the least amount of plugins as possible, as they may conflict with each other. If you have a problem, try disabling all plugins and enabling them one by one to find the culprit.
+
+## Processing tools dissapeared
+Although it looks like a built in part of QGIS, it can be disabled. Check the `Processing` plugin in the `Plugin Manager`.
+
+---
+[toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
diff --git a/site/qgis-toolbox/algo_knapsack.md b/site/qgis-toolbox/algo_knapsack.md
new file mode 100644
index 0000000..addc644
--- /dev/null
+++ b/site/qgis-toolbox/algo_knapsack.md
@@ -0,0 +1,34 @@
+---
+layout: default
+title: Raster knapsack optimization
+nav_order: 2
+has_children: false
+has_toc : false
+parent: QGIS Fire Analytics Toolbox
+---
+## Raster knapsack optimization
+### Intro
+_A proof-of-concept integration of mathematical programming solvers to model and solve optimization problems with GIS entities._
+
+Users can create a new raster layer that selects the most valuable pixels in a raster, according to a capacity constraint defined by another -optional- raster and a fractional ratio.
+
+Several solvers can be used (cbc, glpk, cplex_direct, gurobi, ipopt, NEOS, etc.), thanks to the MIP being modeled and solved through [pyomo](http://www.pyomo.org).
+
+Before running this algorithm, make sure that you have installed the corresponding solvers that you want to use. See [pyomo documentation](https://pyomo.readthedocs.io/en/stable/installation.html#conditional-dependencies) for more details.
+
+| screenshot |
+| --- |
+||
+
+### Detailed description
+By selecting a Values layer and/or a Weights layer, and setting the bound on the total capacity, a layer that maximizes the sum of the values of the selected pixels is created.
+
+The capacity constraint is set up by choosing a ratio (between 0 and 1), that multiplies the sum of all weights (except no-data). Hence 1 selects all pixels that aren't no-data in both layers.
+
+This raster knapsack problem is NP-hard, so a MIP solver engine is used to find "nearly" the optimal solution, because -often- is asymptotically hard to prove the optimal value. So a default gap of 0.5% and a timelimit of 5 minutes cuts off the solver run. The user can experiment with these parameters to trade-off between accuracy, speed and instance size(*). On Windows closing the blank terminal window will abort the run!
+
+By using Pyomo, several MIP solvers can be used: CBC, GLPK, Gurobi, CPLEX or Ipopt; If they're accessible through the system PATH, else the executable file can be selected by the user.
+
+Installation of solvers is up to the user, although the windows version is bundled with CBC unsigned binaries, so their users will face a "Windows protected your PC" warning, please avoid pressing the "Don't run" button, follow the "More info" link, scroll then press "Run anyway".
+
+(*): Complexity can be reduced greatly by rescaling and/or rounding values into integers, or even better coarsing the raster resolution (see gdal translate resolution).
diff --git a/site/qgis-toolbox/algo_polygonize_rasters.md b/site/qgis-toolbox/algo_polygonize_rasters.md
new file mode 100644
index 0000000..8d8ed80
--- /dev/null
+++ b/site/qgis-toolbox/algo_polygonize_rasters.md
@@ -0,0 +1,43 @@
+---
+layout: default
+title: Polygonize weighted rasters
+nav_order: 2
+has_children: false
+has_toc : false
+parent: QGIS Fire Analytics Toolbox
+---
+# Polygonize weighted rasters
+
+Create polygons from multiple raster layers; with nodata and scaling strategies, categorical rasters handling and __arbitrary weight attributes__ that modifies the underlying agglomerative clustering algorithm.
+
+
+
+Can also plot a summary of the data distributions and clustering sizes history.
+
+
+## Overview
+A scikit-learn pipeline that:
+1. Handles nodata with [SimpleImputer](https://scikit-learn.org/stable/modules/generated/sklearn.impute.SimpleImputer.html)
+2. Scales data with [StandardScaler](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.StandardScaler.html), [RobustScaler](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.RobustScaler.html) which removes outliers or [OneHotEncoder](https://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.OneHotEncoder.html) for categorical data like fuel models.
+3. Rescales all observations to [0, 1], then multiplies a prioritization (weight) to each raster.
+4. Clusterizes the map using the [Agglomerative](https://scikit-learn.org/stable/modules/generated/sklearn.cluster.AgglomerativeClustering.html) clustering algorithm.
+
+## Usage
+1. Select the rasters: notice you can drag & drop to *reorder* them.
+2. Optionally fill the matrix *in the same order* than the selected rasters, with
+- scaling_strategy = ["standard", "robust", "onehot"] (default is "standard")
+- no_data_strategy = ["mean", "median", "most_frequent", "constant"] (default is "mean")
+- fill_value = any number (only for "constant" no_data_strategy) (default is 0)
+- weight = any number (default is 1)
+**Categorical rasters (like fuel models) should use "onehot" and "most_frequent"**
+3. Experiment with the distance threshold until you get the desired number of clusters. Less distance (until 0) yields more clusters and processing time.
+4. Fine tune the output, ensuring clusters have a minimum number of pixels using the advanced parameter -that invokes GDAL's: [gdal_sieve](https://gdal.org/en/latest/programs/gdal_sieve.html#gdal-sieve)
+
+5. Outputs: The output polygon layer has the attribute 'number of pixels'. The raster layer can be skipped.
+6. Data debug: There's an additional option to raise a (mat)plot(lib) window with original & rescaled data distributions, clustering sizes history & histogram labels. Available outside QGIS, by executing the shown command adding the '--plots' flag in the terminal (OSGeo4WShell).
+
+In depth documentation and source code can be found [here](https://fire2a.github.io/fire2a-lib/fire2a/agglomerative_clustering.html)
+
diff --git a/site/qgis-toolbox/algo_simulator.md b/site/qgis-toolbox/algo_simulator.md
new file mode 100644
index 0000000..826e778
--- /dev/null
+++ b/site/qgis-toolbox/algo_simulator.md
@@ -0,0 +1,140 @@
+---
+layout: default
+title: C2FW Fire Simulator
+nav_order: 1
+has_children: false
+has_toc : false
+parent: QGIS Fire Analytics Toolbox
+---
+
+{: .no_toc}
+
+
+
+# Filling the dialog
+The simulator dialog is divided in four main sections: *Landscape, ignitions, weather and outputs*. And two optional: run-configuration and advanced options.
+Altough intuitive (e.g. match each dimensional unit shown in square brackets), each section is commented below:
+
+## Landscape
+{: width="85%"}
+* The surface fuel model must match the fuel raster codification (see [lookup tables])
+* The style fuel raster checkbox not only "paints" using 'native:setlayerstyle' algorithm according to each [qml layer style], but also show the classification on the Layers panel
+* Enabling crown fire behavior makes sense *even without canopy rasters because there are fixed standard numbers* for them according to the fuel codification (Only available in Canada's fuel model)
+
+back to top
+{: style="text-align: right;"}
+
+## Ignitions
+{: width="85%"}
+* When simulating **one or few simulations**, a detailed output is relevant (like **propagation digraph and propagation scars**)
+* When simulating **hundreds or thousands**, mean and std.dev. statistics are more important than detailed output that can choke the computer unnecessarily (use **final scar** instead of propagation scars; propagation digraph is input for DPV and Centrality measures; but it can't be loaded into view!)
+* There are 3 ways to generate ignitions:
+ 0. Draw a **uniformly distributed** random but burnable pixel
+ 1. Draw using a **probability map** raster
+ 2. Specify a **point** and optionally a radius to specify a **circle** from where uniformly draw
+* If passing various points in the "single point layer", only the last[?] will be taken into consideration (see feature id (fid) in layer attribute table)
+* Note that afterwards there's a random seed input, hence same seed implies drawing the same point(s sequence)
+
+back to top
+{: style="text-align: right;"}
+
+## Weather
+{: width="85%"}
+* The simulator assumes **constant weather parameters across the grid**, they can change over time, but not space
+* These parameters are passed into the simulator using a `.csv` file
+* In a regular simulation **each row lasts 1 hour**, when the rows end, the simulation ends
+* There are two options:
+ 0. Using just one `Weather.csv`
+ 1. Drawing at random from a directory `Weathers/WeatherN.csv : N = 1,2,...` correlatively named
+* WIP: A weather database; meanwhile weathers can be obtained from *weather.org from any location from 1970 until present day*
+
+back to weather spec. \| top
+{: style="text-align: right;"}
+
+## Run Configuration
+{: width="85%"}
+* Only lower the simulation cpu threads if you plan to keep working on something else while the simulations run in the background (for office or web-browsing you'll never need more than 2)
+* Keeping track of the seed yields reproducibility for all generated random numbers
+
+back to top
+{: style="text-align: right;"}
+
+## Outputs
+This section has three main parts: options, advanced and destination directories.
+{: width="85%"}
+
+### Options
+* Access the multiple selection by clicking the `...` on the right
+{: width="85%"}
+* Most outputs adapt according to being 1 or >1 simulations
+* When simulating **one or few simulations**, a detailed output is relevant (like **propagation digraph and propagation scars**)
+* When simulating **hundreds or thousands**, mean and std.dev. statistics are more important than detailed output that can choke the computer unnecessarily (use **final scar** instead of propagation scars; propagation digraph is input for DPV and Centrality measures; but it can't be loaded into view!)
+
+| output name | unit-type | description |
+|:-------------|:------------------|:------|
+| Propagation Fire Scars | polygons | _animate adding the column_ `=now()+ make_interval(hours:=time)` |
+| Propagation Directed Graph | vector lines `periods` | edges labeled with simulation event time `min` |
+| Ignition Points | points | pixel id |
+| Hit Rate Of Spread | raster float32 `m/min` | multiband x simulation and bi-band mean&std |
+| Final Fire Scars | raster `0,1` | |
+| Surface Flame Length| raster float32 `m` | multiband x simulation and bi-band mean&std |
+| Byram Fireline Intensity | raster float32 `kW/m` | multiband x simulation and bi-band mean&std |
+| Crown Fire Scar | raster `0,1` | multiband x simulation and bi-band mean&std |
+| Crown Fire Fuel Consumption Ratio raster | `0,1` | multiband x simulation and bi-band mean&std |
+| Surface Burn Fraction | `0,1` | multiband x simulation and bi-band mean&std (only Canada FBP) |
+| Crown Intensity | raster `kW/m` | multiband x simulation and bi-band mean&std (only Spain S&B) |
+| Crown Flame Length | raster `m` | multiband x simulation and bi-band mean&std (only Spain S&B) |
+| Max Flame Length | raster `m` | multiband x simulation and bi-band mean&std (only Spain S&B) |
+
+back to top
+{: style="text-align: right;"}
+
+### Advanced options
+- + Table of contents +
+ {: .text-delta } +1. TOC +{:toc} +Un/Fold the block using the triangle
at the left of Advanced Parameters+Fire Analytics Toolbox +
+{: .no_toc} +
+
+# Overview
+Our applied fire research as **user friendly graphical GIS tools**:
+- *Simulate* large scale wildfires using Cell2Fire++
+- Get threat and risk *metrics*
+- Use the firebreak location *decision support system*
+- *Combine* our algorithms with any other [QGIS] algorithms easily
+
+Without leaving the graphical environment of [QGIS], just by installing our **processing algorithm plugin** *fire2a-toolbox*.
+
+This type of plugins differ from the regular plugins -by being much more than a pop-up dialog- because they follow a data-science-pipeline architecture.
+Clearly delimites: inputs, outputs, algorithms and contexts; achieving seamless integration with all other provided algorithms in the [toolbox], providing 5 ways of being run.
+
+# Usage alternatives
+1. Simple as *filling a **[form dialog]*** (checkboxes, dropdowns, file-choosers, etc.); with the minimal inputs being a fuel raster and a weather scenario.
+2. **[Batch of forms]**: Execute sequential runs configuring them in data-sheet-style where each row is one (column-wise displayed) form, *easily experiment parameter sensitivities*.
+3. As part of a **[graphical model] workflow**: Drag and drop boxes of parameters and algorithms, conect arrows as input-ouputs between them, into a [custom] *GIS-data-science-pipeline*.
+4. From a **command line tool**, run `qgis_process` [cli wrapper] to call any processing algorithm *without QGIS graphical overhead*.
+5. **Python script**, working *both* [calling it] from the QGIS [python console] *or* as [standalone code]
+
+# Installing
+[Full guide here]({{ site.baseurl }}/qgis-management) or overview (with video):
+1. Install [QGIS] latest version
+ - Support >= 3.36.2
+
+1. Add fire2a's [plugin store URL][toolbox-server] as a custom plugin source
+ - `QGIS menu > Plugins > Manage and Install Plugins > Settings > Add > paste the URL > Ok`
+ - _Why custom? Audit our [binaries](https://github.com/fire2a/C2F-W/actions)_
+
+1. Click "Not installed" tab, search "fire", select and install "Fire Analytics Processing-Toolbox"
+
+1. Accept on the dialog asking permission to install the plugin's python dependencies (if needed)
+ - _Save any open work before installing/updating the plugin. Installing & reloading dependencies on the fly_ __could crash QGIS__
+ - You can deny and disable this check, that happens every time the plugin is loaded. ([Manually][fire2a-lib-pypi] install [them](https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/blob/main/fireanalyticstoolbox/dependencies_handler.txt))
+ - Restart QGIS if any install or reloading doesn't succeed (details at: Log Messages > Plugins)
+ - Toggle the plugin checkbox (left of + Table of contents +
+ {: .text-delta } +1. TOC +{:toc} + its icon on the Manager list) if it doesn't appear immediately on the Processing Toolbox Panel
+
+**All Done!** On the Processing Toolbox Panel, look for " Fire Analytics"
+
+
+
+# First test run
+(Check the video at the end!) Getting or generating a fuel model raster can be challenging (tutorial coming soon), so the simplest way is to:
+1. Use the downloader algorithm to get a prepared instance
+2. Save an empty [project] into the downloaded folder (where fuels, elevation and Weather.csv files are)
+3. Drag and drop layers from the project home (file Browser Panel) into the Layer Panel
+4. Set the same CRS to the layers and project (any in meters suffices)
+5. Open the simulator algorithm , select the proper fuelmodel (Canada, Kitral or S&B), select the fuel layer in the fuel dropdown, press run.
+
+
+
+
+Note: Step 2 can be skipped but it is cumbersome to select each layer from file explorers than to use the dropdown to select between current loaded layers; Also `Weather.csv` is automatically selected when there's a saved project.
+
+# Deployed algorithms
+
+## ** Fire Analytics Toolbox**
+
+
+: [**Cell2 Fire Simulator**](./algo_simulator.html)
+
+**Utils**
+
+
+: Simulator **Instances Downloader**, gets ready to simulate instances
+
+
+: **Match AII Grid** Rasters: Simplifies using gdal translate thrice, to clip extent, then resize and replace geotransform to match an ascii raster into another
+
+
+: **Meteo**: Simplifies creating Chilean -Kitral fuel model compatible- weather files
+
+
+: **Polygonize weighted rasters**: A pipeline for creating polygons from multiple raster layers; with nodata and scaling strategies, categorical rasters handling and weight attribute. [algorithm][fire2a-lib-clustering-docs]
+
+**Simulator Post Processing (simpp)**
+
+
+: **Bundle**: all following algorithms combined for convenience
+
+
+: **Ignition Point(s)**: reads the ignition history file from the simulator outputs, creates a point layer
+
+
+: **Fire Scar(s)**: reads the csv.Grids files from the simulator outputs, creates: final scars raster layer, propagation scars polygons & burn probability
+
+
+: **Propagation Digraph**: reads the csv.Messages files from the simulator outputs, creates a directed graph of the fire propagation, each arrow labeled with the time spread
+
+
+: **Spatial Statistics**:, any of: Hit Rate Of Spread, Flame Length, Byram Fire Line Intensity, Crown Fire Scar, Crown Fire Fuel Consumption Ratio, Surface Burn Fraction
+
+**Simulator Risk Metrics**
+
+
+: **DownStream Protection Value**
+
+
+: **Betweenness Centrality**
+
+
+: **Burn Probability**, a subset of the fire scar algorithm
+
+**Decision optimization**
+
+
+: [Raster knapsack optimization](./algo_knapsack.html)
+
+
+: Polygon knapsack optimization : Optimizes the classical knapsack problem using polygons with values and/or weights attributes, returns a polygon layer with the selected polygons.
+
+
+: Polygon treatment optimization : Using possible treatments for each polygon, Maximize the changed value of the treated polygons
+
+
+: Raster treatment optimization : Maximize the changed value of the treated raster, deciding which treatment to apply to each pixel (or no change), subject to budget and area constraints
+
+
+: Raster treatment & teams optimization : Maximize the changed value of the treated raster, deciding which treatment to apply by which team to each pixel (or no change), subject to budget, area constraints and team capabilities
+
+{: .warning}
+By default QGIS limits the processing algorithms log to about 5000 lines. In the rare case you really need the full log, see number 4 and 5 of [usage alternatives](https://fire2a.github.io/docs/qgis-toolbox/index.html#usage-alternatives)
+
+| 
|
+| :--- |
+| QGIS processing tools snapshot |
+
+---
+[QGIS]: https://qgis.org
+
+[requirements.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/fireanalyticstoolbox/requirements.txt
+[requirements.dev.txt]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/requirements.dev.txt
+
+[Scott&Burgan-dialog-server]: https://fdobad.github.io/qgis-processingplugin-template/plugins.xml
+[Kitral simulator dialog-server]: https://fdobad.github.io/fire2am-kitral/plugins.xml
+[toolbox-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
+[c2f-repo]: https://www.github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin
+[fire2a-lib-repo]: https://www.github.com/fire2a/fire2a-lib
+[fire2a-lib-requirements]: https://github.com/fire2a/fire2a-lib/blob/d6a08bd78ba1388e6548170ebfcc20077eff7f5e/pyproject.toml#L20
+[fire2a-lib-pypi]: https://pypi.org/project/fire2a-lib/
+[fire2a-lib-clustering-docs]: https://fire2a.github.io/fire2a-lib/fire2a/agglomerative_clustering.html
+
+
+[graphical model]: https://docs.qgis.org/latest/en/docs/user_manual/processing/modeler.html
+[toolbox]: https://docs.qgis.org/latest/en/docs/user_manual/processing/toolbox.html
+[form dialog]: https://docs.qgis.org/latest/en/docs/user_manual/processing/toolbox.html#the-algorithm-dialog
+[Batch of forms]: https://docs.qgis.org/latest/en/docs/user_manual/processing/batch.html#processing-batch
+[cli wrapper]: https://docs.qgis.org/latest/en/docs/user_manual/processing/standalone.html
+[python console]: https://docs.qgis.org/latest/en/docs/user_manual/plugins/python_console.html#console
+[calling it]: https://docs.qgis.org/latest/en/docs/user_manual/processing/console.html
+[standalone code]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/script_samples/standalone.py
+[custom]: https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/tree/main/graphical_models
+[plugin manager]: https://docs.qgis.org/latest/en/docs/training_manual/qgis_plugins/fetching_plugins.html
+
+[toolbox-server]: https://fire2a.github.io/fire-analytics-qgis-processing-toolbox-plugin/plugins.xml
+[toolbox-releases]: https://github.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/releases
+[project]: https://docs.qgis.org/3.28/en/docs/user_manual/introduction/project_files.html
+
+[forestfire]: https://raw.githubusercontent.com/fire2a/fire-analytics-qgis-processing-toolbox-plugin/main/fireanalyticstoolbox/assets/forestfire.svg