[JOSS] Final Docs (probably)

.gitattributes

@@ -1,4 +1,12 @@
-*.ipynb linguist-detectable=false
+
+# handles large files via git-lfs
 *.ref filter=lfs diff=lfs merge=lfs -text
+
+# handles lf and crlf for those using git on windows with wsl
 * text=auto
-*.sh text eol=lf
+*.sh    text eol=lf
+*.bash  text eol=lf
+*.csv   text eol=lf
+
+# makes ipynb extension not detectable by linguist
+*.ipynb linguist-detectable=false

.github/workflows/main.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - "master"
-      - "dev-ci"
+      - "dev"
   pull_request:
     branches: [ "master" ]
   workflow_dispatch:
@@ -16,7 +16,7 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
-          lfs: true # Keep enabled as you use LFS
+          lfs: true # we use LFS to store large files (e.g. data.nc)
 
       - name: Install Dependencies (Build + Test)
         run: |
@@ -39,7 +39,6 @@ jobs:
       - name: Check ForeFire version
         run: ./bin/forefire -v
 
-      # --- KEEPING DIAGNOSTIC STEPS ---
       - name: Add Build/Runtime Diagnostics
         run: |
           echo "--- ForeFire Linkage ---"
@@ -49,7 +48,6 @@ jobs:
           # Install ncdump tool and check the format kind
           sudo apt-get install -y --no-install-recommends netcdf-bin
           ncdump -k tests/runff/data.nc || echo "Could not check data.nc format"
-      # --- END DIAGNOSTIC STEPS ---
 
       - name: Run 'runff' Test Script
         run: |

CONTRIBUTING.md

@@ -47,7 +47,7 @@ We welcome code contributions, from bug fixes to new features.
 
 2.  **Set Up Development Environment:**
 
-    Follow the instructions in the [Installation Guide](https://firefront.readthedocs.io/en/latest/getting_started/installation.html) to build ForeFire from source. *(Update link if RTD URL changes)*
+    Follow the instructions in the [Installation Guide](https://forefire.readthedocs.io/en/latest/getting_started/installation.html) to build ForeFire from source. *(Update link if RTD URL changes)*
 
 3.  **Fork the Repository:**
 
@@ -64,7 +64,7 @@ We welcome code contributions, from bug fixes to new features.
     Implement your code changes, following existing coding style and conventions where possible.
 6.  **Add Tests (if applicable):**
 
-    For new features or significant bug fixes, please add corresponding tests or update existing ones. See the [Testing Documentation](https://firefront.readthedocs.io/en/latest/developer_guide/testing.html) *(Placeholder: Link to testing section once created)* for details on how to run tests. Ensure all tests pass locally.
+    For new features or significant bug fixes, please add corresponding tests or update existing ones. See the [Testing Documentation](https://forefire.readthedocs.io/en/latest/developer_guide/testing.html) *(Placeholder: Link to testing section once created)* for details on how to run tests. Ensure all tests pass locally.
     ```bash
     # Example command to run tests (adjust as needed)
     cd tests && bash run.bash

README.md

@@ -9,15 +9,15 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 ![Language](https://img.shields.io/badge/C++-00599C?logo=c%2B%2B&logoColor=white)
 ![Language](https://img.shields.io/badge/Python-3776AB?logo=python&logoColor=white)
-[![Documentation Status](https://readthedocs.org/projects/firefront/badge/?version=latest)](https://firefront.readthedocs.io/en/latest/?badge=latest) 
+[![Documentation Status](https://readthedocs.org/projects/forefire/badge/?version=latest)](https://forefire.readthedocs.io/en/latest/?badge=latest) 
 [![DOI](https://img.shields.io/badge/DOI-10.14195/978--989--26--0884--6_29-blue)](https://www.researchgate.net/publication/278769168_ForeFire_open-source_code_for_wildland_fire_spread_models) <!-- Or use Zenodo DOI if available -->
 
 
 **ForeFire** is an open-source **wildfire simulation engine** written in C++. Developed by CNRS at the [Université de Corse Pascal Paoli](https://www.univ-corse.fr/), it is used for research and operational forecasting. The engine implements various fire behavior models and enables high-fidelity coupled fire-atmosphere simulations, aiming to improve wildfire prediction and understanding for complex environments.
 
 
 **Key Links:**
-- 📚 **Full Documentation:** [forefire.readthedocs.io](https://firefront.readthedocs.io/en/latest/)
+- 📚 **Full Documentation:** [forefire.readthedocs.io](https://forefire.readthedocs.io/en/latest/)
 - 🚀 **Live Demo:** [forefire.univ-corse.fr/sim](http://forefire.univ-corse.fr/sim)
 - 🌍 **Website:** [forefire.univ-corse.fr](https://forefire.univ-corse.fr/)
 
@@ -74,7 +74,7 @@ The easiest way to get started is often using Docker and the interactive console
     forefire> listenHTTP[]
 
     # the output should be
-    >> HTTP command server listening at http://localhost:8000
+    >> ForeFire HTTP command server listening at http://localhost:8000
     ```
 
     This server provides a grafical user interface that you can access on your browser at http://localhost:8000/

bindings/python/setup.py

@@ -6,7 +6,7 @@
 
 # Determine current directory (where setup.py resides)
 this_dir = os.path.abspath(os.path.dirname(__file__))
-# Compute the top-level ForeFire directory (two levels up: bindings/python -> bindings -> firefront)
+# Compute the top-level ForeFire directory (two levels up: bindings/python -> bindings -> forefire)
 FOREFIRE_DIR = os.path.abspath(os.path.join(this_dir, "..", ".."))
 FOREFIRE_LIB = "forefireL"  # as used in lib/libforefireL.dylib (or .so/.dll)
 

docs/source/getting_started/installation.rst

@@ -33,7 +33,7 @@ The repository provides a convenience script (`install-forefire.sh`) that automa
   .. code-block:: bash
 
     git clone https://github.com/forefireAPI/forefire.git
-    cd firefront
+    cd forefire
 
 2.  **Run the install script:**
 
@@ -66,7 +66,7 @@ Use this method if you are not on Debian/Ubuntu, prefer manual control, or don't
   .. code-block:: bash
 
     git clone https://github.com/forefireAPI/forefire.git
-    cd firefront
+    cd forefire
 
 2.  **Install Prerequisites Manually:**
 
@@ -102,21 +102,21 @@ The main executable `forefire` will be located at `../bin/forefire` (relative to
 
   .. code-block:: bash
 
-    # Execute this from the root of the firefront repository
+    # Execute this from the root of the forefire repository
     export PATH=$PATH:`pwd`/bin
 
   **Permanently:**
 
-  Add the following line to your shell's configuration file (e.g., `~/.bashrc`, `~/.zshrc`, `~/.profile`, or `~/.config/fish/config.fish`). Replace `/path/to/firefront` with the actual absolute path to the cloned repository.
+  Add the following line to your shell's configuration file (e.g., `~/.bashrc`, `~/.zshrc`, `~/.profile`, or `~/.config/fish/config.fish`). Replace `/path/to/forefire` with the actual absolute path to the cloned repository.
 
   .. code-block:: bash
 
-    export PATH="/path/to/firefront/bin:$PATH"
+    export PATH="/path/to/forefire/bin:$PATH"
 
-  *Optional:* The install script also sets `export FOREFIREHOME="/path/to/firefront"`. You may want to add this line as well, as some scripts or components might potentially use it.
+  *Optional:* The install script also sets `export FOREFIREHOME="/path/to/forefire"`. You may want to add this line as well, as some scripts or components might potentially use it.
 
   .. code-block:: bash
 
-    export FOREFIREHOME="/path/to/firefront"
+    export FOREFIREHOME="/path/to/forefire"
 
   After editing your configuration file, either restart your terminal or reload the configuration (e.g., `source ~/.bashrc`).

docs/source/getting_started/quickstart.rst

@@ -23,7 +23,7 @@ Steps
 
   .. code-block:: bash
 
-    cd firefront
+    cd forefire
     docker build . -t forefire:latest
 
   This might take a few minutes the first time as it downloads base images and installs dependencies inside the Docker build environment.
@@ -58,7 +58,7 @@ Steps
 
     forefire> listenHTTP[]
 
-  You should see output like: `>> HTTP command server listening at http://localhost:8000`
+  You should see the output : `>> ForeFire HTTP command server listening at http://localhost:8000`
 
 7.  **Access the Web Console:**
 

docs/source/getting_started/running_the_example.rst

@@ -29,7 +29,7 @@ This is the simplest way to run a simulation non-interactively by feeding the en
 
 1.  **Navigate to the test directory:**
 
-  Ensure your terminal's current directory is the root of the cloned `firefront` repository. Then navigate:
+  Ensure your terminal's current directory is the root of the cloned `forefire` repository. Then navigate:
 
   .. code-block:: bash
 
@@ -100,16 +100,30 @@ This method uses the built-in HTTP server to provide a web-based console and map
 
     cd tests/runff
 
-2.  **Start the ForeFire interpreter** (as shown in Method 2, ensuring you start it from *within* the `tests/runff` directory for simplicity with file paths in the next steps).
+2.  **Start the ForeFire interpreter and launch the HTTP server:**
 
-3.  **Launch the HTTP server:**
+  Assuming ``forefire`` is in your PATH:
+
+  .. code-block:: bash
+
+    forefire
 
   At the ``forefire>`` prompt, type:
 
   .. code-block:: none
 
     forefire> listenHTTP[]
 
+  You should see the output: `>> ForeFire HTTP command server listening at http://localhost:8000`.
+
+  **Alternative Shortcut** using ``-l`` (listen) flag:
+
+  Alternatively, to launch the HTTP server directly without entering the interactive console first, you can use the `-l` command-line option. This is convenient if you primarily want to use the web interface.
+
+  .. code-block:: none
+
+    forefire -l
+
 4.  **Use the Web Interface:**
 
   - Open your browser to ``http://localhost:8000/`` (or the specified port).

docs/source/reference/api_reference.rst

@@ -1,22 +1,30 @@
 C++ API Reference
 =================
 
-This section will contain the C++ API reference, automatically generated from source code comments using Doxygen and Breathe.
+This section provides a high-level overview of the most fundamental C++ classes and interfaces that constitute the ForeFire simulation engine. For a comprehensive, detailed API reference for all classes and functions, please consult the full Doxygen-generated documentation.
 
-Key C++ classes providing the core functionality of ForeFire include:
+Core Simulation Objects
+-----------------------
+
+These classes represent the primary entities in a wildfire simulation.
 
 .. doxygenclass:: libforefire::FireDomain
    :project: ForeFire
    :members:
 
-.. doxygenclass:: libforefire::FireNode
+.. doxygenclass:: libforefire::FireFront
    :project: ForeFire
    :members:
 
-.. doxygenclass:: libforefire::FireFront
+.. doxygenclass:: libforefire::FireNode
    :project: ForeFire
    :members:
 
+Data Management
+---------------
+
+These classes are central to how ForeFire handles environmental and simulation data.
+
 .. doxygenclass:: libforefire::DataBroker
    :project: ForeFire
    :members:
@@ -25,13 +33,26 @@ Key C++ classes providing the core functionality of ForeFire include:
    :project: ForeFire
    :members:
 
-.. .. doxygenclass:: libforefire::PropagationModel
-..    :project: ForeFire
-..    :members:
+.. rubric:: Note
+   ForeFire provides various specializations of ``DataLayer`` (e.g., for 2D/3D arrays, NetCDF files, fuel properties, atmospheric data) to handle different data sources and types. Refer to the full Doxygen documentation for details on specific implementations like ``Array2DdataLayer``, ``NCXYZTDataLayer``, ``FuelDataLayer``, etc.
+
+Scientific Model Interfaces
+---------------------------
+
+These abstract base classes define how new scientific models for fire spread and flux calculations can be integrated.
+
+.. doxygenclass:: libforefire::PropagationModel
+   :project: ForeFire
+   :members:
+
+.. doxygenclass:: libforefire::FluxModel
+   :project: ForeFire
+   :members:
+
+User Interaction & Configuration
+--------------------------------
 
-.. .. doxygenclass:: libforefire::FluxModel
-..    :project: ForeFire
-..    :members:
+These components manage user commands and simulation parameters.
 
 .. doxygenclass:: libforefire::Command
    :project: ForeFire
@@ -41,6 +62,15 @@ Key C++ classes providing the core functionality of ForeFire include:
    :project: ForeFire
    :members:
 
-.. doxygenclass:: libforefire::Simulator
+Fundamental Utilities
+---------------------
+
+Basic geometric data types used throughout the simulation.
+
+.. doxygenclass:: libforefire::FFPoint
    :project: ForeFire
    :members:
+
+.. doxygenclass:: libforefire::FFVector
+   :project: ForeFire
+   :members: