Updated Sphinx documentation with more precise explenations of Malpol…

…on's examples scenarios and more friendly front page.
plantnet · Feb 29, 2024 · d84de07 · d84de07
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -76,6 +76,12 @@
 html_static_path = ["_static"]
 
 
+# These paths are either relative to html_static_path
+# or fully qualified paths (eg. https://...)
+html_css_files = [
+    'css/custom.css',
+]
+
 # -- Options for autodoc ----------------------------------------------------
 
 # autodoc_class_signature = "separated"

diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -7,16 +7,19 @@
 Experiment examples
 *******************
 
+The repository contains examples of how to use Malpolon for different scenarios.
+The examples are organized by the type of user and the type of dataset used.
+
 .. toctree::
    :maxdepth: 10
 
 
-Ecologists scenario
-*******************
+I. Ecologists scenario
+**********************
 
-I have a dataset of my own and I want to train a model on it. I want to be able to easily customize the training process and the model architecture.
+I have a dataset of **pre-extracted image patches** or **raster files** *(e.g. bioclimatic data, satellite rasters...)* of my own and I want to train a **deep image neural network model** on it. I want to be able to easily customize the training process and the model architecture.
 
-- *Drop and play* : I have an observations file (.csv) and I want to train a model on different environmental variables (rasters, satellite imagery) without having to worry about the data loading.
+- *Drop and play* : I have a file (.csv) of Presence/Absence (PA) or Presence Only (PO) observations and I want to train a model on different environmental variables (rasters, satellite imagery) without having to worry about the data loading and on-the-fly extraction.
 
 - *Custom dataset* : I have my own dataset consisting of pre-extracted image patches and/or rasters and I want to train a model on it.
 
@@ -31,10 +34,10 @@ MicroGeoLifeCLEF2022
 `See MicroGeoLifeCLEF2022 (training) GitHub README 🔗 <https://github.com/plantnet/malpolon/tree/main/examples/ecologists/micro_geolifeclef2022>`_
 
 
-Inference scenario
-******************
+II. Inference scenario
+**********************
 
-I have an observations file (.csv) and I want to predict the presence of species on a given area using a model I trained previously and a selected dataset or a shapefile I would provide.
+I have a file (.csv) of Presence/Absence (PA) or Presence Only (PO) observations and I want to predict the presence of species on a given area using a model I trained previously and a selected dataset I would provide.
 
 Sentinel-2A
 ===========
@@ -47,8 +50,8 @@ MicroGeoLifeCLEF2022
 `See MicroGeoLifeCLEF2022 (inference) GitHub README 🔗 <https://github.com/plantnet/malpolon/tree/main/examples/inference/micro_geolifeclef2022>`_
 
 
-Kaggle scenario
-***************
+III. Kaggle scenario
+********************
 
 I am a potential kaggle participant on the GeoLifeClef challenge. I want to train a model on the provided datasets without having to worry about the data loading, starting from a plug-and-play example.
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -7,6 +7,16 @@
 Welcome to Malpolon's documentation !
 =====================================
 
+.. figure:: ../resources/Malpolon_transparent.png
+  :width: 300
+  :alt: Malpolon_logo
+  :align: center
+
+
+Malpolon is a framework facilitating the training and sharing of Deep Species Distribution models using various types of input covariates including bioclimatic rasters, remote sensing images, land-use rasters, etc...
+
+If you're not a deep learning or PyTorch expert but nonetheless want to use visual deep learning models on satellite and/or bioclimatic rasters to predict the presence of species on a given area, this framework is for you.
+
 .. toctree::
    :maxdepth: 1
 
@@ -139,30 +149,6 @@ Examples using the GeoLifeCLEF 2022 and 2023 datasets, as well as Sentinel-2A ra
 
 Build your own scripts by modifying the provided examples!
 
-.. API documentation
-.. =================
-
-.. malpolon.data.data_module
-.. =========================
-.. .. automodule:: malpolon.data.data_module
-..    :members: BaseDataModule
-.. .. automodule:: malpolon.data.environmental_raster
-..     :members:
-
-.. Datasets
-.. ========
-.. .. automodule:: malpolon.data.datasets
-..     :members:
-
-.. Models
-.. ======
-.. .. automodule:: malpolon.models
-..    :members:
-
-.. Plot
-.. ====
-.. .. automodule:: malpolon.plot
-..    :members:
 
 Indices and tables
 ==================