From afa5bb6573bc81d94159a7a5a7f09f3fdfc9df8f Mon Sep 17 00:00:00 2001
From: DIANE <abderrahim.diane@cefe.cnrs.fr>
Date: Tue, 21 Jan 2025 15:41:43 +0100
Subject: [PATCH] update

---
 docs/USE CASES/DataVisualization.md |  2 +-
 docs/USE CASES/EDA.md               |  4 +--
 docs/USE CASES/ModelCreation.md     |  2 +-
 docs/USE CASES/SamplesSelection.md  |  2 +-
 mkdocs.yml                          | 48 +++++++++++++++++++++++++----
 5 files changed, 47 insertions(+), 11 deletions(-)

diff --git a/docs/USE CASES/DataVisualization.md b/docs/USE CASES/DataVisualization.md
index 1f0d0d9..e73239b 100644
--- a/docs/USE CASES/DataVisualization.md	
+++ b/docs/USE CASES/DataVisualization.md	
@@ -1,3 +1,3 @@
 With NIRS workflow, you can efficiently visualize your spectra to see their trend.
 
-![Image Alt Text](../figs/DataVisualization.png)
\ No newline at end of file
+![Image Alt Text](./figs/DataVisualization.png)
\ No newline at end of file
diff --git a/docs/USE CASES/EDA.md b/docs/USE CASES/EDA.md
index 3453925..1dad48e 100644
--- a/docs/USE CASES/EDA.md	
+++ b/docs/USE CASES/EDA.md	
@@ -2,11 +2,11 @@
 With NIRS Workflow, you can perform an exploratory data analysis on your spectral data, specifically you can perform dimensionality reduction to concentrate the information provided by spectra on the samples, allowing you to see similarities and differences between samples based on compressed spectra that are visualized in 1D, 2D, or 3D space. 
 </p>
 
-![Image Alt Text](../figs/DimensionalityReduction.png)
+![Image Alt Text](./figs/DimensionalityReduction.png)
 
 
 <p style='text-align: justify;'>
 If you find it difficult to discern similarities and differences between spectra, the app proposes specific Machine Learning methods, specifically clustering methods, to automatically accomplish the task.
 </p>
 
-![Image Alt Text](../figs/Clustering.png)
\ No newline at end of file
+![Image Alt Text](./figs/Clustering.png)
\ No newline at end of file
diff --git a/docs/USE CASES/ModelCreation.md b/docs/USE CASES/ModelCreation.md
index be8465e..a9a90e4 100644
--- a/docs/USE CASES/ModelCreation.md	
+++ b/docs/USE CASES/ModelCreation.md	
@@ -1,3 +1,3 @@
 NIRS Workflow features a section that serve for supervised predictive modelling. It enables you to create a predictive model that is supposed to predict your target variable from spectral data.
 
-![Image Alt Text](../figs/PredictiveModeling.png)
\ No newline at end of file
+![Image Alt Text](./figs/PredictiveModeling.png)
\ No newline at end of file
diff --git a/docs/USE CASES/SamplesSelection.md b/docs/USE CASES/SamplesSelection.md
index 636f8a4..80cd8bb 100644
--- a/docs/USE CASES/SamplesSelection.md	
+++ b/docs/USE CASES/SamplesSelection.md	
@@ -1,3 +1,3 @@
 If you have a large set of spectra, and want to sample a representative subset to use for any objective. NIRS Workflow features a functionality that can accomplish the task for you.
 
-![Image Alt Text](../figs/Sampling.png)
\ No newline at end of file
+![Image Alt Text](./figs/Sampling.png)
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 8cc5bcb..1d0294e 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,11 +1,42 @@
-site_name: NIRS Workflow
+site_name: NIRS Workflow - Documentation
+site_author: 'Nicolas.barthes@cefe.cnrs.fr'
+copyright: 'Est. 2016, Copr. <a href="https://0x4447.com">0x4447, LLC.</a>'
+use_directory_urls: true
 
 nav:
-  - Home: 'index.md'
-  - Dimensionality Reduction: 'DimensionalityReduction.md'
-  - Clustering Methods: 'ClusteringAnalysis.md'
-  - Models Creation: 'ModelCreation.md'
-  - Prediction Making: 'PredictionMaking.md'
+  - HOME: 'index.md'
+  - USE CASES: 
+    - DATA VISUALIZATION: 'USE CASES/DataVisualization.md'
+    - EXPLORATORY DATA ANALYSIS(EDA): 'USE CASES/EDA.md'
+    - SAMPLES SELECTION: 'USE CASES/SamplesSelection.md'
+    - PREDICTIVE MODELLING: 'USE CASES/ModelCreation.md'
+    - PREDICTION MAKING: 'USE CASES/PredictionMaking.md'
+  - GETTING STARTED:
+    - HOME WORKSPACES:
+      - Initial webpage load: 'GETTING STARTED/Initial webpage load.md'
+      - Simple or advanced interface: 'GETTING STARTED/Simple or advanced interface.md'
+      - Tabs : 'GETTING STARTED/Tabs.md'
+    - QUICK-START GUIDE:
+      - Form completion: 'GETTING STARTED/Input.md'
+      - Uploading your data: 'GETTING STARTED/DataImport.md'
+      - Data visualization (for tabs requiring data uploading): 'GETTING STARTED/DataVisualization.md'
+      - Exploratory data analysis: 'GETTING STARTED/EDA.md'
+      - Samples selection: 'GETTING STARTED/SamplesSelection.md'
+      - Predictive modeling: 'GETTING STARTED/ModelCreation.md'
+      - Prediction making: 'GETTING STARTED/PredictionMaking.md'
+      - Reporting and results downloading: 'GETTING STARTED/Reporting.md'
+  - RESOURCES:
+      - Frameworks and algorithms: 'RESOURCES/Frameworks and algorithms.md'
+      - SOURCE CODE:
+        - data visualization: 'RESOURCES/ModelCreation.md'
+        - samples selection: 'RESOURCES/ModelCreation.md'
+        - calibration development: 'RESOURCES/ModelCreation.md'
+        - prediction: 'RESOURCES/ModelCreation.md'
+      - REFERENCES: 'RESOURCES/References.md'
+  - CITATION: 'GETTING STARTED/CitationPermission.md'
+  - SUPPORT: 'Support.md'
+
+      
 
 
 theme:
@@ -13,7 +44,11 @@ theme:
 
   features:
     - navigation.tabs
+    - navigation.tabs.sticky
     - navigation.sections
+    - navigation.expand
+    - navigation.path
+    - navigation.indexes
     - toc.integrate
     - navigation.top
     - search.suggest
@@ -21,6 +56,7 @@ theme:
     - content.tabs.link
     - content.code.annotation
     - content.code.copy
+    - toc.integrate
   language: en
   palette:
     - scheme: default
-- 
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