rst updates for rtd

rtd/source/configure_sen2cor/sen2cor_2_10.rst

+Sen2cor 2.10.01
+===============
+
+.. role:: bash(code)
+    :language: bash
+
+* Download `Sen2Cor v2.10.01 <https://step.esa.int/thirdparties/sen2cor/2.10.0/Sen2Cor-02.10.01-Linux64.run>`_ and put it to its final install directory.
+
+* Make it executable :bash:`chmod +x Sen2Cor-02.10.01-Linux64.run`
+	
+* Install Sen2Cor :bash:`./Sen2Cor-02.10.01-Linux64.run`
+
+* Update your configuration:
+
+1. Move or symlink `ESACCI-LC package for SC module <https://earth.esa.int/eogateway/ftp/Sentinel-2/ESACCI-LC-L4-ALL-FOR-SEN2COR-2.10.tar.gz>`_ content to Sen2Cor directory:
+  
+.. code-block:: bash
+
+	ln -s /path/to/ESACCI-LC-L4-ALL-FOR-SEN2COR-2.10/ESACCI-LC-L4-LCCS-Map-300m-P1Y-2015-v2.0.7.tif /Path/to/Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data
+	ln -s /path/to/ESACCI-LC-L4-WB-Map-150m-P13Y-2000-v4.0.tif Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/
+	ln -s /path/to/ESACCI-LC-L4-Snow-Cond-500m-MONTHLY-2000-2012-v2.4 Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/
+
+
+2. Create or symlink DEM directory
+  
+.. code-block:: bash
+	
+    ln -s /path/to/dem ~/sen2cor/2.10/dem
+
+3. Update Sen2Cor config file :bash:`nano ~/sen2cor/2.10/cfg/L2A_GIPP.xml`
+  
+.. code-block:: html
+
+	<DEM_Directory>dem/srtm</DEM_Directory>
+	<DEM_Reference>http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/</DEM_Reference>
+	<DEM_Terrain_Correction>FALSE</DEM_Terrain_Correction>  # If you don't want DEM terrain correction
+
+4. Update Sen2Chain config file :bash:`nano ~/sen2chain_data/config/config.cfg`
+
+.. code-block:: bash
+
+    sen2cor_bashrc_path = /path/to/Sen2Cor-02.10.01-Linux64/L2A_Bashrc
+
+
+* Of course you have to update Sen2Chain

rtd/source/getting_started/configuration.rst

@@ -6,7 +6,7 @@ Installation
 
 Download Sen2Chain and install the python dependencies
 
-.. code-block::
+.. code-block:: bash
 
     git clone https://framagit.org/espace-dev/sen2chain.git 
     cd sen2chain
@@ -15,7 +15,7 @@ Download Sen2Chain and install the python dependencies
     
 Or install directly from Git :
 
-.. code-block::
+.. code-block:: bash
     
     python3 -m pip install git+https://framagit.org/espace-dev/sen2chain.git
     
@@ -24,24 +24,23 @@ Or install directly from Git :
 Update sen2chain
 -----------------
 
-Updates are regularly made on the processing chain, it can be easily retrieved with Git. Go to the install directory, pull the last updates from Framagit, and if necessary reinstall Sen2Chain (to get new requirement libraries).
+| Updates are regularly made on the processing chain, it can be easily retrieved with Git.
+| Go to the install directory, pull the last updates from Framagit, and if necessary reinstall Sen2Chain (to get new requirement libraries).
 
-.. code-block::
+.. code-block:: bash
 
 	cd sen2chain 
 	git pull 
 	pip3 install --user -e .
 	
 
-
-| The different configuration files are located in ~/sen2chain_data. This files are only created after the first sen2chain import in python.  
+| The different configuration files are located in ~/sen2chain_data. These files are only created after the first sen2chain import in python.  
 | To initialize the config files you can launch:
 
-.. code-block::
+.. code-block:: python
 
-    python3
-    >>> from sen2chain import Tile
-	>>> exit()
+    from sen2chain import Tile
+    exit()
 
 
 Sen2chain Configuration
@@ -49,24 +48,24 @@ Sen2chain Configuration
 
 After the first launch of sen2chain, default folders are created in: 
 
-.. code-block::
+.. code-block:: bash
 
 	~/sen2chain_data/data
 
 
 You can change the settings by editing the configuration file:
 
-.. code-block::
+.. code-block:: bash
 
 	~/sen2chain_data/data/config.cfg
 
-Here you can configure all the paths that will receive the different data from the processing steps of sen2chain. 
-| In this file indicate the full path to the bashrc of your sen2cor installation to process L1C to L2A _**(ajouter ici la possibilité de mettre un autre sen2cor pour les données pré 2018)**_:
+| Here you can set directory paths that will receive the different products from the processing steps of sen2chain.
+| In this file indicate the full path to the L2A_Bashrc file of your sen2cor installation to process L1C to L2A _**(ajouter ici la possibilité de mettre un autre sen2cor pour les données pré 2018)**_:
 
-.. code-block::
+.. code-block:: bash
 
 	/path/to/Sen2Cor-02.10.01-Linux64/L2A_Bashrc
 
 
  
-**Sen2Chain is now ready to run!*
+**Sen2Chain is now ready to run!**

rtd/source/getting_started/eodag.rst

 EODAG
 ======
 
-| `EODDAG <https://eodag.readthedocs.io/en/stable/>`_ is a command-line tool and a Python package for searching and downloading remotely sensed images while offering a unified API for data access regardless of the data provider. 
+| `EODAG <https://eodag.readthedocs.io/en/stable/>`_ is a command-line tool and a Python package for searching and downloading remotely sensed images while offering a unified API for data access regardless of the data provider. 
 
 | A specific plugin was released for the Scihub provider. Both can be installed with pip.
 
 
-.. code-block::    
+.. code-block:: bash
     
     python3 -m pip install eodag-sentinelsat
     
@@ -19,7 +19,7 @@ Register to Scihub, PEPS and any provider you deem relevant for your work, and g
 | Follow the guidelines provided in `EODAG's documentation <https://eodag.readthedocs.io/en/stable/getting_started_guide/configure.html>`_ to configure the plugin. 
 | You can create a dedicated configuration file or edit the default one: 
 
-.. code-block::
+.. code-block:: bash
     
     ~/.config/eodag/eodag.yml
 

rtd/source/getting_started/index.rst

@@ -12,5 +12,6 @@ Why sen2chain, how to install, configure it, go!
    intro
    my_install
    eodag
-   configuration
    sen2cor
+   configuration
+   

rtd/source/getting_started/my_install.rst

@@ -5,19 +5,19 @@ Sen2chain requires pip, GDAL, Git and Sen2Cor 2.10.01
 
 pip
 -----
-.. code-block::
+.. code-block:: bash
     
     python -m pip install --upgrade pip
 
 GDAL
 -----
-.. code-block::
+.. code-block:: bash
     
     sudo apt install gdal-bin libgdal-dev python3-gdal
 
 Git
 ----
-.. code-block::
+.. code-block:: bash
 
     sudo apt-get install git
 
@@ -26,27 +26,27 @@ Sen2cor v2.10.01
 
 1. Download Sen2Cor v2.10.01
 
-.. code-block::
+.. code-block:: bash
 
     wget https://step.esa.int/thirdparties/sen2cor/2.10.0/Sen2Cor-02.10.01-Linux64.run
 
 
 2. Make it executable
 
-.. code-block::
+.. code-block:: bash
 
     chmod +x Sen2Cor-02.10.01-Linux64.run
     
 
 3. Install Sen2Cor 
 
-.. code-block::
+.. code-block:: bash
 
     ./Sen2Cor-02.10.01-Linux64.run
 
 
 .. note::
-   Installation guide and requirements for previous versions of Sen2Chain and Sen2Cor are available :ref:`here <sen2cor>`. This may be needed to process imagery from 2018 and before.
+   Installation guide and requirements for previous versions of Sen2Chain and Sen2Cor are available :ref:`here <sen2cor>`. Previous versions are needed to process imagery before 2018.
 
 
 | You can add extra data to improve some features of sen2chain. 

rtd/source/getting_started/sen2cor.rst

 .. _sen2cor:
 
-Sen2cor
-=========
-
 Configuration of Sen2cor v2.10.01
 ----------------------------------
 
-1. Move or create symlink to `ESACCI-LC package for SC module <https://earth.esa.int/eogateway/ftp/Sentinel-2/ESACCI-LC-L4-ALL-FOR-SEN2COR-2.10.tar.gz>` content to Sen2Cor directory:
+1. Move or create symlink to `ESACCI-LC package for SC module <https://earth.esa.int/eogateway/ftp/Sentinel-2/ESACCI-LC-L4-ALL-FOR-SEN2COR-2.10.tar.gz>`_ content to Sen2Cor directory:
 
-.. code-block::
+.. code-block:: bash
 
 	ln -s /path/to/ESACCI-LC-L4-ALL-FOR-SEN2COR-2.10/ESACCI-LC-L4-LCCS-Map-300m-P1Y-2015-v2.0.7.tif /Path/to/Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data
-	
-.. code-block::
-
 	ln -s /path/to/ESACCI-LC-L4-WB-Map-150m-P13Y-2000-v4.0.tif Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/
-	
-.. code-block::
-
 	ln -s /path/to/ESACCI-LC-L4-Snow-Cond-500m-MONTHLY-2000-2012-v2.4 Sen2Cor-02.10.01-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/
 	
 2. Create or symlink DEM directory
 
-.. code-block::
+.. code-block:: bash
 
 	ln -s /path/to/dem ~/sen2cor/2.10/dem
 	
-3. Update Sen2cor configuration file ```nano ~/sen2cor/2.10/cfg/L2A_GIPP.xml```
+3. Update Sen2cor configuration file ``nano ~/sen2cor/2.10/cfg/L2A_GIPP.xml``
 
-.. code-block::
+.. code-block:: html
 
 	<DEM_Directory>dem/srtm</DEM_Directory>
 	<DEM_Reference>http://srtm.csi.cgiar.org/wp-content/uploads/files/srtm_5x5/TIFF/</DEM_Reference>
 	<DEM_Terrain_Correction>FALSE</DEM_Terrain_Correction>  # If you don't want DEM terrain correction
 
-4. Update sen2chain config file ```nano ~/sen2chain_data/config/config.cfg```
+4. Update sen2chain config file ``nano ~/sen2chain_data/config/config.cfg``
 
-.. code-block::
+.. code-block:: bash
 
 	sen2cor_bashrc_path = /path/to/Sen2Cor-02.10.01-Linux64/L2A_Bashrc
 	

rtd/source/index.rst

@@ -46,6 +46,7 @@ Content
    :caption: Contents:
    
    getting_started/index
+   product_user_guide/index
    first_steps/index
    going_further/index
    package_content

rtd/source/package_content.rst

-=====================
-User Guide
-=====================
+===========================
+Python Reference User Guide
+===========================
 
 Every package
 =====================

rtd/source/product_user_guide/index.rst

+========================
+Product User Guide
+========================
+
+.. toctree::
+    L1C
+    L2A
+    Cloudmasks
+    Indices
+    Time Series