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18 changes: 11 additions & 7 deletions docs/source/cli/gdal.rst
Original file line number Diff line number Diff line change
@@ -1,7 +1,11 @@
Geospatial Data Abstraction Library
===================================
GDAL
====

GDAL is a translator library for raster and vector geospatial data formats that is released under an `MIT style license <https://gdal.org/license.html#license>`__ by the `Open Source Geospatial Foundation <http://www.osgeo.org/>`__. As a library, it presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. The `News <https://github.com/OSGeo/gdal/blob/v3.4.0/gdal/NEWS.md>`__ page describes the latest release.
**Geospatial Data Abstraction Library (GDAL)** is a translator library for raster and vector geospatial data formats that is released under an `MIT style license <https://gdal.org/license.html#license>`__ by the `Open Source Geospatial Foundation <http://www.osgeo.org/>`__.

As a library, **GDAL** presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing.

For information on the newest release of **GDAL**, see `News <https://github.com/OSGeo/gdal/blob/v3.4.0/gdal/NEWS.md>`__.

.. note::

Expand All @@ -10,7 +14,7 @@ GDAL is a translator library for raster and vector geospatial data formats that
Available commands
------------------

The complete documentation of GDAL commands can be found on the `GDAL website <https://gdal.org/programs/index.html>`__.
The complete documentation of **GDAL** commands can be found on the `GDAL website <https://gdal.org/programs/index.html>`__.

Raster programmes
^^^^^^^^^^^^^^^^^
Expand All @@ -28,7 +32,7 @@ Raster programmes
$ rgb2pct.py # Convert a 24bit RGB image to 8bit paletted.
$ pct2rgb.py # Convert an 8bit paletted image to 24bit RGB.
$ gdalattachpct.py # Attach a color table to a raster file from an input file.
$ gdal_merge.py # Mosaicks a set of images.
$ gdal_merge.py # Mosaics a set of images.
$ gdal2tiles.py # Generates directory with TMS tiles, KMLs and simple web viewers.
$ gdal2xyz.py # Translates a raster file into xyz format.
$ gdal_rasterize # Burns vector geometries into a raster.
Expand Down Expand Up @@ -76,5 +80,5 @@ Geographic network programmes

.. code-block:: bash

$ gnmmanage # Manages networks
$ gnmanalyse # Analyses networks
$ gnmmanage # Manages networks.
$ gnmanalyse # Analyses networks.
12 changes: 6 additions & 6 deletions docs/source/cli/gdrive.rst
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
Google Drive
============
Drive
=====

The **Drive** CLI is a utility that allows managing a Google Drive account from the SEPAL console (for more information, see the Readme file directly in the GitHub repository https://github.com/odeke-em/drive).
The **Google Drive (Drive)** CLI is a utility that allows managing a Google Drive account from the SEPAL console (for more information, see `the Readme file in the GitHub repository <https://github.com/odeke-em/drive>`__.

Usage
-----

Initialize drive connection
Initialize Drive connection
^^^^^^^^^^^^^^^^^^^^^^^^^^^

Before running any of the **Drive** commands, start a session by running the following line:
Expand All @@ -15,7 +15,7 @@ Before running any of the **Drive** commands, start a session by running the fol

$ drive init

Copy the URL that is displayed in the terminal and paste it into your browser. Log in to your Google account and "trust the connection" by selecting the "allow" button. An authorization code will be displayed; copy and paste it into the SEPAL terminal. You are now ready to use the :code:`Drive` CLI tool.
Copy the URL that is displayed in the terminal and paste it into your browser. Log in to your Google account and "trust the connection" by selecting the **Allow** button. An authorization code will be displayed; copy and paste it into the SEPAL terminal. You are now ready to use the :code:`Drive` CLI tool.

.. note::

Expand All @@ -37,7 +37,7 @@ You can upload files from your SEPAL environment by using the :code:`Push` comma
Download files
--------------

To download files, use the :code:`Pull` command. This command will create files that don't exist locally but do remotely.
To download files, use the :code:`Pull` command, which will create files that don't exist locally (but do remotely).

.. code-block:: bash

Expand Down
38 changes: 22 additions & 16 deletions docs/source/cli/gee.rst
Original file line number Diff line number Diff line change
@@ -1,19 +1,21 @@
Google Earth Engine
===================
GEE
===

The **earthengine** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line. It is installed automatically when you install the Python API. To check whether the tool is installed and functioning correctly, enter the following in a command line:
The **Google Earth Engine (GEE)** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line.

The tool is installed automatically when you install the Python API. To check whether it is installed and functioning correctly, enter the following in a command line:

.. code-block:: console

$ earthengine

If the tool is properly installed, it will print out a short summary of available commands. To get help on a specific command, use:
If the tool is properly installed, it will display a short summary of available commands. To get help on a specific command, use:

.. code-block:: console

$ earthengine command -h

When you first install the Python API, you will need to login using the :code:`Authenticate` command described below.
When you first install the Python API, you will need to log in using the :code:`Authenticate` command, as described below.

Available commands
------------------
Expand All @@ -40,19 +42,23 @@ More information on the available command can be found on the `Google API websit
$ upload_manifest # Uploads an image to GEE using the given manifest file.
$ upload_table_manifest # Uploads a table to GEE using the given manifest file.

Use Google Earth Engine in the Jupyter interface
------------------------------------------------
Use GEE in the Jupyter interface
--------------------------------

We highly suggest working directly from the Python interface of GEE, as Python has been extended by the community (gee_tools, geemap, ipygee, sepal_ui, etc.) and is more user-friendly.

It's also the best way to prototype a script before using it in a SEPAL application, as the translation from Python to Javascript is not always straightforward.

We highly suggest to work directly from the Python interface of Google Earth Engine as the Pythonhas been extended by the community (gee_tools, geemap, ipygee, sepal_ui etc.) and is more user-friendly.
It's also the best way to prototype a script before using it in a SEPAL application as the translation from Python to Javascript is not always straightforward.
The main advantages of the **GEE code editor** are:

The main advantages of the GEE code editor are:
- the access to a live map
- the value inspector

SEPAL and Jupyter lab can help you bring this to the next level by providing both tools in a Python notebook, allowing you to also access all the Python geospatil tools created by the Eart obseervation community.
SEPAL and JupyterLab can help you bring this to the next level by providing both tools in a Python notebook, allowing you to also access all Python geospatial tools created by the Earth observation community.

First open a JupyterLab instance and start a notebook. In the first cell create a map and place it the sidecar by running the following code:
First, open a JupyterLab instance and start a notebook.

In the first cell, create a map and place it the sidecar by running the following code:

.. code-block:: python

Expand All @@ -67,15 +73,15 @@ First open a JupyterLab instance and start a notebook. In the first cell create
.. thumbnail:: ../_images/cli/gee/create_a_sidecar.png
:title: Some code that will be run in the sidecar

As displayed in the previous image, the list of available sidecars is displayed on the right side of the frame. You can create as many sidecars as you want and display any widget in it. We chose to use the sepal_ui mappping widget as it's including key features such as:
As displayed in the previous image, the list of available sidecars is displayed on the right side of the frame. You can create as many sidecars as you want and display any widget in it. We chose to use the **sepal_ui mappping** widget as it includes key features, such as:

- GEE full compatibility
- an extended layer manager
- a value inspector

From now the map will be displayed in a sidecar next to thenotebook. The map is running live so in any cell you can add extra layers to it. It's more powerful than the Code editor map as you don't need to run all your cells again to get the map updated.
The map will be displayed in a sidecar next to the notebook. It is running live, so you can add extra layers to it in any cell. Also, it is more powerful than the **Code editor map** as you don't need to run all your cells again to update the map.

.. thumbnail:: ../_images/cli/gee/sidecar_with_data.png
:title: The map displayed in the sidecar

Now you are all set to create your own GEE script. You can use the GEE Python API documentation to get started.

Now you are all set to create your own **GEE script** – you can use the **GEE Python API documentation** to get started.
12 changes: 7 additions & 5 deletions docs/source/cli/gwb.rst
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@@ -1,16 +1,18 @@
GuidosToolbox Workbench
=======================
GWB
===

The GuidosToolbox Workbench (**GWB**) is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB <https://forest.jrc.ec.europa.eu/en/activities/lpa/gwb/>`_ or `GTB <https://forest.jrc.ec.europa.eu/en/activities/lpa/gtb/>`_). Citation reference: `GuidosToolbox Workbench: Spatial analysis of raster maps for ecological applications <https://doi.org/10.1111/ecog.05864>`_.
**GuidosToolbox Workbench (GWB)** is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB <https://forest.jrc.ec.europa.eu/en/activities/lpa/gwb/>`_ or `GTB <https://forest.jrc.ec.europa.eu/en/activities/lpa/gtb/>`_).

Citation reference: `GuidosToolbox Workbench: Spatial analysis of raster maps for ecological applications <https://doi.org/10.1111/ecog.05864>`_.

.. note::

The current version available on SEPAL is 1.9.0
The current version available in SEPAL is 1.9.0

Available commands
------------------

The complete documentation of GWB commands can be found in the `GWB manual <https://gwbdoc.readthedocs.io>`__
The complete documentation of GWB commands can be found in the `GWB manual <https://gwbdoc.readthedocs.io>`__.

.. code-block:: console

Expand Down
32 changes: 16 additions & 16 deletions docs/source/cli/index.rst
Original file line number Diff line number Diff line change
@@ -1,22 +1,23 @@
SEPAL environment
=================
CLI utilities and coding tools
==============================
*Use command-line interface (CLI) utilities and coding tools in SEPAL*

CLI tools
---------

The SEPAL platform includes a variety of useful command-line interface (CLI) utilities to help resolve specific problems such as:
The SEPAL platform includes a variety of useful command-line interface (CLI) utilities to help resolve specific problems, such as:

- Geospatial Data Abstraction Library (GDAL)
- Google Drive (Drive)
- Google Earth Engine (GEE)
- GuidosToolbox Workbench (GWB)
- Open Foris Geospatial Toolkit (OFGT)
- Orfeo Toolbox (OTB)
- **Geospatial Data Abstraction Library (GDAL)**
- **Google Drive (Drive)**
- **Google Earth Engine (GEE)**
- **GuidosToolbox Workbench (GWB)**
- **Open Foris Geospatial Toolkit (OFGT)**
- **Orfeo Toolbox (OTB)**

These tools can be called directly from the terminal or any programming language sending commands to the kernel, including R and Python (installed by default on any SEPAL account).
These tools can be called directly from the terminal or via any programming language sending commands to the kernel, including R and Python (installed by default on any SEPAL account).

.. thumbnail:: ../_images/cli/index/cli_gdalinfo.gif
:title: How to use the gdalinfo command in a SEPAL terminal
:title: How to use the **gdalinfo** command in the SEPAL terminal

.. note::

Expand All @@ -38,25 +39,24 @@ These tools can be called directly from the terminal or any programming language

nohup gdalinfo example.tif

All the console outputs will be redirected to a :code:`nohup.out` in your home directory, but the execution will be running in the background. Thus, you will be able to safely close the terminal or even the browser window without killing your process (for more information about :code:`nohup`, see `here <https://en.wikipedia.org/wiki/Nohup>`__.

All console outputs will be redirected to a :code:`nohup.out` in your home directory, but the execution will be running in the background. Thus, you will be able to safely close the terminal or even the browser window without killing your process (for more information about :code:`nohup`, see `this article <https://en.wikipedia.org/wiki/Nohup>`__.

Coding tools
------------

In the **App** section, you'll find three coding tools at the top of the list:
In the **Apps** section, there are three coding tools at the top of the list:

- JupyterLab
- JupyterNotebook
- RStudio

.. thumbnail:: ../_images/cli/index/code_editor.png
:title: The three code editor in the SEPAL environment
:title: The three code editors in the SEPAL environment

They will allow the user to code wokflows in any of the available languages using the coresponding environment in SEPAL. These environments are fully customizable (select the :code:`Python` or :code:`R` section to know more).

.. thumbnail:: ../_images/cli/index/jupyter_example.png
:title: Example of rasterio code running in SEPAL JupyterLab (code extracted from rasterio documentation: https://rasterio.readthedocs.io/en/latest/topics/plotting.html)
:title: Example of **rasterio** code running in SEPAL JupyterLab (code extracted from **rasterio** documentation: https://rasterio.readthedocs.io/en/latest/topics/plotting.html)

.. toctree::
:hidden:
Expand Down
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