rtd build test

.readthedocs.yaml

+# readthedocs.yaml
+# RTD configuration file
+
+# Required
+version: 2
+
+sphinx:
+	configuration: rtd/conf.py

rtd/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

rtd/make.bat

+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

rtd/source/automatization.rst

+=====================
+automatization
+=====================
+
+.. automodule:: sen2chain.automatization
+   :members:

rtd/source/cloud_mask.rst

+=====================
+cloud_mask
+=====================
+
+.. automodule:: sen2chain.cloud_mask
+   :members:

rtd/source/colormap.rst

+=====================
+colormap
+=====================
+
+.. automodule:: sen2chain.colormap
+   :members:

rtd/source/conf.py

+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'sen2chain'
+copyright = '2023, ESPACE-DEV'
+author = 'ESPACE-DEV'
+release = '0.1'
+
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+# math
+from sphinx_math_dollar import NODE_BLACKLIST
+from docutils.nodes import header,FixedTextElement, literal,math
+from docutils.nodes import  comment, doctest_block, image, literal_block, math_block, paragraph, pending, raw, rubric, substitution_definition, target
+math_dollar_node_blacklist = (literal,math,doctest_block, image, literal_block,  math_block,  pending,  raw,rubric, substitution_definition,target)
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["myst_parser",'sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.napoleon','sphinx.ext.autosummary','sphinx_math_dollar','sphinx.ext.mathjax']
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+autodoc_member_order = 'bysource'
+
+mathjax_config = {
+    'tex2jax': {
+        'inlineMath': [ ["\\(","\\)"] ],
+        'displayMath': [["\\[","\\]"] ],
+    },
+}
+
+mathjax3_config = {
+  "tex": {
+    "inlineMath": [['\\(', '\\)']],
+    "displayMath": [["\\[", "\\]"]],
+  }
+}
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+html_permalinks_icon = '<span>#</span>'
+html_static_path = ['_static']

rtd/source/config.rst

+=====================
+config
+=====================
+
+.. automodule:: sen2chain.config
+   :members:
+

rtd/source/configure_sen2cor/index.rst

+==================================
+Configure sen2cor
+==================================
+ 
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   
+   sen2cor_2_5
+   sen2cor_2_8
+   sen2cor_2_9
+   sen2cor_2_10

rtd/source/configure_sen2cor/sen2cor_2_10.md

+# Sen2cor 2.10
+
+* 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 `chmod +x Sen2Cor-02.10.01-Linux64.run`
+* Install Sen2Cor `./Sen2Cor-02.10.01-Linux64.run`
+* Update config
+  * 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:
+    * `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/`
+  * Create or symlink DEM directory
+    * `ln -s /path/to/dem ~/sen2cor/2.10/dem`
+  * Update Sen2Cor config file `nano ~/sen2cor/2.10/cfg/L2A_GIPP.xml`
+    * <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
+  * Update Sen2Chain config file `nano ~/sen2chain_data/config/config.cfg`
+    * sen2cor_bashrc_path = /path/to/Sen2Cor-02.10.01-Linux64/L2A_Bashrc
+* Of course you have to update Sen2Chain

rtd/source/configure_sen2cor/sen2cor_2_5.md

+## Sen2cor 2.5
+
+Sen2Cor v02.05.05 is still supported by Sen2Chain latest version.
+
+Sen2Cor install path (sen2cor_bashrc_path) in config file (\~/sen2chain_data/config/config.cfg) is used to retrieve info of the Sen2Cor version and process L1C accordingly. So please keep the default Sen2Cor install directory name unchanged (ie Sen2Cor-02.0\*.0\*-Linux64) so that Sen2Chain finds this pattern.
+
+_Pas certain de comment configurer 2.5.5 donc le texte suivant n'est peut etre pas utile_
+
+**Sen2Cor default config**\
+Sen2Chain will not override your Sen2Cor config. You have to directly edit your Sen2Cor configuration file (default path: `\~/sen2cor/2.5/cfg/L2A_GIPP.xml`) : -> DEM_Directory and DEM_Reference paths in order to auto-download and use DEM correction. If a DEM is used the land cover data should be used to improve Sen2Cor classification algorithms. Please refer to 4.1 of Sen2Cor Configuration and User Manual (http://step.esa.int/thirdparties/sen2cor/2.8.0/docs/S2-PDGS-MPC-L2A-SUM-V2.8.pdf) for more install and configuration infos.\
+At SEAS-OI we still don't use the DEM correction as it seems not relevant in high shadow / steep slope environments (as in Reunion Island). Config file example: [L2A_GIPP.xml](/espace-dev/sen2chain/-/wikis/uploads/975660b0f1d6806891c4dd3b36feda7c/L2A_GIPP.xml)

rtd/source/configure_sen2cor/sen2cor_2_8.md

+# Sen2cor 2.8
+
+Starting from last tag version (v0.6-rc1), Sen2Chain should be compatible with Sen2Cor v02.08.00 (Sen2Cor v02.05.05 is still supported). 
+
+Sen2Cor install path (sen2cor_bashrc_path) in config file (~/sen2chain_data/config/config.cfg) is used to retrieve info of the Sen2Cor version and process L1C accordingly. So please keep the default Sen2Cor install directory name unchanged (ie Sen2Cor-02.0*.0*-Linux64) so that Sen2Chain finds this pattern.
+
+
+**Sen2Cor default config**\
+Sen2Chain will not override your Sen2Cor config. You have to directly edit your Sen2Cor configuration file (default path: `~/sen2cor/2.8/cfg/L2A_GIPP.xml`) : 
+-> DEM_Directory and DEM_Reference paths in order to auto-download and use DEM correction. If a DEM is used the land cover data should be used to improve Sen2Cor classification algorithms. Please refer to 4.1 of Sen2Cor Configuration and User Manual (http://step.esa.int/thirdparties/sen2cor/2.8.0/docs/S2-PDGS-MPC-L2A-SUM-V2.8.pdf) for more install and configuration infos.   
+At SEAS-OI we still don't use the DEM correction as it seems not relevant in high shadow / steep slope environments (as in Reunion Island). Config file example: [L2A_GIPP.xml](uploads/975660b0f1d6806891c4dd3b36feda7c/L2A_GIPP.xml)
+
+With Sen2Cor 2.8.0, default L2A naming convention has been changed, we forced it back to the Sen2Cor 2.5.5 way, to preserve compatibility with Sen2Chain functions:
+- Sen2Cor 2.8.0 default processing_baseline number is set to 99.99 => Sen2Chain forces it to previous L1C processing_baseline number
+- product discriminator is now set to the time the file is processed with Sen2Cor 2.8.0 => Sen2Chain forces it to previous L1C product discriminator

rtd/source/configure_sen2cor/sen2cor_2_9.md

+# Sen2cor 2.9
+
+* Download [Sen2Cor v2.09.00 ](http://step.esa.int/main/snap-supported-plugins/sen2cor/sen2cor-v2-9/)and put it to its final install directory 
+* Make it executable `chmod +x Sen2Cor-02.09.00-Linux64.run`
+* Install Sen2Cor `./Sen2Cor-02.09.00-Linux64.run`
+* Update config
+  * Move or symlink <span dir="ltr">ESACCI-LC package for SC module</span> to Sen2Cor directory
+    * `ln -s /path/to/ESACCI-LC-L4-LCCS-Map-300m-P1Y-2015-v2.0.7.tif Sen2Cor-02.09.00-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-02.09.00-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/`
+    * `ln -s /path/to/ESACCI-LC-L4-Snow-Cond-500m-P13Y7D-2000-2012-v2.0 Sen2Cor-02.09.00-Linux64/lib/python2.7/site-packages/sen2cor/aux_data/`
+  * Create or symlink DEM directory
+    * `ln -s /path/to/dem ~/sen2cor/2.9/dem`
+  * Update Sen2Cor config file `nano ~/sen2cor/2.9/cfg/L2A_GIPP.xml`
+    * <DEM_Directory>dem/srtm</DEM_Directory>
+    * <DEM_Reference><http://data_public:GDdci@data.cgiar-csi.org/srtm/tiles/GeoTIFF/></DEM_Reference>
+    * <DEM_Terrain_Correction>FALSE</DEM_Terrain_Correction>  # If you don't want DEM terrain correction
+  * Update Sen2Chain config file `nano ~/sen2chain_data/config/config.cfg`
+    * sen2cor_bashrc_path = /path/to/Sen2Cor-02.09.00-Linux64/L2A_Bashrc

rtd/source/contribute.rst

+==========
+Contribute
+==========
+
+You can submit your own developments and branches to our 'framagit <https://framagit.org/espace-dev/sen2chain>'

rtd/source/credits.rst

+=======
+Credits
+=======
+
+Sen2chain was developped in the frame of Sentinel-2 Malaria project, funded by `CNES <https://cnes.fr/en>`_ (TOSCA 2017-2019), under the coordination of Vincent Herbreteau (`IRD <https://en.ird.fr>`_ - `UMR ESPACE-DEV <http://www.espace-dev.fr>`_) and Christophe Révillion (`Univ La Réunion <http://www.univ-reunion.fr/university-of-reunion-island>`_ - UMR ESPACE-DEV). This project aims to use Sentinel-2 imagery for malaria monitoring in Madagascar and South Africa.
+
+
+.. image:: logos.png
+    :align: center
+    :alt: logos
\ No newline at end of file

rtd/source/data_request.rst

+=====================
+data_request
+=====================
+
+.. automodule:: sen2chain.data_request
+   :members:

rtd/source/download_and_process.rst

+=====================
+download_and_process
+=====================
+
+.. automodule:: sen2chain.download_and_process
+   :members:
+