Merge pull request #16 from openalea/doc

Doc

Author: jbdurand

.gitignore

@@ -89,4 +89,4 @@ site/
 out
 
 # Sphinx
-_static
+#_static

README.md

@@ -1,42 +1,41 @@
 # stat_tool
 
-_________________
+---
 
 [![Docs](https://readthedocs.org/projects/stat_tool/badge/?version=latest)](https://stat_tool.readthedocs.io/)
 [![Build Status](https://github.com/openalea/stat_tool/actions/workflows/conda-package-build.yml/badge.svg?branch=main)](https://github.com/openalea/stat_tool/actions/workflows/conda-package-build.yml?query=branch%3Amaster)
 [![License](https://img.shields.io/badge/License--CeCILL-C-blue)](https://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html)
 [![Anaconda-Server Badge](https://anaconda.org/openalea3/stat_tool/badges/version.svg)](https://anaconda.org/openalea3/stat_tool)
 
-_________________
+---
 
 [Read Latest Documentation](https://stat_tool.readthedocs.io/) - [Browse GitHub Code Repository](https://github.com/openalea/stat_tool/)
 
-_________________
+---
 
 **stat_tool** Basic Statistical tools used by different Structure Analysis libraries.
 
-### Contributors
+## Contributors
 
 Thanks to all that ontribute making this package what it is !
 
 <a href="https://github.com/openalea/stat_tool/graphs/contributors">
   <img src="https://contrib.rocks/image?repo=openalea/stat_tool" />
 </a>
 
-### Note for developers
- * Compile and install with
+## Note for developers
 
-     pip install -e .
+- Compile and install with
+
+  pip install -e .
 
 after activation of the conda environment depicted in the online documentation.
 
- * Comilation options for developers such are WITH_TEST, WITH_EFENCE are defined in pyproject.toml. They can be used with
+  * Compilation options for developers such as WITH_TEST, WITH_EFENCE are defined in pyproject.toml. They can be used with
 
-    pip install --no-build-isolation --config-settings=cmake.define.WITH_TEST=TRUE -e .
-    pip install --no-build-isolation --config-settings=cmake.build-type="Debug" -e .
+  pip install --no-build-isolation --config-settings=cmake.define.WITH_TEST=TRUE -e .
+  pip install --no-build-isolation --config-settings=cmake.build-type="Debug" -e .
 
 and also combined:
 
     pip install --no-build-isolation --config-settings=cmake.define.WITH_TEST=TRUE --config-settings=cmake.define.WITH_EFENCE=TRUE --config-settings=cmake.build-type="Debug" -e .
-
-

doc/Doxyfile

@@ -1779,7 +1779,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of

doc/_static/openalea_web.svg

@@ -0,0 +1,27 @@
+C++ Documentation
+#################
+
+.. toctree
+    :maxdepth: 2
+
+
+    .. doxygenclass:: stat_tool::
+        :project: stat_tool
+        :members:
+
+    .. autodoxygenindex::
+        :project: stat_tool
+
+    .. doxygennamespace:: stat_tool::Clusters
+
+    .. doxygennamespace:: stat_tool
+
+.. contents::
+    :local:
+    :depth: 2
+
+.. doxygenindex::
+
+
+
+

doc/api.md

@@ -0,0 +1,77 @@
+Classes
+-------
+
+.. doxygenclass:: stat_tool::CategoricalProcess
+   :members:
+.. doxygenclass:: stat_tool::Chain
+   :members:
+.. doxygenclass:: stat_tool::ChainData
+   :members:
+.. doxygenclass:: stat_tool::ChainReestimation
+   :members:
+.. doxygenclass:: stat_tool::Clusters
+   :members:
+.. doxygenclass:: stat_tool::Compound
+   :members:
+.. doxygenclass:: stat_tool::CompoundData
+   :members:
+.. doxygenclass:: ContinousParametric
+   :members:
+.. doxygenclass:: ContinousParametricProcess
+   :members:
+.. doxygenclass:: stat_tool::Convolution
+   :members:
+.. doxygenclass:: stat_tool::ConvolutionData
+   :members:
+.. doxygenclass:: stat_tool::Curves
+   :members:
+.. doxygenclass:: stat_tool::Dendrogram
+   :members:
+.. doxygenclass:: stat_tool::DiscreteDistributionData
+   :members:
+.. doxygenclass:: stat_tool::DiscreteMixture
+   :members:
+.. doxygenclass:: stat_tool::DiscreteMixtureData
+   :members:
+.. doxygenclass:: stat_tool::DiscreteParametric
+   :members:
+.. doxygenclass:: stat_tool::DiscreteParametricModel
+   :members:
+.. doxygenclass:: stat_tool::DiscreteParametricProcess
+   :members:
+.. doxygenclass:: stat_tool::DistanceMatrix
+   :members:
+.. doxygenclass:: stat_tool::Distribution
+   :members:
+.. doxygenclass:: stat_tool::Forward
+   :members:
+.. doxygenclass:: stat_tool::FrequencyDistribution
+   :members:
+.. doxygenclass:: stat_tool::Histogram
+   :members:
+.. doxygenclass:: stat_tool::MultiPlot
+   :members:
+.. doxygenclass:: stat_tool::MultivariateMixture
+   :members:
+.. doxygenclass:: stat_tool::MultivariateMixtureData
+   :members:
+.. doxygenclass:: stat_tool::Reestimation
+   :members:
+.. doxygenclass:: stat_tool::Regression
+   :members:
+.. doxygenclass:: stat_tool::RegressionKernel
+   :members:
+.. doxygenclass:: stat_tool::SinglePlot
+   :members:
+.. doxygenclass:: stat_tool::StatError
+   :members:
+.. doxygenclass:: stat_tool::StatInterface
+   :members:
+.. doxygenclass:: stat_tool::TemplateMultiPlotSet
+   :members:
+.. doxygenclass:: stat_tool::Test
+   :members:
+.. doxygenclass:: stat_tool::VectorDistance
+   :members:
+.. doxygenclass:: stat_tool::Vectors
+   :members: