Add code layout + wrapping section in README

README.md

@@ -10,17 +10,20 @@ This package provides tools for statistical analysis of the structure of a plant
 ## Install
 
 ### Dependencies
+
 We recommand to use python virtual environments to install the package (conda is a good choice, especialy since conda-only packages are required as dependencies).
 
 Required dependencies available from `conda-forge` channel are :
+
 - boost
 - scons
 - openalea.deploy
 - openalea.sconsx
 - nose (for tests, only via pip install)
 
 ### Doing the development install
-To install the package for developments, you can use the `multisetup.py` script. It will use the `Multisetup` from `openalea.deploy` to compile `stat_tools` and `sequence_analysis` packages.
+
+To install the package for developments, you can use the `multisetup.py` script. It will use the `Multisetup` from `openalea.deploy` to compile `stat_tool` and `sequence_analysis` packages.
 
 ```bash
 python multisetup.py develop
@@ -29,7 +32,7 @@ python multisetup.py develop
 However, compilation can be a bit long and you may want to install using parallel compilation. To do so, you can use the following sequence (compilation with 4 cores, but you can adapt to your ressources):
 
 ```bash
-cd stat_tools
+cd stat_tool
 scons -j4
 pip install -e .
 cd ../sequence_analysis
@@ -39,7 +42,267 @@ cd ..
 ```
 
 ### After-install issues
+
 Observed only on OSX (so far), you may need to extend your `LD_LIBRARY_PATH` environment variable to include the path of your newly built libraries:
-```
+
+```bash
 export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/path/to/your/conda/env/lib:/path/to/StructureAnalysis/stat_tool/build-scons/lib/:/path/to/StructureAnalysis/sequence_analysis/build-scons/lib/
-```
+```
+
+## Wrapping C++ code
+
+The C++ code is wrapped using `boost::python`. The wrapping is done using `Scons` and `openalea.sconsx` (thin additional layer on top of `Scons` for `OpenAlea` projects).
+
+> warning::
+> We still need to make sure that all the C++ code is properly wrapped, and no requirements are missing. Is running all the tests enough ?
+
+## Code layout
+
+As a first step, we focus on two packages: `stat_tool` and `sequence_analysis`. The other packages are either becoming irrelevant (based on original `AML` code) or are not yet implemented.
+
+### stat_tool
+
+You can find below the structure of the `stat_tool` package. The `Scosntruct` file is used to compile the C++ code. The `src/cpp` directory contains the C++ code, and the `src/wrapper` directory contains the code to wrap the C++ code into Python. `src/openalea/stat_tool` contains the Python code that uses the wrapped C++ code.
+
+```bash
+.
+├── AUTHORS.txt
+├── ChangeLog.txt
+├── LICENSE.txt
+├── README.txt
+├── SConstruct
+├── conda
+│   └── meta.yaml
+├── debian
+│   ├── changelog
+│   ├── compat
+│   ├── control
+│   ├── copyright
+│   ├── rules
+│   └── source
+│       └── format
+├── doc
+│   ├── Doxyfile
+│   ├── Makefile
+│   ├── README
+│   ├── _static
+│   │   ├── fig7_1.png
+│   │   └── fig7_2.png
+│   ├── conf.py
+│   ├── contents.rst
+│   ├── cpp
+│   │   └── doxygen.conf
+│   ├── make.bat
+│   ├── pyplots
+│   │   └── example1.py
+│   └── user
+│       ├── admin.rst
+│       ├── ...
+│       └── visualea_oak_demo.rst
+├── examples
+│   ├── Model
+│   │   ├── Markov
+│   │   │   ├── belren1.hsc
+│   │   │   ├── ...
+│   │   │   └── wij1.hsc
+│   │   └── align1.a
+│   ├── Sample
+│   │   ├── Histogram
+│   │   │   ├── meri1.his
+│   │   │   ├── ...
+│   │   │   └── peup6.his
+│   │   └── Sequences
+│   │       ├── belren1.seq
+│   │       ├── ...
+│   │       └── wij1.seq
+│   ├── exploratory.aml
+│   └── exploratory.py
+├── install_stool.sh
+├── merge_info.txt
+├── methodo.txt
+├── setup.py
+├── share
+│   └── data
+│       ├── chene_sessile.vec
+│       ├── ...
+│       └── peup6.his
+├── src
+│   ├── cpp
+│   │   ├── SConscript
+│   │   ├── SConscriptWIG
+│   │   ├── categorical_process.cpp
+│   │   ├── chain.cpp
+│   │   ├── chain_algorithms.cpp
+|   |   ├── ...
+│   │   ├── chain_reestimation.h
+│   │   ├── chain_reestimation.hpp
+│   │   ├── vectors.cpp
+│   │   └── vectors.h
+│   ├── openalea
+│   │   └── stat_tool
+│   │       ├── __init__.py
+│   │       ├── cluster.py
+│   │       ├── ...
+│   │       └── vectors.py
+│   └── wrapper
+│       ├── SConscript
+│       ├── boost_python_aliases.h
+│       ├── export_base.cpp
+│       ├── export_base.h
+|       ├── ...
+│       ├── export_vectors.cpp
+│       ├── export_vectors.h
+│       ├── stat_tool_wrap.cpp
+│       └── wrapper_util.h
+└── test
+    ├── README.md
+    ├── aml
+    │   ├── stat_tool_test.aml
+    │   ├── stat_tool_test.ipynb
+    │   └── stat_tool_test.py
+    ├── cpp
+    │   ├── SConscript
+    │   ├── np_model.mix
+    │   └── test_multivariate_mixture.cpp
+    ├── data
+    │   ├── angles_ahp6_10.seq
+    |   ├── ...
+    │   └── vectors2.vec
+    ├── stat_tool_examples.py
+    ├── stat_tool_sequence_analysis_class.txt
+    ├── test_cluster.py
+    ├── ...
+    ├── test_vectors_functional.py
+    └── tools.py
+```
+
+### sequence_analysis
+
+You can find below the structure of the `sequence_analysis` package, which is similar to `stat_tool`. The `Scosntruct` file is used to compile the C++ code. The `src/cpp` directory contains the C++ code, and the `src/wrapper` directory contains the code to wrap the C++ code into Python. `src/openalea/sequint`and `src/openalea/sequence_analysis` contains the Python code that uses the wrapped C++ code.
+
+```bash
+.
+├── AUTHORS.txt
+├── ChangeLog.txt
+├── LICENSE.txt
+├── README.txt
+├── SConstruct
+├── conda
+│   └── meta.yaml
+├── debian
+│   ├── changelog
+│   ├── compat
+│   ├── control
+│   ├── copyright
+│   ├── rules
+│   └── source
+│       └── format
+├── doc
+│   ├── Doxyfile
+│   ├── Makefile
+│   ├── conf.py
+│   ├── contents.rst
+│   ├── cpp
+│   │   └── doxygen.conf
+│   ├── make.bat
+│   ├── pyplots
+│   │   ├── example_oak_1.py
+│   │   ├── ...
+│   │   └── sequence_plot_values.py
+│   └── user
+│       ├── admin.rst
+│       ├── autosum.rst
+│       ├── index.rst
+│       ├── overview.txt
+│       ├── scripts
+│       │   ├── example_oak.py
+│       │   └── example_oak.rst
+│       └── tutorial.rst
+├── sequence_analysis.py
+├── setup.py
+├── share
+│   ├── README.txt
+│   └── data
+│       ├── abri13.ren
+│       ├── abricotier_suivi_11.seq
+│       ├── belren1.hsc
+│       ├── belren1.seq
+│       ├── ...
+│       ├── wij1.hsc
+│       └── wij1.seq
+├── src
+│   ├── cpp
+│   │   ├── SConscript
+│   │   ├── alignment.cpp
+│   │   ├── ...
+│   │   └── vomc_distributions2.cpp
+│   ├── openalea
+│   │   ├── seqint
+│   │   │   ├── README.txt
+│   │   │   ├── __init__.py
+│   │   │   ├── config.py
+│   │   │   ├── ...
+│   │   │   └── xl_io.py
+│   │   └── sequence_analysis
+│   │       ├── __init__.py
+│   │       ├── _sequence_analysis.so
+│   │       ├── compare.py
+│   │       ├── ...
+│   │       └── variable_order_markov.py
+│   ├── sequence_analysis_wralea
+│   │   ├── __init__.py
+│   │   ├── __wralea__.py
+│   │   ├── demo
+│   │   │   ├── __init__.py
+│   │   │   ├── change_point
+│   │   │   │   ├── Demo_ChangePoint_stat_tool_wralea.py
+│   │   │   │   ├── __init__.py
+│   │   │   │   ├── angelique_internode_length.seq
+│   │   │   │   ├── change_point_demo.aml
+│   │   │   │   ├── icon.png
+│   │   │   │   ├── pin_laricio_7x.seq
+│   │   │   │   └── reinet1.hsc
+│   │   │   └── stat_tool_tutorial
+│   │   │       ├── __init__.py
+│   │   │       ├── __wralea__.py
+│   │   │       ├── angelique_internode_length.seq
+│   │   │       ├── icon.png
+│   │   │       ├── pin_laricio_7x.seq
+│   │   │       └── reinet1.hsc
+│   │   ├── icon.png
+│   │   └── stat.py
+│   └── wrapper
+│       ├── SConscript
+│       ├── boost_python_aliases.h
+│       ├── csequence.cpp
+│       ├── export_base.cpp
+│       ├── export_base.h
+│       ├── ...
+│       ├── sequence_analysis_wrap.cpp
+│       └── wrapper_util.h
+├── test
+│   ├── _test_variable_order_markov.py
+│   ├── functional1.py
+│   ├── functional2.py
+│   ├── functional3.py
+│   ├── test_add_absorbing_run.py
+│   ├── ...
+│   ├── test_transcode.py
+│   └── tools.py
+└── tutorials
+    ├── Code
+    │   ├── __init__.py
+    │   ├── amlseq2R.py
+    │   ├── matrix_plot.py
+    │   └── python_dics2R.py
+    ├── Utils
+    │   ├── __init__.py
+    │   ├── __pycache__
+    │   │   └── __init__.cpython-310.pyc
+    │   ├── dos2unix.py
+    │   └── unix2dos.py
+    ├── scratch
+    ├── seq1v_5s_LR_init.hsmc
+    ├── sequences.ipynb
+    └── sim_v_5s_LR.hsmc
+```