openalea · jbdurand · Feb 25, 2026 · Feb 25, 2026 · Mar 9, 2026 · Mar 12, 2026
diff --git a/.gitignore b/.gitignore
@@ -88,6 +88,3 @@ venv/
 docs/preconvert
 site/
 out
-
-# Sphinx
-_static
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-24.04"
+  tools:
+    python: "mambaforge-22.9"
+
+conda:
+  environment: conda/environment.yml
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: doc/conf.py
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -92,6 +92,8 @@ endif()
 # Options
 option(WITH_EFENCE "Build with efence library" OFF)
 option(WITH_TEST "Build tests" OFF)
+message(STATUS "WITH_EFENCE = ${WITH_EFENCE}")
+message(STATUS "WITH_TEST = ${WITH_TEST}")
 
 ##################################################
 # Add a library for sequence_analysis and its Python wrappers

diff --git a/README.md b/README.md
@@ -13,11 +13,13 @@ _________________
 
 _________________
 
-**sequence analysis** Basic Statistical tools used by different Structure Analysis libraries.
+**sequence_analysis** is a python module for the analysis of time series (discrete time). It is mainly dedicated to the analysis of botanical sequences but can be used for general purposes. The module contains procedures for estimating semi-Markov, hidden semi-Markov, variable-order Markov and hidden variable-order Markov models. It also has procedure to estimate renewal processes and offers diverse tools to edit sets of sequences (filter, merge sets merge variables, select, etc.)
+
+sequence_analysis is relies on [OpenAlea](https://github.com/openalea/) and particularly the  [stat_tool module](https://github.com/openalea/stat_tool)
 
 ### Contributors
 
-Thanks to all that ontribute making this package what it is !
+Thanks to everone who ontribute making this package what it is!
 
 </a>
 <a href="https://github.com/openalea/sequence_analysis/graphs/contributors">

diff --git a/README.txt b/README.txt
diff --git a/TODO b/TODO
@@ -0,0 +1,2 @@
+[ ] Remove plots from pytests
+[ ] Make a list from tests to be updated
diff --git a/conda/environment.yml b/conda/environment.yml
@@ -1,13 +1,15 @@
 name: sequence_analysis_dev
 channels:
   - conda-forge
+  - openalea3/label/dev
   - openalea3
 dependencies:
   - python
   - pip
   - boost
   - matplotlib-base
   - openalea.stat_tool
+  - compilers
+  - doxygen
   - pip:
       - -e '..[test,dev,doc]'
-
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -33,13 +33,13 @@ requirements:
     {% for dep in build_deps %}
     - {{ dep }}
     {% endfor  %}
-    - cmake
-    - make                                 # [not win]
     - openalea.stat_tool
     - boost
 
   build:
     - {{ compiler("cxx") }}
+    - cmake
+    - make                                 # [not win]
 
   run:
     - python
@@ -62,7 +62,9 @@ test:
   source_files:
     - test/
   commands:
-    - pytest
+    - cd test
+    - pytest -v --ignore=aml          # [not win]
+
 
 
 about:
@@ -74,3 +76,5 @@ about:
 extra:
   recipe-maintainers:
     - Jean-Baptiste Durand
+    - Thomas Arsouze
+    - Christophe Pradal
diff --git a/doc/_static/openalea_web.svg b/doc/_static/openalea_web.svg
diff --git a/tutorials/Code/__init__.py → doc/examples/Code/__init__.py b/tutorials/Code/__init__.py → doc/examples/Code/__init__.py
diff --git a/tutorials/Code/amlseq2R.py → doc/examples/Code/amlseq2R.py b/tutorials/Code/amlseq2R.py → doc/examples/Code/amlseq2R.py
diff --git a/tutorials/Code/matrix_plot.py → doc/examples/Code/matrix_plot.py b/tutorials/Code/matrix_plot.py → doc/examples/Code/matrix_plot.py
diff --git a/tutorials/Code/python_dics2R.py → doc/examples/Code/python_dics2R.py b/tutorials/Code/python_dics2R.py → doc/examples/Code/python_dics2R.py
diff --git a/tutorials/Utils/__init__.py → doc/examples/Utils/__init__.py b/tutorials/Utils/__init__.py → doc/examples/Utils/__init__.py
diff --git a/tutorials/Utils/dos2unix.py → doc/examples/Utils/dos2unix.py b/tutorials/Utils/dos2unix.py → doc/examples/Utils/dos2unix.py
diff --git a/tutorials/Utils/unix2dos.py → doc/examples/Utils/unix2dos.py b/tutorials/Utils/unix2dos.py → doc/examples/Utils/unix2dos.py
diff --git a/tutorials/example_oak.ipynb → doc/examples/example_oak.ipynb b/tutorials/example_oak.ipynb → doc/examples/example_oak.ipynb
-Original file line number
+Diff line change
@@ Expand Up / @@ -88,6 +88,3 @@ venv/ @@
     docs/preconvert
     site/
     out
-    # Sphinx
-    _static
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		[ ] Remove plots from pytests
		[ ] Make a list from tests to be updated