First packaging...

.github/workflows/conda-package-build.yml

@@ -19,7 +19,5 @@ on:
 jobs:
   build:
     uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
-    with:
-      conda-directory: "./stat_tool/conda"
     secrets:
       anaconda_token: ${{ secrets.ANACONDA_TOKEN }}

.gitignore

@@ -0,0 +1,93 @@
+*.py[cod]
+.DS_Store
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+build
+eggs
+.eggs
+parts
+var
+sdist
+debian/
+develop-eggs
+.installed.cfg
+lib
+lib64
+MANIFEST
+**/__pycache__
+**/vpsequence_analysis
+CMakeFiles
+
+# Installer logs
+pip-log.txt
+npm-debug.log
+pip-selfcheck.json
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+htmlcov
+.cache
+.pytest_cache
+.mypy_cache
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# SQLite
+test_exp_framework
+
+# npm
+node_modules/
+
+# dolphin
+.directory
+libpeerconnection.log
+
+# setuptools
+dist
+
+# IDE Files
+atlassian-ide-plugin.xml
+.idea/
+*.swp
+*.kate-swp
+.ropeproject/
+
+# Python3 Venv Files
+.venv/
+bin/
+include/
+lib/
+lib64
+pyvenv.cfg
+share/
+venv/
+.python-version
+
+# Cython
+*.c
+
+# Emacs backup
+*~
+
+# VSCode
+/.vscode
+
+# Automatically generated files
+docs/preconvert
+site/
+out
+
+# Sphinx
+_static

CMakeLists.txt

@@ -0,0 +1,198 @@
+# Initialize the CMake project
+cmake_minimum_required(VERSION 3.20)
+
+##################################################
+# If we are running in a Conda environment, we automatically
+# add the Conda env prefix to the CMAKE_PREFIX_PATH
+
+if(DEFINED ENV{CONDA_PREFIX})
+  list(APPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}")
+  #TODO: Windows Conda environments are structured differently,
+  #      how unfortunate is this?
+  list(APPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}/Library")
+endif()
+
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+include("Anaconda")
+
+##################################################
+# Define the version
+
+if(SKBUILD)
+  set(SEQANA_TOOL_VERSION ${SKBUILD_PROJECT_VERSION})
+else()
+  set(SEQANA_VERSION "2.0.0")
+endif()
+
+project(openalea.sequence_analysis
+  VERSION ${SEQANA_VERSION}
+  LANGUAGES CXX
+  DESCRIPTION "Statistical analysis of plant architecture sequences")
+
+##################################################
+# Set CMake policies for this project
+
+# We allow <Package>_ROOT (env) variables for locating dependencies using find_paclage
+cmake_policy(SET CMP0074 NEW)
+# We allow target_sources to convert relative paths to absolute paths
+cmake_policy(SET CMP0076 NEW)
+ # for Python*_FIND_STRATEGY=LOCATION
+cmake_policy(SET CMP0094 NEW)
+cmake_policy(SET CMP0167 NEW)
+##################################################
+# Initialize some default paths
+# See https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html
+include(GNUInstallDirs)
+
+##################################################
+# Set C++ standard and compile options
+
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+# set(CMAKE_CXX_EXTENSIONS ON)
+
+# This may be set in pyproject.toml
+set(CMAKE_VERBOSE_MAKEFILE ON)
+
+##################################################
+# For Python bindings, we need to enable position-independent code
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)  # For shared libs
+
+##################################################
+# TODO : REMOVE?
+# if(WIN32)
+#   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -enable-stdcall-fixup -enable-auto-import -enable-runtime-pseudo-reloc -s")
+# endif()
+
+
+# RPath settings
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+list(
+  FIND
+  CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES
+  ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}
+  isSystemDir
+)
+if("${isSystemDir}" STREQUAL "-1")
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+endif("${isSystemDir}" STREQUAL "-1")
+
+
+if (WIN32)
+    string(REGEX REPLACE "/W3" "/W0" ${CMAKE_CXX_FLAGS} "${${CMAKE_CXX_FLAGS}}") 
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MD")
+
+    # To fix compilation error with vc14 and boost
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /DHAVE_SNPRINTF")
+endif()
+
+# Options
+option(WITH_EFENCE "Build with efence library" OFF)
+option(WITH_TEST "Build tests" OFF)
+
+##################################################
+# Add a library for sequence_analysis and its Python wrappers
+add_library(oasequence_analysis SHARED)
+
+##################################################
+# Find external dependencies
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(Boost REQUIRED COMPONENTS python)
+# TODO
+
+find_library(STAT_TOOL_LIB NAMES oastat_tool)
+
+#find_package(openalea.stat_tool REQUIRED)
+
+##################################################
+# Setup lib, inc, defines for C++ oastat_tool lib
+
+target_link_libraries(oasequence_analysis PUBLIC ${STAT_TOOL_LIB})
+
+target_include_directories(oasequence_analysis
+  PUBLIC
+    ${Boost_INCLUDE_DIRS}
+    ${CONDA_ENV}include
+)
+
+# Export symbols on Windows
+# if (WIN32 OR MSVC)
+#   target_compile_definitions(oasequence_analysis PUBLIC STAT_TOOL_MAKEDLL)
+# endif()
+
+# Optionally add efence
+if(WITH_EFENCE)
+  find_library(EFENCE_LIBRARY NAMES efence)
+  if(EFENCE_LIBRARY)
+    target_link_libraries(oasequence_analysis PUBLIC efence)
+    target_compile_definitions(oasequence_analysis PUBLIC DEBUG)
+  else()
+    message(WARNING "Could not find efence library, disabling it")
+  endif()  
+endif()
+
+# Add files to build
+add_subdirectory(src/cpp/sequence_analysis)
+
+
+##################################################
+# Add a Python binding library 
+python_add_library(_sequence_analysis MODULE)
+
+target_include_directories(oasequence_analysis
+  PUBLIC
+    "src/cpp"
+)
+
+target_link_libraries(_sequence_analysis
+  PRIVATE
+    ${OASTAT_LIB}
+    oasequence_analysis
+    Boost::python
+    Python::Module
+  )
+
+  target_compile_definitions(_sequence_analysis PRIVATE BOOST_ALL_NO_LIB)
+
+  # Control the output name of the produced shared library
+  set_target_properties(_sequence_analysis PROPERTIES PREFIX "")
+  set_target_properties(_sequence_analysis PROPERTIES OUTPUT_NAME "_sequence_analysis")
+  if(WIN32)
+    set_target_properties(_sequence_analysis PROPERTIES SUFFIX ".pyd")
+  elseif(APPLE)
+    set_target_properties(_sequence_analysis PROPERTIES SUFFIX ".so")
+  endif()
+
+add_subdirectory("src/wrapper/")
+
+
+if(APPLE)
+    set_target_properties(_sequence_analysis PROPERTIES INSTALL_RPATH "@loader_path/.")
+elseif(UNIX)
+    set_target_properties(_sequence_analysis PROPERTIES INSTALL_RPATH "$ORIGIN/.")
+endif()
+
+##################################################
+# Install targets and headers for sequence_analysis lib
+install(TARGETS oasequence_analysis
+            RUNTIME DESTINATION "${CONDA_ENV}bin/"
+            LIBRARY DESTINATION "${CONDA_ENV}lib/"
+            ARCHIVE DESTINATION "${CONDA_ENV}lib/"
+)
+
+install(
+  TARGETS
+    _sequence_analysis
+  DESTINATION "${SKBUILD_PLATLIB_DIR}/openalea/sequence_analysis"
+)
+
+# Optionally handle tests
+# TODO TO TEST
+if(WITH_TEST)
+  enable_testing()
+  add_subdirectory(test/cpp)
+endif()
+

README.md

@@ -0,0 +1,25 @@
+# Sequence Analysis
+
+_________________
+
+[![Docs](https://readthedocs.org/projects/sequence_analysis/badge/?version=latest)](https://sequence_analysis.readthedocs.io/)
+[![Build Status](https://github.com/openalea/sequence_analysis/actions/workflows/conda-package-build.yml/badge.svg?branch=main)](https://github.com/openalea/sequence_analysis/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/sequence_analysis/badges/version.svg)](https://anaconda.org/openalea3/sequence_analysis)
+
+_________________
+
+[Read Latest Documentation](https://sequence_analysis.readthedocs.io/) - [Browse GitHub Code Repository](https://github.com/openalea/sequence_analysis/)
+
+_________________
+
+**sequence analysis** Basic Statistical tools used by different Structure Analysis libraries.
+
+### Contributors
+
+Thanks to all that ontribute making this package what it is !
+
+</a>
+<a href="https://github.com/openalea/sequence_analysis/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=openalea/sequence_analysis" />
+</a>

README.txt

@@ -1,4 +1,4 @@
-vplants.stat_tool
+openalea.sequence_analysis
 -----------------
 
 Description
@@ -31,5 +31,4 @@ qt >= 4.2 (on windows)
 Dependencies
 ---------------------
 
-vplants.tool
-vplants.stat_tool
+openalea.stat_tool