Add a dependency to ipython v2.4.1

Build the OpenALea.Visualea recipes on windows and upload it on anaconda.

Add tool, stat_tool and sequence analysis to the process.

Check if all these packages are currently compatible with the other ones.

Conda simplify the installation process of binary packages and their dependencies for end users.

Making OpenAlea installable with conda will solve the "installation nightmare" users face today.

To do that, OpenAlea packages and deps have to be packaged with conda and adapt when needed like:

• qt and pyqt
• scons and sconsx
• deploy

At least, on Windows, old packages (win-64) are removed during the build.
The error may come from appveyor-ci

Add CONDA 3 information with Travis and appveyor

Hello,
I tried following conda recipe on Ubuntu 14.04:

name: plg_lineage_editor
channels:
  - openalea
  - defaults
dependencies:
  - python=2.7
  - openalea.sconsx
  - openalea.components
  - pyqglviewer

But importing PyQGLViewer fails as follow:

$ source activate plg_lineage_editor
(pgl_lineage_editor) $ python -c 'import PyQGLViewer'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/jlegrand/miniconda2/envs/pgl_lineage_editor/lib/python2.7/site-packages/../../libQGLViewer.so.2)

Thanks a lot for the rest of the recepies!
Jo

SCons and openalea.misc are not building.
Add them to travis and appveyor

We need to add fractalysis to the openalea-recipes

The share directory is copied directly in site-packages.
Use preserve_egg = True in recipe to install share_dir in an egg

@fredboudon : Can you change the flag ANACONDA_UPLOAD from unstable to release.
The packages will then be upload directly on main channel of anaconda/openalea

@christian34 : How can we amange the build of the deps of Alinea?

Can we build a new set of recipes on OpenAlea based on the release?
Or do we add these recipes to the release openalea?
Add Caribu (https://github.com/openalea-incubator/caribu) at the release

Add an ANN recipe for vplants.plantgl.
See ANN recipe provided by ilastik

Create and upload an openalea metapackage

The idea is to move all the recipes to conda-forge.
This will induce major modification in the code:

• Code need to work with non-patched software:
  Each package needs to run natively, with current version of all the dependencies (bison, boost, ...)

To support ABI compatibiliy between all the recipes, I propose to use the conda-forge toolchain.
The toolchain defines all the flags (CXXFLAGS, ...), the compiler, ... that is the same for all the packages we build.

conda install toolchain -c conda-forge
See https://github.com/conda-forge/toolchain-feedstock

Create recipes to build all packages of VPlants

Add a PyQGLViewer recipe to conda.
This is needed for LPy and OpenAleaLab

libCGAL reference wrong libraries:

ImportError: dlopen(/Users/pradal/miniconda2/envs/cereal/lib/python2.7/site-packages/OpenAlea.PlantGL-2.23.2-py2.7-macosx-10.6-x86_64.egg/openalea/plantgl/math/_pglmath.so, 2): Library not loaded: /usr/local/opt/gmp/lib/libgmp.10.dylib
Referenced from: /Users/pradal/miniconda2/envs/cereal/lib/libCGAL.13.0.1.dylib
Reason: image not found

Create a recipe for Caribu (https://github.com/openalea-incubator/caribu)

astk is a library that contains some utilities.
Move this package, create conda package and review it.

Using the following config file to create a conda environment (ubuntu 16.04):

name: lineage_editor
channels:
  - openalea
  - defaults
dependencies:
  - python=2.7
  - openalea.sconsx
  - openalea.components
  - vplants.plantgl
  - pyqglviewer

I get an error when testing python import:

>>> from vplants.plantgl.all import Scene
Exception Boost.Python.ArgumentError: 'Python argument types in\n    SceneCodec.__del__(AscCodec)\ndid not match C++ signature:\n    __del__(PySceneCodec*)' in <bound method AscCodec.__del__ of <openalea.plantgl.codec.asc.AscCodec object at 0x7fa841ba6368>> ignored
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jonathan/.miniconda2/envs/lineage_editor/lib/python2.7/site-packages/VPlants.PlantGL-2.21.0-py2.7.egg/openalea/plantgl/all.py", line 8, in <module>
    import codec
  File "/home/jonathan/.miniconda2/envs/lineage_editor/lib/python2.7/site-packages/VPlants.PlantGL-2.21.0-py2.7.egg/openalea/plantgl/codec/__init__.py", line 1, in <module>
    import asc
  File "/home/jonathan/.miniconda2/envs/lineage_editor/lib/python2.7/site-packages/VPlants.PlantGL-2.21.0-py2.7.egg/openalea/plantgl/codec/asc.py", line 110, in <module>
    codec = AscCodec()
  File "/home/jonathan/.miniconda2/envs/lineage_editor/lib/python2.7/site-packages/VPlants.PlantGL-2.21.0-py2.7.egg/openalea/plantgl/codec/asc.py", line 16, in __init__
    sg.SceneCodec.__init__(self,"ASC",sg.SceneCodec.Mode.ReadWrite)
Boost.Python.ArgumentError: Python argument types in
    SceneCodec.__init__(AscCodec, str, Mode)
did not match C++ signature:
    __init__(_object*)
    __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > name)
    __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > name, PGL::SceneCodec::Mode mode)

Both SCons and bison are available and working on the anaconda channel.
Remove the ones in the recipes and in the openalea channel

The Python version was chosen using CONDA_VERSION.
When CONDA_VERSION was 2, Python 2 was selected.
Otherelse, Python 3 was chosen.

However, this is not longer true. We have to specify explictly both CONDA_VERSION and PYTHON_VERSION in travis and appveyor

Build a new conda recipe of Boost libs on Windows

Provide usefull informations about howto build and install the conda recipes.
Also add a guide on howto create your own recipe.

openalea.deploy has a method that detects if the commands are run in a conda environment.
In this case, the modification of environment variables are disable.

The method is_conda_env check if CONDA_ENV_PATH is defined.
However, this variable is no more define by conda activate script (see conda/conda#2312)

Please, replace it with CONDA_PREFIX variable.