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plantgl's Introduction

https://img.shields.io/badge/license-CeCILL--C-blue

Distribution based on Python 2:

https://ci.appveyor.com/api/projects/status/pbfi5p0bfslqij3s/branch/master?svg=true https://readthedocs.org/projects/plantgl/badge/?version=latest

Distribution based on Python 3:

https://ci.appveyor.com/api/projects/status/5a4xss61gm8v88yo/branch/master?svg=true Documentation Status

PlantGL

PlantGL is an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants.

Several methods are provided to create plant architectures from field measurements or from procedural algorithms. Because they reveal particularly useful in plant design and simulation, special attention has been paid to the definition and use of branching system envelops.

PlantGL is design to be :

  • Open source : PlantGL is an open source software and can thus be freely used and extended. Providing a standard graphic toolkit to the plant modeling community, it benefits in return of the tests and improvements of users.
  • Portable : PlantGL is available on major operating systems (GNU Linux, Microsoft Windows). It is also compatible with various plant modeling systems (L-studio, AMAP, etc.) and graphic toolkits (Pov-Ray, Vrml, etc.).
  • Simple : The intended audience is researchers of the plant modeling community with no knowledge in computer graphics. Researchers could create images to illustrate and explore their results.
  • Modular : PlantGL is composed of several independent modules like a geometric library, GUI components and Python wrappers. They can be used alone or combined in a specific application.
  • Hybrid System : Core computational components of PlantGL are implemented in the C++ compiled language for performance. In addition for flexibility of use, these components are also exported in the Python interpreted language.

doc/_images/pglteaser.png

Installation

PlantGL distribution is based on the conda software environment management system. To install conda, you may refer to its installation page: https://docs.conda.io/projects/conda/en/latest/user-guide/install/

To install PlantGL, you need to create an environment (named for instance pgl) :

conda create -n pgl openalea.plantgl -c fredboudon -c conda-forge

The package openalea.plantgl is retrieved from the fredboudon channel (developement) and its dependencies will be taken from conda-forge channel.

Then, you need to activate the pgl environment

conda activate pgl

You can then run the PlantGL viewer

pglviewer

Or use the PlantGL modules in Python

ipython
>>> %gui qt
>>> from openalea.plantgl.all import *
>>> Viewer.display(Sphere())

Compiling

The simplest way to build PlantGL is to use conda (see below).

Then, setup your Conda environment with all required dependencies :

# Linux or macOS
conda env create -f build-util/plantgl-devel.yaml

# Windows
conda env create -f build-util/plantgl-devel-win.yaml

conda activate plantgl-devel

Now, you can build, then install PlantGL :

cd plantgl
mkdir build
cd build

# Linux
cmake .. -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX}

# Windows -> Visual Studio 2015 is required
cmake .. -G "NMake Makefiles" -DCMAKE_INSTALL_PREFIX=%LIBRARY_PREFIX%  ..

cmake --build . --target install --config Release

cd ..
python setup.py install --prefix=${CONDA_PREFIX}

You're done !

Documentation

Documentation is available at https://plantgl-fb.readthedocs.io/en/latest

Help and Support

Please open an Issue if you need support or that you run into any error (Installation, Runtime, etc.). We'll try to resolve it as soon as possible.

Authors

PlantGL was developed by Frédéric Boudon, Christophe Pradal, Christophe Nouguier with contributions of Christophe Godin, Nicolas Dones, Boris Adam, Pierre Barbier de Reuille, etc.

Citation

If you find our work useful in your research, please consider citing:

Pradal C., Boudon F., Nouguier C., Chopard J., Godin C.. 2009. PlantGL : A python-based geometric library for 3D plant modelling at different scales. Graphical Models, 71 : p. 1-21.

plantgl's People

Contributors

artzet-s avatar cgodin avatar christian34 avatar cokelaer avatar cxaviermarchand avatar dbarbeau avatar ethan13310 avatar ferraro-simbals avatar fredboudon avatar gbaty avatar gcerutti avatar jlegrand62 avatar jvail avatar jwintz avatar karamokos avatar pfernique avatar pradal avatar ricomos avatar rocsg avatar thomasarsouze avatar tristancabel avatar witherj avatar

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plantgl's Issues

Host pyqglviewer on openalea

PlantGl depends on pyqglviewer, but the package is not hosted on openalea, which can lead to broken builds in the future.
Currently (30/03/2022), compiled conda packages from fredboudon channel have been directly uploaded on openalea3.

CaribuScene ImportError: DLL load failed while importing _pglsg: The specified module could not be found.

Dear all,

An error related to plantgl occurs when I import CaribuScene with from alinea.caribu.CaribuScene import CaribuScene, while I have followed the ReadMe instruction to install plantgl in a conda environment.

Error message listed below:

(base) PS C:\Users\twang> conda activate phm
(phm) PS C:\Users\twang> ipython
Python 3.8.11 (default, Aug  6 2021, 09:57:55) [MSC v.1916 64 bit (AMD64)]
Type 'copyright', 'credits' or 'license' for more information
IPython 7.26.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from alinea.caribu.CaribuScene import CaribuScene^M
   ...: from alinea.caribu.light import diffuse_source
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-c039d1534a24> in <module>
----> 1 from alinea.caribu.CaribuScene import CaribuScene
      2 from alinea.caribu.light import diffuse_source

c:\users\twang\.conda\envs\phm\lib\site-packages\alinea.caribu-8.0.7-py3.8.egg\alinea\caribu\CaribuScene.py in <module>
     18
     19 from openalea.mtg.mtg import MTG
---> 20 from openalea.plantgl.all import Scene as pglScene, Viewer
     21
     22 from alinea.caribu.file_adaptor import read_can, read_light, read_pattern, \

c:\users\twang\.conda\envs\phm\lib\site-packages\openalea.plantgl-3.11.0-py3.8.egg\openalea\plantgl\all.py in <module>
      1 from .math import *
----> 2 from .scenegraph import *
      3 from .algo import *
      4 if not pgl_support_extension('PGL_NO_QT_GUI'):
      5     from .gui import *

c:\users\twang\.conda\envs\phm\lib\site-packages\openalea.plantgl-3.11.0-py3.8.egg\openalea\plantgl\scenegraph\__init__.py in <module>
      1 import openalea.plantgl.math
----> 2 from ._pglsg import *
      3
      4 from . import cspline
      5 from . import bezier_nurbs

ImportError: DLL load failed while importing _pglsg: The specified module could not be found.

I suspect it is a problem to do with my Windows 11 operating system (Win11 Home 10.0.22).
In addition, I put my conda list here:
conda_list.txt

Do you have any idea to solve this error?
Thanks.
Tien-Cheng.

How to use Plantgl for modeling apical meristem?

Hi @fredboudon, and @pradal, I want to use PlantGL to model a 3D apical meristem and add a gene network into it, but I can't find how to model a tissue using it. Could you please tell me where I can find the guide to do that (example in the picture in your paper)
image

Thanks!

Best,
Ziyi

Meet ResolvePackageNotFound when compiling

OS: Windows 11 64bit
run conda env create -f build-util\plantgl-devel.yaml then report

Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
  - gmp
  - flex
  - bison

Error when creating a Tapered from a Shape geometry.

As the title say. When creating a Tapered from the geometry from a Shape, there's an argument error. But the types are correct...

In [9]: from openalea.plantgl.all import *

In [10]: s = Sphere()

In [11]: t = Tapered(1,1,s)

In [12]: m = Material(Color3(127,72,0))

In [13]: f = Shape(s,m)

In [14]: t2 = Tapered(1,1,f.geometry)

ArgumentError Traceback (most recent call last)
in
----> 1 t2 = Tapered(1,1,f.geometry)

ArgumentError: Python argument types in
Tapered.init(Tapered, int, int, Sphere)
did not match C++ signature:
init(_object*, double baseRadius=0.5, double topRadius=0.5, PGL::RefCountPtrPGL::Primitive primitive=None)

Blank Canvas (Unflushed Rendering) of PlantGL from L-Py animate()

I would like to report a rendering issue that appears since the migration of L-py / PlantGL libraries from Python 2 to Python 3.

From third-party program, OpenAlea.lpy.lsystem.animate() will open PlantGL Viewer to show animation of an L-system in Python 2 without problem.

However, if I run animate() in Python 3, it results in a blank canvas on PlantGL Viewer. I can only display the last frame of the animation if I put some input line such as "input()" or "raw_input()" following the animate() that seems to flush the rendering to show the last frame onto the blank canvas.

I tried to locate the implementation of lsystem.animate() in openalea Github repo to fix it on my end but could not find it. Kindly help. Thanks!

Build PlantGL with CMake on Linux x64

Après avoir porté le système de compilation sous CMake et fait la mise à jour vers Qt 5 et Python 3.7, je cherche à build PlantGL sous Linux x64 (Ubuntu 14.04 LTS) en utilisant Conda.

Suivant le scénario, avec Conda Build, j'obtiens différentes erreurs :

Scénario 1)

  • Je compile avec GCC 7.4, installé via APT.

La compilation et l'installation de PlantGL se déroulent correctement. Cependant, arrivé à l'exécution des tests unitaires, j'obtiens l'erreur :

  File "/home/travis/miniconda/conda-bld/[...]/lib/python3.7/site-packages/OpenAlea.PlantGL-2.4.0-py3.7.egg/openalea/plantgl/all.py", line 4, in <module>
    if not pgl_support_extension('PGL_NO_QT_GUI'):
Boost.Python.ArgumentError: Python argument types in
    openalea.plantgl.scenegraph._pglsg.pgl_support_extension(str)
did not match C++ signature:
    pgl_support_extension(std::string ext)

La version de Boost est la 1.67.0, compilée avec GCC 7.2.

Même chose en utilisant le compilateur natif de ma version d'Ubuntu (GCC 4.8.4).

Scénario 2)

  • Je compile en utilisant le compilateur fourni par Conda, en rajoutant {{ compiler('cpp') }} au fichier meta.yaml.

Dans ce cas là, CMake échoue à trouver les libraries OpenGL/GLU/GLX :

CMake Error at /home/[...]/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY)
Call Stack (most recent call first):
  /home/[...]/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  /home/[...]/cmake-3.14/Modules/FindOpenGL.cmake:394 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  CMakeLists.txt:78 (find_package)

Les différentes approches que j'ai tenté afin de résoudre ce problème sont :

  • Ajout de différentes libraries CDT dans le meta.yaml de PlantGL :
- {{ cdt('xorg-x11-proto-devel') }}  # [linux]
- {{ cdt('mesa-libgl-devel') }}      # [linux]
- {{ cdt('libx11-devel') }}          # [linux]
- {{ cdt('libxext-devel') }}         # [linux]
- {{ cdt('libxrender-devel') }}      # [linux]
- {{ cdt('mesa-libgl-devel') }}      # [linux]
- {{ cdt('mesa-libegl-devel') }}     # [linux]
- {{ cdt('mesa-dri-drivers') }}      # [linux]
- {{ cdt('libxau-devel') }}          # [linux]
- {{ cdt('libdrm-devel') }}          # [linux]
- {{ cdt('libxcomposite-devel') }}   # [linux]
- {{ cdt('libxcursor-devel') }}      # [linux]
- {{ cdt('libxi-devel') }}           # [linux]
- {{ cdt('libxrandr-devel') }}       # [linux]
- {{ cdt('libxscrnsaver-devel') }}   # [linux]
- {{ cdt('libxtst-devel') }}         # [linux]
- {{ cdt('libselinux-devel') }}      # [linux]
  • Suppression/modification des variables d'environnement créées par Conda Build et son compilateur (via activate-binutils_linux-64.sh, activate-gcc_linux-64.sh et activate-gxx_linux-64.sh).

Dans ces deux cas, CMake ne parvient toujours pas à trouver OpenGL et affiche toujours la même erreur (ci-dessus).

Scénario 3)

  • Comme pour le scénario 2), je compile en utilisant le compilateur fourni par Conda, cette fois en rajoutant les chemins vers libGL.so, libGLU.so et libxcb-glx.so.

Cette fois-ci, CMake parvient à lancer la compilation, au prix de quelques warnings :

CMake Warning at src/wrapper/gui/CMakeLists.txt:5 (add_library):
  Cannot generate a safe runtime search path for target _pglgui because there
  is a cycle in the constraint graph:

    dir 0 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/_build_env/lib]
      dir 6 must precede it due to runtime library [libGLU.so.1]
    dir 1 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/work/build/src/cpp/plantgl/gui]
    dir 2 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/work/build/src/cpp/plantgl/algo]
    dir 3 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/work/build/src/cpp/plantgl/scenegraph]
    dir 4 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/work/build/src/cpp/plantgl/math]
    dir 5 is [/home/ethan/miniconda3/envs/plantgl/conda-bld/openalea.plantgl_1558355395596/work/build/src/cpp/plantgl/tool]
    dir 6 is [/usr/lib/x86_64-linux-gnu]
      dir 0 must precede it due to runtime library [libgmp.so.10]

  Some of these libraries may not be found correctly.

Cependant, la compilation finit par planter suite à l'absence de GL/gl.h. Rajouter include_directories("/usr/include") (là où ce trouve le fichier gl.h) ne change rien.

Add local conda recipe

Add a conda recipe locally to enhance Continuous Integration and improve robustness.
SconsX adapts the build flags and all the paths (include, lib, install) when building with conda.
So it is worth a while to use it

Can't open pglviewer.exe

Hi all,
I have installed plantgl in a conda environment and get a binary pglviewer.exe from there.
Although I can call the viewer from a Python script, I can't open the binary directly : a message indicates that some Qt related dlls are missing, but they are in the same path than the binary. I tried to add my conda path to the environment variables, the error is now Runtime error R6034. Maybe it's due conflicts between different dll paths.
Could ou tell me how to solve it please?
Tks

pgl.TriangleSet([],[]) causes conda terminated with exit code -1073741819 (0xC0000005).

Hi all,

I have just updated and specified the question:
This error can be reproduce on windows 10 with the following two lines.

import openalea.plantgl.all as pgl
pgl.TriangleSet([],[])

image

Which version of pgl are you using?
With conda list, I found that I have even two plantgl!

    openalea-plantgl         3.9.3           pypi_0                 pypi
    openalea.plantgl         3.9.3           py38h2272212_1         fredboudon

It seems that I am using openalea.plantgl, should** I switch to openalea-plantgl instead ?

Here you will find the current conda list result:
condalist_10_04_2022.txt
@pradal Could you please help me to find out where the problem is?

Many thanks,
Tien-Cheng.

Problem of visualization with PlantGL

Hello,

I have installed the PlantGL library (from https://github.com/openalea/plantgl) through "python setup.py install" and everything seems ok but i am trying to visualize an object (through openalea.plantgl.all.Viewer.display(object)), python.exe crashed. Does anyone have any idea about that?Thanks in advance!

Cheers,

Adama

Almost completed install with conda Qt5

I tried to compile PlantGL with a Qt5 coming from conda (5.6.2. from the conda forge) and I made it! I mean, the compilation almost went through, except for an error when compiling the viewer binary. The error was about my Qt not being built properly:

"You must build your code with position independent code if Qt was built with -reduce-relocations. " "Compile your code with -fPIC (-fPIE is not enough)."

Which i fixed in the SconsScript of plantgl/gui/exe by adding exe_env.Append(CXXFLAGS='-fPIC') and LIBRARIES.extend( [ 'icui18n','icuuc','icudata'] ) (no idea why, but these were the ones missing).

In the end, compilation goes through, and i try to import plantgl in ipython where i get a nasty message:

In [2]: import openalea.plantgl.all as pgl
---------------------------------------------------------------------------
ArgumentError                             Traceback (most recent call last)
<ipython-input-2-2ffec001cb25> in <module>()
----> 1 import openalea.plantgl.all as pgl

/home/tissuelab-env/Develop/plantgl/src/plantgl/all.py in <module>()
      2 from scenegraph import *
      3 from algo import *
----> 4 if not pgl_support_extension('PGL_NO_QT_GUI'):
      5     from gui import *
      6 

ArgumentError: Python argument types in
    openalea.plantgl.scenegraph._pglsg.pgl_support_extension(str)
did not match C++ signature:
    pgl_support_extension(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > ext)

But the components can be imported fine, and I could run the following commands without error:

In [1]: %gui qt5
In [2]: from openalea.plantgl.gui import Viewer
In [3]: from openalea.plantgl.scenegraph import Scene, Sphere
In [4]: scene = Scene()
In [5]: scene += Sphere(1)
In [6]: Viewer.add(scene)

Yet, the content of the viewer isn't what i expected... :(

image

Anything familiar in there??

core dumped with numpy > 1.20 at runtime

Due to runtime incompatbilities between boost and numpy > 1.20 (core dumped), versions had to be blocked and lead to python dependant release. This should be investigated to achieve standard release

Crash on MacOSX

On Mac, with the lastest conda version, the foolowing lines crash on my computer

from openalea.plantgl.all import *
l= Point3Array([(0,0,0), (1,0,0)])

The code itself has not changed. However, current conda package broke on mac. Surely due to dependencies (boost or something else).

Hull from photographs

Sorry if this is obvious, but your paper alludes to the fact that a 3D hull of a plant can be reconstructed from photographs, using PlantGL.
If you could point me to any documentation or examples which relate to this functionality, it would be much appreciated.
Thanks!

Troubles importing PlantGL 'AscCodec'

After installing PlantGL & PyQGLviewer I cannot load lineage éditor 'pgl_lineage_editor.py'.
When loading 'Scene' I have an error related to AscCodec

from openalea.plantgl.codec.asc import AscCodec
Traceback (most recent call last):
  File "/home/jonathan/miniconda2/envs/lineage_editor/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2881, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-10-4cc08f87f278>", line 1, in <module>
    from openalea.plantgl.codec.asc import AscCodec
  File "/home/jonathan/Softwares/pycharm-community-2017.2.3/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  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/Softwares/pycharm-community-2017.2.3/helpers/pydev/_pydev_bundle/pydev_import_hook.py", line 21, in do_import
    module = self._system_import(name, *args, **kwargs)
  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)
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)
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 0x7fed781bef18>> ignored

I have installed everything using Conda:
conda install -c openalea vplants.plantgl pyqglviewer
The full list of installed conda packages:

# packages in environment at /home/jonathan/miniconda2/envs/lineage_editor:
#
alabaster                 0.7.10                   py27_0    defaults
ann                       1.1.2                         0    openalea
babel                     2.5.0                    py27_0    defaults
backports                 1.0                      py27_0    defaults
backports.shutil-get-terminal-size 1.0.0                     <pip>
boost                     1.57.0                        4    defaults
cairo                     1.14.8                        0    defaults
certifi                   2016.2.28                py27_0    defaults
cgal                      4.6.3                         0    openalea
cycler                    0.10.0                   py27_0    defaults
dbus                      1.10.20                       0    defaults
decorator                 4.1.2                    py27_0    defaults
docutils                  0.14                     py27_0    defaults
enum34                    1.1.6                    py27_0    defaults
expat                     2.1.0                         0    defaults
fontconfig                2.12.1                        3    defaults
freeglut                  2.8.1                         0    defaults
freetype                  2.5.5                         2    defaults
functools32               3.2.3.2                  py27_0    defaults
get_terminal_size         1.0.0                    py27_0    defaults
glib                      2.50.2                        1    defaults
gmp                       6.1.0                         0    defaults
gst-plugins-base          1.8.0                         0    defaults
gstreamer                 1.8.0                         0    defaults
harfbuzz                  0.9.39                        2    defaults
icu                       54.1                          0    defaults
imagesize                 0.7.1                    py27_0    defaults
ipython                   5.3.0                    py27_0    defaults
ipython-genutils          0.2.0                     <pip>
ipython_genutils          0.2.0                    py27_0    defaults
jinja2                    2.9.6                    py27_0    defaults
jpeg                      9b                            0    defaults
libffi                    3.2.1                         1    defaults
libgcc                    5.2.0                         0    defaults
libgfortran               3.0.0                         1    defaults
libiconv                  1.14                          0    defaults
libpng                    1.6.30                        1    defaults
libqglviewer              2.6.4                         1    openalea
libxcb                    1.12                          1    defaults
libxml2                   2.9.4                         0    defaults
markupsafe                1.0                      py27_0    defaults
matplotlib                1.5.1               np111py27_0    defaults
mkl                       2017.0.3                      0    defaults
mpfr                      3.1.5                         0    defaults
numpy                     1.11.3                   py27_0    defaults
openalea.components       1.4.0                    py27_1    openalea
openalea.container        2.3.0                     <pip>
openalea.core             1.4.0                    py27_0    openalea
openalea.deploy           2.0.0                    py27_0    openalea
openalea.image            1.2.0                     <pip>
openalea.misc             1.3.0                    py27_0    openalea
openalea.numpy            1.2.0                     <pip>
openalea.pkgbuilder       1.2.0                     <pip>
openalea.pylab            1.2.0                     <pip>
openalea.scheduler        1.2.0                     <pip>
openalea.sconsx           2.0.1                    py27_0    openalea
openalea.stdlib           1.2.0                     <pip>
openalea.svgdraw          1.2.0                     <pip>
openssl                   1.0.2l                        0    defaults
pango                     1.40.3                        1    defaults
path.py                   10.3.1                   py27_0    defaults
pathlib2                  2.3.0                    py27_0    defaults
pcre                      8.39                          1    defaults
pexpect                   4.2.1                    py27_0    defaults
pickleshare               0.7.4                    py27_0    defaults
pip                       9.0.1                    py27_1    defaults
pixman                    0.34.0                        0    defaults
prompt-toolkit            1.0.15                    <pip>
prompt_toolkit            1.0.15                   py27_0    defaults
ptyprocess                0.5.2                    py27_0    defaults
pycairo                   1.10.0                   py27_0    defaults
pygments                  2.2.0                    py27_0    defaults
pyopengl                  3.1.1a1             np111py27_0    defaults
pyparsing                 2.2.0                    py27_0    defaults
pyqglviewer               0.14                     py27_0    openalea
pyqt                      4.11.4                   py27_4    defaults
python                    2.7.13                        0    defaults
python-dateutil           2.6.1                    py27_0    defaults
pytz                      2017.2                   py27_0    defaults
qhull                     2012.1                        0    openalea
qt                        4.8.7                         4    defaults
readline                  6.2                           2    defaults
requests                  2.14.2                   py27_0    defaults
scandir                   1.5                      py27_0    defaults
scipy                     0.19.0              np111py27_0    defaults
scons                     2.4.1                    py27_0    openalea
setuptools                36.4.0                   py27_0    defaults
simplegeneric             0.8.1                    py27_1    defaults
sip                       4.18                     py27_0    defaults
six                       1.10.0                   py27_0    defaults
snowballstemmer           1.2.1                    py27_0    defaults
sphinx                    1.6.3                    py27_0    defaults
sphinxcontrib             1.0                      py27_0    defaults
sphinxcontrib-websupport  1.0.1                    py27_0    defaults
sqlite                    3.13.0                        0    defaults
subprocess32              3.2.7                    py27_0    defaults
tk                        8.5.18                        0    defaults
traitlets                 4.3.2                    py27_0    defaults
typing                    3.6.2                    py27_0    defaults
vplants.marsalt (/home/jonathan/Projects/LineageEditor/marsalt/imaging/mars_alt/src) 0.9.3.dev0                <pip>
vplants.plantgl           2.21.0                   py27_0    openalea
vplants.tissue-analysis (/home/jonathan/Projects/LineageEditor/marsalt/tissue_analysis/src) 0.9.1.0                   <pip>
wcwidth                   0.1.7                    py27_0    defaults
wheel                     0.29.0                   py27_0    defaults
zlib                      1.2.11                        0    defaults

Did I miss something ?!
Thanks, Jo

Test test_pointmanipulation.test_median_point failed only on Windows 64bits

Here is the error (see AppVeyor CI

======================================================================
ERROR: test_pointmanipulation.test_median_point

Traceback (most recent call last):
File "C:\Miniconda\conda-bld\openalea.plantgl_1518250173049_test_env\lib\site-packages\nose\case.py", line 197, in runTest
self.test(*self.arg)
File "C:\Miniconda\conda-bld\openalea.plantgl_1518250173049\test_tmp\test\test_pointmanipulation.py", line 34, in test_median_point
raise ValueError(k,j,dist_to_points(p3list[i],p3list),dist_to_points(p3list[j],p3list),p3list[i],p3list[j])
ValueError: (80, 99, 5300.545823832321, 5300.545823832321, Vector3(69.4804,61.5419,47.4436), Vector3(69.4804,61.5419,47.4436))

Ran 131 tests in 12.093s

Fix namespace

OpenAlea namespace package has to be declared in the setup.py

Trouble installing PlantGL with Qt4 on Mac OS with conda

@fredboudon We (@oalii and I) came across several errors when running setup.py (with the right options_conda.py) with a Qt4.8.7:

  • SconsEnvironment has no attribute EnableQtModules : corrected adding this bit a code to the SConstruct :
    if qt_version == 4: env.EnableQtModules = env.EnableQt4Modules elif qt_version == 5: env.EnableQtModules = env.EnableQt5Modules

  • Linker error, unable to find qt symbols : corrected by adding "qtcore" to the EXTRA_LIBS variable in options.py

  • Unable to finish setup due to missing file "build-scons/include/plantgl/algo/codec/scne_parser.cpp.h"

Feels we're very close, but unable to overcome this last bit. Any help appreciated...

PlantGL & Numpy

Which version of Numpy is required?

conda recipe asks for
numpy=1.20|>=1.21.5

BUT

CI define CONDA_NPY as

CONDA_NPY: "119"

installation fail on linux

I created an environment with just plantgl in a brand new linux (debian:buster with just miniconda). Creation is fine but importing plantgl fails searching for libglut.

I attach the full environment creation and python error
fail.txt

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