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visualea's Introduction

OpenAlea.Visualea

OpenAlea.Visualea is an application that allows to use OpenAlea packages and to build dataflow graphically.

License

OpenAlea.Visualea is released under a Cecill v2 license.

See LICENSE.txt Nota : Cecill v2 license is a GPL compatible license.

Dependencies

  • Python >= 3.7
  • Qt >= 5.12
  • QtPy (PyQt >= 5.12)

Installation user mode

conda install openalea.visualea -c openalea3 -c conda-forge  

Installation dev mode

  • Create a conda environment

    conda create -n visualea -c openalea3 -c conda-forge openalea.plantgl pyqglviewer  
    conda activate visualea  
    conda install -c openalea3 -c conda-forge numpy scipy qtconsole pandas matplotlib openalea.sconsx networkx ipykernel ipyparallel
    
  • clone from the openalea org

    1 core
    2 grapheditor
    3 openalea-components
    4 visualea

  • Checkout the visualea branch
    python setup.py develop

visualea's People

Contributors

baugetfa avatar cokelaer avatar dbarbeau avatar fredboudon avatar gbaty avatar jlegrand62 avatar pradal avatar revesansparole avatar ricomos avatar thomasarsouze avatar

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visualea's Issues

Missing dependencies during win64 anaconda installation

Hello,

On win64 platform with anaconda installation of visualea from openalea channels :

conda create -n visualea python
activate visualea
conda install -c openalea openalea.visualea

I'had execution error when a launch visualea :

ipython
from openalea.visualea.visualea_script import start_gui
start_gui()

Resulting error like :

ImportError: You must install pyqt-tools due to pyqt package absence
ImportError: No module named rich_ipython_widget due to qtconsole absence
AttributeError: 'module' object has no attribute 'QTextEdit' due to pyqt version 5

So I fix my problem with :

conda install -c openalea pyqt=4.10.4
conda install -c openalea qtconsole

[VisuAlea] Error due to a local import

When running visualea, there is an error:

Traceback (most recent call last):
File "", line 1, in
File "/Users/pradal/miniconda3/envs/tstvisu/lib/python3.10/site-packages/OpenAlea.Visualea-2.3.1-py3.9.egg/openalea/visualea/visualeagui.py", line 32, in
from openalea.visualea.mainwindow import MainWindow
File "/Users/pradal/miniconda3/envs/tstvisu/lib/python3.10/site-packages/OpenAlea.Visualea-2.3.1-py3.9.egg/openalea/visualea/mainwindow.py", line 51, in
from openalea.visualea import dataflowview, helpwidget, metainfo, ui_mainwindow
File "/Users/pradal/miniconda3/envs/tstvisu/lib/python3.10/site-packages/OpenAlea.Visualea-2.3.1-py3.9.egg/openalea/visualea/ui_mainwindow.py", line 445, in
import images_rc
ModuleNotFoundError: No module named 'images_rc'

Ubuntu fail

Hello,

I installed everything in Ubuntu with a conda environment openalea3 and with setup.py develop, and when I try to run visualeagui.py I get this message

Traceback (most recent call last):
File "/home/jazzsta/Model/visualea/src/openalea/visualea/visualeagui.py", line 197, in
main(sys.argv)
File "/home/jazzsta/Model/visualea/src/openalea/visualea/visualeagui.py", line 103, in main
app = Openalea(args)
File "/home/jazzsta/Model/visualea/src/openalea/visualea/visualeagui.py", line 67, in init
self.win = MainWindow(None)
File "/home/jazzsta/Model/visualea/src/openalea/visualea/mainwindow.py", line 228, in init
self.read_settings()
File "/home/jazzsta/Model/visualea/src/openalea/visualea/mainwindow.py", line 370, in read_settings
settings = Settings()
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/site-packages/openalea.core-2.2.0-py3.9.egg/openalea/core/singleton.py", line 42, in call
return weakref.proxy(Singleton.call(cls, *args, **kw))
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/site-packages/openalea.core-2.2.0-py3.9.egg/openalea/core/singleton.py", line 33, in call
cls._instance = super(Singleton, cls).call(*args, **kw)
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/site-packages/openalea.core-2.2.0-py3.9.egg/openalea/core/settings.py", line 153, in init
self.read()
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/site-packages/openalea.core-2.2.0-py3.9.egg/openalea/core/settings.py", line 168, in read
settingsLogger.debug("Reading configuration file from " + self.configfile)
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/logging/init.py", line 1434, in debug
self._log(DEBUG, msg, args, **kwargs)
File "/home/jazzsta/miniconda3/envs/openalea3/lib/python3.9/logging/init.py", line 1577, in _log
fn, lno, func, sinfo = self.findCaller(stack_info, stacklevel)
TypeError: findCaller() takes 1 positional argument but 3 were given
Process finished with exit code 1

Error when using send to console

In VisuAlea, when running sendtoconsole, the following error is raised:

  File "/Users/pradal/devlp/git/visualea/src/openalea/visualea/graph_operator/__init__.py", line 115, in wrappedGOPNoBool
    return func(*args, **kwargs)
  File "/Users/pradal/devlp/git/visualea/src/openalea/visualea/graph_operator/port.py", line 107, in port_send_to_console
    interpreter.runsource("%s\n" % result)
  File "/Users/pradal/devlp/git/core/src/openalea/core/interpreter/__init__.py", line 71, in runsource
    code = compile(source, filename, symbol)
TypeError: expected a readable buffer object

Bug when return iterable with one element

Hi, I encounter problem :

def test_bug_0():  
    return {"A": 0, "B": 1}

def test_bug_1():
    return {"A": 0, "B": 1, "C": 2}

def test_bug_2():
    return {"A": {0: 42, 1: 21}, "B": 1, "C": 2}

def test_bug_3():
    return {"A": {0: 42, 1: 21}}

def test_bug_4():
    return {"A": {0: 42}, "B": {1: 21}}

test_bug_3() bug and return :

Traceback (most recent call last):
  File "c:\users\artzetsi\miniconda2\envs\develop\lib\site-packages\openalea.core-2.0.2-py2.7.egg\openalea\core\algo\dataflow_evaluation.py", line 227, in eval_vertex_code
    ret = node.eval()
  File "c:\users\artzetsi\miniconda2\envs\develop\lib\site-packages\openalea.core-2.0.2-py2.7.egg\openalea\core\node.py", line 654, in eval
    self.outputs[0] = outlist[0]
KeyError: 0

Worst with a collection.defaultdict like :

def test_bug_5():
    d = collections.defaultdict(dict)
    d["A"][0] = 42
    return d

don't throw error; just return a empty dict {}

Same for you ?

standalone application

  • a workflow exported with a node marked as user application
  • run the app.py with python
  • in tab "user applications" click the button "Widget"
  • get error AttributeError: 'GraphOperator' object has no attribute 'vertex_open'

And indeed, GraphOperator has no vertex_open. See line 165 in src/openalea/visualea/compositenode_widget.py

What was the purpose of it

Visuala: python 3, Qt5, WIP to be able to open the main window, issue with connect

In order to have the main window of visualea ( #14 ) open the following lines have been commented or modified:

  • visualeagui.py: l. 124 modified
    splash.showMessage(message, QtCore.Qt.AlignCenter|QtCore.Qt.AlignBottom) changed to splash.showMessage(message)
  • mainwindow.py: l. 145 commented
    self.connect(self.tabWorkspace, QtCore("contextMenuEvent(QContextMenuEvent)"), self.contextMenuEvent)
  • node_treeview.py: l. 211 commented
    l.sort(item_compare)# (lambda x,y : cmp(x.get_id(), y.get_id())))
  • node_treeview.py: l. 914-915 commented
    self.expanded(QtCore.QModelIndex).connect(self.expanded)
    self.collapsed(QtCore.QModelIndex).connect(self.collapsed)

All these modifications are referenced in the code with # F. Bauget 2023-01-18.

Then, connect management is one major issue.

Missing python base function in visualea like getitem

1

2

Tested with win64 conda installation :

conda create -n visualea python
activate visualea
conda install -c openalea openalea.visualea pyqt=4.10.4 qtconsole
visualea

And with "git clone" + "python setup.py install" on openalea repository : core, vpltk, grapheditor, misc, oalab, visualea

Installation issues

Hi, I've been trying to install and run visualea but I've been running into issues. I was on macOS Mojave but I've tried updating to the newest macOS Monterey version 12.3.1 and am still running into the same issues.

For example, I tried conda create -n openalea -c conda-forge -c openalea openalea.visualea. This went through without issues but when I typed visualea, I received the following error message:

Traceback (most recent call last):
File "", line 1, in
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.Visualea-2.0.1-py2.7.egg/openalea/visualea/visualeagui.py", line 26, in
from openalea.vpltk import qt
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.vpltk-2.0.1-py2.7.egg/openalea/vpltk/qt/init.py", line 157, in
import openalea.vpltk.qt.designer
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.vpltk-2.0.1-py2.7.egg/openalea/vpltk/qt/designer.py", line 94, in
from openalea.vpltk.qt.uic import compileUi, compile_args
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.vpltk-2.0.1-py2.7.egg/openalea/vpltk/qt/uic.py", line 28, in
message = 'You must install %s-tools' % os.environ['QT_API']
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/UserDict.py", line 40, in getitem
raise KeyError(key)
KeyError: 'QT_API'

I then tried to solve this with conda install pyqt. Then I did "visualea" again and got this error message:

Traceback (most recent call last):
File "", line 1, in
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.Visualea-2.0.1-py2.7.egg/openalea/visualea/visualeagui.py", line 29, in
from openalea.visualea.mainwindow import MainWindow
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.Visualea-2.0.1-py2.7.egg/openalea/visualea/mainwindow.py", line 30, in
from openalea.oalab.shell import get_shell_class
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.OALab-2.0.1-py2.7.egg/openalea/oalab/shell/init.py", line 2, in
from .shellwidget import ShellWidget
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.OALab-2.0.1-py2.7.egg/openalea/oalab/shell/shellwidget.py", line 1, in
from qtconsole.rich_jupyter_widget import RichJupyterWidget
ImportError: No module named qtconsole.rich_jupyter_widget

I then tried to solve this with conda install qtconsole, then I did "visualea" again and got this error message:
Traceback (most recent call last):
File "", line 1, in
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.Visualea-2.0.1-py2.7.egg/openalea/visualea/visualeagui.py", line 29, in
from openalea.visualea.mainwindow import MainWindow
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.Visualea-2.0.1-py2.7.egg/openalea/visualea/mainwindow.py", line 30, in
from openalea.oalab.shell import get_shell_class
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.OALab-2.0.1-py2.7.egg/openalea/oalab/shell/init.py", line 3, in
from .shell import get_shell_class
File "/Users/syralie/miniconda3/envs/openalea/lib/python2.7/site-packages/OpenAlea.OALab-2.0.1-py2.7.egg/openalea/oalab/shell/shell.py", line 48, in
class PyCutExt(QtGui.QTextEdit, GraphicalStreamRedirection):
AttributeError: 'module' object has no attribute 'QTextEdit'.

Here's the conda list now:

Name Version Build Channel
alabaster 0.7.12 py_0 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
babel 2.9.1 pyh44b312d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.os 0.1.1 py27_1001 conda-forge
backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge
backports_abc 0.5 py_1
brotlipy 0.7.0 py27h0b31af3_1000 conda-forge
ca-certificates 2022.3.29 hecd8cb5_0
certifi 2020.6.20 pyhd3eb1b0_3
cffi 1.14.0 py27h356ff06_0 conda-forge
chardet 3.0.4 py27h8c360ce_1006 conda-forge
configparser 3.7.3 py27h8c360ce_2 conda-forge
contextlib2 0.6.0.post1 py_0 conda-forge
cryptography 2.8 py27hab9f8d5_2 conda-forge
dbus 1.13.18 h18a8e69_0
decorator 4.4.2 py_0 conda-forge
docutils 0.16 py27h8c360ce_1 conda-forge
enum34 1.1.10 py27h8c360ce_1 conda-forge
expat 2.4.4 he9d5cce_0
future 0.18.2 py27h8c360ce_1 conda-forge
futures 3.3.0 py27_0
gettext 0.19.8.1 hb0f4f8b_2
glib 2.53.6 ha08cb78_1
icu 58.2 h0a44026_3
idna 2.10 pyh9f0ad1d_0 conda-forge
imagesize 1.2.0 py_0 conda-forge
importlib-metadata 1.5.0 py27h8c360ce_1 conda-forge
importlib_metadata 1.5.0 1 conda-forge
ipaddress 1.0.23 py_0 conda-forge
ipykernel 4.10.0 py27_0
ipython 4.2.1 py27_1 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jinja2 2.11.3 pyh44b312d_0 conda-forge
jpeg 9d h9ed2024_0
jupyter_client 5.3.4 py27_0
jupyter_core 4.6.1 py27_0
libcxx 13.0.1 hc203e6f_0 conda-forge
libffi 3.2.1 hb1e8313_1007 conda-forge
libiconv 1.14 3 openalea
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 h1de35cc_0
libzlib 1.2.11 h6c3fc93_1014 conda-forge
markupsafe 1.1.1 py27h89ed719_1 conda-forge
more-itertools 5.0.0 py_0 conda-forge
ncurses 6.3 h96cf925_1 conda-forge
openalea-core 1.3.0 pypi_0 pypi
openalea-deploy 2.1.8 pypi_0 pypi
openalea-grapheditor 2.0.1 pypi_0 pypi
openalea-misc 2.0.0 pypi_0 pypi
openalea-oalab 2.0.1 pypi_0 pypi
openalea-visualea 2.0.1 pypi_0 pypi
openalea-vpltk 2.0.1 pypi_0 pypi
openalea.core 1.4.1 py27_0 openalea
openalea.deploy 2.1.8 py27h8c360ce_2 conda-forge
openalea.grapheditor 2.0.1 0 openalea
openalea.misc 2.0.0 1 openalea
openalea.oalab 2.0.1 2 openalea
openalea.visualea 2.0.1 0 openalea
openalea.vpltk 2.0.1 py27_0 openalea
openssl 1.1.1n h6c3fc93_0 conda-forge
packaging 20.9 pyh44b312d_0 conda-forge
path.py 11.5.2 py_0 conda-forge
pathlib2 2.3.5 py27h8c360ce_1 conda-forge
pcre 8.45 h23ab428_0
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py27h8c360ce_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.5.2 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.9.2 py27h655552a_2
pysocks 1.7.1 py27h8c360ce_1 conda-forge
python 2.7.15 h8e446fc_1011_cpython conda-forge
python-dateutil 2.8.2 pyhd3eb1b0_0
python.app 1.3 py27h89ed719_1 conda-forge
python_abi 2.7 1_cp27m conda-forge
pytz 2020.1 pyh9f0ad1d_0 conda-forge
pyzmq 18.1.0 py27h0a44026_0
qt 5.9.7 h468cd18_1
qtconsole 4.7.7 py_0
qtpy 1.11.2 pyhd3eb1b0_0
readline 8.1 h05e3726_0 conda-forge
requests 2.25.1 pyhd3deb0d_0 conda-forge
scandir 1.10.0 py27h89ed719_1 conda-forge
setuptools 44.0.0 py27_0 conda-forge
simplegeneric 0.8.1 py_1 conda-forge
singledispatch 3.7.0 pyhd3eb1b0_1001
sip 4.19.8 py27h0a44026_0
six 1.16.0 pyh6c4a22f_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sphinx 1.8.5 py27_0 conda-forge
sphinxcontrib-websupport 1.2.4 pyh9f0ad1d_0 conda-forge
sqlite 3.38.2 hb516253_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
tornado 5.1.1 py27h1de35cc_0
traitlets 4.3.3 py27h8c360ce_1 conda-forge
typing 3.7.4.1 py27h8c360ce_1 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
zeromq 4.3.4 h23ab428_0
zipp 1.0.0 py_0 conda-forge
zlib 1.2.11 h6c3fc93_1014 conda-forge

I saw on another closed issue thread that it should be openalea.vpltk 2.0.2 instead. However when I tried conda install -c openalea openalea.visualea openalea.vpltk=2.0.2, I got the following error message:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  • openalea.vpltk=2.0.2 -> python[version='>=3.10,<3.11.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.6|>=3.7|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']

Your python: python=2.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions


Another type of error I've previously gotten when entering "visualea" into the terminal was "ImportError: No module named asyncio" since I'm using python2.7 for this installation. When I try using python3 when installing visualea I'd get error messages about conflicts etc. but I believe asyncio is a python3 module? I have since deleted the env which gave that error though.


I also tried this on a Linux server and I ran into same/similar error messages.

gui not starting after install with conda on win64

Hi,

I just test the visualea conda intall on my win64 (conda install -c openalea openalea.visualea).
When I tried runing visualea, nothing append.

I investigate a little bit more launching from ipython using:

from openalea.visualea.visualea_script import start_gui
start_gui()

I got a first error asking for openalea.oalab (for the interpreter). Is this dependency expected ?
After (conda) install of oalab, I got a second message for importing openalea.misc (same question ?)
After installng openalea.misc, I got the following error

image

That's all folks !

SyntaxError: invalid syntax (trunk_parameters.py, line 51)

I have installed openalea on a windows 10 machine.

I am not a python expert.
I use Python 3.9
Installed visualea but could not get it to run with the command "visualea" as stated in the documentation.

So i went to my ......\anaconda3\envs\openalea\Scripts directory.

There i run

python visualea

I get the program started but when i try to open Demo_WeberPenn i get:

Traceback (most recent call last):
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.visualea-2.3.3-py3.9.egg\openalea\visualea\util.py", line 78, in wrapped
    return f(*args)
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.visualea-2.3.3-py3.9.egg\openalea\visualea\node_treeview.py", line 859, in edit_node
    self.main_win().open_compositenode(obj)
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.visualea-2.3.3-py3.9.egg\openalea\visualea\mainwindow.py", line 495, in open_compositenode
    node = factory.instantiate()
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.core-2.3.1-py3.9.egg\openalea\core\compositenode.py", line 163, in instantiate
    node = self.instantiate_node(vid, call_stack)
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.core-2.3.1-py3.9.egg\openalea\core\compositenode.py", line 358, in instantiate_node
    node = factory.instantiate(call_stack)
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.core-2.3.1-py3.9.egg\openalea\core\node.py", line 1156, in instantiate
    module = self.get_node_module()
  File "c:\my_path\anaconda3\envs\openalea\lib\site-packages\openalea.core-2.3.1-py3.9.egg\openalea\core\node.py", line 1301, in get_node_module
    importlib.import_module(_nodemodule_name)
  File "C:\my_path\anaconda3\envs\openalea\lib\importlib\__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "", line 1030, in _gcd_import
  File "", line 1007, in _find_and_load
  File "", line 986, in _find_and_load_unlocked
  File "", line 680, in _load_unlocked
  File "", line 846, in exec_module
  File "", line 983, in get_code
  File "", line 913, in source_to_code
  File "", line 228, in _call_with_frames_removed
SyntaxError: invalid syntax (trunk_parameters.py, line 51)

There seems to be a pull request that is not merged.

https://github.com/openalea/weberpenn/pulls

When i manualy added the diffs i got it to work, only it does not seem very stable though.

Installation/running visualea

Hi, I'm having trouble in running visualea/openalea in general. I've installed OpenAlea (Windows) through https://openalea.readthedocs.io/en/latest/install.html#openalea-installation. Then I wanted to add the package of Visualea through https://anaconda.org/search?q=visualea, but ran into the same problem that my python version was to 'new' for Visualea. So I brought the version back to 2.7.15 in the anaconda navigator, but now I'm having several problems:

  • The 'pglviewer' command is not recognized in the anaconda command prompt anymore --> PlantGL doesn't appear
  • A window of visualea doesn't appear when typing 'visualea'
  • Several times that the following error occurs: Microsoft Visual C++ Run Time Library: Run time error! Program: C:\ Users\u0158557\Anaconda3\python.exe R6034: 'An application has made an attempt to load the C runtime library incorrectly . Please contact the application's support team for more information
  • Looking into the packages installed in this environment, it is quite different from the packages that were installed before installing visualea

I have no experience with the program, so if someone can give me the right steps that I have to undertake to get OpenAlea up and running (regarding packages, versions,... in Windows), this would be quite helpful.
Thank you in advance

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