Error on startup with pre release 1.1.7

[sthiele]

Following the install instruction I get the following error.

❯  conda activate cnapy-1.1.7
❯ cnapy
Traceback (most recent call last):
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/bin/cnapy", line 6, in <module>
    from cnapy.__main__ import main_cnapy
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/cnapy/__main__.py", line 31, in <module>
    from cnapy.application import Application
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/cnapy/application.py", line 42, in <module>
    from cnapy.gui_elements.main_window import MainWindow
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/cnapy/gui_elements/main_window.py", line 10, in <module>
    from cnapy.core import model_optimization_with_exceptions
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/cnapy/core.py", line 15, in <module>
    import efmtool_link.efmtool4cobra as efmtool4cobra
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/efmtool_link/efmtool4cobra.py", line 1, in <module>
    import efmtool_link.efmtool_intern as efmtool_intern
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/efmtool_link/efmtool_intern.py", line 9, in <module>
    jpype.startJVM()
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/jpype/_core.py", line 184, in startJVM
    jvmpath = getDefaultJVMPath()
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/jpype/_jvmfinder.py", line 74, in getDefaultJVMPath
    return finder.get_jvm_path()
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7/lib/python3.8/site-packages/jpype/_jvmfinder.py", line 212, in get_jvm_path
    raise JVMNotFoundException("No JVM shared library file ({0}) "
jpype._jvmfinder.JVMNotFoundException: No JVM shared library file (libjvm.so) found. Try setting up the JAVA_HOME environment variable properly.

[sthiele]

Maybe it has something to do with openjdk which is now on version openjdk=8.0.332=h166bdaf_0 for me?

[axelvonkamp]

What is the jpype1 version of your environment?

[sthiele]

What is the jpype1 version of your environment?

• jpype1=1.4.1=py38h43d8883_1

[axelvonkamp]

Can you try an older version of jpype1? I still have got 1.2.1. Strangely though, the PR checks did not show this issue.

[sthiele]

I downgraded to jpype1=1.2.1=py38h1fd1430_0 and have the same issue.

Strangely though, the PR checks did not show this issue.

Might be because I'm not on an ubuntu machine.

[sthiele]

It is probably because i use fish. conda issue

But with zsh I get another error:

openjdk version "1.8.0_332"
OpenJDK Runtime Environment (Zulu 8.62.0.19-CA-linux64) (build 1.8.0_332-b09)
OpenJDK 64-Bit Server VM (Zulu 8.62.0.19-CA-linux64) (build 25.332-b09, mixed mode)
Restricted license - for non-production use only - expires 2024-10-28
Could not find font_size in cnapy-config.txt
Traceback (most recent call last):
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/bin/cnapy", line 10, in <module>
    sys.exit(main_cnapy())
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/__main__.py", line 34, in main_cnapy
    Application()
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/application.py", line 76, in __init__
    self.window = MainWindow(self.appdata)
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/gui_elements/main_window.py", line 68, in __init__
    self.central_widget = CentralWidget(self)
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/gui_elements/central_widget.py", line 72, in __init__
    self.reaction_list = ReactionList(self)
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/gui_elements/reactions_list.py", line 131, in __init__
    self.reaction_mask = ReactionMask(self)
  File "/home/sthiele/miniconda3/envs/cnapy-1.1.7p/lib/python3.8/site-packages/cnapy/gui_elements/reactions_list.py", line 678, in __init__
    self.grp_test_model.add_reaction(reaction)
AttributeError: 'Model' object has no attribute 'add_reaction'

[axelvonkamp]

Can you try to replace the line 678 in reactions_list.py with

self.grp_test_model.add_reactions([reaction])

add_reaction is deprecated but should actually still work.

[sthiele]

That works. I did not test thoroughly but CNApy is up and running. 😄

[sthiele]

Oh yeah, some other things I noted.

• The scenario name is in an unfortunate position I think I can click on it but nothing happens.
• Idea: Maybe replace the icon for scenario open with the name of the scenario
• The other toolbar buttons (reload/save scenario) if they are disabled should be greyed out
• How do I know that the scenario has been changed/unsaved? I think there should be some indication if the current scenario is not the same as the one that is on the label.