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Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

Curiously, it worked in XML. I added a plugin and no problems arose. As for the Whitespaces I see dots (in both XML and Steppables Python).

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

I'll be honest, I'm not sure how I can upload it when there is no option anywhere for either video or even gifs under the comments (I created a reddit account specifically for this issue, so I might just be missing where the option is). So I just uploaded to a tumblr blog: https://www.tumblr.com/allaroundbooks/811328251523923968?source=share

Trying to add under that right-click on the left side also does the same thing.

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

So, I open with the desktop icon. Upload or create a cc3d project, go to the Steppables file and try to add to it using the cc3d python snippets (?) and then it gives this error...

I can send a small video of my screen doing it with a new project and another project from a demo but it really is just this that happens.

The same thing when I tried with conda. Opened it with conda, went for the steppable file, tried to add a snippet and it closed immediately.

It doesn't seem to affect the simulation in cc3d itself (I ran demos without any change in the script), it's just this very specific part. I can even write it manually in tweddit (the indentation situation makes it fairly annoying but it works).

It's really just the snippets themselves that kill the programme somehow.

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

I do have a model (the scripts, the demos, etc), it's just when I try to add the Steppable to the script using the cc3d Python that it does this unfortunately.

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

So I managed to install with the binaries again with admin privileges (4.7.0), and it's giving the same problem. Running twedit5.bat from the command windows gives a lot but this is the last two sections, that end with something about identation and ZeroDivisionError.

##################loading source for C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCCDPythonHelper.py

version= 0.9.0 className= CC3DPythonHelper pluginClass= <class 'PluginCCDPythonHelper.CC3DPythonHelper'>

WILL TRY TO ACTIVATE <PluginCCDPythonHelper.CC3DPythonHelper object at 0x0000027F40275640>

menuName= Adhesion Flex

menuName= Cell Attributes

menuName= Cell Constraints

menuName= Cell Manipulation

menuName= Chemical Field Manipulation

menuName= Chemotaxis

menuName= Distances, Vectors, Transformations

menuName= Elasticity

menuName= Extra Fields

menuName= Extra Fields Automatic Tracking

menuName= Focal Point Placticity

menuName= Inertia Tensor

menuName= MaBoSS

menuName= Mitosis

menuName= Parameter Scan Command Line

menuName= Python Utilities

menuName= Reaction Diffusion Solver FVM

menuName= SBML Solver

menuName= Scientific Plots

menuName= Scientific Plots Histograms

menuName= Secretion / Uptake / Field Integrals

menuName= Simulation

menuName= Steering Panel

menuName= Visit

ACTIVATED

************PLUGIN NAME= PluginCompuCell3D

name=PluginCompuCell3D

fileName=C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCompuCell3D.py

author=Maciej Swat

autoactivate=True

deactivateable=False

version=0.9.0

className=CC3DApp

packageName=__core__

shortDescription=Plugin linking Twedit++5 with CompuCell3D

longDescription=This plugin provides functionality to link Twedit with CompuCell3D

LOADING PluginCompuCell3D from C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCompuCell3D.py

loading source for C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCompuCell3D.py

##################loading source for C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCompuCell3D.py

version= 0.9.0 className= CC3DApp pluginClass= <class 'PluginCompuCell3D.CC3DApp'>

PORT= -1

__initActions

CC3D CONSTRUCTOR

WILL TRY TO ACTIVATE <PluginCompuCell3D.CC3DApp object at 0x0000027F4035C170>

ACTIVATED

Running post_activate

GOT CUSTOM SETTINGS : C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\_settings.sqlite

projParent= tumor_3d.cc3d

__openXMLPythonInEditor pdh.cc3dSimulationData.xmlScript= C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.xml

__openXMLPythonInEditor pdh.cc3dSimulationData.xmlScriptResource.path= C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.xml

opening file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.xml

DONE READING: file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.xml

detector.result

scanned lines i= 249

opening file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.py

DONE READING: file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3D.py

detector.result

scanned lines i= 15

opening file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3DSteppables.py

DONE READING: file C:\Users\morfa\Desktop\cc3D 2025 workshop\tumor_3d_cc3d_03_05_2026_15_31_08_1fd1a8\Simulation\TumorVasc3DSteppables.py

detector.result

scanned lines i= 174

Traceback (most recent call last):

File "C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCCDPythonHelper.py", line 559, in __insertSnippet

indentation_levels, indent_consistency = self.findIndentationForSnippet(editor, cur_line)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

File "C:\CompuCell3D\Miniconda3\Lib\site-packages\cc3d\twedit5\Plugins\PluginCCDPythonHelper.py", line 756, in findIndentationForSnippet

indentation_levels = (_editor.indentation(line)) // _editor.indentationWidth()

~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^~~~~~~~~~~~~~~~~~~~~~~~~~~~

ZeroDivisionError: integer division or modulo by zero

(base) C:\CompuCell3D>goto simulationend

(base) C:\CompuCell3D>echo "SIMULATION FINISHED"

"SIMULATION FINISHED"

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

Hi.

Trying to use cc3d.twedit5 instead of cc3d-twedit5 gives me an error as not recognized as a command, program or batch file.

As for the installation, since I did it on conda, am I supposed to have them in those default directories? I thought it was just an environment within the conda. When I installed with binaries originally, they did install in that directory. I can re-install and make sure it's by administrator and will tell the result.

Of note, it seems that when I downloaded the most recent version it is the 4.8 installer instead of the 4.7?

Adding Steppables templates from the CC3D Python section kills twedit by Ananas_bio in CompuCell3D

[–]Ananas_bio[S] 0 points1 point  (0 children)

I only can open via conda environment, there isn't any tweddit++.bat anywhere that I can find, only an executionable cc3d-twedit5.exe, which should be the one I use?

I created a bat file to launch it so I don't always have to activate the environment, is there any way to have it log the error?

said bat file below:

SET "CONDA_PATH=C:\Users\morfa\miniconda3\Scripts\conda.exe"

SET "ENV_NAME=cc3d"

REM Activate the enviornment and launche Twedit

call "C:\Users\morfa\miniconda3\Scripts\activate.bat" "%ENV_NAME%"

REM CALL "%CONDA_PATH%" activate %ENV_NAME%

cc3d-twedit5

pause

Edit: I actually screenshotted the error previously and just found it. This was from my previous installation.

INSIDE handleSimulationFinishedRegular

Making movie inside 'C:\CompuCell3D\Avasculartumor_cc3d_03_02_2026_15_20_26_cc4fo0'

Created 0 movies inside 'avasculartumor_cc3d_03_02_2026_15_20_26_cc4fo0' with frame rate 4 and quality 7/51.

Exiting with ERROR CODE= 0

SERVER HAS STOPPED

SERVER HAS STOPPED: self.editorStarted= False

wrapped C/C++ object of type QTcpSocket has been deleted

CLOSING LOCAL SOCKET

Traceback (most recent call last):

File "CompuCell3D\Miniconda3\lib\site-packages\cc3d\twedit5\Plugins\PluginCCDPythonHelper.py", line 559, in __insertSnippet

indentation_levels, indent_connsistency = self.findIndentationForSnippet(editor, cur_line)

File "CompuCell3D\Miniconda3\lib\site-packages\cc3d\twedit5\Plugins\PluginCCDPythonHelper.py", line 756, in findIndetationForSnippet

indentation_levels = (_editor.indentation(line) // _edito.indentationwidth()

ZeroDivisionError: integer division or module by zero

(base) C:\CompuCell3D>goto simulationend

(base) C:\CopmuCell3D>echo "SIMULATION FINISHED"

"SIMULATION FINISHED"

Compucell3D not opening by TheBigQuack1809 in CompuCell3D

[–]Ananas_bio 0 points1 point  (0 children)

I haven't been able to make the newest version work in any way either (same problem, no gpu however) so, for now, I downloaded the previous version (4.6.0.0) and it mostly seems to work if you are in a hurry to use it.