topic Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5 in ArcGIS Pro Questions

Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

KonradBostrom — Wed, 03 Sep 2025 15:40:41 GMT

I've recently upgraded Pro from 3.0.3 to 3.5.2, and several of my Custom Python Toolboxes will now crash Pro if I run them a second time in a row. The tool works as expected, if I close and reopen Pro before running it again, but this isn't an issue I had on 3.0.3.

My code and input data are unchanged.

I'm curious if anyone else has experienced this behavior or has any insight into what might be causing this.

Thanks!

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Robert_LeClair — Wed, 03 Sep 2025 18:03:24 GMT

I wonder if the Python environment may need to be repaired? You can learn more about this workflow here - Repair an environment—ArcGIS Pro | Documentation

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

KonradBostrom — Wed, 03 Sep 2025 19:42:29 GMT

Hi Robert,

Thanks for the suggestion! My environment manager doesn't show the 'Warning icon' for the environment, and I didn't have the option to repair it. I did try to run the toolbox twice with a new clone of the default python environment and had the same issue.

Any other suggestions?

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Robert_LeClair — Wed, 03 Sep 2025 20:20:58 GMT

Well at least we know it's not a bad environment. Another thing to try is to create a new Python in a new Project. Add the old Python toolbox to the new project and copy and paste the original tool to the new toolbox. Run the tool again. Does ArcGIS Pro still crash?

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Chris_Ste — Fri, 17 Oct 2025 07:16:17 GMT

Hi,

I'm having the same Problem: First run works, the second crashes PRO. After I reopen the project it works again for one time then crashes again.

Tried with different projects and Data, always crashes on the second run.
Tested the code again with PRO Version 3.3 and it runs several times without crashing.

There's a bug-report (BUG-000176923) on that issue, with what I can only assume is a joke as a workaround ("Use ArcGIS Pro 3.3, where the tool completes successfully.").
It specifies Windows 10 as OS, but PRO also crashes on my Windows 11 machine.

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

KonradBostrom — Tue, 02 Dec 2025 18:56:23 GMT

Hi Chris,

Have you found a solution for this? I haven't had any luck personally.

Best, Konrad

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Robert_LeClair — Tue, 02 Dec 2025 20:41:27 GMT

In reviewing the BUG-000176923 report, it does say it's currently under review. Hopefully it is fixed at ArcGIS Pro 3.7!

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

DFarming — Thu, 18 Dec 2025 00:55:10 GMT

I have a script that reads a shapefile into a geodataframe, it always crashes the second time it is ran as of upgrading to 3.6 (from 3.5).

If I run the script it works the first time, if I run it again it crashes.
If I run the script it works, if I then make any changes to the script code and save, I can run it a second time with no crash. Is it not properly clearing the kernel or something?

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Chris_Ste — Wed, 22 Apr 2026 06:18:16 GMT

There has been an update on BUG-000176923. It seems to not be reproducible.
I did some testing and it might have something to do with modules imported within the toolbox. We use an environment that has several modules more than the base-env. When we use toolboxes with that environment that only uses modules found in the base-env, it seems to work. As soon as we use toolboxes that use e.g. geopandas and/or psycopg2 the tool crashes on the second run.
@DFarming seems like geopandas could be the culprit, as it crashes on a geodataframe
@KonradBostrom is geopandas also imported in the toolboxes that crash your PRO-instances? This would second my suspicion on geopandas

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

KonradBostrom — Tue, 28 Apr 2026 17:45:16 GMT

Chris, that's an interesting observation. I do use several opensource GIS libraries in my tool. I might rewrite it to only use base modules and see if that fixes it. Thanks for mentioning.

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

KonradBostrom — Tue, 28 Apr 2026 21:18:15 GMT

Rewriting my toolbox and removing all opensource / non-default modules stopped it from crashing on rerun.

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Chris_Ste — Wed, 29 Apr 2026 08:44:58 GMT

Glad this solved the issue.
Unfortunately rewriting all toolboxes within our company is no viable option.
On further research I found another BUG that also mentions geopandas: BUG-000151279 for ArcGIS Pro
Maybe @Robert_LeClair can forward that information, so the issue might be fixed in 3.7 or any following patches/hotfixes.

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Robert_LeClair — Wed, 29 Apr 2026 21:57:07 GMT

@KoryKramer - does the ArcGIS Pro Dev Team know about this item/issue?

Re: Custom Python Toolbox Crashes Pro on 2nd Run after upgrading to 3.5

Chris_Ste — Mon, 22 Jun 2026 07:30:48 GMT

I finally had a chance to test PRO 3.7 on a separate machine. Cloned the base-env, upgraded to 3.7, installed geopandas via python command prompt (conda install -c conda-forge geopandas) and tested our toolboxes:

1. tools within toolboxes that do not import geopandas run perfectly several times in a row without crashing

2. tools within toolboxes that import geopandas crash PRO on the second run

This is highly frustrating as our company would like to use several new features implemented in PRO since 3.3 and this bug forces us to stay with 3.3 and its limitations...

@KoryKramer Is there any chance this bug might be fixed with a patch in the near future as it was in BUG-000176923?

Update:
I did some further research and found the following:
Apparently on import of third party libraries in .pyt-toolboxes pointers to C-libraries are loaded in PROs application memory and are NOT deleted after tool-execution to make further runs of python processes faster. Good thinking, but this causes a memory access violation that terminates ArcGISPro.exe on OS-level.

To stop this I moved all imports from the top of the .pyt file to within the def execute() part of the tool to isolate imports and keep them out of the main toolbox (and therefore application?) scope.
Then added

def isLicensed(self): return True

to force an external process execution thread (as suggested by Gemini).
The import of geopandas within the execute function (and therefore an isolated thread?) works, but then the tool crashes again on the second run, which again hints to a polluted memory in the main memory caused by the non-isolated python-process.

Another approach was to add the following to the top of the pyt-file, again resulting in crashing on the second run:

import geopandas as gpd import importlib importlib.reload(gpd)

I'm out of ideas and time to try find a solution but hope this might help to find out, why those tools still work in PRO 3.3 and crash in PRO 3.5/3.7.

Update 2:

The env for 3.3 has geopandas 1.0.1 installed, the env for 3.5 my colleague currently has 0.14.4 installed. Could it be, that dependencies in newer ArcPRO Versions require geopandas to downgrade to the last 0.X Version of geopandas (and some of its dependencies) and that this causes the crash on the second run?
Our env for 3.2 used 0.12.2 and ran perfectly, so it might be the combination of "new ArcPRO (3.4 or higher)" + "old geopandas (0.X)"