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I created a script tool in the custom toolbox, it runs like this:

The GUI of my python script tool

But the default progress dialog keep stealing focus from the Tkinter GUI, that makes me so hard to move/resize the OpenFileDialog, expand the dropdown menu, double-click to choose item... ...

I have to right-click on the file to select it, paste the path into the inputbox to change the location.

Is there any way to avoid this or disable the default progress dialog?

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If you place your Tkinter code into the tool validation part (Tool>Properties>Validation>Edit), around parameter initialization, you should be fine. However this is not an advised method due to architectural discordances. Still you can use Python add-ins as suggested in Recommendations about graphic interface for ArcPy/Python script and Trying to use Tkinter to open dialog box in ArcMap.

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