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A lot of people use WP CLI to script the setup using Bash scripting. Here are some articles that discuss this.
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Another approach is to hardcode PHP scripts with embedded SQL to do the setup.
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A third approach is something I have been working on recently; a set of PHP objects to make setup and configuration easier for automated testing. The objects do not have nearly the breadth of functionality that WP CLI has, but if you prefer scripting in PHP over scripting in BASH you can always send pull requests for things you need to add.
Hope this helps.
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