what is the best way to test a flask modular app [ GUI & CLI ]

First of all I'm relatively new for the field of automated testing and it comes as a must for me to use it

I'm open to any idea or tool

I'm used to write modular flask apps, then testing it manually,

now when starting learning automated testing I can't get in tree things

1. [ test two origins ] I need to be able to call test as a part of the application or separate from it to test both application behavior within the functional context & GUI views
2. [ call it from two origins ] I need to call it either within CLI context or GUI view (consider protected views)
3. [ secure it ] writing tests for sensitive modules should have it's rules, also as it's own risks

what I've tried or found:

• Flask documentation - Testing Flask Applications (don't cover modular app)
• pytest, unittest (only covers CLI)
• some articles like this, and this... (all are handling same aspects | no securty basis)

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I'm seeking for a well documented secure approach for testing flask regarding the tree aspects I've mentioned above