SMAPI Malware blocking in Stardew Valley on macOS

You will need to codesign the app. Some background:

https://www.reddit.com/r/StardewValley/comments/1h071jl/mac_deleted_stardew_modding_api_because_of_malware/

(This is also more of an app development question, so probably better suited to the Apple Developer forums.)

Even very popular and respected applications are occasionally affected by what are called supply chain attacks that result in malware ending up in a typically trusted app. Therefore, you may want to do quite a bit more research before stating that a mod such as this is ever "100%" safe. Although the Mac's Gatekeeper could be flagging this due to a false positive, it may actually contain malware.

I would suggest first downloading the app and submitting it online to: https://www.virustotal.com/gui/home/upload

Then, if you are willing to risk it: Safely open apps on your Mac - Apple Support

It's possible that that option is only available when an application is simply unsigned, but not for "known malware". That document states:

"If macOS detects known malware, your Mac notifies you that the app can't be opened and moves it to the Trash. You might be asked to anonymously share a copy of the malware with Apple to help improve macOS security. If you choose to share, macOS uploads only the malware executable itself (or the containing app bundle, if the executable is contained in a bundle) and nothing else."

If the file ends up in the trash, try uploading to VirusTotal to see what they think. You should also use the "Send to Apple" button on the pop-up so they can analyze the app to determine if it really is a false positive detection (and correct Gatekeeper's classification).

If you insist on trusting this app, there are instructions in the following discussion for possibly allowing it to run: MacOS Sequoia -- "Allow Apps from Anywher… - Apple Community