Suspicious unknown folders and files appear in the cloud.

• If a Python script installed Malware, it would be seen in one of these 3 folders and also require that you entered your Administrator Password:

/Library/LaunchDaemons

/Library/LaunchAgents

~/Library/LaunchAgents

• If you did give Python access to your training files in iCloud, it can certainly install files/folders in the root directory without any further authorization on your part. Authorization has already been given. You can turn off Python access to iCloud at  > System Settings > [name on top] > iCloud > See All. Also on the iCloud screen, tap Drive, then review Apps syncing to iCloud Drive.

• Malicious Python scripts can also ask for your Apple Account password and send it to a third party. If that was the case, the person that has your Apple Account password can add files to your iCloud Drive. This would not have anything to do with your Mac being compromised, but certainly your Apple Account would be. Changing the Apple Account password is all that would be needed to prevent further access.

• As for viruses being installed by just clicking a link, that is not true although certainly would be told to you by an Antivirus company. First, viruses cannot be installed on a Mac because there is no access to the System files that are locked on a read only partition of the Hard Drive. A virus refers to a self propagating process that spreads across system files and other devices and is not possible. It may be a semantic difference in the use of the word "virus" to scare you, because certainly Malware can be installed on a Mac, and that would require you to enter your Administrator Password to install it and will not happen automatically by clicking a link. Malware is installed in one of the 3 folders listed above so it can run on startup.

• A Trojan would be an app that you installed, and could have come from a python script, that was meant to do one thing but does something else. This app/script would then be set to run on startup in your Login Settings. For example, it may have been told to you that it simply displays the time in a window on your Desktop, but actually sends Notification that will appear on your Mac that claims you have a virus and suggest you install some software to prevent it.

My guess is that, in one of those "Terms and Conditions" things that pop up when you access an app or web page, you did authorize PyCharm to leave little pieces behind without telling you.

But, of course, there is no way that any of us could know exactly what happened.

Do you think I need to do a full system reset to factory defaults with a reinstallation of Mac OS to avoid future threats?

No. And antivirus software is more likely to do harm than good.