You could write a custom application which uses the Power BI REST API to accomplish this. If writing a custom application in C# is an option for you, you can write your application code to upload PBIX files to either a personal workspace or a group worksapce in PowerBI.com. This gives you the same result as publishing a project in Power BI Desktop. If you go down this road, you must learn how to register your application with Azure AD and how to configure permissions for the Power BI REST API.
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