There are definitely options outside of Jupyter if you are willing to give up the Read-Eval-Print-Loop pattern, as it sounds like you are.
You could just write a python script that people put alongside their data. You can generate a report other ways and that generation can be part of the script. The main way I have used in the past is via ReportLab because it can do everything and make composited PDFs. But you can go simpler by using Matplotlib and annotation or PIL to control placing the parts of your report.
Or if you want you can make the output go to Plotly I believe. Where the ‘report’ could be a webpage with the resulting plots if that works. I have old example code with composting with ReportLab here.
Although it doesn’t have the report making aspect, the first part of this notebook I have here sort of illustrates putting data alongside a script with sample data and then suggest user to add their data. The goal is just to really get users pointing the script plot_expression_across_chromosomes.py at their data and then they get a plot. The overarching script is stored in a different repo and obtained in the preparation steps. (However, that particular script I haven’t overhauled to my current, clearer coding style. So if you need a model, I’d suggest the one named ‘nucleotide_difference_imbalance_plot_stylized_like_Figure_8_of_Morrill_et_al_2016.py’ available here; the blurb about it at that page tells you how you can run the demo page via MyBinder.)
That type of combination can also be dockerized so they would just need to place their data in a directory that you then tell them how to attach to a Docker container and then trigger the processing with a single command. This example here builds to something like that while teaching about Docker. I say ‘something like that’ because the software triggered isn’t a Python script as far as I know but the idea is the same.
As for giving people a place to put their data with your code, you can go even fancier and make an actual Python-based web app using Django or Flask. Because it is Python, you can use thePython modules that you have mentioned. I have done this on PythonAnywhere with some really simple items before I discovered Jupyter and the MyBinder combination, for examples see http://fomightez.pythonanywhere.com/ammonium_screen/ or http://fomightez.pythonanywhere.com/spartan_fixer/ . However, that adds overhead of learning another ecosystem and adds hosting fees if you are allowing people to process a lot of data. Jupyter allows much more complex interaction between users and your code though without focusing on the overhead of web development. In fact I never quite got around to implementing the upload part and was just working with web forms at the time, as you’ll see if you look at my examples being served from PythonAnywhere.