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SciCompMod / memilio

Modular spatio-temporal models for epidemic and pandemic simulations
https://scicompmod.github.io/memilio/
Apache License 2.0
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Update memilio-simulation setup.py and documentation #295

Open AgathaSchmidt opened 2 years ago

AgathaSchmidt commented 2 years ago

When installing the memilio python bindings there are some packages like pandas missing. You need to run the setup.py of memilio-epidata first. If the intention is that you can set up these two independently they should each have complete setup.py 's .

dabele commented 2 years ago

I'm surprised the memilio-simulation package requires pandas

AgathaSchmidt commented 2 years ago

I think I mixed something up in the issue description. The goal was to run the pycode/examples/simulation/secir_simple file. It was unclear which setup.py has to be executed. Intuitively the memilio-simulation setup.py comes into mind. But without running the memilio-epidata setup.py not all packages needed are installed. Maybe it could be sufficent to add a ReadMe to the pycode/examples folder.

dabele commented 2 years ago

I don't think we should install pandas with the python bindings just so a user can run the examples, even the examples that specifically demonstrate the use of the python bindings. Note that the examples are not installed with the package. I agree there could be a hint somwhere. Ideally the examples are mentioned in the README of pycode or pycode/memilio-simulation. Adding a README to pycode/examples may be enough.

Maybe a pip requirements file to install all the packages needed for the examples? Installing memilio-epidata to run the memilio-simulation examples is not the ideal solution. The requirements just happen to be similar by chance.