add dockerfile - Githubissues

vivarium-collective / vivarium-biosimulators

A Vivarium wrapper for BioSimulators

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add dockerfile #10

Closed eagmon closed 3 years ago

eagmon commented 3 years ago

This PR will add a dockerfile, which sets the BioSimulators docker image as its base: https://github.com/orgs/biosimulators/packages?repo_name=Biosimulators.

jonrkarr commented 3 years ago

I suggest making the individual simulators optional dependencies. Making every simulator required would make it hard to get started without the Docker image.

Let's see if we can find a simple way to manage the combination of versions of simulators. I think two things would help

create a new python package which has all of the simulators as optional dependencies whose main purpose is to track their compatibility with core libraries
apply the same version tags for that to the Docker image

eagmon commented 3 years ago

So far the simulators with checks are passing:

[X] tellurium
[ ] cobrapy
[ ] bionetgen
[X] gillespy2
[X] libsbmlsim
[ ] rbapy
[X] xpp

The failing simulators fails for different reasons:

cobrapy:

Need to configure the SteadyStateSimulation

bionetgen:

need a model to load in

rbapy:

File "/Users/eranagmon/.pyenv/versions/v-tellurium/lib/python3.9/site-packages/biosimulators_utils/model_lang/rba/validation.py", line 10, in <module>
    import rba
ModuleNotFoundError: No module named 'rba'

jonrkarr commented 3 years ago

Note on RBA

RBApy will be included in the next version of the Docker image. Until recently, RBApy required CPLEX which requires python <= 3.8. We forked and patched RBApy to have additional options for GLPK and Gurobi, which can be run with Python 3.9. I'm pushing the French group that created RBApy to publish RBApy to PyPI to make it easier to install. Presently, RBApy needs to be installed from our fork.