Fixing some bugs and active development #28
Conversation
vishnumahamkali
commented
Dec 19, 2023
vishnumahamkali
commented
- Bug causing problems with accessing equilibrator accessions
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@timmccubbin, FYI |
| @@ -261,6 +262,60 @@ def calculate_transport_charge(self): | |||
| {key: sum(val) for key, val in n_proton.items()}, | |||
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| def update_variable_bounds(self): | |||
| """Updating the method from cobra to update the flux bounds in cplex_interface. Currently not doing it for gurobi_interface as I don't have a licence to test this""" | |||
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I have a Gurobi license, could give it a try and make a PR to this branch or in a follow-up after this is merged. Or would you rather stop support for gurobi? My use case for gurobi so far has been that the constraint relaxation is more flexible, but I have managed to get CPLEX to do what I want. Not sure if the "Debugging" part of the docs would still work, although I don't think that gurobi's computeIIS function takes the quadratic constraint into account anyways.
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| logs_dir = cwd + os.sep + "logs" | ||
| if not os.path.exists(logs_dir): | ||
| os.makedirs(logs_dir) | ||
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| def variability(model_variability, variable_list=None): |
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I have been using this branch with CPLEX for a couple of days, including the variability, and it's been working great so far.
| @@ -31,7 +28,7 @@ | |||
| R = 8.31e-3 # "kJ / mol / K" | |||
| FARADAY = 96.485 # "kJ / mol" | |||
| Vmax = 1000 | |||
| K = 1e8 | |||
| K = 1e6 | |||
| default_T = 298.15 # , "K") | |||
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I have opened an issue about this #29.
| equilibrator-api==0.3.2b7 | ||
| component-contribution==0.3.2b4 | ||
| equilibrator-cache==0.3.2b2 | ||
| equilibrator-api |
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It would be nice to pin it, since the different equilibrator packages usually need to coordinated. This version set works for me with this branch:
equilibrator-api==0.6.0
equilibrator-cache==0.6.0
component-contribution==0.6.0
I think stating only equilibrator-api>=0.6.0 and letting pip do the dependency resolution might also be fine.
