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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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The current solver interface glpk doesn't support setting the optimality tolerance #724

Closed helenaherand closed 2 years ago

helenaherand commented 2 years ago

Yesterday, I ran into "The current solver interface glpk doesn't support setting the optimality tolerance" when running memote in the terminal. I tried to change the interface to CPLEX and Gurobi (glpk) by the solver option but cplex did not seem to be a valid interface and "--solver glpk" did not solve the issue. Does anyone know why glpk does not support setting the optimality tolerance and/or how I may solve it?

helenaherand commented 2 years ago

memote report snapshot Human-GEM.xml Scaling... A: min|aij| = 1.000e+00 max|aij| = 1.000e+00 ratio = 1.000e+00 Problem data seem to be well scaled The current solver interface glpk doesn't support setting the optimality tolerance. ============================= test session starts ============================== platform linux -- Python 3.6.7, pytest-6.2.5, py-1.10.0, pluggy-1.0.0 rootdir: /home/helena plugins: anyio-3.3.4 collected 191 items / 1 skipped / 190 selected

../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py . [ 0%] ..FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFFF.F..F....FFF.FFF.FFFF.. [ 34%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_basic.py . [ 34%] .....FF.......F.F.F.FF [ 46%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py . [ 46%] FFFFFFFFFFF.FFFFF.............FFFFFFFFFFF.......FFFFFF [ 74%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_consistency.py . [ 75%] ..ssssssssssssssssFFFFFF.FFF [ 90%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_essentiality.py s [ 90%] [ 90%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_growth.py s [ 91%] [ 91%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_matrix.py . [ 91%] F.. [ 93%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbml.py . [ 93%] . [ 94%] ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_sbo.py F [ 94%] FFFFFFFss. [100%]

=============================== warnings summary =============================== .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR00021] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR04413] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09931] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR09932] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR12140] .local/lib/python3.6/site-packages/memote/suite/tests/test_biomass.py::test_biomass_consistency[MAR13082] /home/helena/.local/lib/python3.6/site-packages/cobra/core/metabolite.py:135: UserWarning: The element 'R' does not appear in the periodic table warn("The element %s does not appear in the periodic table" % e)

-- Docs: https://docs.pytest.org/en/stable/warnings.html =========================== short test summary info ============================ FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[pubchem.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[kegg.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[seed.compound] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[inchikey] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[inchi] FAILED ../../../.local/lib/python3.6/site-packages/memote/suite/tests/test_annotation.py::test_metabolite_annotation_overview[chebi] FAILED 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carrascomj commented 2 years ago

Hello Helena!

It is just a warning, you can safely ignore it. Some solvers, like glpk, in some versions of cobrapy (which ultimately depends on the version of optlang it is using) do not implement or do not expose setting the tolerance of the solver and that generates a warning.

By the way, in order to use cplex or gurobi, you have to install them first separately. Both provide academic licenses.

helenaherand commented 2 years ago

Thanks, carrascomj!