AMICI/pytest.ini at main · AMICI-dev/AMICI · GitHub

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[pytest]

addopts = -vv --strict-markers --doctest-modules --ignore-glob=*.template.py

filterwarnings =
    # warnings are errors
    error
    # Unrelated to our code, unclosed SSL socket when downloading test assets
    #  (probably improper cleanup upstream in case of exceptions)
    ignore:Exception ignored while finalizing socket:pytest.PytestUnraisableExceptionWarning
    ignore:Exception ignored in. .ssl\.SSLSocket :pytest.PytestUnraisableExceptionWarning
    # Known issue with numpy under valgrind - don't error on this
    once:Signature .* for <class 'numpy.longdouble'> does not match any known type. falling back to type probe function:UserWarning
    # petab
    ignore:Using petab.v1.Problem with PEtab2.0 is deprecated:DeprecationWarning
    # pandas>=3.1 deprecations (Pandas4Warning) in petab and petabtests
    ignore:The inplace keyword in .* is deprecated:DeprecationWarning:petab
    ignore:The 'float_precision' argument is deprecated:DeprecationWarning:petab
    ignore:'str' is not supported as a fill value:DeprecationWarning:petab
    # petab1to2 warns-and-falls-back for v1-only noise distributions not
    # supported in v2 (e.g. log10-normal -> log-normal); this is an
    # intentional, documented conversion decision, not an error
    ignore:Noise distribution .* is not supported in PEtab v2\. Using .* instead\.:UserWarning
    # petab1to2 drops PEtab v1's parameterScale column when upgrading to v2
    # (v2 has no equivalent); nominal/simulation values are unaffected since
    # petab v1's nominalValue is always stored in linear units regardless of
    # parameterScale, so this only affects estimation-scale metadata, not
    # simulation correctness
    ignore:Parameter scales are not supported in PEtab v2\.:UserWarning
    # petab1to2 renames a v1 measurement table column `experimentId`, which is
    # reserved in v2; it is not used for simulation
    ignore:The measurement table has a column `experimentId`, which is reserved in PEtab v2\.:UserWarning
    # amici
    ignore:Conservation laws for non-constant species in models with RateRules are currently not supported and will be turned off.:UserWarning
    ignore:Conservation laws for non-constant species in models with Species-AssignmentRules are currently not supported and will be turned off.:UserWarning
    ignore:Conservation laws for non-constant species in combination with parameterized stoichiometric coefficients are not currently supported and will be turned off.:UserWarning
    ignore:Support for PEtab2.0.*experimental:UserWarning
    ignore:The JAX module is experimental and the API may change in the future.:ImportWarning
    # hundreds of SBML <=5.17 warnings
    ignore:.*inspect.getargspec\(\) is deprecated.*:DeprecationWarning
    # pysb warnings
    ignore:the imp module is deprecated in favour of importlib.*:DeprecationWarning:pysb\.core
    ignore:Model.initial_conditions will be removed in a future version. Instead, you can get a list of Initial objects with Model.initials.:DeprecationWarning:pysb\.core
    # https://github.com/pytest-dev/pytest-xdist/issues/825#issuecomment-1292283870
    ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning
    ignore:.*:ImportWarning:tellurium
    ignore:.*PyDevIPCompleter6.*:DeprecationWarning
    # ignore numpy log(0) warnings (np.log(0) = -inf)
    ignore:divide by zero encountered in log:RuntimeWarning
    # ignore jax deprecation warnings
    ignore:jax.* is deprecated:DeprecationWarning
    # swig 4.3 issues
    ignore:builtin type .* has no __module__ attribute:DeprecationWarning

norecursedirs = .git amici_models build doc documentation models ThirdParty _installation examples *build* petab_test_problems pysb_test_models