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Tests fail with version 0.7.3 with installed extras #111

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yurivict opened this issue Sep 21, 2018 · 7 comments
Open

Tests fail with version 0.7.3 with installed extras #111

yurivict opened this issue Sep 21, 2018 · 7 comments

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@yurivict
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Thanks for fixing some other failures yesterday. Today I installed extras, and some tests fail again:

================================================================================= FAILURES ==================================================================================
____________________________________________________________ test_get_native__a_substance_no_composition[solve0] ____________________________________________________________

solve = ()

    @pytest.mark.veryslow
    @requires('pygslodeiv2', 'pyodesys')
    @pytest.mark.parametrize('solve', [(), ('H2O',)])
    def test_get_native__a_substance_no_composition(solve):
        rsys = ReactionSystem.from_string('\n'.join(['H2O -> H2O+ + e-(aq); 1e-8', 'e-(aq) + H2O+ -> H2O; 1e10']))
        odesys, extra = get_odesys(rsys)
        c0 = {'H2O': 0, 'H2O+': 2e-9, 'e-(aq)': 3e-9}
        if len(solve) > 0:
            from pyodesys.symbolic import PartiallySolvedSystem
            odesys = PartiallySolvedSystem(odesys, extra['linear_dependencies'](solve))
>       odesys = get_native(rsys, odesys, 'gsl')

/usr/local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

rsys = <chempy.reactionsystem.ReactionSystem object at 0x812b501d0>, odesys = <pyodesys.symbolic.SymbolicSys object at 0x8162bda90>, integrator = 'gsl', skip_keys = (0,)
steady_state_root = False, conc_roots = None

    def get_native(rsys, odesys, integrator, skip_keys=(0,), steady_state_root=False, conc_roots=None):
        comp_keys = Substance.composition_keys(rsys.substances.values(), skip_keys=skip_keys)
        if PartiallySolvedSystem is None:
>           raise ValueError("Failed to import 'native_sys' from 'pyodesys.native'")
E           ValueError: Failed to import 'native_sys' from 'pyodesys.native'

/usr/local/lib/python2.7/site-packages/chempy/kinetics/_native.py:113: ValueError
____________________________________________________________ test_get_native__a_substance_no_composition[solve1] ____________________________________________________________

solve = ('H2O',)

    @pytest.mark.veryslow
    @requires('pygslodeiv2', 'pyodesys')
    @pytest.mark.parametrize('solve', [(), ('H2O',)])
    def test_get_native__a_substance_no_composition(solve):
        rsys = ReactionSystem.from_string('\n'.join(['H2O -> H2O+ + e-(aq); 1e-8', 'e-(aq) + H2O+ -> H2O; 1e10']))
        odesys, extra = get_odesys(rsys)
        c0 = {'H2O': 0, 'H2O+': 2e-9, 'e-(aq)': 3e-9}
        if len(solve) > 0:
            from pyodesys.symbolic import PartiallySolvedSystem
            odesys = PartiallySolvedSystem(odesys, extra['linear_dependencies'](solve))
>       odesys = get_native(rsys, odesys, 'gsl')

/usr/local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

rsys = <chempy.reactionsystem.ReactionSystem object at 0x816468610>, odesys = <pyodesys.symbolic.PartiallySolvedSystem object at 0x8130a33d0>, integrator = 'gsl'
skip_keys = (0,), steady_state_root = False, conc_roots = None

    def get_native(rsys, odesys, integrator, skip_keys=(0,), steady_state_root=False, conc_roots=None):
        comp_keys = Substance.composition_keys(rsys.substances.values(), skip_keys=skip_keys)
        if PartiallySolvedSystem is None:
>           raise ValueError("Failed to import 'native_sys' from 'pyodesys.native'")
E           ValueError: Failed to import 'native_sys' from 'pyodesys.native'

/usr/local/lib/python2.7/site-packages/chempy/kinetics/_native.py:113: ValueError
========================================================================== short test summary info ==========================================================================
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:808: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [3] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:181: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:915: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [2] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:49: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [2] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:108: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/util/tests/test_graph.py:30: graphviz not installed? (dot command missing)
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:569: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/util/tests/test_table.py:58: latex not installed? (pdflatex command missing)
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:710: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:539: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/util/tests/test_graph.py:48: graphviz not installed? (dot command missing)
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:858: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:497: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:675: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:510: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:757: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test__native.py:156: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [1] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:949: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [4] ../../../../../local/lib/python2.7/site-packages/chempy/kinetics/tests/test_ode.py:475: Unfulfilled requirements. Missing modules: pycvodes.
SKIP [2] ../../../../../local/lib/python2.7/site-packages/chempy/util/tests/test_table.py:46: latex not installed? (pdflatex command missing)
============================================================================= warnings summary ==============================================================================
chempy/kinetics/tests/test_ode.py::test_get_ode__Radiolytic__units__multi
  /usr/local/lib/python2.7/site-packages/pyodesys/core.py:519: UserWarning: 'adaptive' mode with SciPy's integrator (vode/lsoda) may overshoot (itask=2)
    warnings.warn("'adaptive' mode with SciPy's integrator (vode/lsoda) may overshoot (itask=2)")
  /usr/local/lib/python2.7/site-packages/pyodesys/core.py:520: UserWarning: 'adaptive' mode with SciPy's integrator is unreliable, consider using e.g. cvode
    warnings.warn("'adaptive' mode with SciPy's integrator is unreliable, consider using e.g. cvode")

chempy/kinetics/tests/test_rates.py::test_RateExpr__subclass_from_callback
  /usr/local/lib/python2.7/site-packages/chempy/kinetics/tests/test_rates.py:52: ChemPyDeprecationWarning: subclass_from_callback is deprecated. Use from_callback instead.
    lambda v, a, backend: a[0]*v['H2']*v['Br2']**(3/2) / (v['Br2'] + a[1]*v['HBr'])

chempy/kinetics/tests/test_rates.py::test_MassAction__subclass_from_callback
  /usr/local/lib/python2.7/site-packages/chempy/kinetics/tests/test_rates.py:100: ChemPyDeprecationWarning: subclass_from_callback is deprecated. Use MassAction.from_callback instead.
    rate_coeff, cls_attrs=dict(parameter_keys=('temperature',), nargs=2))
  /usr/local/lib/python2.7/site-packages/chempy/kinetics/rates.py:180: ChemPyDeprecationWarning: subclass_from_callback is deprecated. Use from_callback instead.
    _RateExpr = super(MassAction, cls).subclass_from_callback(cb, cls_attrs=cls_attrs)

chempy/tests/test__equilibrium.py::test_solve_equilibrium_1
  /usr/local/lib/python2.7/site-packages/chempy/chemistry.py:859: RuntimeWarning: divide by zero encountered in double_scalars
    tot *= conc**nr

chempy/tests/test_henry.py::test_Henry__with_units
  /usr/local/lib/python2.7/site-packages/chempy/tests/test_henry.py:23: ChemPyDeprecationWarning: get_kH_at_T is deprecated since (not including) 0.3.1, it will be missing in 0.5.0. Use __call__ instead.
    assert allclose(kH_H2.get_kH_at_T(

chempy/tests/test_reactionsystem.py::test_ReactionSystem__html_tables
  /usr/local/lib/python2.7/site-packages/chempy/tests/test_reactionsystem.py:101: ChemPyDeprecationWarning: unimolecular_html_table is deprecated since (not including) 0.5.7, it will be missing in 0.8.0. Use chempy.printing.tables.UnimolecularTable instead.
    ut, unc = rs.unimolecular_html_table()
  /usr/local/lib/python2.7/site-packages/chempy/tests/test_reactionsystem.py:106: ChemPyDeprecationWarning: bimolecular_html_table is deprecated since (not including) 0.5.7, it will be missing in 0.8.0. Use chempy.printing.tables.BimolecularTable instead.
    bt, bnc = rs.bimolecular_html_table()

chempy/util/tests/test_expr.py::test_mk_Poly
  /usr/local/lib/python2.7/site-packages/chempy/util/tests/test_expr.py:165: ChemPyDeprecationWarning: _mk_Poly is deprecated. Use create_Poly instead.
    Poly = mk_Poly('T', reciprocal=True)

chempy/util/tests/test_expr.py::test_PiecewisePoly
  /usr/local/lib/python2.7/site-packages/chempy/util/tests/test_expr.py:208: ChemPyDeprecationWarning: _mk_PiecewisePoly is deprecated. Use create_Piecewise instead.
    TPiecewisePoly = mk_PiecewisePoly('temperature')

chempy/util/tests/test_parsing.py::test_formula_to_composition
  /usr/local/lib/python2.7/site-packages/chempy/util/tests/test_parsing.py:16: ChemPyDeprecationWarning: / depr. (before 0.5.0): use 'Fe+3' over 'Fe/3+'
    assert formula_to_composition('Fe/3+') == {0: 3, 26: 1}
  /usr/local/lib/python2.7/site-packages/chempy/util/tests/test_parsing.py:16: ChemPyDeprecationWarning: 'Fe/3+' deprecated, use e.g. 'Fe+3'
    assert formula_to_composition('Fe/3+') == {0: 3, 26: 1}

chempy/util/tests/test_parsing.py::test_formula_to_latex
  /usr/local/lib/python2.7/site-packages/chempy/util/parsing.py:435: ChemPyDeprecationWarning: / depr. (before 0.5.0): use 'Fe+3' over 'Fe/3+'
    formula, prefixes, infixes, **kwargs)
  /usr/local/lib/python2.7/site-packages/chempy/util/parsing.py:435: ChemPyDeprecationWarning: 'Fe/3+' deprecated, use e.g. 'Fe+3'
    formula, prefixes, infixes, **kwargs)

chempy/util/tests/test_periodic.py::test_mass_from_composition__formula
  /usr/local/lib/python2.7/site-packages/chempy/util/tests/test_periodic.py:44: ChemPyDeprecationWarning: / depr. (before 0.5.0): use 'Fe+3' over 'Fe/3+'
    Fminus = mass_from_composition(formula_to_composition('F/-'))

-- Docs: http://doc.pytest.org/en/latest/warnings.html
====================================================== 2 failed, 274 passed, 28 skipped, 16 warnings in 11.71 seconds =======================================================
*** Error code 1
@bjodah
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bjodah commented Sep 21, 2018 •
edited

Is pygslodeiv2 properly installed? (i.e. are tests passing for pytest --pyargs pygslodeiv2?)
Edit: and are tests passing for pytest --pyargs pyodesys?

@yurivict
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The example from their page works, but tests (pytest) fail in a similar way.
I will report this to them,

@yurivict
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Tests still fail in 0.7.4.

@bjodah
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bjodah commented Oct 19, 2018

still because of this?:
bjodah/pygslodeiv2#36

that one looked like a packaging issue to me (see last comment)

@yurivict
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The package pygslodeiv2 is installed and can be imported, yet the tests fail.
I can't tell what is the problem.

This statement

from pygslodeiv2 import (
    integrate_adaptive, integrate_predefined, requires_jac
)

succeeds when run by itself.

@bjodah
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bjodah commented Oct 19, 2018

does python -m pytest --pyargs pygslodeiv2 pass in that environment?

@yurivict
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does python -m pytest --pyargs pygslodeiv2 pass in that environment?

No, it fails the same way.

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