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loriab / pylibefp

python wrapper to I. Kaliman's libefp for effective fragment potentials
BSD 3-Clause "New" or "Revised" License
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Tests fail: LIBEFP: cannot find "h2o" in any of .efp files #7

Open yurivict opened 6 years ago

yurivict commented 6 years ago

libefp-1.5.0 has the file /usr/local/share/libefp/fraglib/h2o.efp installed. FRAGLIB_DEEP=OFF in libefp. libefp says: option_with_print(FRAGLIB_DEEP "Installed fragment libary has hierarchical, not flat, filestructure. Psi4 wants OFF" ON)

============================================================================ test session starts ============================================================================
platform freebsd11 -- Python 2.7.15, pytest-3.6.4, py-1.6.0, pluggy-0.6.0 -- /usr/local/bin/python2.7
cachedir: ../../.pytest_cache
hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/usr/ports/science/py-pylibefp/work-py27/.build/tests/.hypothesis/examples')
rootdir: /usr/ports/science/py-pylibefp/work-py27, inifile:
plugins: hypothesis-3.71.10
collected 61 items                                                                                                                                                          

../../pylibefp-0.4/tests/test_coverage.py::test_grad_fail LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                      [  1%]
../../pylibefp-0.4/tests/test_coverage.py::test_frag_missing_fail LIBEFP: cannot find "h2o" in any of .efp files
PASSED                                                                                              [  3%]
../../pylibefp-0.4/tests/test_coverage.py::test_multifrag_fail LIBEFP: parameters for fragment "NH3_L" are already loaded
PASSED                                                                                                 [  4%]
../../pylibefp-0.4/tests/test_coverage.py::test_multifrag_pass LIBEFP: parameters for fragment "NH3_L" are already loaded
LIBEFP: cannot find "nh3" in any of .efp files
FAILED                                                                                                 [  6%]
../../pylibefp-0.4/tests/test_coverage.py::test_frag_fail_1 LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                    [  8%]
../../pylibefp-0.4/tests/test_coverage.py::test_frag_fail_2 LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                    [  9%]
../../pylibefp-0.4/tests/test_dict.py::test_dict_1 LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                             [ 11%]
../../pylibefp-0.4/tests/test_dict.py::test_dict_2a LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                            [ 13%]
../../pylibefp-0.4/tests/test_dict.py::test_dict_3a LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                            [ 14%]
../../pylibefp-0.4/tests/test_dict.py::test_dict_4a LIBEFP: cannot find "acetone" in any of .efp files
FAILED                                                                                                            [ 16%]
../../pylibefp-0.4/tests/test_dict.py::test_dict_5 PASSED                                                                                                             [ 18%]
../../pylibefp-0.4/tests/test_efpefp.py::test_elec_1a LIBEFP: cannot find "h2o" in any of .efp files
FAILED                                                                                                          [ 19%]
../../pylibefp-0.4/tests/test_efpefp.py::test_elec_1b LIBEFP: cannot find "h2o" in any of .efp files
^C

================================================================================= FAILURES ==================================================================================
______________________________________________________________________________ test_grad_fail _______________________________________________________________________________

    def test_grad_fail():
>       asdf = system_1()

../../pylibefp-0.4/tests/test_coverage.py:9: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:13: in system_1
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'h2o'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: h2o

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment h2o read from /usr/local/share/libefp/fraglib/h2o.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
____________________________________________________________________________ test_multifrag_pass ____________________________________________________________________________

    def test_multifrag_pass():
        asdf = pylibefp.core.efp()

        asdf.add_potential(['nh3', 'nh3'])
        asdf.add_potential('nh3', duplicates_ok=True)
>       asdf.add_fragment(['nh3'] * 5)

../../pylibefp-0.4/tests/test_coverage.py:44: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'nh3'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: nh3

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
_____________________________________________________________________________ test_frag_fail_1 ______________________________________________________________________________

    def test_frag_fail_1():
>       asdf = system_1()

../../pylibefp-0.4/tests/test_coverage.py:49: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:13: in system_1
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'h2o'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: h2o

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment h2o read from /usr/local/share/libefp/fraglib/h2o.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
_____________________________________________________________________________ test_frag_fail_2 ______________________________________________________________________________

    def test_frag_fail_2():
>       asdf = system_1()

../../pylibefp-0.4/tests/test_coverage.py:55: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:13: in system_1
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'h2o'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: h2o

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment h2o read from /usr/local/share/libefp/fraglib/h2o.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
________________________________________________________________________________ test_dict_1 ________________________________________________________________________________

    def test_dict_1():
>       sys1 = system_1()

../../pylibefp-0.4/tests/test_dict.py:9: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:13: in system_1
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'h2o'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: h2o

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment h2o read from /usr/local/share/libefp/fraglib/h2o.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
_______________________________________________________________________________ test_dict_2a ________________________________________________________________________________

    def test_dict_2a():
>       sys1 = system_2()

../../pylibefp-0.4/tests/test_dict.py:33: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:26: in system_2
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

res = efp_result.EFP_RESULT_UNKNOWN_FRAGMENT, msg = 'h2o'

    def _result_to_error(res, msg=''):

        if res == core.efp_result.EFP_RESULT_SUCCESS:
            return
        elif res == core.efp_result.EFP_RESULT_FATAL:
            raise Fatal(msg)
        elif res == core.efp_result.EFP_RESULT_NO_MEMORY:
            raise NoMemory(msg)
        elif res == core.efp_result.EFP_RESULT_FILE_NOT_FOUND:
            raise FileNotFound(msg)
        elif res == core.efp_result.EFP_RESULT_SYNTAX_ERROR:
            raise EFPSyntaxError(msg)
        elif res == core.efp_result.EFP_RESULT_UNKNOWN_FRAGMENT:
>           raise UnknownFragment(msg)
E           UnknownFragment: h2o

../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:69: UnknownFragment
--------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------
  EFP fragment h2o read from /usr/local/share/libefp/fraglib/h2o.efp
  EFP fragment nh3 read from /usr/local/share/libefp/fraglib/nh3.efp
_______________________________________________________________________________ test_dict_3a ________________________________________________________________________________

    def test_dict_3a():
>       sys1 = system_3()

../../pylibefp-0.4/tests/test_dict.py:45: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../pylibefp-0.4/tests/systems.py:42: in system_3
    sys.add_fragment(frags)
../stage/usr/local/lib/python2.7/site-packages/pylibefp/wrapper/wrapper.py:188: in add_fragment
    _result_to_error(res, frag)
loriab commented 6 years ago

Curious. Is libefp an independent package and detected as pre-built through -Dlibefp_DIR or are you building it in the course of the pylibefp superbuild?

Btw, I just killed off python 2.7 (though not in the last tagged version). Hereafter, 3.5+

yurivict commented 6 years ago

libefp is a separate package. I didn't use -Dlibefp_DIR because it is in the standard directory /usr/local.

Btw, I just killed off python 2.7

We have a lot of python versions, of which 2.7 is the oldest. Python bindings need to be separate packages because multiple versions of python can be installed. I don't have any nostalgic feelings about python-2.7, but some people have such about Qt4, curiously.