Failure in two diomira tests. #299

Aretno · 2017-08-23T17:07:31Z

I updated today to the current status of nextic/master and now two diomira tests are failing (in addition to the blr one mentioned in #263). Using python 3.6. I tried to do a clean also just to make sure nothing was messing with it.

_____________________________________________________________________________________ test_command_line_run[diomira] _____________________________________________________________________________________

city = 'diomira', tmpdir_factory = <_pytest.tmpdir.TempdirFactory object at 0x1055f7358>

    @mark.slow
    # @mark.parametrize('city',
    #                   'diomira isidora irene dorothea zaira penthesilea'.split())
    # TODO understand what's wrong with isidora (in Travis)
    @mark.parametrize('city',
                      'diomira irene dorothea zaira penthesilea'.split())
    
    def test_command_line_run(city, tmpdir_factory):
        ICTDIR = getenv('ICTDIR')
        # Use the example config file included in the repository
        config_file_name = join(ICTDIR, 'invisible_cities/config', city+'.conf')
        # Ensure that output does not pollute: send it to a temporary dir
        temp_dir = tmpdir_factory.mktemp('output_files')
        out_file_name = join(temp_dir, city+'.out')
        # The actual command that we want to test
        command = ('city {city} {config_file_name} -o {out_file_name}'
                   .format(**locals()))
        try:
>           check_output(command, shell = True, stderr=STDOUT)

invisible_cities/cities/command_line_execution_test.py:28: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../../../anaconda/envs/IC3.6/lib/python3.6/subprocess.py:336: in check_output
    **kwargs).stdout
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input = None, timeout = None, check = True
popenargs = ('city diomira /Users/ansimez/Documents/InvCit/IC/invisible_cities/config/diomira.conf -o /private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/output_files0/diomira.out',)
kwargs = {'shell': True, 'stderr': -2, 'stdout': -1}, process = <subprocess.Popen object at 0x11327d128>
stdout = b'acum_discharge_length    = 5000     # deconvolution_city.conf\ncompression              = ZLIB4    # city.conf\nconf...imum(a, axis, None, out, keepdims)\nValueError: zero-size array to reduction operation minimum which has no identity\n'
stderr = None, retcode = 1

    def run(*popenargs, input=None, timeout=None, check=False, **kwargs):
        """Run command with arguments and return a CompletedProcess instance.
    
        The returned instance will have attributes args, returncode, stdout and
        stderr. By default, stdout and stderr are not captured, and those attributes
        will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them.
    
        If check is True and the exit code was non-zero, it raises a
        CalledProcessError. The CalledProcessError object will have the return code
        in the returncode attribute, and output & stderr attributes if those streams
        were captured.
    
        If timeout is given, and the process takes too long, a TimeoutExpired
        exception will be raised.
    
        There is an optional argument "input", allowing you to
        pass a string to the subprocess's stdin.  If you use this argument
        you may not also use the Popen constructor's "stdin" argument, as
        it will be used internally.
    
        The other arguments are the same as for the Popen constructor.
    
        If universal_newlines=True is passed, the "input" argument must be a
        string and stdout/stderr in the returned object will be strings rather than
        bytes.
        """
        if input is not None:
            if 'stdin' in kwargs:
                raise ValueError('stdin and input arguments may not both be used.')
            kwargs['stdin'] = PIPE
    
        with Popen(*popenargs, **kwargs) as process:
            try:
                stdout, stderr = process.communicate(input, timeout=timeout)
            except TimeoutExpired:
                process.kill()
                stdout, stderr = process.communicate()
                raise TimeoutExpired(process.args, timeout, output=stdout,
                                     stderr=stderr)
            except:
                process.kill()
                process.wait()
                raise
            retcode = process.poll()
            if check and retcode:
                raise CalledProcessError(retcode, process.args,
>                                        output=stdout, stderr=stderr)
E               subprocess.CalledProcessError: Command 'city diomira /Users/ansimez/Documents/InvCit/IC/invisible_cities/config/diomira.conf -o /private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/output_files0/diomira.out' returned non-zero exit status 1.

../../../anaconda/envs/IC3.6/lib/python3.6/subprocess.py:418: CalledProcessError
------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------
acum_discharge_length    = 5000     # deconvolution_city.conf
compression              = ZLIB4    # city.conf
config_file              = /Users/ansimez/Documents/InvCit/IC/invisible_cities/config/diomira.conf # <command line>
#          data_mc_ratio = 0.8      # trigger_emulation_city.conf  OVERRIDDEN
data_mc_ratio            = 0.8      # diomira.conf
#               file_out = /tmp/electrons_40keV_z250_PMP.h5 # city.conf  OVERRIDDEN
file_out                 = /private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/output_files0/diomira.out # diomira.conf
#               files_in = $ICDIR/database/test_data/electrons_40keV_z250_RWF.h5 # city.conf  OVERRIDDEN
files_in                 = $ICDIR/database/test_data/electrons_40keV_z250_MCRD.h5 # diomira.conf
#             max_charge = 500000   # trigger_emulation_city.conf  OVERRIDDEN
max_charge               = 50000    # diomira.conf
#             max_height = 2000     # trigger_emulation_city.conf  OVERRIDDEN
max_height               = 500      # diomira.conf
#              max_width = 500000.0 # trigger_emulation_city.conf  OVERRIDDEN
max_width                = 40000.0  # diomira.conf
#             min_charge = 1000     # trigger_emulation_city.conf  OVERRIDDEN
min_charge               = 5000     # diomira.conf
#             min_height = 10       # trigger_emulation_city.conf  OVERRIDDEN
min_height               = 10       # diomira.conf
#    min_number_channels = 2        # trigger_emulation_city.conf  OVERRIDDEN
min_number_channels      = 2        # diomira.conf
#              min_width = 2000.0   # trigger_emulation_city.conf  OVERRIDDEN
min_width                = 2000.0   # diomira.conf
n_baseline               = 28000    # deconvolution_city.conf
n_mau                    = 100      # calibrated_city.conf
n_mau_sipm               = 100      # calibrated_city.conf
#                   nmax = 1        # city.conf  OVERRIDDEN
nmax                     = 2        # diomira.conf
nprint                   = 1        # city.conf
#          raw_data_type = RWF      # raw_city.conf  OVERRIDDEN
raw_data_type            = MCRD     # monte_carlo_city.conf
run_all                  = False    # city.conf
run_number               = 0        # city.conf
s1_lmax                  = 20       # pmap_city.conf
s1_lmin                  = 8        # pmap_city.conf
s1_rebin_stride          = 1        # pmap_city.conf
s1_stride                = 4        # pmap_city.conf
s1_tmax                  = 101000.0 # pmap_city.conf
s1_tmin                  = 99000.0  # pmap_city.conf
#                s2_lmax = 100000   # pmap_city.conf  OVERRIDDEN
s2_lmax                  = 100000   # diomira.conf
#                s2_lmin = 100      # pmap_city.conf  OVERRIDDEN
s2_lmin                  = 100      # diomira.conf
#        s2_rebin_stride = 40       # pmap_city.conf  OVERRIDDEN
s2_rebin_stride          = 1        # diomira.conf
#              s2_stride = 40       # pmap_city.conf  OVERRIDDEN
s2_stride                = 40       # diomira.conf
#                s2_tmax = 1199000.0 # pmap_city.conf  OVERRIDDEN
s2_tmax                  = 799000.0 # diomira.conf
#                s2_tmin = 101000.0 # pmap_city.conf  OVERRIDDEN
s2_tmin                  = 101000.0 # diomira.conf
sipm_noise_cut           = 1.0      # monte_carlo_city.conf
skip                     = 0        # city.conf
thr_csum_s1              = 0.5      # calibrated_city.conf
thr_csum_s2              = 1.0      # calibrated_city.conf
thr_mau                  = 3        # calibrated_city.conf
thr_sipm                 = 3.5      # calibrated_city.conf
thr_sipm_s2              = 10       # pmap_city.conf
thr_trigger              = 5        # deconvolution_city.conf
#            tr_channels = [0, 1]   # trigger_emulation_city.conf  OVERRIDDEN
tr_channels              = [0, 1]   # diomira.conf
#           trigger_type = S2       # trigger_emulation_city.conf  OVERRIDDEN
trigger_type             = S2       # diomira.conf
verbosity                = 0        # city.conf
1

                 Diomira will run a max of 2 events
                 Input Files = ['/Users/ansimez/Documents/InvCit/IC/invisible_cities//database/test_data/electrons_40keV_z250_MCRD.h5']
                 Output File = /private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/output_files0/diomira.out
                          
Opening /Users/ansimez/Documents/InvCit/IC/invisible_cities//database/test_data/electrons_40keV_z250_MCRD.h5... Traceback (most recent call last):
  File "/Users/ansimez/Documents/InvCit/IC/bin/city", line 19, in <module>
    city_class.drive(args)
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/base_cities.py", line 143, in drive
    instance.go()
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/base_cities.py", line 152, in go
    self.run()
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/base_cities.py", line 178, in run
    self.file_loop()
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/base_cities.py", line 367, in file_loop
    self.event_loop(NEVT, first_event_no, dataVectors)
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/diomira.py", line 107, in event_loop
    peak_data = self.emulate_trigger(RWF)
  File "/Users/ansimez/Documents/InvCit/IC/invisible_cities/cities/base_cities.py", line 824, in emulate_trigger
    s2 =  cpf.find_s2(CWF[pmt_id], wfm_index, **self.s2_params._asdict())
  File "invisible_cities/reco/peak_functions_c.pyx", line 236, in invisible_cities.reco.peak_functions_c.find_s2 (invisible_cities/reco/peak_functions_c.c:7708)
    cpdef find_s2(double [:] csum,  int [:] index,
  File "invisible_cities/reco/peak_functions_c.pyx", line 242, in invisible_cities.reco.peak_functions_c.find_s2 (invisible_cities/reco/peak_functions_c.c:7519)
    return S2(find_s12(csum, index, time, length, stride, rebin_stride))
  File "invisible_cities/reco/peak_functions_c.pyx", line 267, in invisible_cities.reco.peak_functions_c.find_s12 (invisible_cities/reco/peak_functions_c.c:7976)
    csum, find_peaks(index, time, length, stride=stride), rebin_stride=rebin_stride)
  File "invisible_cities/reco/peak_functions_c.pyx", line 193, in invisible_cities.reco.peak_functions_c.find_peaks (invisible_cities/reco/peak_functions_c.c:6149)
    i_i   = np.where(np.asarray(index) >= i_min)[0].min() # index in index corresponding to t.min
  File "/Users/ansimez/anaconda/envs/IC3.6/lib/python3.6/site-packages/numpy/core/_methods.py", line 29, in _amin
    return umr_minimum(a, axis, None, out, keepdims)
ValueError: zero-size array to reduction operation minimum which has no identity

____________________________________________________________________________________ test_diomira_copy_mc_and_offset _____________________________________________________________________________________

config_tmpdir = local('/private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/configure_tests0')

    @mark.slow
    def test_diomira_copy_mc_and_offset(config_tmpdir):
        PATH_IN = os.path.join(os.environ['ICDIR'], 'database/test_data/', 'electrons_40keV_z250_MCRD.h5')
        PATH_OUT = os.path.join(config_tmpdir,                             'electrons_40keV_z250_RWF.h5')
        # PATH_OUT = os.path.join(os.environ['IC_DATA'],                             'electrons_40keV_z250_test_RWF.h5')
    
        start_evt  = Diomira.event_number_from_input_file_name(PATH_IN)
        run_number = 0
        nrequired = 2
    
        conf = configure('diomira invisible_cities/config/diomira.conf'.split()).as_dict
    
        conf.update(dict(run_number = run_number,
                         files_in   = PATH_IN,
                         file_out   = PATH_OUT,
                         first_evt  = start_evt,
                         nmax       = nrequired))
    
        diomira = Diomira(**conf)
>       diomira.run()

invisible_cities/cities/diomira_test.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
invisible_cities/cities/base_cities.py:178: in run
    self.file_loop()
invisible_cities/cities/base_cities.py:367: in file_loop
    self.event_loop(NEVT, first_event_no, dataVectors)
invisible_cities/cities/diomira.py:107: in event_loop
    peak_data = self.emulate_trigger(RWF)
invisible_cities/cities/base_cities.py:824: in emulate_trigger
    s2 =  cpf.find_s2(CWF[pmt_id], wfm_index, **self.s2_params._asdict())
invisible_cities/reco/peak_functions_c.pyx:236: in invisible_cities.reco.peak_functions_c.find_s2 (invisible_cities/reco/peak_functions_c.c:7708)
    cpdef find_s2(double [:] csum,  int [:] index,
invisible_cities/reco/peak_functions_c.pyx:242: in invisible_cities.reco.peak_functions_c.find_s2 (invisible_cities/reco/peak_functions_c.c:7519)
    return S2(find_s12(csum, index, time, length, stride, rebin_stride))
invisible_cities/reco/peak_functions_c.pyx:267: in invisible_cities.reco.peak_functions_c.find_s12 (invisible_cities/reco/peak_functions_c.c:7976)
    csum, find_peaks(index, time, length, stride=stride), rebin_stride=rebin_stride)
invisible_cities/reco/peak_functions_c.pyx:193: in invisible_cities.reco.peak_functions_c.find_peaks (invisible_cities/reco/peak_functions_c.c:6149)
    i_i   = np.where(np.asarray(index) >= i_min)[0].min() # index in index corresponding to t.min
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

a = array([], dtype=int64), axis = None, out = None, keepdims = False

    def _amin(a, axis=None, out=None, keepdims=False):
>       return umr_minimum(a, axis, None, out, keepdims)
E       ValueError: zero-size array to reduction operation minimum which has no identity

../../../anaconda/envs/IC3.6/lib/python3.6/site-packages/numpy/core/_methods.py:29: ValueError
------------------------------------------------------------------------------------------ Captured stdout call ------------------------------------------------------------------------------------------
1

                 Diomira will run a max of 2 events
                 Input Files = ['/Users/ansimez/Documents/InvCit/IC/invisible_cities/database/test_data/electrons_40keV_z250_MCRD.h5']
                 Output File = /private/var/folders/2j/9g3ngw197b3fp5_yhn8lzt3h0000gp/T/pytest-of-ansimez/pytest-5/configure_tests0/electrons_40keV_z250_RWF.h5
                          
Opening /Users/ansimez/Documents/InvCit/IC/invisible_cities/database/test_data/electrons_40keV_z250_MCRD.h5...

The text was updated successfully, but these errors were encountered:

jjgomezcadenas · 2017-08-23T19:50:35Z

Have you compiled cython (source manage compile_and_run)

Aretno · 2017-08-24T06:24:00Z

Yes, I think after the clean the setup does the compile automatically. I tried to do it again, this was the output (mostly deprecated numpy API warnings and two warnings on pmaps_functions_c which shouldn't affect Diomira, if I'm not mistaken)


building 'invisible_cities.core.core_functions_c' extension
creating build/temp.macosx-10.6-x86_64-3.5
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities/core
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/core/core_functions_c.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/core/core_functions_c.o
In file included from invisible_cities/core/core_functions_c.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
creating build/lib.macosx-10.6-x86_64-3.5
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities/core
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/core/core_functions_c.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/core/core_functions_c.cpython-35m-darwin.so
building 'invisible_cities.core.system_of_units_c' extension
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/core/system_of_units_c.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/core/system_of_units_c.o
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/core/system_of_units_c.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/core/system_of_units_c.cpython-35m-darwin.so
building 'invisible_cities.evm.pmaps' extension
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities/evm
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/evm/pmaps.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/evm/pmaps.o
In file included from invisible_cities/evm/pmaps.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities/evm
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/evm/pmaps.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/evm/pmaps.cpython-35m-darwin.so
building 'invisible_cities.reco.peak_functions_c' extension
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities/reco
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/reco/peak_functions_c.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/reco/peak_functions_c.o
In file included from invisible_cities/reco/peak_functions_c.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities/reco
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/reco/peak_functions_c.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/reco/peak_functions_c.cpython-35m-darwin.so
building 'invisible_cities.reco.pmaps_functions_c' extension
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/reco/pmaps_functions_c.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/reco/pmaps_functions_c.o
In file included from invisible_cities/reco/pmaps_functions_c.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
invisible_cities/reco/pmaps_functions_c.c:23092:17: warning: code will never be executed [-Wunreachable-code]
        value = __Pyx_PyObject_CallMethod2(d, __pyx_n_s_setdefault, key, default_value);
                ^~~~~~~~~~~~~~~~~~~~~~~~~~
invisible_cities/reco/pmaps_functions_c.c:23063:9: note: silence by adding parentheses to mark code as explicitly dead
    if (1) {
        ^
        /* DISABLES CODE */ ( )
2 warnings generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/reco/pmaps_functions_c.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/reco/pmaps_functions_c.cpython-35m-darwin.so
building 'invisible_cities.sierpe.blr' extension
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities/sierpe
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/sierpe/blr.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/blr.o
In file included from invisible_cities/sierpe/blr.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities/sierpe
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/blr.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/blr.cpython-35m-darwin.so
building 'invisible_cities.sierpe.cblr' extension
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/sierpe/cblr.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/cblr.o
In file included from invisible_cities/sierpe/cblr.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/cblr.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/cblr.cpython-35m-darwin.so
building 'invisible_cities.types.ic_types_c' extension
creating build/temp.macosx-10.6-x86_64-3.5/invisible_cities/types
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/ansimez/anaconda/include -arch x86_64 -I/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include -I/Users/ansimez/anaconda/include/python3.5m -I/Users/ansimez/anaconda/include/python3.5m -c invisible_cities/types/ic_types_c.c -o build/temp.macosx-10.6-x86_64-3.5/invisible_cities/types/ic_types_c.o
In file included from invisible_cities/types/ic_types_c.c:444:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1788:
/Users/ansimez/anaconda/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by "
      "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
 ^
1 warning generated.
creating build/lib.macosx-10.6-x86_64-3.5/invisible_cities/types
/usr/bin/clang -bundle -undefined dynamic_lookup -L/Users/ansimez/anaconda/lib -arch x86_64 build/temp.macosx-10.6-x86_64-3.5/invisible_cities/types/ic_types_c.o -L/Users/ansimez/anaconda/lib -o build/lib.macosx-10.6-x86_64-3.5/invisible_cities/types/ic_types_c.cpython-35m-darwin.so
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/core/core_functions_c.cpython-35m-darwin.so -> invisible_cities/core
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/core/system_of_units_c.cpython-35m-darwin.so -> invisible_cities/core
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/evm/pmaps.cpython-35m-darwin.so -> invisible_cities/evm
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/reco/peak_functions_c.cpython-35m-darwin.so -> invisible_cities/reco
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/reco/pmaps_functions_c.cpython-35m-darwin.so -> invisible_cities/reco
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/blr.cpython-35m-darwin.so -> invisible_cities/sierpe
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/sierpe/cblr.cpython-35m-darwin.so -> invisible_cities/sierpe
copying build/lib.macosx-10.6-x86_64-3.5/invisible_cities/types/ic_types_c.cpython-35m-darwin.so -> invisible_cities/types
Creating /Users/ansimez/anaconda/lib/python3.5/site-packages/invisible-cities.egg-link (link to .)
Adding invisible-cities IC-Kr-prod-March-659-gf2ef764- to easy-install.pth file

Installed /Users/ansimez/Documents/InvCit/IC

jjgomezcadenas · 2017-08-24T08:04:14Z

This is OK, cython just being chatty...

Aretno · 2017-08-24T09:30:09Z

I don't know if this is solved, on my last post I just copied the part of chatty cython but the test failure still happened afterwards. Sorry, I did not explain myself properly.

jmbenlloch · 2017-08-24T09:41:40Z

I think we have an issue with the versions of the dependencies we use. @Aretno can you execute conda env export on a shell where you have the IC env and copy here the output?

jjgomezcadenas · 2017-08-24T09:43:35Z

Now, this is strange, tests are not failing in any other machine that I know, including Travis. All the errors seem to be related with cython. Which version doyou have (cython --version)? which version of conda (conda --version)?

Aretno · 2017-08-24T09:48:24Z

@jmbenlloch

name: IC3.6
channels:
- conda-forge
- https://conda.anaconda.org/gijzelaerr
- https://conda.anaconda.org/mhworth
- defaults
dependencies:
- lmfit=0.9.7=py36_0
- alabaster=0.7.10=py36_0
- appnope=0.1.0=py36_0
- astropy=2.0=np113py36_0
- babel=2.4.0=py36_0
- bleach=1.5.0=py36_0
- cycler=0.10.0=py36_0
- cython=0.25.2=py36_0
- decorator=4.0.11=py36_0
- docutils=0.13.1=py36_0
- entrypoints=0.2.2=py36_1
- freetype=2.5.5=2
- hdf5=1.8.17=1
- html5lib=0.999=py36_0
- icu=54.1=0
- imagesize=0.7.1=py36_0
- ipykernel=4.6.1=py36_0
- ipython=6.1.0=py36_0
- ipython_genutils=0.2.0=py36_0
- ipywidgets=6.0.0=py36_0
- jedi=0.10.2=py36_2
- jinja2=2.9.6=py36_0
- jsonschema=2.6.0=py36_0
- jupyter=1.0.0=py36_3
- jupyter_client=5.0.1=py36_0
- jupyter_console=5.1.0=py36_0
- jupyter_core=4.3.0=py36_0
- libpng=1.6.27=0
- markupsafe=0.23=py36_2
- matplotlib=2.0.2=np113py36_0
- mistune=0.7.4=py36_0
- mkl=2017.0.1=0
- nbconvert=5.2.1=py36_0
- nbformat=4.3.0=py36_0
- networkx=1.11=py36_0
- notebook=5.0.0=py36_0
- numexpr=2.6.2=np113py36_0
- numpy=1.13.0=py36_0
- openssl=1.0.2l=0
- pandas=0.20.2=np113py36_0
- pandocfilters=1.4.1=py36_0
- path.py=10.3.1=py36_0
- pexpect=4.2.1=py36_0
- pickleshare=0.7.4=py36_0
- pip=9.0.1=py36_1
- prompt_toolkit=1.0.14=py36_0
- ptyprocess=0.5.1=py36_0
- py=1.4.34=py36_0
- pygments=2.2.0=py36_0
- pymysql=0.7.9=py36_0
- pyparsing=2.1.4=py36_0
- pyqt=5.6.0=py36_2
- pytables=3.3.0=np113py36_0
- pytest=3.1.1=py36_0
- python=3.6.1=2
- python-dateutil=2.6.0=py36_0
- pytz=2017.2=py36_0
- pyzmq=16.0.2=py36_0
- qt=5.6.2=2
- qtconsole=4.3.0=py36_0
- readline=6.2=2
- requests=2.14.2=py36_0
- scipy=0.19.0=np113py36_0
- setuptools=27.2.0=py36_0
- simplegeneric=0.8.1=py36_1
- sip=4.18=py36_0
- six=1.10.0=py36_0
- snowballstemmer=1.2.1=py36_0
- sphinx=1.6.2=py36_0
- sphinxcontrib=1.0=py36_0
- sphinxcontrib-websupport=1.0.1=py36_0
- sqlite=3.13.0=0
- terminado=0.6=py36_0
- testpath=0.3.1=py36_0
- tk=8.5.18=0
- tornado=4.5.1=py36_0
- traitlets=4.3.2=py36_0
- wcwidth=0.1.7=py36_0
- wheel=0.29.0=py36_0
- widgetsnbextension=2.0.0=py36_0
- xz=5.2.2=1
- zlib=1.2.8=3
- pip:
  - apipkg==1.4
  - execnet==1.4.1
  - flaky==3.3.0
  - hypothesis==3.11.3
  - 'invisible-cities (/Users/ansimez/Documents/InvCit/IC)==IC Kr prod March 659 gf2ef764 '
  - ipython-genutils==0.2.0
  - jupyter-client==5.0.1
  - jupyter-console==5.1.0
  - jupyter-core==4.3.0
  - prompt-toolkit==1.0.14
  - pytest-xdist==1.17.1
  - tables==3.3.0
prefix: /Users/ansimez/anaconda/envs/IC3.6

@jjgomezcadenas

Cython version 0.25.2
conda 4.3.22

jjgomezcadenas · 2017-08-24T10:01:13Z

My conda version is 4.3.21. Cython version is the same.

jacg · 2017-08-30T12:23:47Z

What is the status of this?

A completely fresh check out and install of IC and all its dependencies, from scratch, works fine here.

Aretno · 2017-09-01T11:22:48Z

I still have the same problems, I have tried to do a clean install of IC (but not of the dependancies that live in conda) and still having the same failures.

jacg · 2017-09-07T22:24:23Z

@jjgomezcadenas This is whole issue could have been avoided if #170 were ready; then we could write in the manual: "If tests fail mysteriously on your machine but not on Travis and elsewhere, then try

bash manage.sh update_all

Or words to that effect.

Without #170 we will periodically waste our time on this sort of stuff.

jjgomezcadenas closed this as completed Aug 24, 2017

jjgomezcadenas reopened this Aug 24, 2017

jacg mentioned this issue Sep 1, 2017

Failure in tests #263

Closed

jacg closed this as completed Sep 7, 2017

gonzaponte mentioned this issue Oct 3, 2017

Fix dependencies versions #349

Merged

jacg mentioned this issue Oct 3, 2017

Version control #353

Closed

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Failure in two diomira tests. #299

Failure in two diomira tests. #299

Aretno commented Aug 23, 2017

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jacg commented Sep 7, 2017

Failure in two diomira tests. #299

Failure in two diomira tests. #299

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