An error for nosetests isochrones #173
Comments
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I'm having a similar set of errors starting from scratch with python 3.10: `Ran 33 tests in 183.888s FAILED (errors=10, failures=2)` I had more errors just trying to add to an existing 3.8 environment, so followed the advice to create a custom isochrones environment. |
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Based on @timothydmorton's suggestion in another issue, I deleted my ~/.isochrones directory and tried again after installing multinest and pymultinest. (I have installed earlier versions in the past) This time there were just two failures: ======================================================================
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Hi,
When I run nosetests isochrones, those error is reported. Can you give me some suggestions?
Thanks!
(base) [linj@psr ~]$ nosetests isochrones
/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_fits.py:6: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
from pandas.util.testing import assert_frame_equal
/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py:97: DtypeWarning: Columns (17) have mixed types.Specify dtype option on import or set low_memory=False.
df = pd.concat([self.to_df(f) for f in self.get_filenames()])
/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/series.py:726: RuntimeWarning: divide by zero encountered in log10
result = getattr(ufunc, method)(*inputs, **kwargs)
EEE....E/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py:97: DtypeWarning: Columns (17) have mixed types.Specify dtype option on import or set low_memory=False.
df = pd.concat([self.to_df(f) for f in self.get_filenames()])
/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/series.py:726: RuntimeWarning: divide by zero encountered in log10
result = getattr(ufunc, method)(*inputs, **kwargs)
E.EEE/home/linj/anaconda3/lib/python3.9/site-packages/numpy/core/shape_base.py:65: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
ary = asanyarray(ary)
./home/linj/anaconda3/lib/python3.9/site-packages/numpy/core/shape_base.py:65: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
ary = asanyarray(ary)
...........E/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py:97: DtypeWarning: Columns (17) have mixed types.Specify dtype option on import or set low_memory=False.
df = pd.concat([self.to_df(f) for f in self.get_filenames()])
/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/series.py:726: RuntimeWarning: divide by zero encountered in log10
result = getattr(ufunc, method)(*inputs, **kwargs)
EEE....
ERROR: isochrones.tests.test_basic.test_mist_basic
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 14, in test_mist_basic
_basic_ic_checks(ic)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 92, in _basic_ic_checks
eep = ic.get_eep(1.0, age, feh, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
matplotlib: DEBUG: matplotlib data path: /home/linj/anaconda3/lib/python3.9/site-packages/matplotlib/mpl-data
matplotlib: DEBUG: CONFIGDIR=/home/linj/.config/matplotlib
matplotlib: DEBUG: interactive is False
matplotlib: DEBUG: platform is linux
matplotlib: DEBUG: loaded modules: [']
matplotlib: DEBUG: CACHEDIR=/home/linj/.cache/matplotlib
matplotlib.font_manager: DEBUG: Using fontManager instance from /home/linj/.cache/matplotlib/fontlist-v330.json
matplotlib.pyplot: DEBUG: Loaded backend qtagg version unknown.
matplotlib.pyplot: DEBUG: Loaded backend QtAgg version unknown.
h5py._conv: DEBUG: Creating converter from 7 to 5
h5py._conv: DEBUG: Creating converter from 5 to 7
h5py._conv: DEBUG: Creating converter from 7 to 5
h5py._conv: DEBUG: Creating converter from 5 to 7
numexpr.utils: INFO: Note: detected 72 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
numexpr.utils: INFO: Note: NumExpr detected 72 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
numexpr.utils: INFO: NumExpr defaulting to 8 threads.
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: isochrones.tests.test_basic.test_closest_eep
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 107, in read_hdf
df = pd.read_hdf(h5file, path)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/io/pytables.py", line 387, in read_hdf
raise FileNotFoundError(f"File {path_or_buf} does not exist")
FileNotFoundError: File /home/linj/.isochrones/mist/mist_v1.2_vvcrit0.4_full_isos.h5 does not exist
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 143, in na_arithmetic_op
result = expressions.evaluate(op, left, right)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 233, in evaluate
return _evaluate(op, op_str, a, b) # type: ignore
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 119, in _evaluate_numexpr
result = _evaluate_standard(op, op_str, a, b)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 68, in _evaluate_standard
return op(a, b)
TypeError: unsupported operand type(s) for -: 'str' and 'float'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 24, in test_closest_eep
_check_closest_eep(mist, n=n)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 65, in _check_closest_eep
eeps = [
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 66, in
ic.get_eep(m, a, f, return_nan=True, resid_tol=resid_tol, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
======================================================================
ERROR: isochrones.tests.test_basic.test_spec
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 29, in test_spec
_check_spec(mist)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_basic.py", line 124, in _check_spec
eep = ic.get_eep(1.0, 9.6, 0.1, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Building ObservationTree...
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Failure: ModuleNotFoundError (No module named 'flaky')
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/failure.py", line 39, in runTest
raise self.exc_val.with_traceback(self.tb)
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/loader.py", line 416, in loadTestsFromName
module = self.importer.importFromPath(
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/home/linj/anaconda3/lib/python3.9/imp.py", line 234, in load_module
return load_source(name, filename, file)
File "/home/linj/anaconda3/lib/python3.9/imp.py", line 171, in load_source
module = _load(spec)
File "", line 711, in _load
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_fits.py", line 7, in
from flaky import flaky
ModuleNotFoundError: No module named 'flaky'
======================================================================
ERROR: isochrones.tests.test_ini.test_ini
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_ini.py", line 14, in test_ini
_check_ini(MIST)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_ini.py", line 26, in _check_ini
SingleCheck().check(ic, os.path.join(FOLDER, d))
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_ini.py", line 70, in check
self.check_asserts(mod)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_ini.py", line 49, in check_asserts
eep_pars = mod.convert_pars_to_eep(self.pars)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/starmodel.py", line 447, in convert_pars_to_eep
eeps = {s: self.ic.get_eep(*p[0:3], accurate=True) for s, p in pardict.items()}
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/starmodel.py", line 447, in
eeps = {s: self.ic.get_eep(*p[0:3], accurate=True) for s, p in pardict.items()}
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured stdout << ---------------------
checking /home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/star1
root
╚═ WISE W1=(12.00, 0.05) @(0.00, 0 [4.00])
╚═ WISE W2=(11.50, 0.05) @(0.00, 0 [4.00])
╚═ twomass H=(12.85, 0.02) @(0.00, 0 [4.00])
╚═ twomass J=(13.51, 0.02) @(0.00, 0 [4.00])
╚═ twomass K=(12.69, 0.02) @(0.00, 0 [4.00])
╚═ 0_0, Teff=[4135.0, 98.0], feh=[-0.46, 0.16], logg=[4.711, 0.1]
--------------------- >> end captured stdout << ----------------------
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Initializing StarModel from /home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/star1/star.ini
isochrones: DEBUG: Obs is root
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: isochrones.tests.test_likelihood.test_compare_starmodels
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_likelihood.py", line 23, in test_compare_starmodels
assert np.isclose(m1.lnlike(pars), m2.lnlike(pars))
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/starmodel.py", line 549, in lnlike
Teff, logg, feh, mags = self.ic.interp_mag(pars, self.bands)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 436, in interp_mag
self.model_grid.interp.grid,
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Building ObservationTree...
isochrones: DEBUG: Adding (3.58, 0.05) @(0.0, 0.0) (-J)
isochrones: DEBUG: Adding (3.22, 0.05) @(0.0, 0.0) (-K)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: isochrones.tests.test_likelihood.test_compare_spec
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_likelihood.py", line 53, in test_compare_spec
test_compare_starmodels(props_spec)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_likelihood.py", line 23, in test_compare_starmodels
assert np.isclose(m1.lnlike(pars), m2.lnlike(pars))
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/starmodel.py", line 549, in lnlike
Teff, logg, feh, mags = self.ic.interp_mag(pars, self.bands)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 436, in interp_mag
self.model_grid.interp.grid,
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Building ObservationTree...
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: isochrones.tests.test_likelihood.test_compare_phot
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_likelihood.py", line 57, in test_compare_phot
test_compare_starmodels(props_phot)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_likelihood.py", line 23, in test_compare_starmodels
assert np.isclose(m1.lnlike(pars), m2.lnlike(pars))
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/starmodel.py", line 549, in lnlike
Teff, logg, feh, mags = self.ic.interp_mag(pars, self.bands)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 436, in interp_mag
self.model_grid.interp.grid,
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Building ObservationTree...
isochrones: DEBUG: Adding (3.58, 0.05) @(0.0, 0.0) (-J)
isochrones: DEBUG: Adding (3.22, 0.05) @(0.0, 0.0) (-K)
--------------------- >> end captured logging << ---------------------
======================================================================
ERROR: Testing with first entry from Gaia DR1 TGAS table
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/numpy/ma/core.py", line 3187, in view
output = ndarray.view(self, dtype)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 692, in array_finalize
super().array_finalize(obj)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/units/quantity.py", line 549, in array_finalize
self._set_unit(unit)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 160, in _set_unit
super()._set_unit(self._convert_unit_to_angle_unit(unit))
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/units/quantity.py", line 1931, in _set_unit
raise UnitTypeError(
astropy.units.core.UnitTypeError: Longitude instances require units equivalent to 'rad', so cannot set it to ''.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/test_query.py", line 38, in test_queries
assert tm.get_id() == b("03000819+0014074") # force byte literal b/c that's what gets returned
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/query/catalog.py", line 73, in get_id
row = self.closest
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/query/catalog.py", line 60, in closest
df = self.df.sort_values(by=self._distance_column)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/query/catalog.py", line 52, in df
df = self.table.to_pandas()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/query/catalog.py", line 46, in table
self._run_query()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/query/vizier.py", line 26, in _run_query
self._coords = SkyCoord(self._table["_RAJ2000"], self._table["_DEJ2000"], unit="deg")
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/sky_coordinate.py", line 331, in init
skycoord_kwargs, components, info = _parse_coordinate_data(
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/sky_coordinate_parsers.py", line 296, in _parse_coordinate_data
_components[frame_attr_name] = attr_class(arg, unit=unit)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 669, in new
self = super().new(cls, angle, unit=unit, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 138, in new
return super().new(cls, angle, unit, dtype=dtype, copy=copy,
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/units/quantity.py", line 524, in new
value = value.view(cls)
File "/home/linj/anaconda3/lib/python3.9/site-packages/numpy/ma/core.py", line 3192, in view
output = ndarray.view(self, dtype)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 692, in array_finalize
super().array_finalize(obj)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/units/quantity.py", line 549, in array_finalize
self._set_unit(unit)
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/coordinates/angles.py", line 160, in _set_unit
super()._set_unit(self._convert_unit_to_angle_unit(unit))
File "/home/linj/anaconda3/lib/python3.9/site-packages/astropy/units/quantity.py", line 1931, in _set_unit
raise UnitTypeError(
astropy.units.core.UnitTypeError: Longitude instances require units equivalent to 'rad', so cannot set it to ''.
======================================================================
ERROR: isochrones.tests.tests.test_mist_basic
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 107, in read_hdf
df = pd.read_hdf(h5file, path)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/io/pytables.py", line 387, in read_hdf
raise FileNotFoundError(f"File {path_or_buf} does not exist")
FileNotFoundError: File /home/linj/.isochrones/mist/mist_v1.2_vvcrit0.4_full_isos.h5 does not exist
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 143, in na_arithmetic_op
result = expressions.evaluate(op, left, right)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 233, in evaluate
return _evaluate(op, op_str, a, b) # type: ignore
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 119, in _evaluate_numexpr
result = _evaluate_standard(op, op_str, a, b)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 68, in _evaluate_standard
return op(a, b)
TypeError: unsupported operand type(s) for -: 'str' and 'float'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 14, in test_mist_basic
_basic_ic_checks(ic)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 92, in _basic_ic_checks
eep = ic.get_eep(1.0, age, feh, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
======================================================================
ERROR: isochrones.tests.tests.test_closest_eep
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 107, in read_hdf
df = pd.read_hdf(h5file, path)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/io/pytables.py", line 387, in read_hdf
raise FileNotFoundError(f"File {path_or_buf} does not exist")
FileNotFoundError: File /home/linj/.isochrones/mist/mist_v1.2_vvcrit0.4_full_isos.h5 does not exist
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 143, in na_arithmetic_op
result = expressions.evaluate(op, left, right)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 233, in evaluate
return _evaluate(op, op_str, a, b) # type: ignore
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 119, in _evaluate_numexpr
result = _evaluate_standard(op, op_str, a, b)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/computation/expressions.py", line 68, in _evaluate_standard
return op(a, b)
TypeError: unsupported operand type(s) for -: 'str' and 'float'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 24, in test_closest_eep
_check_closest_eep(mist, n=n)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 65, in _check_closest_eep
eeps = [
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 66, in
ic.get_eep(m, a, f, return_nan=True, resid_tol=resid_tol, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
======================================================================
ERROR: isochrones.tests.tests.test_spec
Traceback (most recent call last):
File "/home/linj/anaconda3/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 29, in test_spec
_check_spec(mist)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/tests/tests.py", line 124, in _check_spec
eep = ic.get_eep(1.0, 9.6, 0.1, accurate=True)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 509, in get_eep
return self.get_eep_accurate(mass, age, feh, **kwargs)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 558, in get_eep_accurate
while np.isnan(self.mass_age_resid(eep0, mass, age, feh)):
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 712, in mass_age_resid
mass_interp = self.interp_value([eep, age, feh], ["initial_mass"])
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 400, in interp_value
return self.model_grid.interp(pars, props)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 136, in interp
self._interp = DFInterpolator(self.df, filename=filename, is_full=self.is_full)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 158, in df
self._df = self.read_hdf()
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 109, in read_hdf
df = self.write_hdf(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/grid.py", line 113, in write_hdf
df = self.get_df(orig=orig)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/models.py", line 117, in get_df
df = self.compute_additional_columns(df)
File "/home/linj/anaconda3/lib/python3.9/site-packages/isochrones/mist/models.py", line 84, in compute_additional_columns
df["feh"] = df["log_surf_z"] - np.log10(df["surface_h1"]) - np.log10(0.0181) # Aaron Dotter says
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/common.py", line 65, in new_method
return method(self, other)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/init.py", line 343, in wrapper
result = arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 190, in arithmetic_op
res_values = na_arithmetic_op(lvalues, rvalues, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 150, in na_arithmetic_op
result = masked_arith_op(left, right, op)
File "/home/linj/anaconda3/lib/python3.9/site-packages/pandas/core/ops/array_ops.py", line 92, in masked_arith_op
result[mask] = op(xrav[mask], yrav[mask])
TypeError: unsupported operand type(s) for -: 'str' and 'float'
-------------------- >> begin captured logging << --------------------
isochrones: DEBUG: Building ObservationTree...
--------------------- >> end captured logging << ---------------------
Ran 33 tests in 223.684s
FAILED (errors=12)
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