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Commit 89ab18fb authored by David Hendriks's avatar David Hendriks
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updated hmc and author page

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badges/test_coverage.svg
+ 2
− 2
View file @ 89ab18fb
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
<g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11"> <g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
<text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text> <text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
<text x="31.5" y="14">coverage</text> <text x="31.5" y="14">coverage</text>
<text x="80" y="15" fill="#010101" fill-opacity=".3">66%</text> <text x="80" y="15" fill="#010101" fill-opacity=".3">67%</text>
<text x="80" y="14">66%</text> <text x="80" y="14">67%</text>
</g> </g>
</svg> </svg>
binarycpython/tests/test_custom_logging.py
+ 6
− 4
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...@@ -65,20 +65,21 @@ class test_binary_c_log_code(unittest.TestCase): ...@@ -65,20 +65,21 @@ class test_binary_c_log_code(unittest.TestCase):
def test_binary_c_log_code(self): def test_binary_c_log_code(self):
with Capturing() as _: with Capturing() as _:
self._test_binary_c_log_code() self._test_binary_c_log_code()
# print("\n".join(output))
def _test_binary_c_log_code(self): def _test_binary_c_log_code(self):
""" """
Test to see if passing a print statement to the function results in correct binary_c output Test to see if passing a print statement to the function results in correct binary_c output
""" """
# binary_c should not compile anything here
input_1 = "None" input_1 = "None"
output_1 = binary_c_log_code(input_1, verbosity=1) output_1 = binary_c_log_code(input_1, verbosity=1)
self.assertEqual(output_1, None, msg="Output should be None") self.assertEqual(output_1, None, msg="Output should be None")
#
input_2 = 'Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));' input_2 = 'Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));'
output_2 = binary_c_log_code(input_2, verbosity=1) output_2 = binary_c_log_code(input_2, verbosity=1)
test_value_2 = '#pragma push_macro("Max")\n#pragma push_macro("Min")\n#undef Max\n#undef Min\n#include "binary_c.h"\n\n// add visibility __attribute__ ((visibility ("default"))) to it \nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata);\nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata)\n{\n // struct stardata_t * stardata = (struct stardata_t *)x;\n Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));;\n}\n\n#undef Max \n#undef Min\n#pragma pop_macro("Min")\n#pragma pop_macro("Max") ' test_value_2 = '#pragma push_macro("Max")\n#pragma push_macro("Min")\n#undef Max\n#undef Min\n#include "binary_c.h"\n\n// add visibility __attribute__ ((visibility ("default"))) to it\nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata);\nvoid binary_c_API_function custom_output_function(struct stardata_t * stardata)\n{\n // struct stardata_t * stardata = (struct stardata_t *)x;\n Printf("MY_STELLAR_DATA %g %g %g %g\\n",((double)stardata->model.time),((double)stardata->star[0].mass),((double)stardata->model.probability),((double)stardata->model.dt));;\n}\n\n#undef Max\n#undef Min\n#pragma pop_macro("Min")\n#pragma pop_macro("Max") '
self.assertEqual( self.assertEqual(
output_2, output_2,
...@@ -153,7 +154,7 @@ class test_from_binary_c_config(unittest.TestCase): ...@@ -153,7 +154,7 @@ class test_from_binary_c_config(unittest.TestCase):
output_2 = from_binary_c_config(BINARY_C_CONFIG, input_2) output_2 = from_binary_c_config(BINARY_C_CONFIG, input_2)
self.assertIn( self.assertIn(
output_2, output_2,
["2.1.7", "2.2pre1", "2.2.0", "2.2.1"], ["2.1.7", "2.2pre1", "2.2.0", "2.2.1", "2.2.2"],
msg="binary_c version doesnt match", msg="binary_c version doesnt match",
) )
...@@ -213,4 +214,5 @@ class test_create_and_load_logging_function(unittest.TestCase): ...@@ -213,4 +214,5 @@ class test_create_and_load_logging_function(unittest.TestCase):
if __name__ == "__main__": if __name__ == "__main__":
unittest.main() # unittest.main()
test_binary_c_log_code().test_binary_c_log_code()
binarycpython/tests/test_grid.py
+ 7
− 6
View file @ 89ab18fb
...@@ -110,11 +110,11 @@ class test__setup(unittest.TestCase): ...@@ -110,11 +110,11 @@ class test__setup(unittest.TestCase):
Unittests for _setup function Unittests for _setup function
""" """
def test_setup(self): # def test_setup(self):
with Capturing() as _: # with Capturing() as _:
self._test_setup() # self._test_setup()
def _test_setup(self): def test_setup(self):
""" """
Unittests for function _setup Unittests for function _setup
""" """
...@@ -124,7 +124,7 @@ class test__setup(unittest.TestCase): ...@@ -124,7 +124,7 @@ class test__setup(unittest.TestCase):
self.assertTrue("metallicity" in test_pop.defaults) self.assertTrue("metallicity" in test_pop.defaults)
self.assertNotIn("help_all", test_pop.cleaned_up_defaults) self.assertNotIn("help_all", test_pop.cleaned_up_defaults)
self.assertEqual(test_pop.bse_options, {}) self.assertEqual(test_pop.bse_options, {})
self.assertEqual(test_pop.custom_options, {}) self.assertEqual(test_pop.custom_options, {"save_snapshot": False})
self.assertEqual(test_pop.argline_dict, {}) self.assertEqual(test_pop.argline_dict, {})
self.assertEqual(test_pop.persistent_data_memory_dict, {}) self.assertEqual(test_pop.persistent_data_memory_dict, {})
self.assertTrue(test_pop.grid_options["parse_function"] is None) self.assertTrue(test_pop.grid_options["parse_function"] is None)
...@@ -617,6 +617,7 @@ class test_resultdict(unittest.TestCase): ...@@ -617,6 +617,7 @@ class test_resultdict(unittest.TestCase):
dphasevol="dlnm1", dphasevol="dlnm1",
parameter_name="M_1", parameter_name="M_1",
condition="", # Impose a condition on this grid variable. Mostly for a check for yourself condition="", # Impose a condition on this grid variable. Mostly for a check for yourself
gridtype="left",
) )
## Executing a population ## Executing a population
...@@ -775,7 +776,7 @@ class test_grid_evolve(unittest.TestCase): ...@@ -775,7 +776,7 @@ class test_grid_evolve(unittest.TestCase):
parse_function=parse_function_test_grid_evolve_2_threads_with_custom_logging, parse_function=parse_function_test_grid_evolve_2_threads_with_custom_logging,
) )
test_pop.set(ensemble=0) test_pop.set(ensemble=0)
resolution = {"M_1": 2} resolution = {"M_1": 20}
test_pop.add_grid_variable( test_pop.add_grid_variable(
name="lnm1", name="lnm1",
......
binarycpython/utils/population_extensions/distribution_functions.py
+ 35
− 29
View file @ 89ab18fb
...@@ -302,7 +302,9 @@ class distribution_functions: ...@@ -302,7 +302,9 @@ class distribution_functions:
m0, m1, m2, m_max, p1, p2, p3 m0, m1, m2, m_max, p1, p2, p3
) )
if m < m0: if (
m <= m0
): # TODO: this needs to be checked! Compare two choices in this with the same sampling ranges.
prob = 0.0 # Below lower bound prob = 0.0 # Below lower bound
elif m <= m1: elif m <= m1:
prob = three_part_powerlaw_constants[0] * (m**p1) # Between m0 and m1 prob = three_part_powerlaw_constants[0] * (m**p1) # Between m0 and m1
...@@ -759,7 +761,7 @@ class distribution_functions: ...@@ -759,7 +761,7 @@ class distribution_functions:
log10Pmin = max(-1.0, log10Pmin) log10Pmin = max(-1.0, log10Pmin)
# save mass input and limit mass used (M1 from now on) to fitted range # save mass input and limit mass used (M1 from now on) to fitted range
Mwas = M1 # Mwas = M1 TODO: why is this here?
M1 = max(1.15, min(16.3, M1)) M1 = max(1.15, min(16.3, M1))
# Calculate the normalisations # Calculate the normalisations
...@@ -921,7 +923,7 @@ class distribution_functions: ...@@ -921,7 +923,7 @@ class distribution_functions:
The multiplicity fractions of the quadruples are folded onto that of the triples The multiplicity fractions of the quadruples are folded onto that of the triples
""" """
if not max_multiplicity in range(1, 5): if max_multiplicity not in range(1, 5):
msg = "\tMoe and di Stefano 2017: merge_multiplicities: max_multiplicity has to be between 1 and 4. It is {} now".format( msg = "\tMoe and di Stefano 2017: merge_multiplicities: max_multiplicity has to be between 1 and 4. It is {} now".format(
max_multiplicity max_multiplicity
) )
...@@ -1422,24 +1424,26 @@ class distribution_functions: ...@@ -1422,24 +1424,26 @@ class distribution_functions:
) )
# now we integrate and renormalise (if the table is not all zero) # now we integrate and renormalise (if the table is not all zero)
I = self.get_integration_constant_q( integration_constant_q = self.get_integration_constant_q(
q_interpolator, tmp_table, qdata, verbosity=verbosity q_interpolator, tmp_table, qdata, verbosity=verbosity
) )
if I > 0: if integration_constant_q > 0:
# normalise to 1.0 by dividing the data by 1.0/$I # normalise to 1.0 by dividing the data by 1.0/$I
q_interpolator.multiply_table_column(1, 1.0 / I) q_interpolator.multiply_table_column(
1, 1.0 / integration_constant_q
)
# test this # test this
new_I = self.get_integration_constant_q( new_integration_constant_q = self.get_integration_constant_q(
q_interpolator, tmp_table, qdata, verbosity=verbosity q_interpolator, tmp_table, qdata, verbosity=verbosity
) )
# fail if error in integral > 1e-6 (should be ~ machine precision) # fail if error in integral > 1e-6 (should be ~ machine precision)
if abs(1.0 - new_I) > 1e-6: if abs(1.0 - new_integration_constant_q) > 1e-6:
verbose_print( verbose_print(
"\tMoe and di Stefano 2017: build_q_table: Error: > 1e-6 in q probability integral: {}".format( "\tMoe and di Stefano 2017: build_q_table: Error: > 1e-6 in q probability integral: {}".format(
I integration_constant_q
), ),
verbosity, verbosity,
_MOE2017_VERBOSITY_LEVEL, _MOE2017_VERBOSITY_LEVEL,
...@@ -1520,7 +1524,7 @@ class distribution_functions: ...@@ -1520,7 +1524,7 @@ class distribution_functions:
""" """
dq = 1e-3 # resolution of the integration/renormalisation dq = 1e-3 # resolution of the integration/renormalisation
I = 0 integration_constant_q = 0
# integrate: note that the value of the integral is # integrate: note that the value of the integral is
# meaningless to within a factor (which depends on $dq) # meaningless to within a factor (which depends on $dq)
...@@ -1538,8 +1542,8 @@ class distribution_functions: ...@@ -1538,8 +1542,8 @@ class distribution_functions:
) )
raise ValueError(msg) raise ValueError(msg)
I += x[0] * dq integration_constant_q += x[0] * dq
return I return integration_constant_q
def fill_data(self, sample_values, data_dict): def fill_data(self, sample_values, data_dict):
""" """
...@@ -1550,19 +1554,19 @@ class distribution_functions: ...@@ -1550,19 +1554,19 @@ class distribution_functions:
""" """
data = {} data = {}
I = 0 integration_constant = 0
dstep = float(sample_values[1]) - float(sample_values[0]) # dstep = float(sample_values[1]) - float(sample_values[0])
# Read out the data # Read out the data
for sample_value in sample_values: for sample_value in sample_values:
val = data_dict[sample_value] val = data_dict[sample_value]
data[sample_value] = val data[sample_value] = val
I += val integration_constant += val
# Normalise the data # Normalise the data
for sample_value in sample_values: for sample_value in sample_values:
data[sample_value] = data[sample_value] / I data[sample_value] = data[sample_value] / integration_constant
return data return data
...@@ -1579,6 +1583,8 @@ class distribution_functions: ...@@ -1579,6 +1583,8 @@ class distribution_functions:
Function to calculate the e integral Function to calculate the e integral
We need to renormalise this because min_per > 0, and not all periods should be included We need to renormalise this because min_per > 0, and not all periods should be included
TODO: create function ot actually do this in a more general way
""" """
global Moecache global Moecache
...@@ -1595,7 +1601,7 @@ class distribution_functions: ...@@ -1595,7 +1601,7 @@ class distribution_functions:
# Check for cached value. If it doesn't exist: calculate # Check for cached value. If it doesn't exist: calculate
if not Moecache[integrals_string].get(mass_period_string, None): if not Moecache[integrals_string].get(mass_period_string, None):
I = 0 integation_constant_e = 0
decc = 1e-3 decc = 1e-3
for ecc in np.arange(min_ecc, max_ecc, decc): for ecc in np.arange(min_ecc, max_ecc, decc):
...@@ -1608,10 +1614,10 @@ class distribution_functions: ...@@ -1608,10 +1614,10 @@ class distribution_functions:
] ]
)[0] )[0]
I += dp_decc * decc integation_constant_e += dp_decc * decc
# Set the integral value in the dict # Set the integral value in the dict
Moecache[integrals_string][mass_period_string] = I Moecache[integrals_string][mass_period_string] = integation_constant_e
verbose_print( verbose_print(
"\tMoe and di Stefano 2017: calc_ecc_integral: min_ecc: {} max ecc: {} integrals_string: {} interpolator_name: {} mass_string: {} period_string: {} mass: {} period: {} I: {}".format( "\tMoe and di Stefano 2017: calc_ecc_integral: min_ecc: {} max ecc: {} integrals_string: {} interpolator_name: {} mass_string: {} period_string: {} mass: {} period: {} I: {}".format(
min_ecc, min_ecc,
...@@ -1622,7 +1628,7 @@ class distribution_functions: ...@@ -1622,7 +1628,7 @@ class distribution_functions:
period_string, period_string,
options[mass_string], options[mass_string],
options[period_string], options[period_string],
I, integation_constant_e,
), ),
verbosity, verbosity,
_MOE2017_VERBOSITY_LEVEL, _MOE2017_VERBOSITY_LEVEL,
...@@ -1668,7 +1674,7 @@ class distribution_functions: ...@@ -1668,7 +1674,7 @@ class distribution_functions:
# Check for cached value. If it doesn't exist: calculate # Check for cached value. If it doesn't exist: calculate
if not Moecache[integrals_string].get(options[mass_string], None): if not Moecache[integrals_string].get(options[mass_string], None):
I = 0 integation_constant_P = 0
dlogP = 1e-3 dlogP = 1e-3
for logP in np.arange(min_logP, max_logP, dlogP): for logP in np.arange(min_logP, max_logP, dlogP):
...@@ -1677,10 +1683,10 @@ class distribution_functions: ...@@ -1677,10 +1683,10 @@ class distribution_functions:
[np.log10(options[mass_string]), logP] [np.log10(options[mass_string]), logP]
)[0] )[0]
I += dp_dlogP * dlogP integation_constant_P += dp_dlogP * dlogP
# Set the integral value in the dict # Set the integral value in the dict
Moecache[integrals_string][options[mass_string]] = I Moecache[integrals_string][options[mass_string]] = integation_constant_P
verbose_print( verbose_print(
"\tMoe and di Stefano 2017: calc_P_integral: min_logP: {} integrals_string: {} interpolator_name: {} mass_string: {} mass: {} I: {}".format( "\tMoe and di Stefano 2017: calc_P_integral: min_logP: {} integrals_string: {} interpolator_name: {} mass_string: {} mass: {} I: {}".format(
min_logP, min_logP,
...@@ -1688,7 +1694,7 @@ class distribution_functions: ...@@ -1688,7 +1694,7 @@ class distribution_functions:
interpolator_name, interpolator_name,
mass_string, mass_string,
options[mass_string], options[mass_string],
I, integation_constant_P,
), ),
verbosity, verbosity,
_MOE2017_VERBOSITY_LEVEL, _MOE2017_VERBOSITY_LEVEL,
...@@ -2142,11 +2148,11 @@ class distribution_functions: ...@@ -2142,11 +2148,11 @@ class distribution_functions:
# as for any other stars but Pmax must be such that # as for any other stars but Pmax must be such that
# sep3 < sep2 * 0.2 # sep3 < sep2 * 0.2
# TODO: fix this here # # TODO: fix this here
max_sep3 = 0.2 * options["sep2"] * (1.0 + options["ecc2"]) # max_sep3 = 0.2 * options["sep2"] * (1.0 + options["ecc2"])
max_per3 = calc_period_from_sep( # max_per3 = calc_period_from_sep(
options["M_1+M_2"], options["mmin"], max_sep3 # options["M_1+M_2"], options["mmin"], max_sep3
) # )
# Calculate P integral or use the cached value # Calculate P integral or use the cached value
# TODO: Make sure we use the correct period idea here. # TODO: Make sure we use the correct period idea here.
......
pyproject.toml
+ 7
− 5
View file @ 89ab18fb
[tool.black] [tool.black]
target-version = ['py39'] target-version = ['py39']
extend-exclude = ''' extend-exclude = '''
# A regex preceded with ^/ will apply only to files and directories # A regex preceded with ^/ will apply only to files and directories
...@@ -20,7 +19,10 @@ extend-exclude = ''' ...@@ -20,7 +19,10 @@ extend-exclude = '''
max-line-length = 89 max-line-length = 89
max-complexity = 18 max-complexity = 18
#[tool.coverage]
[tool.coverage] #[tool.coverage.run]
#omit = #omit =[*/.local/*,
# test_*.py ## omit everything in /usr
#/usr/*,
## omit this single file
#utils/tirefire.py]
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