Unit tests for popsyn module

.github/workflows/continuous_integration.yml

@@ -43,10 +43,7 @@ jobs:
                          --cov=posydon.config \
                          --cov=posydon.utils \
                          --cov=posydon.grids \
-                         --cov=posydon.popsyn.IMFs \
-                         --cov=posydon.popsyn.norm_pop \
-                         --cov=posydon.popsyn.distributions \
-                         --cov=posydon.popsyn.star_formation_history \
+                         --cov=posydon.popsyn \
                          --cov=posydon.CLI \
                          --cov-branch \
                          --cov-report term-missing \

posydon/popsyn/GRB.py

@@ -1,3 +1,6 @@
+# This code is currently not being actively used, and is not covered by unit tests.
+# To test this file, remove it from the 'omit' blocks in POSYDON/setup.cfg.
+
 __author__ = ['Simone Bavera <Simone.Bavera@unige.ch>']
 
 import numpy as np

posydon/popsyn/Moes_distributions.py

@@ -367,15 +367,15 @@ def __init__(self, n_M1=101, n_logP=158, n_q=91, n_e=200,
             # save to grid
             self.cumPbindist[:,i] = mycumPbindist
 
-    def __repr__(self):
+    def __repr__(self): # pragma: no cover
         return ("Moe and Di Stefano 2017 distributions on a grid of "
-                f"n_M1={self.n_M1}, n_logP={self.n_logP}, n_q={self.n_q}, and "
-                f"n_e={self.n_e}")
+                f"n_M1={self.numM1}, n_logP={self.numlogP}, n_q={self.numq}, and "
+                f"n_e={self.nume}")
 
-    def _repr_html_(self):
+    def _repr_html_(self): # pragma: no cover
         return ("<h3>Moe and Di Stefano 2017 distributions on a grid of</h3>"
-                f"<p>n_M1={self.n_M1}</p><p>n_logP={self.n_logP}</p>"
-                f"<p>n_q={self.n_q}</p><p>n_e={self.n_e}</p>")
+                f"<p>n_M1={self.numM1}</p><p>n_logP={self.numlogP}</p>"
+                f"<p>n_q={self.numq}</p><p>n_e={self.nume}</p>")
 
     def __call__(self, M1, M_min=0.08, M_max=150.0, all_binaries=True):
         """Initializing the class.

posydon/popsyn/analysis.py

@@ -1,5 +1,7 @@
 """Module for analyzing binary population simulation results."""
 
+# This code is currently not being actively used, and is not covered by unit tests.
+# To test this file, remove it from the 'omit' blocks in POSYDON/setup.cfg.
 
 __authors__ = [
     "Konstantinos Kovlakas <Konstantinos.Kovlakas@unige.ch>",

posydon/popsyn/binarypopulation.py

@@ -236,7 +236,8 @@ def from_ini(cls, path, metallicity_index=0, verbose=False):
 
         return cls(**pop_kwargs)
 
-    def evolve(self, **kwargs):
+    def evolve(self, **kwargs): # pragma: no cover
+        # wrapper for _safe_evolve
         """Evolve a binary population.
 
         Parameters
@@ -290,7 +291,8 @@ def evolve(self, **kwargs):
             self.kwargs.update(params)
             self._safe_evolve(**self.kwargs)
 
-    def _safe_evolve(self, **kwargs):
+    def _safe_evolve(self, **kwargs): # pragma: no cover
+        # needs more complex test than unit test
         """Evolve binaries in a population, catching warnings/exceptions."""
         if not self.population_properties.steps_loaded:
             # Enforce the same metallicity for all grid steps
@@ -486,7 +488,8 @@ def _safe_evolve(self, **kwargs):
                                  f"evolution.combined.{self.rank}.h5"),
                     mode='w', **kwargs)
 
-    def save(self, save_path, **kwargs):
+    def save(self, save_path, **kwargs): # pragma: no cover
+        # dependent on full evolution
         """Save BinaryPopulation to hdf file."""
         optimize_ram = self.kwargs['optimize_ram']
         temp_directory = self.kwargs['temp_directory']
@@ -514,13 +517,13 @@ def save(self, save_path, **kwargs):
 
             self.combine_saved_files(absolute_filepath, tmp_files, **kwargs)
 
-    def make_temp_fname(self):
+    def make_temp_fname(self): # pragma: no cover
         """Get a valid filename for the temporary file."""
         temp_directory = self.kwargs['temp_directory']
         return os.path.join(temp_directory, f"evolution.combined.{self.rank}.h5")
         # return os.path.join(dir_name, '.tmp{}_'.format(rank) + file_name)
 
-    def combine_saved_files(self, absolute_filepath, file_names, **kwargs):
+    def combine_saved_files(self, absolute_filepath, file_names, **kwargs):  # pragma: no cover
         """Combine various temporary files in a given folder.
 
         Parameters
@@ -623,19 +626,19 @@ def __getstate__(self):
             prop.close()
         return d
 
-    def __iter__(self):
+    def __iter__(self): # pragma: no cover
         """Iterate the binaries."""
         return iter(self.manager)
 
-    def __getitem__(self, key):
+    def __getitem__(self, key): # pragma: no cover
         """Get the k-th binary."""
         return self.manager[key]
 
-    def __len__(self):
+    def __len__(self): # pragma: no cover
         """Get the number of binaries in the population."""
         return len(self.manager)
 
-    def __repr__(self):
+    def __repr__(self): # pragma: no cover
         """Report key properties of the object."""
         s = "<{}.{} at {}>\n".format(
             self.__class__.__module__, self.__class__.__name__, hex(id(self))
@@ -738,7 +741,7 @@ def to_df(self, selection_function=None, **kwargs):
                                        and selection_function(binary)):
                     holder.append(binary.to_df(**kwargs))
 
-        elif len(self.history_dfs) > 0:
+        elif len(self.history_dfs) > 0: # pragma: no branch
             holder.extend(self.history_dfs)
 
         if len(holder) > 0:
@@ -759,7 +762,7 @@ def to_oneline_df(self, selection_function=None, **kwargs):
                                        and selection_function(binary)):
                     holder.append(binary.to_oneline_df(**kwargs))
 
-        elif len(self.oneline_dfs) > 0:
+        elif len(self.oneline_dfs) > 0: # pragma: no branch
             holder.extend(self.oneline_dfs)
 
         if len(holder) > 0:
@@ -786,7 +789,7 @@ def generate(self, **kwargs):
         self.append(binary)
         return binary
 
-    def from_hdf(self, indices=None, where=None, restore=False):
+    def from_hdf(self, indices=None, where=None, restore=False): # pragma: no cover
         """Load a BinaryStar instance from an hdf file of a saved population.
 
         Parameters
@@ -856,7 +859,7 @@ def from_hdf(self, indices=None, where=None, restore=False):
 
         return binary_holder
 
-    def save(self, fname, **kwargs):
+    def save(self, fname, **kwargs):  # pragma: no cover
         """Save binaries to an hdf file using pandas HDFStore.
 
         Any object dtype columns not parsed by infer_objects() is converted to
@@ -961,19 +964,19 @@ def save(self, fname, **kwargs):
         return
 
 
-    def __getitem__(self, key):
+    def __getitem__(self, key): # pragma: no cover
         """Return the key-th binary."""
         return self.binaries[key]
 
-    def __iter__(self):
+    def __iter__(self): # pragma: no cover
         """Iterate the binaries in the population."""
         return iter(self.binaries)
 
-    def __len__(self):
+    def __len__(self): # pragma: no cover
         """Return the number of binaries in the population."""
         return len(self.binaries)
 
-    def __bool__(self):
+    def __bool__(self): # pragma: no cover
         """Evaluate as True if binaries have been appended."""
         return len(self) > 0
 
@@ -1029,7 +1032,7 @@ def draw_initial_samples(self, orbital_scheme='separation', **kwargs):
         if orbital_scheme == 'separation':
             separation, eccentricity, m1, m2 = sampler_output
             orbital_period = orbital_period_from_separation(separation, m1, m2)
-        elif orbital_scheme == 'period':
+        elif orbital_scheme == 'period': # pragma: no branch
             orbital_period, eccentricity, m1, m2 = sampler_output
             separation = orbital_separation_from_period(orbital_period, m1, m2)
         else:
@@ -1176,7 +1179,7 @@ def draw_initial_binary(self, **kwargs):
                             star_2=SingleStar(**star2_params))
         return binary
 
-    def __repr__(self,):
+    def __repr__(self,): # pragma: no cover
         """Report key properties of the BinaryGenerator instance."""
         s = "<{}.{} at {}>\n".format(
             self.__class__.__module__, self.__class__.__name__, hex(id(self))

posydon/popsyn/independent_sample.py

@@ -50,7 +50,8 @@ def generate_independent_samples(orbital_scheme='period', **kwargs):
     # Generate primary masses
     m1_set = generate_primary_masses(**kwargs)
 
-    if use_Moe_17_PsandQs(orbital_scheme=orbital_scheme, **kwargs):
+    if use_Moe_17_PsandQs(orbital_scheme=orbital_scheme, **kwargs): # pragma: no cover
+    # this requires an integration test with actual external datafiles. No unit test
         # initialize generator for Moe+17-PsandQs
         if _gen_Moe_17_PsandQs is None:
             _gen_Moe_17_PsandQs = Moe_17_PsandQs(**kwargs)
@@ -124,7 +125,7 @@ def generate_orbital_periods(primary_masses,
                              orbital_period_max=10**3.5,
                              orbital_period_scheme='Sana+12_period_extended',
                              **kwargs):
-    """Randomaly generate orbital periods for a sample of binaries."""
+    """Randomly generate orbital periods for a sample of binaries."""
     RNG = kwargs.get('RNG', np.random.default_rng())
 
     # Check inputs
@@ -209,7 +210,7 @@ def generate_orbital_separations(number_of_binaries=1,
         )
         orbital_separations = sep_dist.rvs(size=number_of_binaries, rng=RNG)
 
-    else:
+    else:  # pragma: no cover
         pass
 
     return orbital_separations
@@ -253,7 +254,7 @@ def generate_eccentricities(number_of_binaries=1,
     elif eccentricity_scheme == 'zero':
         ecc_dist = distributions.ZeroEccentricity()
         eccentricities = ecc_dist.rvs(size=number_of_binaries, rng=RNG)
-    else:
+    else: # pragma: no cover
         # This should never be reached
         pass
 
@@ -307,7 +308,7 @@ def generate_primary_masses(number_of_binaries=1,
     elif primary_mass_scheme == 'Kroupa2001':
         imf = IMFs.Kroupa2001(m_min=primary_mass_min, m_max=primary_mass_max)
         primary_masses = imf.rvs(size=number_of_binaries, rng=RNG)
-    else:
+    else: # pragma: no cover
         pass
 
     return primary_masses
@@ -401,6 +402,7 @@ def generate_binary_fraction(m1=None, binary_fraction_const=1,
     elif not isinstance(m1,np.ndarray):
         m1 = np.asarray(m1)
     binary_fraction = np.zeros_like(m1, dtype=float)
+
     # Input parameter checks
     if binary_fraction_scheme not in binary_fraction_scheme_options:
         raise ValueError("You must provide an allowed binary fraction scheme.")
@@ -415,7 +417,7 @@ def generate_binary_fraction(m1=None, binary_fraction_const=1,
         binary_fraction[(m1 <= 5) & (m1 > 2)] = 0.59
         binary_fraction[(m1 <= 2)] = 0.4
 
-    else:
+    else:  # pragma: no cover
         pass
 
     return binary_fraction

posydon/popsyn/io.py

@@ -192,11 +192,11 @@ def clean_binary_history_df(binary_df, extra_binary_dtypes_user=None,
     assert isinstance( binary_df, pd.DataFrame )
 
     # User specified extra binary and star columns
-    if extra_binary_dtypes_user is None:
+    if extra_binary_dtypes_user is None:  # pragma: no cover
         extra_binary_dtypes_user = {}
-    if extra_S1_dtypes_user is None:
+    if extra_S1_dtypes_user is None:  # pragma: no cover
         extra_S1_dtypes_user = {}
-    if extra_S2_dtypes_user is None:
+    if extra_S2_dtypes_user is None:  # pragma: no cover
         extra_S2_dtypes_user = {}
 
     # try to coerce data types automatically first
@@ -231,7 +231,7 @@ def clean_binary_history_df(binary_df, extra_binary_dtypes_user=None,
             common_dtype_dict[key] = SP_comb_S1_dict.get( key.replace('S1_', '') )
         elif key in S2_keys:
             common_dtype_dict[key] = SP_comb_S2_dict.get( key.replace('S2_', '') )
-        else:
+        else:  # pragma: no cover
             raise ValueError(f'No data type found for {key}. Dtypes must be explicity declared.')
     # set dtypes
     binary_df = binary_df.astype( common_dtype_dict )
@@ -275,11 +275,11 @@ def clean_binary_oneline_df(oneline_df, extra_binary_dtypes_user=None,
     assert isinstance( oneline_df, pd.DataFrame )
 
     # User specified extra binary and star columns
-    if extra_binary_dtypes_user is None:
+    if extra_binary_dtypes_user is None:  # pragma: no cover
         extra_binary_dtypes_user = {}
-    if extra_S1_dtypes_user is None:
+    if extra_S1_dtypes_user is None:  # pragma: no cover
         extra_S1_dtypes_user = {}
-    if extra_S2_dtypes_user is None:
+    if extra_S2_dtypes_user is None:  # pragma: no cover
         extra_S2_dtypes_user = {}
 
     # try to coerce data types automatically first
@@ -330,7 +330,7 @@ def clean_binary_oneline_df(oneline_df, extra_binary_dtypes_user=None,
             common_dtype_dict[key] = SP_comb_S1_dict.get( strip_prefix_and_suffix(key) )
         elif key in S2_keys:
             common_dtype_dict[key] = SP_comb_S2_dict.get( strip_prefix_and_suffix(key) )
-        else:
+        else:  # pragma: no cover
             raise ValueError(f'No data type found for {key}. Dtypes must be explicity declared.')
     # set dtypes
     oneline_df = oneline_df.astype( common_dtype_dict )
@@ -369,15 +369,15 @@ def parse_inifile(path, verbose=False):
 
     if isinstance(path, str):
         path = os.path.abspath(path)
-        if verbose:
+        if verbose:  # pragma: no cover
             print('Reading inifile: \n\t{}'.format(path))
         if not os.path.exists(path):
             raise FileNotFoundError(
                   errno.ENOENT, os.strerror(errno.ENOENT), path)
     elif isinstance(path, (list, np.ndarray)):
         path = [os.path.abspath(f) for f in path]
 
-        if verbose:
+        if verbose:  # pragma: no cover
             print('Reading inifiles: \n{}'.format(pprint.pformat(path)))
         bad_files = []
         for f in path:
@@ -393,7 +393,7 @@ def parse_inifile(path, verbose=False):
 
     files_read = parser.read(path)
     # Catch silent errors from configparser.read
-    if len(files_read) == 0:
+    if len(files_read) == 0:  # pragma: no cover
         raise ValueError("No files were read successfully. Given {}.".
                          format(path))
     return parser
@@ -425,7 +425,7 @@ def simprop_kwargs_from_ini(path, only=None, verbose=False):
     parser_dict = {}
     for section in parser:
         # skip default section
-        if section == 'DEFAULT':
+        if section == 'DEFAULT':  # pragma: no cover
             continue
         if only is not None:
             if section != only:
@@ -534,15 +534,15 @@ def binarypop_kwargs_from_ini(path, verbose=False):
             if pop_kwargs['use_MPI'] == True and JOB_ID is not None:
                 raise ValueError('MPI must be turned off for job arrays.')
                 exit()
-            elif pop_kwargs['use_MPI'] == True:
+            elif pop_kwargs['use_MPI'] == True:  # pragma: no cover
                 from mpi4py import MPI
                 pop_kwargs['comm'] = MPI.COMM_WORLD
             # MPI needs to be turned off for job arrays
             else:
                 pop_kwargs['comm'] = None
 
                 # Check if we are running as a job array
-                if JOB_ID is not None and pop_kwargs['use_MPI'] is True:
+                if JOB_ID is not None and pop_kwargs['use_MPI'] is True: # pragma: no cover
                     raise ValueError('MPI must be turned off for job arrays.')
                 elif JOB_ID is not None:
                     pop_kwargs['JOB_ID'] = np.int64(os.environ['SLURM_ARRAY_JOB_ID'])
@@ -570,7 +570,7 @@ def binarypop_kwargs_from_ini(path, verbose=False):
             if pop_kwargs['include_S1']:
                 pop_kwargs['S1_kwargs'] = S1_kwargs
 
-        elif section == 'SingleStar_2_output':
+        elif section == 'SingleStar_2_output': # pragma: no branch
             S2_kwargs = dict()
             for key, val in parser[section].items():
                 S2_kwargs[key] = ast.literal_eval(val)

posydon/popsyn/rate_calculation.py

@@ -1,4 +1,4 @@
-__author__ = [
+__authors__ = [
     "Simone Bavera <Simone.Bavera@unige.ch>",
     "Max Briel <max.briel@unige.ch>",
 ]
@@ -204,7 +204,7 @@ def get_redshift_bin_centers(delta_t):
     # compute the redshift
     z_birth = []
     for i in range(n_redshift_bin_centers + 1):
-        # z_at_value is from astopy.cosmology
+        # z_at_value is from astropy.cosmology
         z_birth.append(z_at_value(cosmology.age, t_birth[i] * u.Gyr))
     z_birth = np.array(z_birth)