From c2259409c46b1b1f744a7e7185a48a1472bd7930 Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 16:33:16 -0600
Subject: [PATCH 1/9] Pep8 changes to test_zheng07.py module

---
 .../hod_models/tests/test_zheng07.py                 | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
index 2cddcf469..81e125949 100644
--- a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
+++ b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
@@ -14,8 +14,7 @@
 
 
 def test_zheng07_composite1():
-    """ Ensure that the ``zheng07`` pre-built model does not accept non-Zheng07Cens.
-    """
+    """Ensure that the ``zheng07`` pre-built model does not accept non-Zheng07Cens."""
     model1 = PrebuiltHodModelFactory("zheng07")
     model2 = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
 
@@ -30,7 +29,7 @@ def test_zheng07_composite1():
 
 
 def test_zheng07_composite2():
-    """ This test ensures that the source code provided in the
+    """This test ensures that the source code provided in the
     ``Advanced usage of the ``zheng07`` model`` tutorial behaves as expected.
     """
 
@@ -76,7 +75,7 @@ def mean_occupation(self, **kwargs):
 
 
 def test_modulate_with_cenocc1():
-    """ Regression test for Issue #646. Verify that the ``modulate_with_cenocc``
+    """Regression test for Issue #646. Verify that the ``modulate_with_cenocc``
     keyword argument is actually passed to the satellite occupation component.
     """
     model1 = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
@@ -86,7 +85,7 @@ def test_modulate_with_cenocc1():
 
 
 def test_modulate_with_cenocc2():
-    """ Regression test for Issue #646. Verify that the ``modulate_with_cenocc``
+    """Regression test for Issue #646. Verify that the ``modulate_with_cenocc``
     keyword argument results in behavior that is properly modified by the centrals.
     """
     model = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
@@ -107,8 +106,7 @@ def test_host_centric_distance():
 
 
 def test_mass_definition_flexibility():
-    """ Regression test for Issue #993.
-    """
+    """Regression test for Issue #993."""
     model = PrebuiltHodModelFactory(
         "zheng07", mdef="200m", halo_boundary_key="halo_radius_arbitrary"
     )

From 0d42df8e319fb50fdcd8f39d5e2f3353956afc5d Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 16:34:12 -0600
Subject: [PATCH 2/9] Added new failing unit test to address #993

---
 .../hod_models/tests/test_zheng07.py            | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
index 81e125949..4d672d54e 100644
--- a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
+++ b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
@@ -116,3 +116,20 @@ def test_mass_definition_flexibility():
         halocat.halo_table["halo_mvir"]
     )
     model.populate_mock(halocat, seed=43)
+
+
+def test_mass_definition_flexibility2():
+    """Regression test for Issue #993."""
+    halocat = FakeSim()
+    halocat.halo_table["halo_mass_custom"] = np.copy(halocat.halo_table["halo_mvir"])
+    halocat.halo_table["halo_radius_custom"] = np.copy(halocat.halo_table["halo_rvir"])
+    halocat.halo_table.remove_column("halo_upid")
+    halocat.halo_table.remove_column("halo_mvir")
+    halocat.halo_table.remove_column("halo_rvir")
+    model = PrebuiltHodModelFactory(
+        "zheng07",
+        mdef="custom",
+        prim_haloprop_key="halo_mass_custom",
+        halo_boundary_key="halo_radius_custom",
+    )
+    model.populate_mock(halocat)

From 98e960a151883e4c7dec62875a3f2644b65f9621 Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 16:56:45 -0600
Subject: [PATCH 3/9] Pep8 changes to model_defaults.py

---
 halotools/empirical_models/model_defaults.py | 49 ++++++++++++--------
 1 file changed, 29 insertions(+), 20 deletions(-)

diff --git a/halotools/empirical_models/model_defaults.py b/halotools/empirical_models/model_defaults.py
index b4789bbd4..1967b547e 100644
--- a/halotools/empirical_models/model_defaults.py
+++ b/halotools/empirical_models/model_defaults.py
@@ -4,7 +4,7 @@
 """
 import numpy as np
 
-__all__ = ['get_halo_boundary_key', 'get_halo_mass_key']
+__all__ = ["get_halo_boundary_key", "get_halo_mass_key"]
 
 
 # Default thresholds for mocks
@@ -15,30 +15,38 @@
 # Used when executing a Monte Carlo realization of a Poission distribution
 # whose mean is formally zero, which causes the built-in
 # scipy method to raise an exception.
-default_tiny_poisson_fluctuation = 1.e-20
+default_tiny_poisson_fluctuation = 1.0e-20
 
 default_smhm_scatter = 0.2
-default_smhm_haloprop = 'halo_mpeak'
+default_smhm_haloprop = "halo_mpeak"
 default_binary_galprop_haloprop = default_smhm_haloprop
 
 # At minimum, the following halo and galaxy properties
 # will be bound to each mock galaxy
-host_haloprop_prefix = 'halo_'
+host_haloprop_prefix = "halo_"
 
-default_haloprop_list_inherited_by_mock = (
-    ['halo_id', 'halo_hostid', 'halo_x', 'halo_y', 'halo_z',
-    'halo_vx', 'halo_vy', 'halo_vz',
-    'halo_mvir', 'halo_rvir', 'halo_upid']
-    )
+default_haloprop_list_inherited_by_mock = [
+    "halo_id",
+    "halo_hostid",
+    "halo_x",
+    "halo_y",
+    "halo_z",
+    "halo_vx",
+    "halo_vy",
+    "halo_vz",
+    "halo_mvir",
+    "halo_rvir",
+    "halo_upid",
+]
 
-prim_haloprop_key = 'halo_mvir'
-sec_haloprop_key = 'halo_nfw_conc'
+prim_haloprop_key = "halo_mvir"
+sec_haloprop_key = "halo_nfw_conc"
 
-halo_mass_definition = 'vir'
+halo_mass_definition = "vir"
 
 
 def get_halo_boundary_key(mdef):
-    """ For the input mass definition,
+    """For the input mass definition,
     return the string used to access halo table column
     storing the halo radius.
 
@@ -56,11 +64,11 @@ def get_halo_boundary_key(mdef):
     --------
     radius_key : str
     """
-    return 'halo_r'+mdef
+    return "halo_r" + mdef
 
 
 def get_halo_mass_key(mdef):
-    """ For the input mass definition,
+    """For the input mass definition,
     return the string used to access halo table column
     storing the halo mass.
 
@@ -78,7 +86,7 @@ def get_halo_mass_key(mdef):
     --------
     mass_key : str
     """
-    return 'halo_m'+mdef
+    return "halo_m" + mdef
 
 
 # Number of bins to use in the lookup table attached to the NFWProfile.
@@ -88,14 +96,15 @@ def get_halo_mass_key(mdef):
 max_permitted_conc = 20.0
 
 default_conc_gal_bias_bins = np.linspace(0.1, 10, 10)
-default_conc_gal_bias_bins = np.insert(default_conc_gal_bias_bins,
-    np.searchsorted(default_conc_gal_bias_bins, 1), 1)
+default_conc_gal_bias_bins = np.insert(
+    default_conc_gal_bias_bins, np.searchsorted(default_conc_gal_bias_bins, 1), 1
+)
 
 Npts_radius_table = 101
 default_lograd_min = -3
 default_lograd_max = 0
-conc_mass_model = 'direct_from_halo_catalog'
-concentration_key = 'halo_nfw_conc'
+conc_mass_model = "direct_from_halo_catalog"
+concentration_key = "halo_nfw_conc"
 
 
 default_rbins = np.logspace(-1, 1.25, 15)

From 106c6d8197cd816d00739d5169a7ea3a198c73ca Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 16:57:09 -0600
Subject: [PATCH 4/9] Changes to profile model template to permit arbitrary
 mdef

---
 .../analytic_models/profile_model_template.py | 35 ++++++++++++-------
 .../satellites/nfw/nfw_profile.py             | 28 +++++++++++----
 2 files changed, 43 insertions(+), 20 deletions(-)

diff --git a/halotools/empirical_models/phase_space_models/analytic_models/profile_model_template.py b/halotools/empirical_models/phase_space_models/analytic_models/profile_model_template.py
index 16831938d..b49528c50 100644
--- a/halotools/empirical_models/phase_space_models/analytic_models/profile_model_template.py
+++ b/halotools/empirical_models/phase_space_models/analytic_models/profile_model_template.py
@@ -26,7 +26,7 @@
 
 @six.add_metaclass(ABCMeta)
 class AnalyticDensityProf(object):
-    r""" Container class for any analytical radial profile model.
+    r"""Container class for any analytical radial profile model.
 
     See :ref:`profile_template_tutorial` for a review of the mathematics of
     halo profiles, and a thorough description of how the relevant equations
@@ -63,16 +63,20 @@ def __init__(self, cosmology, redshift, mdef, halo_boundary_key=None, **kwargs):
         self.redshift = redshift
         self.mdef = mdef
 
-        # The following four attributes are derived quantities from the above,
-        # so that self-consistency between them is ensured
-        self.density_threshold = halo_boundary_functions.density_threshold(
-            cosmology=self.cosmology, redshift=self.redshift, mdef=self.mdef
-        )
         if halo_boundary_key is None:
             self.halo_boundary_key = model_defaults.get_halo_boundary_key(self.mdef)
         else:
             self.halo_boundary_key = halo_boundary_key
-        self.prim_haloprop_key = model_defaults.get_halo_mass_key(self.mdef)
+        # The following four attributes are derived quantities from the above,
+        # so that self-consistency between them is ensured
+        if self.mdef == "custom":
+            self.density_threshold = None
+            self.prim_haloprop_key = kwargs["prim_haloprop_key"]
+        else:
+            self.density_threshold = halo_boundary_functions.density_threshold(
+                cosmology=self.cosmology, redshift=self.redshift, mdef=self.mdef
+            )
+            self.prim_haloprop_key = model_defaults.get_halo_mass_key(self.mdef)
 
         self.gal_prof_param_keys = []
         self.halo_prof_param_keys = []
@@ -169,6 +173,12 @@ def mass_density(self, radius, mass, *prof_params):
             scaled_radius, *prof_params
         )
 
+        if self.density_threshold is None:
+            msg = (
+                "When using mdef=`custom`, "
+                "there is no way to compute the SO mass_density"
+            )
+            raise ValueError(msg)
         density = self.density_threshold * dimensionless_mass
         return density
 
@@ -282,7 +292,7 @@ def enclosed_mass(self, radius, total_mass, *prof_params):
         return mass
 
     def dimensionless_circular_velocity(self, scaled_radius, *prof_params):
-        r""" Circular velocity scaled by the virial velocity,
+        r"""Circular velocity scaled by the virial velocity,
         :math:`V_{\rm cir}(x) / V_{\rm vir}`, as a function of
         dimensionless position :math:`\tilde{r} = r / R_{\rm vir}`.
 
@@ -312,7 +322,7 @@ def dimensionless_circular_velocity(self, scaled_radius, *prof_params):
         )
 
     def virial_velocity(self, total_mass):
-        r""" The circular velocity evaluated at the halo boundary,
+        r"""The circular velocity evaluated at the halo boundary,
         :math:`V_{\rm vir} \equiv \sqrt{GM_{\rm halo}/R_{\rm halo}}`.
 
         Parameters
@@ -369,13 +379,12 @@ def circular_velocity(self, radius, total_mass, *prof_params):
         ) * self.virial_velocity(total_mass)
 
     def _vmax_helper(self, scaled_radius, *prof_params):
-        """ Helper function used to calculate `vmax` and `rmax`.
-        """
+        """Helper function used to calculate `vmax` and `rmax`."""
         encl = self.cumulative_mass_PDF(scaled_radius, *prof_params)
         return -1.0 * encl / scaled_radius
 
     def rmax(self, total_mass, *prof_params):
-        r""" Radius at which the halo attains its maximum circular velocity.
+        r"""Radius at which the halo attains its maximum circular velocity.
 
         Parameters
         ----------
@@ -405,7 +414,7 @@ def rmax(self, total_mass, *prof_params):
         return result.x[0] * halo_radius
 
     def vmax(self, total_mass, *prof_params):
-        r""" Maximum circular velocity of the halo profile.
+        r"""Maximum circular velocity of the halo profile.
 
         Parameters
         ----------
diff --git a/halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_profile.py b/halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_profile.py
index c547c9c8e..95e61057a 100644
--- a/halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_profile.py
+++ b/halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_profile.py
@@ -25,7 +25,7 @@
 
 
 class NFWProfile(AnalyticDensityProf):
-    r""" Model for the spatial distribution of mass
+    r"""Model for the spatial distribution of mass
     and/or galaxies residing in an NFW halo profile,
     based on Navarro, Frenk and White (1995),
     `arXiv:9508025 <http://arxiv.org/abs/astro-ph/9508025/>`_.
@@ -44,6 +44,7 @@ def __init__(
         conc_mass_model=model_defaults.conc_mass_model,
         concentration_key=model_defaults.concentration_key,
         halo_boundary_key=None,
+        prim_haloprop_key=None,
         **kwargs
     ):
         r"""
@@ -60,9 +61,17 @@ def __init__(
         mdef: str, optional
             String specifying the halo mass definition, e.g., 'vir' or '200m'.
             Default is set in `~halotools.empirical_models.model_defaults`.
+            Use "custom" to allow arbitrary relationshipts between mass and radius.
+            When mdef is set to "custom", the `prim_haloprop_key` must also be passed.
 
         halo_boundary_key : str, optional
             Default behavior is to use the column associated with the input mdef.
+            When mdef is set to "custom", any halo boundary is permitted.
+            When mdef is set to "custom", the `prim_haloprop_key` must also be passed.
+
+        prim_haloprop_key : str, optional
+            Default behavior is to use the column associated with the input mdef.
+            When mdef is set to "custom", the `prim_haloprop_key` must also be passed.
 
         conc_mass_model : string or callable, optional
             Specifies the function used to model the relation between
@@ -85,7 +94,12 @@ def __init__(
         >>> nfw = NFWProfile()
         """
         AnalyticDensityProf.__init__(
-            self, cosmology, redshift, mdef, halo_boundary_key=halo_boundary_key
+            self,
+            cosmology,
+            redshift,
+            mdef,
+            halo_boundary_key=halo_boundary_key,
+            prim_haloprop_key=prim_haloprop_key,
         )
 
         self.gal_prof_param_keys = ["conc_NFWmodel"]
@@ -106,7 +120,7 @@ def _initialize_conc_mass_behavior(self, conc_mass_model, **kwargs):
         self.conc_mass_model = conc_mass_model
 
     def conc_NFWmodel(self, *args, **kwargs):
-        r""" NFW concentration as a function of halo mass.
+        r"""NFW concentration as a function of halo mass.
 
         Parameters
         ----------
@@ -387,7 +401,7 @@ def enclosed_mass(self, radius, total_mass, conc):
         return AnalyticDensityProf.enclosed_mass(self, radius, total_mass, conc)
 
     def virial_velocity(self, total_mass):
-        r""" The circular velocity evaluated at the halo boundary,
+        r"""The circular velocity evaluated at the halo boundary,
         :math:`V_{\rm vir} \equiv \sqrt{GM_{\rm halo}/R_{\rm halo}}`.
 
         Parameters
@@ -455,7 +469,7 @@ def circular_velocity(self, radius, total_mass, conc):
         return AnalyticDensityProf.circular_velocity(self, radius, total_mass, conc)
 
     def rmax(self, total_mass, conc):
-        r""" Radius at which the halo attains its maximum circular velocity,
+        r"""Radius at which the halo attains its maximum circular velocity,
         :math:`R_{\rm max}^{\rm NFW} = 2.16258R_{\Delta}/c`.
 
         Parameters
@@ -492,7 +506,7 @@ def rmax(self, total_mass, conc):
         return 2.16258 * scale_radius
 
     def vmax(self, total_mass, conc):
-        r""" Maximum circular velocity of the halo profile,
+        r"""Maximum circular velocity of the halo profile,
         :math:`V_{\rm max}^{\rm NFW} = V_{\rm cir}^{\rm NFW}(r = 2.16258R_{\Delta}/c)`.
 
         Parameters
@@ -577,7 +591,7 @@ def halo_radius_to_halo_mass(self, radius):
         return AnalyticDensityProf.halo_radius_to_halo_mass(self, radius)
 
     def mc_generate_nfw_radial_positions(self, **kwargs):
-        r""" Return a Monte Carlo realization of points in an NFW profile.
+        r"""Return a Monte Carlo realization of points in an NFW profile.
 
         See :ref:`monte_carlo_nfw_spatial_profile` for a discussion of this technique.
 

From e786fc0a579809cfca616baaeda3e0170caeb74c Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 16:59:15 -0600
Subject: [PATCH 5/9] Pep8 changes to hod_mock_factory.py module

---
 halotools/empirical_models/factories/hod_mock_factory.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/halotools/empirical_models/factories/hod_mock_factory.py b/halotools/empirical_models/factories/hod_mock_factory.py
index 1cab463ea..5b3ab7e7a 100644
--- a/halotools/empirical_models/factories/hod_mock_factory.py
+++ b/halotools/empirical_models/factories/hod_mock_factory.py
@@ -39,7 +39,7 @@
 
 
 class HodMockFactory(MockFactory):
-    """ Class responsible for populating a simulation with a
+    """Class responsible for populating a simulation with a
     population of mock galaxies based on an HOD-style model
     built by the `~halotools.empirical_models.HodModelFactory` class.
 
@@ -101,7 +101,7 @@ def __init__(
         self.preprocess_halo_catalog(halocat)
 
     def preprocess_halo_catalog(self, halocat):
-        """ Method to pre-process a halo catalog upon instantiation of
+        """Method to pre-process a halo catalog upon instantiation of
         the mock object. This pre-processing includes identifying the
         catalog columns that will be used by the model to create the mock,
         building lookup tables associated with the halo profile,
@@ -401,7 +401,7 @@ def populate(self, seed=None, **kwargs):
             self.galaxy_table = self.galaxy_table[mask]
 
     def allocate_memory(self, seed=None):
-        """ Method allocates the memory for all the numpy arrays
+        """Method allocates the memory for all the numpy arrays
         that will store the information about the mock.
         These arrays are bound directly to the mock object.
 
@@ -509,7 +509,7 @@ def allocate_memory(self, seed=None):
             self.galaxy_table[key] = np.zeros(self.Ngals, dtype=dt[key].type)
 
     def estimate_ngals(self, seed=None):
-        """ Method to estimate the number of galaxies produced by the
+        """Method to estimate the number of galaxies produced by the
         mock.populate() method. It runs one realization of all
         mc_occupation methods and reports the total number of galaxies
         produced. However, no extra memory is allocated for the

From 418f5e3e45c45575904676f2b1588157c8be75d3 Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 17:04:57 -0600
Subject: [PATCH 6/9] Changed default behavior of HOD models so that when
 halo_upid column is missing, all halos assumed to be hosts

---
 .../factories/hod_mock_factory.py             |   6 +-
 .../factories/tests/test_hod_model_factory.py | 133 +++++++++---------
 2 files changed, 66 insertions(+), 73 deletions(-)

diff --git a/halotools/empirical_models/factories/hod_mock_factory.py b/halotools/empirical_models/factories/hod_mock_factory.py
index 5b3ab7e7a..fe9094e30 100644
--- a/halotools/empirical_models/factories/hod_mock_factory.py
+++ b/halotools/empirical_models/factories/hod_mock_factory.py
@@ -122,10 +122,8 @@ def preprocess_halo_catalog(self, halocat):
             Default is set in `~halotools.empirical_models.model_defaults`.
 
         """
-        try:
-            assert "halo_upid" in list(halocat.halo_table.keys())
-        except AssertionError:
-            raise HalotoolsError(missing_halo_upid_msg)
+        if "halo_upid" not in list(halocat.halo_table.keys()):
+            halocat.halo_table["halo_upid"] = -1
 
         # Make cuts on halo catalog #
         # Select host halos only, since this is an HOD-style model
diff --git a/halotools/empirical_models/factories/tests/test_hod_model_factory.py b/halotools/empirical_models/factories/tests/test_hod_model_factory.py
index 71d61a004..2cea5e0b4 100644
--- a/halotools/empirical_models/factories/tests/test_hod_model_factory.py
+++ b/halotools/empirical_models/factories/tests/test_hod_model_factory.py
@@ -13,7 +13,7 @@
 from ....empirical_models import zheng07_model_dictionary, OccupationComponent
 from ....custom_exceptions import HalotoolsError
 
-__all__ = ('test_empty_arguments', )
+__all__ = ("test_empty_arguments",)
 
 
 def test_empty_arguments():
@@ -24,29 +24,29 @@ def test_empty_arguments():
 
 
 def test_Num_ptcl_requirement():
-    """ Demonstrate that passing in varying values for
+    """Demonstrate that passing in varying values for
     Num_ptcl_requirement results in the proper behavior.
     """
-    model = PrebuiltHodModelFactory('zheng07')
+    model = PrebuiltHodModelFactory("zheng07")
     halocat = FakeSim()
-    actual_mvir_min = halocat.halo_table['halo_mvir'].min()
+    actual_mvir_min = halocat.halo_table["halo_mvir"].min()
 
     model.populate_mock(halocat)
-    default_mvir_min = model.mock.particle_mass*model.mock.Num_ptcl_requirement
+    default_mvir_min = model.mock.particle_mass * model.mock.Num_ptcl_requirement
     # verify that the cut was applied
-    assert np.all(model.mock.halo_table['halo_mvir'] > default_mvir_min)
+    assert np.all(model.mock.halo_table["halo_mvir"] > default_mvir_min)
     # verify that the cut was non-trivial
-    assert np.any(halocat.halo_table['halo_mvir'] < default_mvir_min)
+    assert np.any(halocat.halo_table["halo_mvir"] < default_mvir_min)
 
     del model.mock
-    model.populate_mock(halocat, Num_ptcl_requirement=0.)
-    assert model.mock.Num_ptcl_requirement == 0.
-    assert np.any(model.mock.halo_table['halo_mvir'] < default_mvir_min)
+    model.populate_mock(halocat, Num_ptcl_requirement=0.0)
+    assert model.mock.Num_ptcl_requirement == 0.0
+    assert np.any(model.mock.halo_table["halo_mvir"] < default_mvir_min)
 
 
 def test_unavailable_haloprop():
     halocat = FakeSim()
-    m = PrebuiltHodModelFactory('zheng07')
+    m = PrebuiltHodModelFactory("zheng07")
     m._haloprop_list.append("Jose Canseco")
     with pytest.raises(HalotoolsError) as err:
         m.populate_mock(halocat=halocat)
@@ -57,13 +57,11 @@ def test_unavailable_haloprop():
 
 def test_unavailable_upid():
     halocat = FakeSim()
-    del halocat.halo_table['halo_upid']
-    m = PrebuiltHodModelFactory('zheng07')
+    del halocat.halo_table["halo_upid"]
+    m = PrebuiltHodModelFactory("zheng07")
 
-    with pytest.raises(HalotoolsError) as err:
-        m.populate_mock(halocat=halocat)
-    substr = "does not have the ``halo_upid`` column."
-    assert substr in err.value.args[0]
+    m.populate_mock(halocat=halocat)
+    assert np.allclose(m.mock.halo_table["halo_upid"], -1)
 
 
 def test_censat_consistency_check():
@@ -81,9 +79,9 @@ def test_censat_consistency_check():
     class DummySatComponent(OccupationComponent):
         def __init__(self):
             self.central_occupation_model = 43
-            self.gal_type = 'satellites'
+            self.gal_type = "satellites"
 
-    model.model_dictionary['dummy_key'] = DummySatComponent()
+    model.model_dictionary["dummy_key"] = DummySatComponent()
     with pytest.raises(HalotoolsError) as err:
         model._test_censat_occupation_consistency(model.model_dictionary)
     substr = "has a ``central_occupation_model`` attribute with an inconsistent "
@@ -91,27 +89,25 @@ def __init__(self):
 
 
 def test_factory_constructor_redshift1():
-    """ Verify that redundantly passing in a compatible redshift causes no problems
-    """
+    """Verify that redundantly passing in a compatible redshift causes no problems"""
     model_dict1 = zheng07_model_dictionary(redshift=1)
     model1 = HodModelFactory(**model_dict1)
     assert model1.redshift == 1
 
     model_dict2 = deepcopy(model_dict1)
-    model_dict2['redshift'] = 1
+    model_dict2["redshift"] = 1
     model2 = HodModelFactory(**model_dict2)
     assert model2.redshift == 1
 
 
 def test_factory_constructor_redshift2():
-    """ Verify that passing in an incompatible redshift raises the correct exception
-    """
+    """Verify that passing in an incompatible redshift raises the correct exception"""
     model_dict1 = zheng07_model_dictionary(redshift=1)
     model1 = HodModelFactory(**model_dict1)
     assert model1.redshift == 1
 
     model_dict2 = deepcopy(model_dict1)
-    model_dict2['redshift'] = 2
+    model_dict2["redshift"] = 2
     #
     with pytest.raises(AssertionError) as err:
         model2 = HodModelFactory(**model_dict2)
@@ -120,141 +116,140 @@ def test_factory_constructor_redshift2():
 
 
 def test_factory_constructor_redshift3():
-    """ Verify correct redshift behavior when using the baseline_model_instance argument
-    """
+    """Verify correct redshift behavior when using the baseline_model_instance argument"""
     model_dict1 = zheng07_model_dictionary(redshift=1)
     model1 = HodModelFactory(**model_dict1)
 
-    model2 = HodModelFactory(baseline_model_instance=model1,
-            redshift=model1.redshift)
+    model2 = HodModelFactory(baseline_model_instance=model1, redshift=model1.redshift)
 
     assert model2.redshift == model1.redshift
 
     with pytest.raises(AssertionError) as err:
-        model3 = HodModelFactory(baseline_model_instance=model1,
-                redshift=model1.redshift+1)
+        model3 = HodModelFactory(
+            baseline_model_instance=model1, redshift=model1.redshift + 1
+        )
     substr = "that is inconsistent with the redshift z ="
     assert substr in err.value.args[0]
 
 
 def test_factory_constructor_redshift4():
-    """ Verify correct redshift behavior when the model dictionary
+    """Verify correct redshift behavior when the model dictionary
     has no components with redshifts defined
     """
     model_dict_no_redshift = zheng07_model_dictionary(redshift=1)
     for component_model in model_dict_no_redshift.values():
         del component_model.redshift
 
-    model_dict_no_redshift['redshift'] = 1.5
+    model_dict_no_redshift["redshift"] = 1.5
     model2 = HodModelFactory(**model_dict_no_redshift)
     assert model2.redshift == 1.5
 
 
 def test_raises_appropriate_exception1():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
     with pytest.raises(HalotoolsError) as err:
-        model.build_model_feature_calling_sequence({'model_feature_calling_sequence': (4, 5)})
-    substr = "does not appear in the keyword arguments you passed to the HodModelFactory"
+        model.build_model_feature_calling_sequence(
+            {"model_feature_calling_sequence": (4, 5)}
+        )
+    substr = (
+        "does not appear in the keyword arguments you passed to the HodModelFactory"
+    )
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception2():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
     with pytest.raises(HalotoolsError) as err:
-        model._test_model_feature_calling_sequence_consistency(
-            ['abc'], model.gal_types)
+        model._test_model_feature_calling_sequence_consistency(["abc"], model.gal_types)
     substr = "input ``model_feature_calling_sequence`` has a ``abc`` element"
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception3():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 
-    model_dictionary_key = 'Air Bud 4: Seventh Inning Fetch'
+    model_dictionary_key = "Air Bud 4: Seventh Inning Fetch"
     gal_type_list = model.gal_types
-    known_gal_type = 'Josh'
+    known_gal_type = "Josh"
     with pytest.raises(HalotoolsError) as err:
         model._infer_gal_type_and_feature_name(
-            model_dictionary_key, gal_type_list, known_gal_type=known_gal_type)
+            model_dictionary_key, gal_type_list, known_gal_type=known_gal_type
+        )
     substr = "The first substring of each key of the ``model_dictionary``"
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception4():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 
-    model_dictionary_key = 'Air Bud 4: Seventh Inning Fetch'.lower()
+    model_dictionary_key = "Air Bud 4: Seventh Inning Fetch".lower()
     gal_type_list = model.gal_types
-    known_gal_type = 'Air Bud 4'.lower()
+    known_gal_type = "Air Bud 4".lower()
     with pytest.raises(HalotoolsError) as err:
         model._infer_gal_type_and_feature_name(
-            model_dictionary_key, gal_type_list, known_gal_type=known_gal_type)
+            model_dictionary_key, gal_type_list, known_gal_type=known_gal_type
+        )
     substr = "The model_dictionary key ``air bud 4: seventh inning fetch`` must be comprised of"
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception5():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 
-    model_dictionary_key = 'Air Bud_: The Dog is in the House'.lower()
+    model_dictionary_key = "Air Bud_: The Dog is in the House".lower()
     gal_type_list = model.gal_types
     with pytest.raises(HalotoolsError) as err:
         model._infer_gal_type_and_feature_name(
-            model_dictionary_key, gal_type_list,
-            known_feature_name="He Sits, He Stays, He Shoots, He Scores")
+            model_dictionary_key,
+            gal_type_list,
+            known_feature_name="He Sits, He Stays, He Shoots, He Scores",
+        )
     substr = "The second substring of each key of the ``model_dictionary`` "
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception6():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 
-    model_dictionary_key = 'Air Bud_: The Dog is in the House'.lower()
+    model_dictionary_key = "Air Bud_: The Dog is in the House".lower()
     gal_type_list = model.gal_types
     with pytest.raises(HalotoolsError) as err:
         model._infer_gal_type_and_feature_name(
-            model_dictionary_key, gal_type_list,
-            known_feature_name="The Dog is in the House".lower())
+            model_dictionary_key,
+            gal_type_list,
+            known_feature_name="The Dog is in the House".lower(),
+        )
     substr = "the ``gal_type`` and ``feature_name`` substrings, separated by a '_', in that order"
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception7():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 
-    model_dictionary_key = 'Air Bud_: The Dog is in the House'.lower()
-    gal_type_list = ['Air', 'Bud']
+    model_dictionary_key = "Air Bud_: The Dog is in the House".lower()
+    gal_type_list = ["Air", "Bud"]
     with pytest.raises(HalotoolsError) as err:
-        model._infer_gal_type_and_feature_name(
-            model_dictionary_key, gal_type_list)
+        model._infer_gal_type_and_feature_name(model_dictionary_key, gal_type_list)
     substr = "The ``_infer_gal_type_and_feature_name`` method was unable to identify"
     assert substr in err.value.args[0]
 
 
 def test_raises_appropriate_exception8():
-    """
-    """
+    """"""
     model_dict_no_redshift = zheng07_model_dictionary()
     model = HodModelFactory(**model_dict_no_redshift)
 

From 2b642246b6f7fb77e09c6e468f3526f0b24d2660 Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 17:16:50 -0600
Subject: [PATCH 7/9] Pep8 changes to subhalo mock factory

---
 .../factories/subhalo_mock_factory.py         | 65 +++++++++++--------
 1 file changed, 38 insertions(+), 27 deletions(-)

diff --git a/halotools/empirical_models/factories/subhalo_mock_factory.py b/halotools/empirical_models/factories/subhalo_mock_factory.py
index 9ff31af66..1e3445695 100644
--- a/halotools/empirical_models/factories/subhalo_mock_factory.py
+++ b/halotools/empirical_models/factories/subhalo_mock_factory.py
@@ -19,15 +19,17 @@
 from ...custom_exceptions import HalotoolsError
 
 
-__all__ = ['SubhaloMockFactory']
-__author__ = ['Andrew Hearin']
+__all__ = ["SubhaloMockFactory"]
+__author__ = ["Andrew Hearin"]
 
-unavailable_haloprop_msg = ("Your model requires that the ``%s`` key appear in the halo catalog,\n"
-    "but this column is not available in the catalog you attempted to populate.\n")
+unavailable_haloprop_msg = (
+    "Your model requires that the ``%s`` key appear in the halo catalog,\n"
+    "but this column is not available in the catalog you attempted to populate.\n"
+)
 
 
 class SubhaloMockFactory(MockFactory):
-    """ Class responsible for populating a simulation with a
+    """Class responsible for populating a simulation with a
     population of mock galaxies based on models generated by
     `~halotools.empirical_models.SubhaloModelFactory`.
 
@@ -61,23 +63,25 @@ def __init__(self, **kwargs):
         """
 
         MockFactory.__init__(self, **kwargs)
-        halocat = kwargs['halocat']
+        halocat = kwargs["halocat"]
 
         # Pre-compute any additional halo properties required by the model
         self.preprocess_halo_catalog(halocat)
         self.precompute_galprops()
 
     def preprocess_halo_catalog(self, halocat):
-        """ Method to pre-process a halo catalog upon instantiation of the mock object.
-        """
+        """Method to pre-process a halo catalog upon instantiation of the mock object."""
         halo_table = halocat.halo_table
 
-        if (('halo_hostid' not in self.additional_haloprops) & ('halo_hostid' in list(halo_table.keys()))):
-            self.additional_haloprops.append('halo_hostid')
+        if ("halo_hostid" not in self.additional_haloprops) & (
+            "halo_hostid" in list(halo_table.keys())
+        ):
+            self.additional_haloprops.append("halo_hostid")
 
-        if (('halo_mvir_host_halo' not in self.additional_haloprops) &
-                ('halo_mvir_host_halo' in list(halo_table.keys()))):
-            self.additional_haloprops.append('halo_mvir_host_halo')
+        if ("halo_mvir_host_halo" not in self.additional_haloprops) & (
+            "halo_mvir_host_halo" in list(halo_table.keys())
+        ):
+            self.additional_haloprops.append("halo_mvir_host_halo")
 
         self.halo_table = Table()
         for key in self.additional_haloprops:
@@ -87,7 +91,7 @@ def preprocess_halo_catalog(self, halocat):
                 raise HalotoolsError(unavailable_haloprop_msg % key)
 
     def precompute_galprops(self):
-        """ Method pre-processes the input subhalo catalog, and pre-computes
+        """Method pre-processes the input subhalo catalog, and pre-computes
         all halo properties that will be inherited by the ``galaxy_table``.
 
         For example, in subhalo-based models, the phase space coordinates of the
@@ -107,13 +111,15 @@ def precompute_galprops(self):
             self.galaxy_table[key] = self.halo_table[key]
             self._precomputed_galprop_list.append(key)
 
-        phase_space_keys = ['x', 'y', 'z', 'vx', 'vy', 'vz']
+        phase_space_keys = ["x", "y", "z", "vx", "vy", "vz"]
         for newkey in phase_space_keys:
-            self.galaxy_table[newkey] = self.galaxy_table[model_defaults.host_haloprop_prefix+newkey]
+            self.galaxy_table[newkey] = self.galaxy_table[
+                model_defaults.host_haloprop_prefix + newkey
+            ]
             self._precomputed_galprop_list.append(newkey)
 
-        self.galaxy_table['galid'] = np.arange(len(self.galaxy_table))
-        self._precomputed_galprop_list.append('galid')
+        self.galaxy_table["galid"] = np.arange(len(self.galaxy_table))
+        self._precomputed_galprop_list.append("galid")
 
         # Component models may explicitly distinguish between certain types of halos,
         # e.g., subhalos vs. host halos. Since this assignment is not dynamic,
@@ -122,21 +128,24 @@ def precompute_galprops(self):
 
             try:
                 f = component_model.gal_type_func
-                newkey = feature + '_gal_type'
+                newkey = feature + "_gal_type"
                 self.galaxy_table[newkey] = f(table=self.galaxy_table)
                 self._precomputed_galprop_list.append(newkey)
             except AttributeError:
                 pass
             except:
                 clname = component_model.__class__.__name__
-                msg = ("\nThe `gal_type_func` attribute of the " + clname +
-                    "\nraises an unexpected exception when passed a halo table as a "
+                msg = (
+                    "\nThe `gal_type_func` attribute of the "
+                    + clname
+                    + "\nraises an unexpected exception when passed a halo table as a "
                     "table keyword argument. \n"
                     "If the features in your component model have explicit dependence "
                     "on galaxy type, \nthen you must implement the `gal_type_func` mechanism "
                     "in such a way that\nthis function accepts a "
                     "length-N halo table as a ``table`` keyword argument, \n"
-                    "and returns a length-N array of strings.\n")
+                    "and returns a length-N array of strings.\n"
+                )
                 raise HalotoolsError(msg)
 
     def populate(self, seed=None):
@@ -237,17 +246,19 @@ def populate(self, seed=None):
                 seed += 1
             func(table=self.galaxy_table, seed=seed)
 
-        if hasattr(self.model, 'galaxy_selection_func'):
+        if hasattr(self.model, "galaxy_selection_func"):
             mask = self.model.galaxy_selection_func(self.galaxy_table)
             self.galaxy_table = self.galaxy_table[mask]
 
     def _allocate_memory(self, seed=None):
-        """
-        """
+        """"""
         Ngals = len(self.galaxy_table)
 
-        new_column_generator = (key for key in self.model._galprop_dtypes_to_allocate.names
-            if key not in self._precomputed_galprop_list)
+        new_column_generator = (
+            key
+            for key in self.model._galprop_dtypes_to_allocate.names
+            if key not in self._precomputed_galprop_list
+        )
 
         for key in new_column_generator:
             dt = self.model._galprop_dtypes_to_allocate[key]

From 2100bb2d983c8c93a74e383675589648c3ddcaf6 Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 17:19:48 -0600
Subject: [PATCH 8/9] Removed halo_upid column from
 default_haloprop_list_inherited_by_mock

---
 halotools/empirical_models/factories/subhalo_mock_factory.py    | 2 ++
 .../empirical_models/factories/tests/test_hod_model_factory.py  | 1 -
 halotools/empirical_models/model_defaults.py                    | 1 -
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/halotools/empirical_models/factories/subhalo_mock_factory.py b/halotools/empirical_models/factories/subhalo_mock_factory.py
index 1e3445695..a678187e6 100644
--- a/halotools/empirical_models/factories/subhalo_mock_factory.py
+++ b/halotools/empirical_models/factories/subhalo_mock_factory.py
@@ -73,6 +73,8 @@ def preprocess_halo_catalog(self, halocat):
         """Method to pre-process a halo catalog upon instantiation of the mock object."""
         halo_table = halocat.halo_table
 
+        self.additional_haloprops.append("halo_upid")
+
         if ("halo_hostid" not in self.additional_haloprops) & (
             "halo_hostid" in list(halo_table.keys())
         ):
diff --git a/halotools/empirical_models/factories/tests/test_hod_model_factory.py b/halotools/empirical_models/factories/tests/test_hod_model_factory.py
index 2cea5e0b4..3017a35d7 100644
--- a/halotools/empirical_models/factories/tests/test_hod_model_factory.py
+++ b/halotools/empirical_models/factories/tests/test_hod_model_factory.py
@@ -61,7 +61,6 @@ def test_unavailable_upid():
     m = PrebuiltHodModelFactory("zheng07")
 
     m.populate_mock(halocat=halocat)
-    assert np.allclose(m.mock.halo_table["halo_upid"], -1)
 
 
 def test_censat_consistency_check():
diff --git a/halotools/empirical_models/model_defaults.py b/halotools/empirical_models/model_defaults.py
index 1967b547e..8fc67120f 100644
--- a/halotools/empirical_models/model_defaults.py
+++ b/halotools/empirical_models/model_defaults.py
@@ -36,7 +36,6 @@
     "halo_vz",
     "halo_mvir",
     "halo_rvir",
-    "halo_upid",
 ]
 
 prim_haloprop_key = "halo_mvir"

From 7cfacdc9531fae6707f0cc5bc4b4acb2f54ee72c Mon Sep 17 00:00:00 2001
From: Andrew Hearin <ahearin@anl.gov>
Date: Fri, 19 Feb 2021 17:49:52 -0600
Subject: [PATCH 9/9] Added dedicated regression testing module for convenience

---
 .../tests/test_github_993_regression.py       | 25 +++++++++++++++++++
 .../hod_models/tests/test_zheng07.py          | 17 -------------
 halotools/empirical_models/model_defaults.py  |  2 --
 3 files changed, 25 insertions(+), 19 deletions(-)
 create mode 100644 halotools/empirical_models/composite_models/hod_models/tests/test_github_993_regression.py

diff --git a/halotools/empirical_models/composite_models/hod_models/tests/test_github_993_regression.py b/halotools/empirical_models/composite_models/hod_models/tests/test_github_993_regression.py
new file mode 100644
index 000000000..65925b771
--- /dev/null
+++ b/halotools/empirical_models/composite_models/hod_models/tests/test_github_993_regression.py
@@ -0,0 +1,25 @@
+"""
+"""
+from .....sim_manager import FakeSim
+from ....factories import PrebuiltHodModelFactory
+import numpy as np
+
+
+def test_mass_definition_flexibility2():
+    """Regression test for Issue #993."""
+    halocat = FakeSim()
+    halocat.halo_table["halo_mass_custom"] = np.copy(halocat.halo_table["halo_mvir"])
+    halocat.halo_table["halo_radius_custom"] = np.copy(halocat.halo_table["halo_rvir"])
+    halocat.halo_table.remove_column("halo_upid")
+    halocat.halo_table.remove_column("halo_mvir")
+    halocat.halo_table.remove_column("halo_rvir")
+    model = PrebuiltHodModelFactory(
+        "zheng07",
+        mdef="custom",
+        halo_mass_column_key="halo_mass_custom",
+        prim_haloprop_key="halo_mass_custom",
+        halo_boundary_key="halo_radius_custom",
+    )
+    assert model.halo_boundary_key == "halo_mass_custom"
+    assert model.prim_haloprop_key == "halo_mass_custom"
+    model.populate_mock(halocat)
diff --git a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
index 4d672d54e..81e125949 100644
--- a/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
+++ b/halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py
@@ -116,20 +116,3 @@ def test_mass_definition_flexibility():
         halocat.halo_table["halo_mvir"]
     )
     model.populate_mock(halocat, seed=43)
-
-
-def test_mass_definition_flexibility2():
-    """Regression test for Issue #993."""
-    halocat = FakeSim()
-    halocat.halo_table["halo_mass_custom"] = np.copy(halocat.halo_table["halo_mvir"])
-    halocat.halo_table["halo_radius_custom"] = np.copy(halocat.halo_table["halo_rvir"])
-    halocat.halo_table.remove_column("halo_upid")
-    halocat.halo_table.remove_column("halo_mvir")
-    halocat.halo_table.remove_column("halo_rvir")
-    model = PrebuiltHodModelFactory(
-        "zheng07",
-        mdef="custom",
-        prim_haloprop_key="halo_mass_custom",
-        halo_boundary_key="halo_radius_custom",
-    )
-    model.populate_mock(halocat)
diff --git a/halotools/empirical_models/model_defaults.py b/halotools/empirical_models/model_defaults.py
index 8fc67120f..8ca09a139 100644
--- a/halotools/empirical_models/model_defaults.py
+++ b/halotools/empirical_models/model_defaults.py
@@ -34,8 +34,6 @@
     "halo_vx",
     "halo_vy",
     "halo_vz",
-    "halo_mvir",
-    "halo_rvir",
 ]
 
 prim_haloprop_key = "halo_mvir"