Merge pull request #995 from aphearin/mdef_bugfix

New keyword argument supports user-defined halo boundary

docs/install.rst

@@ -14,10 +14,14 @@ The simplest way to install the latest release of the code is with pip. Before i
 
 	pip install halotools
 
-Alternatively, you can install using conda::
+Alternatively, you can install using the astropy channel on conda::
 
 	conda install -c astropy halotools
 
+or via conda-forge:
+
+    conda install -c conda-forge halotools
+
 Either pip or conda will install the latest official release of the code.
 If instead you want the latest master branch,
 you will need to build the code from source following the instructions in the next section.
@@ -58,13 +62,13 @@ The first step is to clone the halotools repository::
 Installing one of the official releases
 ------------------------------------------
 
-All official releases of the code are tagged with their version name, e.g., v0.5.
+All official releases of the code are tagged with their version name, e.g., v0.7.
 To install a particular release::
 
-	git checkout v0.5
+	git checkout v0.7
 	python setup.py install
 
-This will install the v0.5 release of the code. Other official release versions (e.g., v0.1) can be installed similarly.
+This will install the v0.7 release of the code. Other official release versions (e.g., v0.5) can be installed similarly.
 
 Installing the most recent master branch
 ------------------------------------------
@@ -113,15 +117,15 @@ The h5py package is used for fast I/O of large simulated datasets.
 
 If you did not use pip, then you should be aware of the following strict requirements:
 
-- `Python <http://www.python.org/>`_: 2.7.x or 3.x
+- `Python <http://www.python.org/>`_: 3.7.x
 
 - `Numpy <http://www.numpy.org/>`_: 1.9 or later
 
 - `Scipy <http://www.scipy.org/>`_: 0.15 or later
 
 - `Cython <http://www.cython.org/>`_: 0.23 or later
 
-- `Astropy`_: 1.0 or later
+- `Astropy`_: 4.0 or later
 
 - `BeautifulSoup <http://www.crummy.com/software/BeautifulSoup/>`_: For crawling the web for halo catalogs.
 

docs/installing_halotools_with_virtualenv.rst

@@ -12,19 +12,19 @@ create a virtual environment that will automatically have compatible versions of
 By installing into a virtual environment, you will not change any of the
 packages that are already installed system-wide on your machine. In the example below, we will use conda to create a virtual environment with all the dependencies handled automatically::
 
-	conda create -n halotools_env python=3.7 astropy numpy scipy h5py requests beautifulsoup4 cython
+    conda create -n ht07 python=3.7 halotools=0.7 h5py ipython jupyter matplotlib
 
 In order to activate this environment::
 
-	source activate halotools_env
+	source activate ht07
 
 Then install halotools into this environment::
 
 	pip install halotools
 
 Or, alternatively, you can install the latest master branch by following the :ref:`install_from_source` instructions.
 
-Any additional packages you install into the ``halotools_env`` virtual environment will not impact your system-wide environment. Whenever you want to do science involving Halotools,
+Any additional packages you install into the ``ht07`` virtual environment will not impact your system-wide environment. Whenever you want to do science involving Halotools,
 just activate the environment and import the code. When you are done
 and wish to return to your normal system environment::
 

halotools/empirical_models/composite_models/hod_models/tests/test_zheng07.py

@@ -10,18 +10,22 @@
 from .....custom_exceptions import HalotoolsError
 from .....sim_manager import FakeSim
 
-__all__ = ('test_zheng07_composite1', 'test_zheng07_composite2')
+__all__ = ("test_zheng07_composite1", "test_zheng07_composite2")
 
 
 def test_zheng07_composite1():
     """ Ensure that the ``zheng07`` pre-built model does not accept non-Zheng07Cens.
     """
-    model1 = PrebuiltHodModelFactory('zheng07')
-    model2 = PrebuiltHodModelFactory('zheng07', modulate_with_cenocc=True)
+    model1 = PrebuiltHodModelFactory("zheng07")
+    model2 = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
 
     with pytest.raises(HalotoolsError) as err:
-        __ = PrebuiltHodModelFactory('zheng07', modulate_with_cenocc=True, cenocc_model=0)
-    substr = "Do not pass in the ``cenocc_model`` keyword to ``zheng07_model_dictionary``"
+        __ = PrebuiltHodModelFactory(
+            "zheng07", modulate_with_cenocc=True, cenocc_model=0
+        )
+    substr = (
+        "Do not pass in the ``cenocc_model`` keyword to ``zheng07_model_dictionary``"
+    )
     assert substr in err.value.args[0]
 
 
@@ -31,31 +35,39 @@ def test_zheng07_composite2():
     """
 
     class MyCenModel(OccupationComponent):
-
         def __init__(self, threshold):
-            OccupationComponent.__init__(self, gal_type='centrals',
-                    threshold=threshold, upper_occupation_bound=1.)
-
-            self.param_dict['new_cen_param'] = 0.5
+            OccupationComponent.__init__(
+                self,
+                gal_type="centrals",
+                threshold=threshold,
+                upper_occupation_bound=1.0,
+            )
+
+            self.param_dict["new_cen_param"] = 0.5
             self._suppress_repeated_param_warning = True
 
         def mean_occupation(self, **kwargs):
-            halo_table = kwargs['table']
-            result = np.zeros(len(halo_table)) + self.param_dict['new_cen_param']
+            halo_table = kwargs["table"]
+            result = np.zeros(len(halo_table)) + self.param_dict["new_cen_param"]
             return result
 
     centrals_occupation = MyCenModel(threshold=-20)
-    satellites_occupation = Zheng07Sats(threshold=-20,
-        modulate_with_cenocc=True, cenocc_model=centrals_occupation,
-        _suppress_repeated_param_warning=True)
+    satellites_occupation = Zheng07Sats(
+        threshold=-20,
+        modulate_with_cenocc=True,
+        cenocc_model=centrals_occupation,
+        _suppress_repeated_param_warning=True,
+    )
 
     centrals_profile = TrivialPhaseSpace()
     satellites_profile = NFWPhaseSpace()
 
-    model_dict = ({'centrals_occupation': centrals_occupation,
-        'centrals_profile': centrals_profile,
-        'satellites_occupation': satellites_occupation,
-        'satellites_profile': satellites_profile})
+    model_dict = {
+        "centrals_occupation": centrals_occupation,
+        "centrals_profile": centrals_profile,
+        "satellites_occupation": satellites_occupation,
+        "satellites_profile": satellites_profile,
+    }
 
     composite_model = HodModelFactory(**model_dict)
 
@@ -67,27 +79,42 @@ def test_modulate_with_cenocc1():
     """ 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)
-    assert model1.model_dictionary[u'satellites_occupation'].modulate_with_cenocc is True
+    model1 = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
+    assert (
+        model1.model_dictionary[u"satellites_occupation"].modulate_with_cenocc is True
+    )
 
 
 def test_modulate_with_cenocc2():
     """ 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)
+    model = PrebuiltHodModelFactory("zheng07", modulate_with_cenocc=True)
     test_mass = 1e12
     ncen1 = model.mean_occupation_satellites(prim_haloprop=test_mass)
-    model.param_dict['logMmin'] *= 1.5
+    model.param_dict["logMmin"] *= 1.5
     ncen2 = model.mean_occupation_satellites(prim_haloprop=test_mass)
     assert ncen1 != ncen2
 
 
 def test_host_centric_distance():
-        model = PrebuiltHodModelFactory('zheng07')
-        halocat = FakeSim(seed=43)
-        model.populate_mock(halocat, seed=43)
+    model = PrebuiltHodModelFactory("zheng07")
+    halocat = FakeSim(seed=43)
+    model.populate_mock(halocat, seed=43)
 
-        msg = "host_centric_distance key was never mapped during mock population"
-        assert np.any(model.mock.galaxy_table['host_centric_distance'] > 0), msg
+    msg = "host_centric_distance key was never mapped during mock population"
+    assert np.any(model.mock.galaxy_table["host_centric_distance"] > 0), msg
 
+
+def test_mass_definition_flexibility():
+    """ Regression test for Issue #993.
+    """
+    model = PrebuiltHodModelFactory(
+        "zheng07", mdef="200m", halo_boundary_key="halo_radius_arbitrary"
+    )
+    halocat = FakeSim(seed=43)
+    halocat.halo_table["halo_m200m"] = np.copy(halocat.halo_table["halo_mvir"])
+    halocat.halo_table["halo_radius_arbitrary"] = np.copy(
+        halocat.halo_table["halo_mvir"]
+    )
+    model.populate_mock(halocat, seed=43)