Merge pull request #712 from mcveanlab/0.7.0-final

0.7.0 final

CHANGELOG.rst

@@ -1,11 +1,21 @@
 ********************
-[0.7.0] - 2019-XX-XX
+[0.7.0] - 2019-02-19
 ********************
 
+Separation of tskit from msprime. Msprime is now solely dedicated to simulating
+the coalescent, and all infrastucture for working with succinct tree sequences
+is now provided by tskit. To ensure compatability, msprime now imports code
+from tskit under the old names, which should ensure that all code continues
+to work without changes.
+
 **New features**
 
 - Ability to record the full ARG (Jere Koskela; #665)
 
+**Bug fixes**:
+
+- Fix deprecation warning (#695).
+
 
 **********************
 [0.7.0a1] - 2019-01-14

README.md

@@ -7,7 +7,6 @@ coalescent with recombination based on [tskit](https://tskit.readthedocs.org/en/
 Please see the [documentation](https://msprime.readthedocs.org/en/latest/)
 for further information and 
 [installation instructions](https://msprime.readthedocs.org/en/latest/installation.html).
-``msprime`` is 
 
 If you would like to help make ``msprime`` better, please see the 
 [developer documentation](https://msprime.readthedocs.org/en/latest/development.html)

msprime/simulations.py

@@ -102,8 +102,6 @@ def almost_equal(a, b, rel_tol=1e-9, abs_tol=0.0):
 def _check_population_configurations(population_configurations):
     err = (
         "Population configurations must be a list of PopulationConfiguration instances")
-    if not isinstance(population_configurations, collections.Iterable):
-        raise TypeError(err)
     for config in population_configurations:
         if not isinstance(config, PopulationConfiguration):
             raise TypeError(err)
@@ -587,8 +585,6 @@ def set_demographic_events(self, demographic_events):
         err = (
             "Demographic events must be a list of DemographicEvent instances "
             "sorted in non-decreasing order of time.")
-        if not isinstance(demographic_events, collections.Iterable):
-            raise TypeError(err)
         self.demographic_events = []
         self.model_change_events = []
         for event in demographic_events:

tests/test_highlevel.py

@@ -474,8 +474,7 @@ def f(Ne):
 
     def test_population_configurations(self):
         def f(configs):
-            return msprime.simulator_factory(
-                population_configurations=configs)
+            return msprime.simulator_factory(population_configurations=configs)
         for bad_type in [10, ["sdf"], "sdfsd"]:
             self.assertRaises(TypeError, f, bad_type)
         # Just test the basic equalities here. The actual
@@ -570,8 +569,7 @@ def test_default_migration_matrix(self):
     def test_demographic_events(self):
         for bad_type in ["sdf", 234, [12], [None]]:
             self.assertRaises(
-                TypeError, msprime.simulator_factory, 2,
-                demographic_events=bad_type)
+                TypeError, msprime.simulator_factory, 2, demographic_events=bad_type)
         # TODO test for bad values.
 
     def test_recombination_rate(self):