Merge pull request #184 from jeromekelleher/update-appveyor

Update appveyor config.

appveyor.yml

@@ -1,10 +1,10 @@
 environment:
   matrix:
-    # Disabling Py37 x64. Some weird problem with h5py. See github.com/tskit-dev/msprime/issues/678
-    # - PYTHON: "C:\\Miniconda37-x64"
-    - PYTHON: "C:\\Miniconda36-x64"
+    # Only using latest version of Python because builds are slow.
+    - PYTHON_VERSION: "3.7"
 
 init:
+  - cmd: SET PYTHON=C:\\Miniconda37-x64
   - cmd: ECHO Using %PYTHON%
 
 install:
@@ -14,13 +14,16 @@ install:
   - cmd: git config core.symlinks true
   - cmd: git reset --hard
   - cmd: conda config --add channels conda-forge
+  - cmd: conda create --yes -n testenv python=%PYTHON_VERSION%
+  - cmd: activate testenv
   - cmd: conda install --yes --file=requirements\conda-minimal.txt
   - cmd: conda info -a
+  - cmd: python --version
 
 build_script:
   - cmd: python setup.py build_ext --inplace
   - cmd: pip install daiquiri # daiquiri isn't available on conda-forge
-  - cmd: nosetests -vs
+  - cmd: python -m nose
 
 after_test:
   - cmd: python setup.py bdist_wheel

tests/test_inference.py

@@ -628,7 +628,8 @@ def verify_inserted_ancestors(self, ts):
             tsinfer.check_ancestors_ts(ancestors_ts)
             self.assertEqual(ancestor_data.num_sites, ancestors_ts.num_sites)
             self.assertEqual(ancestor_data.num_ancestors, ancestors_ts.num_samples)
-            self.assertTrue(np.array_equal(ancestors_ts.genotype_matrix(), A))
+            self.assertTrue(np.array_equal(
+                ancestors_ts.genotype_matrix(impute_missing_data=True), A))
             inferred_ts = tsinfer.match_samples(
                 sample_data, ancestors_ts, engine=engine)
             self.assertTrue(np.array_equal(