Fix pytest and other depreciation warnings / errors (#56)

* fix pytest and other depreciation warnings / errors

* update pinned packages for doc environment (fix nbsphinx)

* fix overwritten input dataset

doc/environment.yml

@@ -3,16 +3,16 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - attrs=18.2.0
-  - python=3.6
-  - numpy=1.14.5
+  - attrs=19.1.0
+  - python=3.7
+  - numpy=1.16.0
   - pandas=0.23.3
-  - xarray=0.10.9
-  - ipython=6.4.0
-  - matplotlib=2.2.2
+  - xarray=0.13.0
+  - ipython=7.8.0
+  - matplotlib=3.0.2
   - graphviz
   - python-graphviz
-  - nbconvert=5.2.1
-  - sphinx=1.7.6
-  - nbsphinx=0.3.3
-  - pandoc=1.19.2
+  - nbconvert=5.6.0
+  - sphinx=1.8.5
+  - nbsphinx=0.4.2
+  - pandoc=2.7.3

xsimlab/drivers.py

@@ -225,7 +225,8 @@ def _get_output_dataset(self):
                 var_name = '__'.join(key)
                 xr_vars[var_name] = self._to_xr_variable(key, clock)
 
-        out_ds = self.dataset.update(xr_vars)
+        out_ds = self.dataset.copy()
+        out_ds.update(xr_vars)
 
         # remove output_vars attributes in output dataset
         for clock in self.output_vars:

xsimlab/tests/fixture_model.py

@@ -19,7 +19,7 @@ def initialize(self):
         self.u_change = np.zeros_like(self.u)
 
     def run_step(self, *args):
-        self.u_change[:] = np.sum((d for d in self.u_diffs))
+        self.u_change[:] = sum((d for d in self.u_diffs))
 
     def finalize_step(self):
         self.u += self.u_change

xsimlab/tests/test_dot.py

@@ -94,8 +94,11 @@ def test_to_graphviz_attributes(model):
                     reason="IPython is not installed")
 @pytest.mark.parametrize('format,typ', [
     ('png', Image),
-    pytest.mark.xfail(('jpeg', Image),
-                      reason='jpeg not always supported in dot'),
+    pytest.param(
+        'jpeg', Image,
+        marks=pytest.mark.xfail(
+            reason='jpeg not always supported in dot')
+    ),
     ('dot', type(None)),
     ('pdf', type(None)),
     ('svg', SVG),
@@ -134,8 +137,11 @@ def test_dot_graph_no_ipython(model):
                     reason="IPython is not installed")
 @pytest.mark.parametrize('format,typ', [
     ('png', Image),
-    pytest.mark.xfail(('jpeg', Image),
-                      reason='jpeg not always supported in dot'),
+    pytest.param(
+        'jpeg', Image,
+        marks=pytest.mark.xfail(
+            reason='jpeg not always supported in dot')
+    ),
     ('dot', type(None)),
     ('pdf', type(None)),
     ('svg', SVG),

xsimlab/tests/test_drivers.py

@@ -119,6 +119,11 @@ def test_set_input_vars(self, in_dataset, xarray_driver,
             actual[0] = -9999
             assert not np.array_equal(actual, expected)
 
+    def test_get_output_dataset(self, in_dataset, xarray_driver):
+        # regression test: make sure a copy of input dataset is used
+        out_ds = xarray_driver.run_model()
+        assert not in_dataset.identical(out_ds)
+
     def test_run_model(self, in_dataset, out_dataset, xarray_driver):
         out_ds_actual = xarray_driver.run_model()
 

xsimlab/tests/test_variable.py

@@ -23,8 +23,8 @@ def test_as_dim_tuple_invalid():
 
     with pytest.raises(ValueError) as excinfo:
         _as_dim_tuple(invalid_dims)
-    assert "following combinations" in str(excinfo)
-    assert "('x',), ('y',) and ('x', 'y'), ('y', 'x')" in str(excinfo)
+    assert "following combinations" in str(excinfo.value)
+    assert "('x',), ('y',) and ('x', 'y'), ('y', 'x')" in str(excinfo.value)
 
 
 def test_foreign():

xsimlab/utils.py

@@ -3,8 +3,8 @@
 
 """
 import threading
-from collections import (Mapping, KeysView, ItemsView, ValuesView,
-                         OrderedDict)
+from collections import OrderedDict
+from collections.abc import Mapping, KeysView, ItemsView, ValuesView
 from contextlib import suppress
 from importlib import import_module