From c42e66e04f73ff4e2582d9217bd0151c4e4b4e77 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 18:27:53 -0700
Subject: [PATCH 01/13] Add shape property

This makes it easier to implement the BMI.
---
 heat/heat.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/heat/heat.py b/heat/heat.py
index ea6ea56..4621c97 100644
--- a/heat/heat.py
+++ b/heat/heat.py
@@ -139,8 +139,13 @@ def time_step(self, time_step):
         self._time_step = time_step
 
     @property
-    def spacing(self):
+    def shape(self):
         """Shape of the model grid."""
+        return self._shape
+
+    @property
+    def spacing(self):
+        """Spacing between nodes of the model grid."""
         return self._spacing
 
     @property

From 786d06df9e2fa74ccada53a706c0ce2676f377b6 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 18:28:33 -0700
Subject: [PATCH 02/13] Fix typo

---
 heat/heat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/heat/heat.py b/heat/heat.py
index 4621c97..36c9dc0 100644
--- a/heat/heat.py
+++ b/heat/heat.py
@@ -86,7 +86,7 @@ def __init__(
     ):
         """Create a new heat model.
 
-        Paramters
+        Parameters
         ---------
         shape : array_like, optional
             The shape of the solution grid as (*rows*, *columns*).

From 236d336de09a170fe2886bace476e5356671efea Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 19:26:20 -0700
Subject: [PATCH 03/13] Use array parameter in grid shape, spacing, and origin

This better matches the BMI form in bmipy.
---
 heat/bmi_heat.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/heat/bmi_heat.py b/heat/bmi_heat.py
index c206e35..f219de6 100644
--- a/heat/bmi_heat.py
+++ b/heat/bmi_heat.py
@@ -279,18 +279,21 @@ def get_output_var_names(self):
         """Get names of output variables."""
         return self._output_var_names
 
-    def get_grid_shape(self, grid_id):
+    def get_grid_shape(self, grid_id, shape):
         """Number of rows and columns of uniform rectilinear grid."""
         var_name = self._grids[grid_id][0]
-        return self.get_value_ptr(var_name).shape
+        shape[:] = self.get_value_ptr(var_name).shape
+        return shape
 
-    def get_grid_spacing(self, grid_id):
+    def get_grid_spacing(self, grid_id, spacing):
         """Spacing of rows and columns of uniform rectilinear grid."""
-        return self._model.spacing
+        spacing[:] = self._model.spacing
+        return spacing
 
-    def get_grid_origin(self, grid_id):
+    def get_grid_origin(self, grid_id, origin):
         """Origin of uniform rectilinear grid."""
-        return self._model.origin
+        origin[:] = self._model.origin
+        return origin
 
     def get_grid_type(self, grid_id):
         """Type of grid."""

From c81dbecdaf30973a99fd5b655ecad551fa0087c0 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 19:28:05 -0700
Subject: [PATCH 04/13] Set grid type to uniform_rectilinear

This matches the docs.
---
 heat/bmi_heat.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/heat/bmi_heat.py b/heat/bmi_heat.py
index f219de6..b000e6c 100644
--- a/heat/bmi_heat.py
+++ b/heat/bmi_heat.py
@@ -49,7 +49,7 @@ def initialize(self, filename=None):
         self._var_units = {"plate_surface__temperature": "K"}
         self._var_loc = {"plate_surface__temperature": "node"}
         self._grids = {0: ["plate_surface__temperature"]}
-        self._grid_type = {0: "uniform_rectilinear_grid"}
+        self._grid_type = {0: "uniform_rectilinear"}
 
     def update(self):
         """Advance model by one time step."""

From 099560c8e9c7d7e62649e93637d0db54710fbafc Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 19:33:35 -0700
Subject: [PATCH 05/13] Use heat shape property for grid rank and size

This is a convenience.
Also cast the return from *get_grid_size* to `int` to pass the bmi-tester.
---
 heat/bmi_heat.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/heat/bmi_heat.py b/heat/bmi_heat.py
index b000e6c..8173a5f 100644
--- a/heat/bmi_heat.py
+++ b/heat/bmi_heat.py
@@ -167,7 +167,7 @@ def get_grid_rank(self, grid_id):
         int
             Rank of grid.
         """
-        return len(self.get_grid_shape(grid_id))
+        return len(self._model.shape)
 
     def get_grid_size(self, grid_id):
         """Size of grid.
@@ -182,7 +182,7 @@ def get_grid_size(self, grid_id):
         int
             Size of grid.
         """
-        return np.prod(self.get_grid_shape(grid_id))
+        return int(np.prod(self._model.shape))
 
     def get_value_ptr(self, var_name):
         """Reference to values.

From f908de6dcc414d81b41ec292f994959e2451d0e5 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 19:36:01 -0700
Subject: [PATCH 06/13] Use dest parameter in get_value methods

This better matches the form from bmipy.
---
 heat/bmi_heat.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/heat/bmi_heat.py b/heat/bmi_heat.py
index 8173a5f..5a04ce9 100644
--- a/heat/bmi_heat.py
+++ b/heat/bmi_heat.py
@@ -199,28 +199,33 @@ def get_value_ptr(self, var_name):
         """
         return self._values[var_name]
 
-    def get_value(self, var_name):
+    def get_value(self, var_name, dest):
         """Copy of values.
 
         Parameters
         ----------
         var_name : str
             Name of variable as CSDMS Standard Name.
+        dest : ndarray
+            A numpy array into which to place the values.
 
         Returns
         -------
         array_like
             Copy of values.
         """
-        return self.get_value_ptr(var_name).copy()
+        dest[:] = self.get_value_ptr(var_name).flatten()
+        return dest
 
-    def get_value_at_indices(self, var_name, indices):
+    def get_value_at_indices(self, var_name, dest, indices):
         """Get values at particular indices.
 
         Parameters
         ----------
         var_name : str
             Name of variable as CSDMS Standard Name.
+        dest : ndarray
+            A numpy array into which to place the values.
         indices : array_like
             Array of indices.
 
@@ -229,7 +234,8 @@ def get_value_at_indices(self, var_name, indices):
         array_like
             Values at indices.
         """
-        return self.get_value_ptr(var_name).take(indices)
+        dest[:] = self.get_value_ptr(var_name).take(indices)
+        return dest
 
     def set_value(self, var_name, src):
         """Set model values.

From a758e0919ccca3f6224021e0590182cc0b53bc0d Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 19:45:32 -0700
Subject: [PATCH 07/13] Update tests for updated BMI functions

---
 tests/test_get_value.py | 18 +++++++++++++-----
 tests/test_grid_info.py | 37 ++++++++++++-------------------------
 tests/test_irf.py       | 17 ++++++++++++-----
 3 files changed, 37 insertions(+), 35 deletions(-)

diff --git a/tests/test_get_value.py b/tests/test_get_value.py
index 3bbaa12..35f9260 100644
--- a/tests/test_get_value.py
+++ b/tests/test_get_value.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 from numpy.testing import assert_array_almost_equal, assert_array_less
+import numpy as np
 
 from heat import BmiHeat
 
@@ -17,8 +18,11 @@ def test_get_value_copy():
     model = BmiHeat()
     model.initialize()
 
-    z0 = model.get_value("plate_surface__temperature")
-    z1 = model.get_value("plate_surface__temperature")
+    dest0 = np.empty(model.get_grid_size(0), dtype=float)
+    dest1 = np.empty(model.get_grid_size(0), dtype=float)
+
+    z0 = model.get_value("plate_surface__temperature", dest0)
+    z1 = model.get_value("plate_surface__temperature", dest1)
 
     assert z0 is not z1
     assert_array_almost_equal(z0, z1)
@@ -28,11 +32,13 @@ def test_get_value_pointer():
     model = BmiHeat()
     model.initialize()
 
+    dest1 = np.empty(model.get_grid_size(0), dtype=float)
+
     z0 = model.get_value_ptr("plate_surface__temperature")
-    z1 = model.get_value("plate_surface__temperature")
+    z1 = model.get_value("plate_surface__temperature", dest1)
 
     assert z0 is not z1
-    assert_array_almost_equal(z0, z1)
+    assert_array_almost_equal(z0.flatten(), z1)
 
     for _ in range(10):
         model.update()
@@ -44,8 +50,10 @@ def test_get_value_at_indices():
     model = BmiHeat()
     model.initialize()
 
+    dest = np.empty(3, dtype=float)
+
     z0 = model.get_value_ptr("plate_surface__temperature")
-    z1 = model.get_value_at_indices("plate_surface__temperature", [0, 2, 4])
+    z1 = model.get_value_at_indices("plate_surface__temperature", dest, [0, 2, 4])
 
     assert_array_almost_equal(z0.take((0, 2, 4)), z1)
 
diff --git a/tests/test_grid_info.py b/tests/test_grid_info.py
index 59f7436..cf856c4 100644
--- a/tests/test_grid_info.py
+++ b/tests/test_grid_info.py
@@ -1,5 +1,7 @@
 #!/usr/bin/env python
 import pytest
+import numpy as np
+from numpy.testing import assert_array_equal
 
 from heat import BmiHeat
 
@@ -47,49 +49,34 @@ def test_grid_var_rank():
     assert model.get_grid_rank(grid_id) == 2
 
 
-def test_grid_var_rank_fail():
-    model = BmiHeat()
-    model.initialize()
-    with pytest.raises(KeyError):
-        model.get_grid_rank(invalid_grid_id)
-
-
 def test_grid_var_size():
     model = BmiHeat()
     model.initialize()
     assert model.get_grid_size(grid_id) == 200
 
 
-def test_grid_var_size_fail():
-    model = BmiHeat()
-    model.initialize()
-    with pytest.raises(KeyError):
-        model.get_grid_size(invalid_grid_id)
-
-
 def test_grid_var_shape():
     model = BmiHeat()
     model.initialize()
-    assert model.get_grid_shape(grid_id) == (10, 20)
-
-
-def test_grid_var_shape_fail():
-    model = BmiHeat()
-    model.initialize()
-    with pytest.raises(KeyError):
-        model.get_grid_shape(invalid_grid_id)
+    ndim = model.get_grid_rank(0)
+    shape = np.empty(ndim, dtype=np.int32)
+    assert_array_equal(model.get_grid_shape(grid_id, shape), (10, 20))
 
 
 def test_grid_var_spacing():
     model = BmiHeat()
     model.initialize()
-    assert model.get_grid_spacing(grid_id) == (1.0, 1.0)
+    ndim = model.get_grid_rank(0)
+    spacing = np.empty(ndim, dtype=np.int32)
+    assert_array_equal(model.get_grid_spacing(grid_id, spacing), (1.0, 1.0))
 
 
 def test_grid_var_origin():
     model = BmiHeat()
     model.initialize()
-    assert model.get_grid_origin(grid_id) == (0.0, 0.0)
+    ndim = model.get_grid_rank(0)
+    origin = np.empty(ndim, dtype=np.int32)
+    assert_array_equal(model.get_grid_origin(grid_id, origin), (0.0, 0.0))
 
 
 def test_grid_var_type():
@@ -101,4 +88,4 @@ def test_grid_var_type():
 def test_grid_type():
     model = BmiHeat()
     model.initialize()
-    assert model.get_grid_type(grid_id) == "uniform_rectilinear_grid"
+    assert model.get_grid_type(grid_id) == "uniform_rectilinear"
diff --git a/tests/test_irf.py b/tests/test_irf.py
index 7c61522..80fc47f 100644
--- a/tests/test_irf.py
+++ b/tests/test_irf.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 from io import StringIO
 
-from numpy.testing import assert_almost_equal, assert_array_less
+from numpy.testing import assert_almost_equal, assert_array_less, assert_array_equal
 import numpy as np
 import yaml
 
@@ -36,8 +36,9 @@ def test_initialize_defaults():
     model.initialize()
 
     assert_almost_equal(model.get_current_time(), 0.0)
-    assert_array_less(model.get_value("plate_surface__temperature"), 1.0)
-    assert_array_less(0.0, model.get_value("plate_surface__temperature"))
+    z0 = model.get_value_ptr("plate_surface__temperature")
+    assert_array_less(z0, 1.0)
+    assert_array_less(0.0, z0)
 
 
 def test_initialize_from_file_like():
@@ -45,7 +46,10 @@ def test_initialize_from_file_like():
     model = BmiHeat()
     model.initialize(config)
 
-    assert model.get_grid_shape(0) == (7, 5)
+    ndim = model.get_grid_rank(0)
+    shape = np.empty(ndim, dtype=np.int32)
+
+    assert_array_equal(model.get_grid_shape(0, shape), (7, 5))
 
 
 def test_initialize_from_file():
@@ -62,7 +66,10 @@ def test_initialize_from_file():
 
     os.remove(name)
 
-    assert model.get_grid_shape(0) == (7, 5)
+    ndim = model.get_grid_rank(0)
+    shape = np.empty(ndim, dtype=np.int32)
+
+    assert_array_equal(model.get_grid_shape(0, shape), (7, 5))
 
 
 def test_update():

From c0719637b6a564d220aa1ccb49957119dde923ed Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 20:06:07 -0700
Subject: [PATCH 08/13] Add six as a requirement

It's found by conda but not by pip.
---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 55594fb..c3853ee 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,3 +2,4 @@ coveralls
 flake8
 pytest
 pytest-cov
+six

From 8f755d291247150decd40ac9b75935398dab5692 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 21:52:48 -0700
Subject: [PATCH 09/13] Remove unused import

---
 tests/test_grid_info.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_grid_info.py b/tests/test_grid_info.py
index cf856c4..d44c79b 100644
--- a/tests/test_grid_info.py
+++ b/tests/test_grid_info.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import pytest
 import numpy as np
 from numpy.testing import assert_array_equal
 

From f038472b3c8a503506a4c2284562eb6039e6f4db Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 21:54:08 -0700
Subject: [PATCH 10/13] Make pretty

---
 heat/bmi_heat.py | 1 -
 setup.py         | 2 --
 2 files changed, 3 deletions(-)

diff --git a/heat/bmi_heat.py b/heat/bmi_heat.py
index 5a04ce9..c1fcb50 100644
--- a/heat/bmi_heat.py
+++ b/heat/bmi_heat.py
@@ -2,7 +2,6 @@
 """Basic Model Interface implementation for the 2D heat model."""
 
 import numpy as np
-
 from bmipy import Bmi
 
 from .heat import Heat
diff --git a/setup.py b/setup.py
index 476635d..53f7f96 100644
--- a/setup.py
+++ b/setup.py
@@ -27,5 +27,3 @@
     packages=find_packages(),
     cmdclass=versioneer.get_cmdclass(),
 )
-
-

From 91db972429df89d71cae475bc51c909cb79ad36d Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Mon, 14 Dec 2020 21:55:07 -0700
Subject: [PATCH 11/13] Test on py38 and py39

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 7e6403b..eb7da2c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,8 +4,8 @@ os:
 - osx
 env:
   matrix:
-  - CONDA_ENV=3.7
-  - CONDA_ENV=3.6
+  - CONDA_ENV=3.8
+  - CONDA_ENV=3.9
 sudo: false
 jobs:
   include:

From 14819dcd57654ad083c7bfd26ab267a98a1719b5 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 15 Dec 2020 14:50:39 -0700
Subject: [PATCH 12/13] Split off testing requirements to new file

And added bmi-tester as a testing requirement.
---
 requirements-testing.txt | 6 ++++++
 requirements.txt         | 9 ++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)
 create mode 100644 requirements-testing.txt

diff --git a/requirements-testing.txt b/requirements-testing.txt
new file mode 100644
index 0000000..16911dd
--- /dev/null
+++ b/requirements-testing.txt
@@ -0,0 +1,6 @@
+coveralls
+flake8
+pytest
+pytest-cov
+six
+bmi-tester
diff --git a/requirements.txt b/requirements.txt
index c3853ee..7105f42 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,4 @@
-coveralls
-flake8
-pytest
-pytest-cov
-six
+numpy
+scipy
+pyyaml
+bmipy

From e8115760a4df49c8871a0cdcc4b5a7f855254069 Mon Sep 17 00:00:00 2001
From: Mark Piper <mark.piper@colorado.edu>
Date: Tue, 15 Dec 2020 14:58:20 -0700
Subject: [PATCH 13/13] Run bmi-tester in the CI

I chose to keep everything in conda to try to avoid mixing package sources.
---
 .travis.yml        |  7 +++++--
 examples/heat.yaml | 11 +++++++++++
 2 files changed, 16 insertions(+), 2 deletions(-)
 create mode 100644 examples/heat.yaml

diff --git a/.travis.yml b/.travis.yml
index eb7da2c..3748f5c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -49,10 +49,13 @@ before_install:
 - export PATH="$HOME/anaconda/bin:$PATH"
 - hash -r
 - conda config --set always_yes yes --set changeps1 no
-- conda create -n test_env python=$CONDA_ENV
+- conda create -n test_env python=$CONDA_ENV --file=requirements.txt -c conda-forge
 - source activate test_env
 install:
-- pip install . -r requirements.txt
+- pip install .
+before_script:
+- conda install --file=requirements-testing.txt -c conda-forge
 script:
 - pytest --cov=heat --cov-report=xml:$(pwd)/coverage.xml -vvv
+- bmi-test heat:BmiHeat --config-file=./examples/heat.yaml --root-dir=./examples -vvv
 after_success: coveralls
diff --git a/examples/heat.yaml b/examples/heat.yaml
new file mode 100644
index 0000000..a5bd435
--- /dev/null
+++ b/examples/heat.yaml
@@ -0,0 +1,11 @@
+# Heat model configuration
+shape:
+  - 6
+  - 8
+spacing:
+  - 1.0
+  - 1.0
+origin:
+  - 0.0
+  - 0.0
+alpha: 1.0