Simplify unit tests to make it easier to read

quasielasticbayes/test/qldata_test.py

@@ -4,13 +4,10 @@
 import numpy as np
 import tempfile
 
-from quasielasticbayes.testing import load_json, add_path
+from quasielasticbayes.testing import add_path, load_json, DATA_DIR, RELATIVE_TOLERANCE_FIT, RELATIVE_TOLERANCE_PROB
 from quasielasticbayes.QLdata import qldata
 
 
-DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
-
-
 class QLdataTest(unittest.TestCase):
     """
     Characterization tests using inputs that have been accepted as correct.
@@ -19,13 +16,11 @@ class QLdataTest(unittest.TestCase):
     """
 
     def test_qlres_minimal_input(self):
-        # reference inputs
-        fin = 'qldata_input.json'
-        with open(os.path.join(DATA_DIR, 'qldata', fin), 'r') as fh:
-            inputs = load_json(fh)
-        with tempfile.TemporaryDirectory() as tmp_dir:
+        inputs = load_json("qldata", "qldata_input.json")
 
+        with tempfile.TemporaryDirectory() as tmp_dir:
             inputs['wrks'] = add_path(tmp_dir, inputs['wrks'])
+
             nd, xout, yout, eout, yfit, yprob = qldata(inputs['numb'],
                                                        inputs['Xv'],
                                                        inputs['Yv'],
@@ -42,16 +37,15 @@ def test_qlres_minimal_input(self):
                                                        inputs['wrkr'],
                                                        inputs['lwrk'])
             # verify
-            cf = 'qldata_output.json'
-            with open(os.path.join(DATA_DIR, 'qldata', cf), 'r') as fh:
+            with open(os.path.join(DATA_DIR, 'qldata', 'qldata_output.json'), 'r') as fh:
                 reference = load_json(fh)
 
             self.assertEqual(reference['nd'], nd)
             np.testing.assert_allclose(reference['xout'], xout)
             np.testing.assert_allclose(reference['yout'], yout)
             np.testing.assert_allclose(reference['eout'], eout)
-            np.testing.assert_allclose(reference['yfit'], yfit, rtol=1e-3)
-            np.testing.assert_allclose(reference['yprob'], yprob, rtol=1e-3)
+            np.testing.assert_allclose(reference['yfit'], yfit, rtol=RELATIVE_TOLERANCE_FIT)
+            np.testing.assert_allclose(reference['yprob'], yprob, rtol=RELATIVE_TOLERANCE_PROB)
 
 
 if __name__ == '__main__':

quasielasticbayes/test/qlres_test.py

@@ -5,11 +5,9 @@
 import numpy as np
 import sys
 
-from quasielasticbayes.testing import add_path, load_json
+from quasielasticbayes.testing import add_path, load_json, DATA_DIR, RELATIVE_TOLERANCE_FIT, RELATIVE_TOLERANCE_PROB
 from quasielasticbayes.QLres import qlres
 
-DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
-
 
 class QLresTest(unittest.TestCase):
     """
@@ -20,9 +18,7 @@ class QLresTest(unittest.TestCase):
 
     @unittest.skipIf(sys.platform == "darwin", "Reading the json reference file causes an unexplained crash.")
     def test_qlres_minimal_input(self):
-        # reference inputs
-        with open(os.path.join(DATA_DIR, 'qlres', 'qlres-input-spec-0.json'), 'r') as fh:
-            inputs = load_json(fh)
+        inputs = load_json("qlres", "qlres-input-spec-0.json")
 
         with tempfile.TemporaryDirectory() as tmp_dir:
             inputs['wrks'] = add_path(tmp_dir, inputs['wrks'])
@@ -41,8 +37,8 @@ def test_qlres_minimal_input(self):
         np.testing.assert_allclose(reference['xout'], xout)
         np.testing.assert_allclose(reference['yout'], yout)
         np.testing.assert_allclose(reference['eout'], eout)
-        np.testing.assert_allclose(reference['yfit'], yfit, rtol=1e-3)
-        np.testing.assert_allclose(reference['yprob'], yprob, rtol=1e-2)
+        np.testing.assert_allclose(reference['yfit'], yfit, rtol=RELATIVE_TOLERANCE_FIT)
+        np.testing.assert_allclose(reference['yprob'], yprob, rtol=RELATIVE_TOLERANCE_PROB)
 
 if __name__ == '__main__':
     unittest.main()

quasielasticbayes/test/qlse_test.py

@@ -4,13 +4,10 @@
 import numpy as np
 import tempfile
 
-from quasielasticbayes.testing import load_json, add_path
+from quasielasticbayes.testing import add_path, load_json, DATA_DIR, RELATIVE_TOLERANCE_FIT, RELATIVE_TOLERANCE_PROB
 from quasielasticbayes.QLres import qlres
 
 
-DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
-
-
 class QLresTest(unittest.TestCase):
     """
     Characterization tests using inputs that have been accepted as correct.
@@ -19,13 +16,11 @@ class QLresTest(unittest.TestCase):
     """
 
     def test_qlres_minimal_input(self):
-        # reference inputs
-        fin = 'qlse_input.json'
-        with open(os.path.join(DATA_DIR, 'qlse', fin), 'r') as fh:
-            inputs = load_json(fh)
-        with tempfile.TemporaryDirectory() as tmp_dir:
+        inputs = load_json("qlse", "qlse_input.json")
 
+        with tempfile.TemporaryDirectory() as tmp_dir:
             inputs['wrks'] = add_path(tmp_dir, inputs['wrks'])
+
             nd, xout, yout, eout, yfit, yprob = qlres(inputs['numb'],
                                                       inputs['Xv'],
                                                       inputs['Yv'],
@@ -51,8 +46,8 @@ def test_qlres_minimal_input(self):
             np.testing.assert_allclose(reference['xout'], xout)
             np.testing.assert_allclose(reference['yout'], yout)
             np.testing.assert_allclose(reference['eout'], eout)
-            np.testing.assert_allclose(reference['yfit'], yfit, rtol=1e-3)
-            np.testing.assert_allclose(reference['yprob'], yprob, rtol=1e-2)
+            np.testing.assert_allclose(reference['yfit'], yfit, rtol=RELATIVE_TOLERANCE_FIT)
+            np.testing.assert_allclose(reference['yprob'], yprob, rtol=RELATIVE_TOLERANCE_PROB)
 
 
 if __name__ == '__main__':

quasielasticbayes/test/testing.py

@@ -0,0 +1,37 @@
+"""Utility code to help with testing
+"""
+import base64
+import json
+import numpy as np
+import os
+
+RELATIVE_TOLERANCE_FIT=1e-3
+RELATIVE_TOLERANCE_PROB=1e-2
+
+
+def _json_numpy_obj_hook(dct):
+    """
+    Decodes a previously encoded numpy ndarray
+    with proper shape and dtype
+    :param dct: (dict) json encoded ndarray
+    :return: (ndarray) if input was an encoded ndarray
+    """
+    if isinstance(dct, dict) and '__ndarray__' in dct:
+        data = base64.b64decode(dct['__ndarray__'])
+        return np.frombuffer(data, dct['dtype']).reshape(dct['shape'])
+    return dct
+
+
+def load_json(*args, **kwargs):
+    """Loads a json-encoded file-like object to a dictionary.
+    Adds supports for decoding numpy arrays
+    See json.load.
+    """
+    kwargs.setdefault('object_hook', _json_numpy_obj_hook)
+    return json.load(*args, **kwargs)
+
+
+def add_path(file_path, file_name):
+    """Sets the path for a file
+    """
+    return os.path.join(file_path, file_name)

quasielasticbayes/testing.py

@@ -5,6 +5,11 @@
 import numpy as np
 import os
 
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
+
+RELATIVE_TOLERANCE_FIT=1e-3
+RELATIVE_TOLERANCE_PROB=1e-2
+
 
 def _json_numpy_obj_hook(dct):
     """
@@ -19,23 +24,16 @@ def _json_numpy_obj_hook(dct):
     return dct
 
 
-def load_json(*args, **kwargs):
+def load_json(sub_directory: str, filename: str):
     """Loads a json-encoded file-like object to a dictionary.
     Adds supports for decoding numpy arrays
     See json.load.
     """
-    kwargs.setdefault('object_hook', _json_numpy_obj_hook)
-    return json.load(*args, **kwargs)
+    with open(os.path.join(DATA_DIR, sub_directory, filename), 'r') as file:
+        return json.load(file, object_hook=_json_numpy_obj_hook)
 
 
 def add_path(file_path, file_name):
     """Sets the path for a file
     """
     return os.path.join(file_path, file_name)
-
-
-# def get_qlse_prob(ref):
-#     if sys.platform == 'win32':
-#         return ref
-#     else:
-#         return [-2.7656994e+04, -1.8887866e+2,  0.0, -5.8251953e-1]