Changeset ecb485c in sasmodels

Timestamp:

Jan 26, 2018 8:16:16 PM (7 years ago)

Author:

Paul Kienzle <pkienzle@…>

Branches:

master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

bb4ff2a

Parents:

a69d8cd (diff), ecf895e (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'master' into pytest

Files:

• sasmodels/mixture.py (modified) (1 diff)
• sasmodels/modelinfo.py (modified) (4 diffs)
• .travis.yml (modified) (2 diffs)
• appveyor.yml (modified) (3 diffs)
• conftest.py (added)
• pytest.ini (added)
• sasmodels/convert.py (modified) (1 diff)
• sasmodels/core.py (modified) (1 diff)
• sasmodels/model_test.py (modified) (4 diffs)
• sasmodels/sasview_model.py (modified) (1 diff)

sasmodels/mixture.py

@@ -94 +94 @@
             # If model is a sum model, each constituent model gets its own scale parameter
             scale_prefix = prefix
-            if prefix == '' and hasattr(part,"operation") and part.operation == '*':
+            if prefix == '' and getattr(part, "operation", '') == '*':
                 # `part` is a composition product model. Find the prefixes of
-                # it's parameters to form a new prefix for the scale, eg:
-                # a model with A*B*C will have ABC_scale
+                # it's parameters to form a new prefix for the scale.
+                # For example, a model with A*B*C will have ABC_scale.
                 sub_prefixes = []
                 for param in part.parameters.kernel_parameters:

sasmodels/modelinfo.py

@@ -69 +69 @@
         processed.append(parse_parameter(*p))
     partable = ParameterTable(processed)
+    partable.check_angles()
     return partable
 
@@ -421 +422 @@
         # type: (List[Parameter]) -> None
         self.kernel_parameters = parameters
-        self._check_angles()
         self._set_vector_lengths()
 
@@ -471 +471 @@
         self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
 
-    def _check_angles(self):
+    def check_angles(self):
+        """
+        Check that orientation angles are theta, phi and possibly psi.
+        """
         theta = phi = psi = -1
         for k, p in enumerate(self.kernel_parameters):
@@ -494 +497 @@
             if psi >= 0 and psi != phi+1:
                 raise TypeError("psi must follow phi")
-            #if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par):
-            #    raise TypeError("orientation parameters must appear at the "
-            #                    "end of the parameter table")
+            if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par):
+                raise TypeError("orientation parameters must appear at the "
+                                "end of the parameter table")
         elif theta >= 0 or phi >= 0 or psi >= 0:
             raise TypeError("oriented shapes must have both theta and phi and maybe psi")

.travis.yml

@@ -37 +37 @@
 - conda update --yes conda
 - conda info -a
-- conda install --yes python=$PY numpy scipy cython mako cffi
+# 2018-01-26 PAK: sasmodels uses yield generator for tests, which isn't supported in pytest 4+
+- conda install --yes python=$PY numpy scipy cython mako cffi "pytest<4"
 install:
 - pip install bumps
@@ -43 +44 @@
 script:
 - python --version
-- python -m sasmodels.model_test -v dll all
+#- python -m sasmodels.model_test -v dll all
+- python -m pytest -v
 before_deploy:
 - echo -e "Host danse.chem.utk.edu\n\tStrictHostKeyChecking no\n" >> ~/.ssh/config

appveyor.yml

@@ -44 +44 @@
 
 install:
-    # Set the CONDA_NPY, although it has no impact on the actual build. 
+    # Set the CONDA_NPY, although it has no impact on the actual build.
     # We need this because of a test within conda-build.
     - cmd: set CONDA_NPY=19
@@ -68 +68 @@
     #- cmd: conda install --yes --quiet obvious-ci
     # 2018-01-19 PAK: skipping toolchain cython and cffi (these were for pyopencl?)
-    - cmd: conda install --yes --quiet numpy scipy
+    # 2018-01-26 PAK: sasmodels uses yield generator for tests, which isn't supported in pytest 4+
+    - cmd: conda install --yes --quiet numpy scipy "pytest<4"
     # 2018-01-19 PAK: skipping pyopencl; this would be needed for deploy but maybe not for test
     #- cmd: conda install --yes --channel conda-forge pyopencl
@@ -86 +87 @@
     #- "%CMD_IN_ENV% python -m sasmodels.model_test dll all"
     #- cmd /E:ON /V:ON /C obvci_appveyor_python_build_env.cmd python -m sasmoels.model_test dll all
-    - python -m sasmodels.model_test dll all
+    #- python -m sasmodels.model_test dll all
+    #- nosetests -v sasmodels/*.py
+    - python -m pytest -v

sasmodels/convert.py

@@ -633 +633 @@
 def test_backward_forward():
     from .core import list_models
+    L = lambda name: _check_one(name, seed=1)
     for name in list_models('all'):
-        L = lambda: _check_one(name, seed=1)
-        L.description = name
-        yield L
+        yield L, name

sasmodels/core.py

@@ -320 +320 @@
     print("\n".join(list_models(kind)))
 
-def test_load():
-    # type: () -> None
-    """Check that model load works"""
+def test_composite_order():
     def test_models(fst, snd):
         """Confirm that two models produce the same parameters"""
         fst = load_model(fst)
         snd = load_model(snd)
-        # Remove the upper case characters frin the parameters, since
-        # they lasndel the order of events and we specfically are
-        # changin that aspect
+        # Un-disambiguate parameter names so that we can check if the same
+        # parameters are in a pair of composite models. Since each parameter in
+        # the mixture model is tagged as e.g., A_sld, we ought to use a
+        # regex subsitution s/^[A-Z]+_/_/, but removing all uppercase letters
+        # is good enough.
         fst = [[x for x in p.name if x == x.lower()] for p in fst.info.parameters.kernel_parameters]
         snd = [[x for x in p.name if x == x.lower()] for p in snd.info.parameters.kernel_parameters]
         assert sorted(fst) == sorted(snd), "{} != {}".format(fst, snd)
 
-
-    test_models(
+    def build_test(first, second):
+        test = lambda description: test_models(first, second)
+        description = first + " vs. " + second
+        return test, description
+
+    yield build_test(
         "cylinder+sphere",
         "sphere+cylinder")
-    test_models(
+    yield build_test(
         "cylinder*sphere",
         "sphere*cylinder")
-    test_models(
+    yield build_test(
         "cylinder@hardsphere*sphere",
         "sphere*cylinder@hardsphere")
-    test_models(
+    yield build_test(
         "barbell+sphere*cylinder@hardsphere",
         "sphere*cylinder@hardsphere+barbell")
-    test_models(
+    yield build_test(
         "barbell+cylinder@hardsphere*sphere",
         "cylinder@hardsphere*sphere+barbell")
-    test_models(
+    yield build_test(
         "barbell+sphere*cylinder@hardsphere",
         "barbell+cylinder@hardsphere*sphere")
-    test_models(
+    yield build_test(
         "sphere*cylinder@hardsphere+barbell",
         "cylinder@hardsphere*sphere+barbell")
-    test_models(
+    yield build_test(
         "barbell+sphere*cylinder@hardsphere",
         "cylinder@hardsphere*sphere+barbell")
-    test_models(
+    yield build_test(
         "barbell+cylinder@hardsphere*sphere",
         "sphere*cylinder@hardsphere+barbell")
 
+def test_composite():
+    # type: () -> None
+    """Check that model load works"""
     #Test the the model produces the parameters that we would expect
     model = load_model("cylinder@hardsphere*sphere")

sasmodels/model_test.py

@@ -123 +123 @@
 
         if is_py:  # kernel implemented in python
-            test_name = "Model: %s, Kernel: python"%model_name
+            test_name = "%s-python"%model_name
             test_method_name = "test_%s_python" % model_info.id
             test = ModelTestCase(test_name, model_info,
@@ -135 +135 @@
             # test using dll if desired
             if 'dll' in loaders or not core.HAVE_OPENCL:
-                test_name = "Model: %s, Kernel: dll"%model_name
+                test_name = "%s-dll"%model_name
                 test_method_name = "test_%s_dll" % model_info.id
                 test = ModelTestCase(test_name, model_info,
@@ -146 +146 @@
             # test using opencl if desired and available
             if 'opencl' in loaders and core.HAVE_OPENCL:
-                test_name = "Model: %s, Kernel: OpenCL"%model_name
+                test_name = "%s-opencl"%model_name
                 test_method_name = "test_%s_opencl" % model_info.id
                 # Using dtype=None so that the models that are only
@@ -469 +469 @@
     loaders = ['opencl', 'dll'] if core.HAVE_OPENCL else ['dll']
     tests = make_suite(loaders, ['all'])
-    for test_i in tests:
-        # In order for nosetest to see the correct test name, need to set
-        # the description attribute of the returned function.  Since we
-        # can't do this for the returned instance, wrap it in a lambda and
-        # set the description on the lambda.  Otherwise we could just do:
-        #    yield test_i.run_all
-        L = lambda: test_i.run_all()
-        L.description = test_i.test_name
-        yield L
+    for test in tests:
+        # In order for nosetest to show the test name, wrap the test.run_all
+        # instance in function that takes the test name as a parameter which
+        # will be displayed when the test is run.
+        yield lambda name: test.run_all(), test.test_name
 
 

sasmodels/sasview_model.py

@@ -859 +859 @@
     # type: () -> None
     """
-    Load and run cylinder model from sas.models.CylinderModel
+    Load and run cylinder model as sas-models-CylinderModel
     """
     if not SUPPORT_OLD_STYLE_PLUGINS: