Merge pull request #97 from scidash/dash

Dash

README.md

@@ -4,7 +4,7 @@
 | [![RTFD](https://readthedocs.org/projects/sciunit/badge/?version=master)](http://sciunit.readthedocs.io/en/latest/?badge=master) | [![RTFD](https://readthedocs.org/projects/sciunit/badge/?version=dev)](http://sciunit.readthedocs.io/en/latest/?badge=dev) |
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-| [![Requirements](https://requires.io/github/scidash/sciunit/requirements.svg?branch=master)](https://requires.io/github/scidash/sciunit/requirements/?branch=master) |  [![Requirements](https://requires.io/github/scidash/sciunit/requirements.svg?branch=dev)](https://requires.io/github/scidash/sciunit/requirements/?branch=dev) | 
+| [![Requirements](https://requires.io/github/scidash/sciunit/requirements.svg?branch=master)](https://requires.io/github/scidash/sciunit/requirements/?branch=master) |  [![Requirements](https://requires.io/github/scidash/sciunit/requirements.svg?branch=dev)](https://requires.io/github/scidash/sciunit/requirements/?branch=dev) |
 | [![Docker Build Status](https://img.shields.io/docker/build/scidash/sciunit.svg)](https://hub.docker.com/r/scidash/sciunit/builds/) |
 
 <img src="https://raw.githubusercontent.com/scidash/assets/master/logos/SciUnit/sci-unit-square-small.png" alt="SciUnit Logo" width="400px">
@@ -15,7 +15,7 @@
 [The conference paper](https://github.com/cyrus-/papers/raw/master/sciunit-icse14/sciunit-icse14.pdf)
 
 ## Documentation
-[Chapter 1](https://github.com/scidash/sciunit/blob/master/docs/chapter1.ipynb) / 
+[Chapter 1](https://github.com/scidash/sciunit/blob/master/docs/chapter1.ipynb) /
 [Chapter 2](https://github.com/scidash/sciunit/blob/master/docs/chapter2.ipynb) /
 [Chapter 3](https://github.com/scidash/sciunit/blob/master/docs/chapter3.ipynb) /
 
@@ -37,7 +37,7 @@ Please join it if you are at all interested!
 ## Contributors
  * [Rick Gerkin](http://rick.gerk.in), Arizona State University (School of Life Science)
  * [Cyrus Omar](http://cs.cmu.edu/~comar), Carnegie Mellon University (Dept. of Computer Science)
- 
+
 ## Reproducible Research ID
 RRID:[SCR_014528](https://scicrunch.org/resources/Any/record/nlx_144509-1/3faed1d9-6579-5da6-b4b4-75a5077656bb/search?q=sciunit&l=sciunit)
 

sciunit/models/base.py

@@ -108,7 +108,7 @@ def __getattr__(self, attr):
                 raise AttributeError("Model %s has no attribute %s"
                                      % (self, attr))
         return result
-        
+
     def __str__(self):
         """Return the model name."""
         return '%s' % self.name

sciunit/suites.py

@@ -118,7 +118,8 @@ def judge(self, models,
                 all the way to the root of the error.
 
         Returns:
-            ScoreMatrix: The resulting scores for all test/model combos."""
+            ScoreMatrix: The resulting scores for all test/model combos.
+        """
         models = self.assert_models(models)
         sm = ScoreMatrix(self.tests, models, weights=self.weights)
         for model in models:

sciunit/tests.py

@@ -65,7 +65,9 @@ def __init__(self, observation, name=None, **params):
 
     observation_schema = None
     """A schema that the observation must adhere to (validated by cerberus).
-    Can also be a list of schemas, one of which the observation must match."""
+    Can also be a list of schemas, one of which the observation must match.
+    If it is a list, each schema in the list can optionally be named by putting
+    (name, schema) tuples in that list."""
 
     params_schema = None
     """A schema that the params must adhere to (validated by cerberus).
@@ -84,7 +86,9 @@ def validate_observation(self, observation):
             raise ObservationError("Observation mean cannot be 'None'.")
         if self.observation_schema:
             if isinstance(self.observation_schema, list):
-                schema = {'oneof_schema': self.observation_schema,
+                schemas = [x[1] if isinstance(x, tuple) else x
+                           for x in self.observation_schema]
+                schema = {'oneof_schema': schemas,
                           'type': 'dict'}
             else:
                 schema = {'schema': self.observation_schema,
@@ -95,6 +99,16 @@ def validate_observation(self, observation):
                 raise ObservationError(v.errors)
         return observation
 
+    @classmethod
+    def observation_schema_names(cls):
+        """Return a list of names of observation schema, if they are set."""
+        names = []
+        if cls.observation_schema:
+            if isinstance(cls.observation_schema, list):
+                names = [x[0] if isinstance(x, tuple) else 'Schema %d' % (i+1)
+                         for i, x in enumerate(cls.observation_schema)]
+        return names
+
     def validate_params(self, params):
         """Validate the params provided to the constructor.
 
@@ -281,14 +295,16 @@ def judge(self, model, skip_incapable=False, stop_on_error=True,
             raise score.score  # An exception.
         return score
 
-    def check(self, model, skip_incapable=True, stop_on_error=True):
+    def check(self, model, skip_incapable=True, stop_on_error=True,
+              require_extra=False):
         """Check to see if the test can run this model.
 
         Like judge, but without actually running the test. Just returns a Score
         indicating whether the model can take the test or not.
         """
         try:
-            if self.check_capabilities(model, skip_incapable=skip_incapable):
+            if self.check_capabilities(model, skip_incapable=skip_incapable,
+                                       require_extra=require_extra):
                 score = TBDScore(None)
             else:
                 score = NAScore(None)

sciunit/validators.py

@@ -1,7 +1,9 @@
 """Cerberus validator classes for SciUnit."""
 
-from cerberus import Validator, TypeDefinition
+import inspect
+
 import quantities as pq
+from cerberus import TypeDefinition, Validator
 
 
 def register_type(cls, name):
@@ -53,27 +55,35 @@ def _validate_units(self, has_units, key, value):
 class ParametersValidator(Validator):
     """Cerberus validator class for observations."""
 
+    units_map = {'time': 's', 'voltage': 'V', 'current': 'A'}
+
     def validate_quantity(self, value):
+        """Validate that the value is of the `Quantity` type."""
         if not isinstance(value, pq.quantity.Quantity):
             self._error('%s' % value, "Must be a Python quantity.")
 
-    def _validate_type_time(self, value):
-        """Validate fields requiring `units` of seconds."""
+    def validate_units(self, value):
+        """Validate units, assuming that it was called by _validate_type_*."""
         self.validate_quantity(value)
-        if not value.simplified.units == pq.s:
-            self._error('%s' % value, "Must have dimensions of time.")
+        self.units_type = inspect.stack()[1][3].split('_')[-1]
+        assert self.units_type, ("`validate_units` should not be called "
+                                 "directly. It should be called by a "
+                                 "_validate_type_* methods that sets "
+                                 "`units_type`")
+        units = getattr(pq, self.units_map[self.units_type])
+        if not value.simplified.units == units:
+            self._error('%s' % value,
+                        "Must have dimensions of %s." % self.units_type)
         return True
 
+    def _validate_type_time(self, value):
+        """Validate fields requiring `units` of seconds."""
+        return self.validate_units(value)
+
     def _validate_type_voltage(self, value):
         """Validate fields requiring `units` of volts."""
-        self.validate_quantity(value)
-        if not value.simplified.units == pq.V:
-            self._error('%s' % value, "Must have dimensions of voltage.")
-        return True
+        return self.validate_units(value)
 
     def _validate_type_current(self, value):
         """Validate fields requiring `units` of amps."""
-        self.validate_quantity(value)
-        if not value.simplified.units == pq.A:
-            self._error('%s' % value, "Must have dimensions of current.")
-        return True
+        return self.validate_units(value)