Merge dae29c4 into 13b9e5e

doc/source/releases/1.0.rst

@@ -0,0 +1,12 @@
+=================
+:mod:`nineml` 1.0
+=================
+
+|date|
+
+The first public release of the Python :mod:`nineml` package,
+which corresponds to the release of version 1.0 of the
+`NineML specification`_.
+
+.. _`NineML specification`: http://nineml-spec.readthedocs.io/
+.. |date| date:: %x

doc/source/releases/index.rst

@@ -8,3 +8,4 @@ All released NineML Python versions:
    :maxdepth: 1
 
    1.0rc1
+   1.0

nineml/abstraction/componentclass/visitors/validators/general.py

@@ -288,7 +288,7 @@ def _flatten_dims(self, expr, element):
             for arg in expr.args:
                 dims = self._flatten_dims(arg, element)
                 # boolean expression == 0
-                if dims != 0 and dims != 1:  # FIXME: allow dimless until bool params @IgnorePep8
+                if dims != 0 and dims != 1:
                     raise NineMLDimensionError(self._construct_error_message(
                         "Logical expression provided non-boolean argument '{}'"
                         .format(arg), dims, expr))

nineml/abstraction/dynamics/base.py

@@ -168,10 +168,6 @@ def __init__(self, name, parameters=(), ports=(), analog_ports=(),
 
         # Set and check event send ports match inferred
         if self.num_event_send_ports:
-            # FIXME: not all OutputEvents are necessarily exposed as Ports,
-            # so really we should just check that all declared output event
-            # ports are in the list of inferred ports, not that the declared
-            # list is identical to the inferred one.
             check_inferred_against_declared(
                 self.event_send_port_names,
                 inferred_struct.event_out_port_names,

nineml/abstraction/dynamics/visitors/validators/general.py

@@ -16,6 +16,9 @@
     DimensionalityComponentValidator)
 from ..base import BaseDynamicsVisitor
 import nineml.units as un
+import logging
+
+logger = logging.getLogger('NineML')
 
 
 class TimeDerivativesAreDeclaredDynamicsValidator(BaseDynamicsVisitor):
@@ -119,10 +122,10 @@ def __init__(self, component_class, **kwargs):  # @UnusedVariable
             # Recursively add all regimes connected to the first regime
             self._add_connected_regimes_recursive(first_regime)
             if len(self.connected) < len(self.regimes):
-                # FIXME: This should probably be a warning not an error
-                raise NineMLUsageError(
-                    "Transition graph of {} contains islands: {} regimes "
-                    "('{}') and {} connected ('{}'):\n\n{}".format(
+                logger.warning(
+                    "Transition graph of {} contains islands: {} "
+                    "regimes ('{}') and {} connected ('{}'):\n\n{}"
+                    .format(
                         component_class,
                         len(self.regimes),
                         "', '".join(r.name for r in self.regimes),

nineml/abstraction/expressions/base.py

@@ -22,7 +22,7 @@
 
 builtin_constants = set(['true', 'false', 'True', 'False'])
 builtin_functions = set([
-    'exp', 'sin', 'cos', 'log', 'log10', 'pow', 'abs',
+    'exp', 'sin', 'cos', 'tan', 'log', 'log10', 'pow', 'abs',
     'sinh', 'cosh', 'tanh', 'sqrt', 'mod',  # 'sum',
     'atan', 'asin', 'acos', 'asinh', 'acosh', 'atanh', 'atan2'])
 reserved_symbols = set(['t'])

nineml/abstraction/ports.py

@@ -78,7 +78,8 @@ class DimensionedPort(
 
     def __init__(self, name, dimension=None):
         super(DimensionedPort, self).__init__(name)
-        self._dimension = dimension if dimension is not None else dimensionless # TODO: This needs checking @IgnorePep8
+        self._dimension = (dimension if dimension is not None
+                           else dimensionless)
 
     @property
     def dimension(self):
@@ -115,7 +116,7 @@ class SendPort(SendPortBase):
 
     Base class for sending ports
     """
-    mode = "send"  # FIXME: This is here for legacy unittest I think (TGC 1/15)
+    mode = "send"
 
     def is_incoming(self):
         return False
@@ -129,7 +130,7 @@ class ReceivePort(object):
 
     Base class for receiving ports
     """
-    mode = "recv"  # FIXME: This is here for legacy unittest I think (TGC 1/15)
+    mode = "receive"
 
     def is_incoming(self):
         return True

test/unittests/abstraction_test/dynamics_test.py

@@ -163,7 +163,7 @@ def test_analog_ports(self):
 
         c = Dynamics(name='C1', analog_ports=[AnalogReceivePort('B')])
         self.assertEqual(len(list(c.analog_ports)), 1)
-        self.assertEqual(list(c.analog_ports)[0].mode, 'recv')
+        self.assertEqual(list(c.analog_ports)[0].mode, 'receive')
         self.assertEqual(len(list(c.analog_send_ports)), 0)
         self.assertEqual(len(list(c.analog_receive_ports)), 1)
         self.assertEqual(len(list(c.analog_reduce_ports)), 0)

test/unittests/units_test.py

@@ -34,8 +34,7 @@ def test_accessors(self):
                 self.assertEqual(getattr(dim, abbrev), dim._dims[i])
                 self.assertEqual(getattr(dim, name), dim._dims[i])
 
-# FIXME: Currently the 'scale' attribute isn't supported, need to work out
-#        whether we want to do this or not.
+
 units_xml_str = """<?xml version="1.0" encoding="UTF-8"?>
 <NineML xmlns="http://nineml.net/9ML/2.0">
   <Annotations>
@@ -74,11 +73,6 @@ def test_accessors(self):
   <Unit symbol="Hz" dimension="per_time" power="0"/>
   <Unit symbol="ms" dimension="time" power="-3"/>
   <Unit symbol="per_ms" dimension="per_time" power="3"/>
-  <!--<Unit symbol="min" dimension="time" power="0" scale="60"/>
-  <Unit symbol="per_min" dimension="per_time" power="0" scale="0.01666666667"/>
-  <Unit symbol="hour" dimension="time" power="0" scale="3600"/>
-  <Unit symbol="per_hour" dimension="per_time" power="0"
-    scale="0.00027777777778"/>-->
   <Unit symbol="m" dimension="length" power="0"/>
   <Unit symbol="cm" dimension="length" power="-2"/>
   <Unit symbol="um" dimension="length" power="-6"/>