Merge branch 'remove-dead-code' into 'master'

vistrails/core/analogy/eigen.py

@@ -309,90 +309,6 @@ def update_elements(spec):
         remove_descriptions(outputs)
         return (inputs, outputs)
 
-##############################################################################
-# EigenPipelineSimilarity
-
-class EigenPipelineSimilarity(EigenBase):
-
-    ##########################################################################
-    # Constructor and initialization
-
-    def __init__(self,
-                 pipeline1,
-                 pipeline2):
-        EigenBase.__init__(self, pipeline1, pipeline2)
-        self.init_operator()
-
-    def init_operator(self):
-        num_verts_p1 = len(self._p1.graph.vertices)
-        num_verts_p2 = len(self._p2.graph.vertices)
-        def ix(a,b): return num_verts_p2 * a + b
-        self._operator = mzeros((num_verts_p1 * num_verts_p2,
-                                 num_verts_p1 * num_verts_p2))
-
-        u = 0.85
-
-        for i in xrange(num_verts_p1):
-            v1_id = self._g1_vertex_map.inverse[i]
-            for j in xrange(num_verts_p2):
-                ix_ij = ix(i,j)
-                self._operator[ix_ij, ix_ij] = u
-                v2_id = self._g2_vertex_map.inverse[j]
-                def edges(pip, v_id):
-                    return chain(imap(lambda (f, t, i): (t, i),
-                                      self._p1.graph.iter_edges_from(v1_id)),
-                                 imap(lambda (f, t, i): (f, i),
-                                      self._p1.graph.iter_edges_to(v1_id)))
-                p1_edges = edges(self._p1, v1_id)
-                p2_edges = edges(self._p2, v2_id)
-                running_sum = 0.0
-                for (_, p1_edge) in p1_edges:
-                    for (_, p2_edge) in p2_edges:
-                        e1_id = self._g1_edge_map[p1_edge]
-                        e2_id = self._g2_edge_map[p2_edge]
-                        running_sum += self._edge_s8y[e1_id, e2_id]
-                p1_edges = edges(self._p1, v1_id)
-                p2_edges = edges(self._p2, v2_id)
-                if not running_sum:
-                    continue
-                for (p1_v, p1_edge_id) in p1_edges:
-                    for (p2_v, p2_edge_id) in p2_edges:
-                        e1_id = self._g1_edge_map[p1_edge_id]
-                        e2_id = self._g2_edge_map[p2_edge_id]
-                        p1_v_id = self._g1_vertex_map[p1_v]
-                        p2_v_id = self._g2_vertex_map[p2_v]
-                        value = self._edge_s8y[e1_id, e2_id]
-                        value *= (1.0 - u) / running_sum
-                        self._operator[ix_ij, ix(p1_v_id, p2_v_id)] = value
-
-    ##############################################################################
-    # Solve
-
-    def step(self, m):
-        v = m.reshape(len(self._p1.modules) *
-                      len(self._p2.modules))
-        v = scipy.dot(self._operator, v)
-        v = v.reshape(len(self._p1.modules),
-                      len(self._p2.modules)).transpose()
-        v = (v / v.sum(0)).transpose()
-        return v
-
-    def solve(self):
-        i = 0
-        while i < 50:
-            i += 1
-            v = self.step(self._vertex_s8y)
-            residue = self._vertex_s8y - v
-            residue *= residue
-            if residue.sum() < 0.0001:
-                break
-            self._vertex_s8y = v
-        mp = [(self._g1_vertex_map.inverse[ix],
-               self._g2_vertex_map.inverse[v])
-              for (ix, v) in
-              enumerate(self._vertex_s8y.argmax(1))]
-        return dict(mp)
-
 ##############################################################################
 # EigenPipelineSimilarity2
 

vistrails/core/api.py

@@ -1,7 +1,7 @@
 import itertools
 
 import vistrails.core.application
-from vistrails.core.db.locator import FileLocator, untitled_locator
+from vistrails.core.db.locator import FileLocator
 import vistrails.core.db.io
 from vistrails.core import debug
 from vistrails.core.modules.basic_modules import identifier as basic_pkg

vistrails/core/db/locator.py

@@ -753,9 +753,3 @@ def guess_extension_from_contents(contents):
                                mashuptrail=mashuptrail,
                                mashupVersion=mashupVersion,
                                parameterExploration=parameterExploration)
-
-
-    ##########################################################################
-
-def untitled_locator():
-    return UntitledLocator()

vistrails/core/interpreter/cached.py

@@ -214,7 +214,6 @@ def create(self):
         self._file_pool = FilePool()
         self._persistent_pipeline = vistrails.core.vistrail.pipeline.Pipeline()
         self._objects = {}
-        self._executed = {}
         self.filePool = self._file_pool
         self._streams = []
 
@@ -224,7 +223,6 @@ def clear(self):
         for obj in self._objects.itervalues():
             obj.clear()
         self._objects = {}
-        self._executed = {}
 
     def __del__(self):
         self.clear()

vistrails/core/interpreter/job.py

@@ -56,13 +56,6 @@
 JOBS_FILENAME = "jobs.json"
 
 
-class BaseMonitor(object):
-    def finished(self):
-        """Indicates whether the job has completed (module can resume).
-        """
-        raise NotImplementedError
-
-
 class JobMixin(NotCacheable):
     """ Mixin for suspendable modules.
 

vistrails/core/modules/config.py

@@ -435,7 +435,6 @@ def parse_documentation():
         field, field_type = line.strip().split(':', 1)
         (cls_name, field_name) = field.split('.')
         doc_lines = []
-        done_with_doc = False
         line = line_iter.next()
         while True:
             line = line_iter.next()

vistrails/core/modules/output_modules.py

@@ -82,10 +82,6 @@ def get_all_fields(cls):
         fields.sort()
         return fields
 
-    @classmethod
-    def get_local_fields(cls):
-        return sorted(cls._fields)
-
     @classmethod
     def get_default(cls, k):
         f = cls.get_field(k)

vistrails/core/vistrail/module_function.py

@@ -52,11 +52,6 @@
 
 ################################################################################
 
-PipelineElementType = enum('PipelineElementType',
-                           ['Module', 'Connection', 'Function', 'Parameter'])
-
-################################################################################
-
 class ModuleFunction(DBFunction):
     __fields__ = ['name', 'returnType', 'params']
     """ Stores a function from a vistrail module """