RF: Remove file-level nx imports in pipeline

Author: effigies

nipype/pipeline/engine/utils.py

@@ -21,7 +21,6 @@
 from functools import reduce
 
 import numpy as np
-import networkx as nx
 from future import standard_library
 
 from ... import logging, config, LooseVersion
@@ -55,12 +54,6 @@
 logger = logging.getLogger('nipype.workflow')
 PY3 = sys.version_info[0] > 2
 
-try:
-    dfs_preorder = nx.dfs_preorder
-except AttributeError:
-    dfs_preorder = nx.dfs_preorder_nodes
-    logger.debug('networkx 1.4 dev or higher detected')
-
 
 def _parameterization_dir(param):
     """
@@ -543,6 +536,7 @@ def _create_dot_graph(graph, show_connectinfo=False, simple_form=True):
     Ensures that edge info is pickleable.
     """
     logger.debug('creating dot graph')
+    import networkx as nx
     pklgraph = nx.DiGraph()
     for edge in graph.edges():
         data = graph.get_edge_data(*edge)
@@ -569,6 +563,7 @@ def _write_detailed_dot(graph, dotfilename):
         struct1:f2 -> struct3:here;
         }
     """
+    import networkx as nx
     text = ['digraph structs {', 'node [shape=record];']
     # write nodes
     edges = []
@@ -748,6 +743,7 @@ def evaluate_connect_function(function_source, args, first_arg):
 
 
 def get_levels(G):
+    import networkx as nx
     levels = {}
     for n in nx.topological_sort(G):
         levels[n] = 0
@@ -891,6 +887,7 @@ def _identity_nodes(graph, include_iterables):
     are included if and only if the include_iterables flag is set
     to True.
     """
+    import networkx as nx
     return [
         node for node in nx.topological_sort(graph)
         if isinstance(node.interface, IdentityInterface) and (
@@ -994,6 +991,12 @@ def generate_expanded_graph(graph_in):
     and b=[3,4] this procedure will generate a graph with sub-graphs
     parameterized as (a=1,b=3), (a=1,b=4), (a=2,b=3) and (a=2,b=4).
     """
+    import networkx as nx
+    try:
+        dfs_preorder = nx.dfs_preorder
+    except AttributeError:
+        dfs_preorder = nx.dfs_preorder_nodes
+
     logger.debug("PE: expanding iterables")
     graph_in = _remove_nonjoin_identity_nodes(graph_in, keep_iterables=True)
     # standardize the iterables as {(field, function)} dictionaries
@@ -1222,6 +1225,7 @@ def _iterable_nodes(graph_in):
 
     Return the iterable nodes list
     """
+    import networkx as nx
     nodes = nx.topological_sort(graph_in)
     inodes = [node for node in nodes if node.iterables is not None]
     inodes_no_src = [node for node in inodes if not node.itersource]
@@ -1349,6 +1353,7 @@ def export_graph(graph_in,
     Indicates whether to show the edge data on the graph. This
     makes the graph rather cluttered. default [False]
     """
+    import networkx as nx
     graph = deepcopy(graph_in)
     if use_execgraph:
         graph = generate_expanded_graph(graph)
@@ -1716,6 +1721,7 @@ def write_workflow_resources(graph, filename=None, append=None):
 def topological_sort(graph, depth_first=False):
     """Returns a depth first sorted order if depth_first is True
     """
+    import networkx as nx
     nodesort = list(nx.topological_sort(graph))
     if not depth_first:
         return nodesort, None

nipype/pipeline/engine/workflows.py

@@ -19,7 +19,6 @@
 import shutil
 
 import numpy as np
-import networkx as nx
 
 from ... import config, logging
 from ...utils.misc import str2bool
@@ -56,6 +55,7 @@ def __init__(self, name, base_dir=None):
             path to workflow storage
 
         """
+        import networkx as nx
         super(Workflow, self).__init__(name, base_dir)
         self._graph = nx.DiGraph()
 
@@ -366,6 +366,7 @@ def get_node(self, name):
     def list_node_names(self):
         """List names of all nodes in a workflow
         """
+        import networkx as nx
         outlist = []
         for node in nx.topological_sort(self._graph):
             if isinstance(node, Workflow):
@@ -482,6 +483,7 @@ def export(self,
            whether to include node and workflow config values
 
         """
+        import networkx as nx
         formats = ["python"]
         if format not in formats:
             raise ValueError('format must be one of: %s' % '|'.join(formats))
@@ -870,6 +872,7 @@ def _reset_hierarchy(self):
     def _generate_flatgraph(self):
         """Generate a graph containing only Nodes or MapNodes
         """
+        import networkx as nx
         logger.debug('expanding workflow: %s', self)
         nodes2remove = []
         if not nx.is_directed_acyclic_graph(self._graph):
@@ -942,6 +945,7 @@ def _get_dot(self,
                  level=0):
         """Create a dot file with connection info
         """
+        import networkx as nx
         if prefix is None:
             prefix = '  '
         if hierarchy is None:

nipype/pipeline/plugins/base.py

@@ -20,7 +20,7 @@
 from ... import logging
 from ...utils.filemanip import loadpkl
 from ...utils.misc import str2bool
-from ..engine.utils import (nx, dfs_preorder, topological_sort)
+from ..engine.utils import topological_sort
 from ..engine import MapNode
 from .tools import report_crash, report_nodes_not_run, create_pyscript
 
@@ -391,6 +391,8 @@ def _task_finished_cb(self, jobid, cached=False):
     def _generate_dependency_list(self, graph):
         """ Generates a dependency list for a list of graphs.
         """
+        import networkx as nx
+
         self.procs, _ = topological_sort(graph)
         try:
             self.depidx = nx.to_scipy_sparse_matrix(
@@ -403,6 +405,11 @@ def _generate_dependency_list(self, graph):
         self.proc_pending = np.zeros(len(self.procs), dtype=bool)
 
     def _remove_node_deps(self, jobid, crashfile, graph):
+        import networkx as nx
+        try:
+            dfs_preorder = nx.dfs_preorder
+        except AttributeError:
+            dfs_preorder = nx.dfs_preorder_nodes
         subnodes = [s for s in dfs_preorder(graph, self.procs[jobid])]
         for node in subnodes:
             idx = self.procs.index(node)
@@ -538,6 +545,7 @@ def __init__(self, plugin_args=None):
         super(GraphPluginBase, self).__init__(plugin_args=plugin_args)
 
     def run(self, graph, config, updatehash=False):
+        import networkx as nx
         pyfiles = []
         dependencies = {}
         self._config = config

nipype/pipeline/plugins/linear.py

@@ -7,11 +7,9 @@
                         absolute_import)
 
 import os
-
-import networkx as nx
 from .base import (PluginBase, logger, report_crash, report_nodes_not_run,
                    str2bool)
-from ..engine.utils import dfs_preorder, topological_sort
+from ..engine.utils import topological_sort
 
 
 class LinearPlugin(PluginBase):
@@ -27,6 +25,11 @@ def run(self, graph, config, updatehash=False):
         graph : networkx digraph
             defines order of execution
         """
+        import networkx as nx
+        try:
+            dfs_preorder = nx.dfs_preorder
+        except AttributeError:
+            dfs_preorder = nx.dfs_preorder_nodes
 
         if not isinstance(graph, nx.DiGraph):
             raise ValueError('Input must be a networkx digraph object')