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from ...interfaces .base import (traits , TraitedSpec , TraitDictObject ,
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TraitListObject )
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- from ...utils .filemanip import save_json , makedirs , to_str
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+ from ...utils .filemanip import save_json
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from .utils import (generate_expanded_graph , export_graph , write_workflow_prov ,
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write_workflow_resources , format_dot , topological_sort ,
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get_print_name , merge_dict , format_node )
@@ -218,12 +218,12 @@ def connect(self, *args, **kwargs):
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edge_data = self ._graph .get_edge_data (srcnode , destnode , None )
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if edge_data :
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logger .debug ('(%s, %s): Edge data exists: %s' , srcnode ,
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- destnode , to_str (edge_data ))
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+ destnode , str (edge_data ))
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for data in connects :
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if data not in edge_data ['connect' ]:
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edge_data ['connect' ].append (data )
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if disconnect :
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- logger .debug ('Removing connection: %s' , to_str (data ))
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+ logger .debug ('Removing connection: %s' , str (data ))
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edge_data ['connect' ].remove (data )
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if edge_data ['connect' ]:
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self ._graph .add_edges_from ([(srcnode , destnode ,
@@ -240,7 +240,7 @@ def connect(self, *args, **kwargs):
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})])
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edge_data = self ._graph .get_edge_data (srcnode , destnode )
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logger .debug ('(%s, %s): new edge data: %s' , srcnode , destnode ,
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- to_str (edge_data ))
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+ str (edge_data ))
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def disconnect (self , * args ):
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"""Disconnect nodes
@@ -256,7 +256,7 @@ def disconnect(self, *args):
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for srcnode , dstnode , conn in connection_list :
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logger .debug ('disconnect(): %s->%s %s' , srcnode , dstnode ,
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- to_str (conn ))
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+ str (conn ))
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if self in [srcnode , dstnode ]:
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raise IOError (
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'Workflow connect cannot contain itself as node: src[%s] '
@@ -277,10 +277,10 @@ def disconnect(self, *args):
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# idx = ed_conns.index(edge)
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remove .append ((edge [0 ], edge [1 ]))
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- logger .debug ('disconnect(): remove list %s' , to_str (remove ))
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+ logger .debug ('disconnect(): remove list %s' , str (remove ))
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for el in remove :
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edge_data ['connect' ].remove (el )
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- logger .debug ('disconnect(): removed connection %s' , to_str (el ))
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+ logger .debug ('disconnect(): removed connection %s' , str (el ))
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if not edge_data ['connect' ]:
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self ._graph .remove_edge (srcnode , dstnode )
@@ -410,7 +410,7 @@ def write_graph(self,
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base_dir = op .join (base_dir , self .name )
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else :
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base_dir = os .getcwd ()
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- base_dir = makedirs (base_dir , exist_ok = True )
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+ os . makedirs (base_dir , exist_ok = True )
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if graph2use in ['hierarchical' , 'colored' ]:
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if self .name [:1 ].isdigit (): # these graphs break if int
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raise ValueError ('{} graph failed, workflow name cannot begin '
@@ -576,7 +576,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
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flatgraph = self ._create_flat_graph ()
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self .config = merge_dict (deepcopy (config ._sections ), self .config )
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logger .info ('Workflow %s settings: %s' , self .name ,
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- to_str (sorted (self .config )))
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+ str (sorted (self .config )))
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self ._set_needed_outputs (flatgraph )
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execgraph = generate_expanded_graph (deepcopy (flatgraph ))
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for index , node in enumerate (execgraph .nodes ()):
@@ -609,7 +609,7 @@ def _write_report_info(self, workingdir, name, graph):
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if workingdir is None :
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workingdir = os .getcwd ()
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report_dir = op .join (workingdir , name )
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- makedirs (report_dir , exist_ok = True )
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+ os . makedirs (report_dir , exist_ok = True )
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shutil .copyfile (
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op .join (op .dirname (__file__ ), 'report_template.html' ),
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op .join (report_dir , 'index.html' ))
@@ -821,7 +821,7 @@ def _set_node_input(self, node, param, source, sourceinfo):
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newval = dict (val )
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if isinstance (val , TraitListObject ):
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newval = val [:]
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- logger .debug ('setting node input: %s->%s' , param , to_str (newval ))
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+ logger .debug ('setting node input: %s->%s' , param , str (newval ))
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node .set_input (param , deepcopy (newval ))
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def _get_all_nodes (self ):
@@ -881,9 +881,9 @@ def _generate_flatgraph(self):
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# dj: added list() for networkx ver.2
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for u , _ , d in list (
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self ._graph .in_edges (nbunch = node , data = True )):
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- logger .debug ('in: connections-> %s' , to_str (d ['connect' ]))
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+ logger .debug ('in: connections-> %s' , str (d ['connect' ]))
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for cd in deepcopy (d ['connect' ]):
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- logger .debug ("in: %s" , to_str (cd ))
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+ logger .debug ("in: %s" , str (cd ))
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dstnode = node ._get_parameter_node (cd [1 ], subtype = 'in' )
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srcnode = u
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srcout = cd [0 ]
@@ -896,9 +896,9 @@ def _generate_flatgraph(self):
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# dj: for ver 2 use list(out_edges)
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for _ , v , d in list (
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self ._graph .out_edges (nbunch = node , data = True )):
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- logger .debug ('out: connections-> %s' , to_str (d ['connect' ]))
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+ logger .debug ('out: connections-> %s' , str (d ['connect' ]))
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for cd in deepcopy (d ['connect' ]):
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- logger .debug ("out: %s" , to_str (cd ))
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+ logger .debug ("out: %s" , str (cd ))
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dstnode = v
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if isinstance (cd [0 ], tuple ):
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parameter = cd [0 ][0 ]
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