neurondm LabelMake hasAnatomicalSystemPhenotype, fix namespaces

after tracking down an issue where abbreviations were not showing up
in generaged labels correctly (which was fixed in the previous commit,
and was due to junk namespaces being inserted silently by calls from
infixowl to bad Graph.compute_qname defaults which is what we fixed)
we now need to make sure that the namespaces are not empty, otherwise
infixowl calls will cause an error

also remove remaining direct usage of makeGraph

neurondm/neurondm/core.py

@@ -19,7 +19,7 @@
 from ttlser import natsort
 from augpathlib import RepoPath
 from pyontutils import combinators as cmb
-from pyontutils.core import Ont, makeGraph, OntId as bOntId, OntTerm as bOntTerm
+from pyontutils.core import Ont, OntId as bOntId, OntTerm as bOntTerm
 from pyontutils.core import OntConjunctiveGraph, OntResAny, OntResIri, OntResPath
 from pyontutils.utils import stack_magic, injective_dict, makeSimpleLogger, cacheout
 from pyontutils.utils import TermColors as tc, subclasses, get_working_dir
@@ -424,6 +424,9 @@ def hasConnectionPhenotype(self, phenotypes):
     def hasExperimentalPhenotype(self, phenotypes):
         yield from self._default(phenotypes)
     @od
+    def hasAnatomicalSystemPhenotype(self, phenotypes):
+        yield from self._default(phenotypes)
+    @od
     def hasClassificationPhenotype(self, phenotypes):
         yield from self._default(phenotypes)
     @od
@@ -1470,7 +1473,7 @@ def makeLocalRemote(suffixes):
         for ig in use_in_paths:
             in_graph.parse(ig, format='turtle')
 
-        nin_graph = makeGraph('', prefixes=PREFIXES, graph=in_graph)
+        in_graph.namespace_manager.populate_from(PREFIXES)
         graphBase.in_graph = in_graph
         graphBase.ignore_existing = ignore_existing
 
@@ -1501,15 +1504,14 @@ class NeurOnt(Ont):  # FIXME this is super misleading wrt the source ...
             NeuronBase.existing_ids = {}
         else:
             no = None
-            graphBase.ng = makeGraph('', prefixes=PREFIXES, graph=out_graph)
-        #new_graph = makeGraph('', prefixes=PREFIXES, graph=out_graph)
+            out_graph.namespace_manager.populate_from(PREFIXES)
+
         graphBase.out_graph = out_graph
 
         # python output setup
         graphBase.compiled_location = compiled_location
 
-        # makeGraph setup
-        new_graph = graphBase.ng #= new_graph
+        new_graph = graphBase.ng  # FIXME remove this usage
         new_graph.filename = out_graph_path
 
         if iri is not None:
@@ -3630,6 +3632,7 @@ def getLocalContext():
 else:
     # note: this solves part of the problem, but mostly defers it until later
     _g = OntConjunctiveGraph()
+    _g.namespace_manager.populate_from(uPREFIXES)
     graphBase.core_graph = _g