Turn off and rename by_second

tests/test_query.py

@@ -220,7 +220,7 @@ def test_query_specific_aspects(self):
             results={TEST.wf1, TEST.wf2})
 
         self.assertQuery(lang, graph,
-            [B], by_io=True, by_chronology=False, by_penultimate=False,
+            [B], by_io=True, by_chronology=False, by_penultimate_output=False,
             results={TEST.wf1}
         )
         self.assertQuery(lang, graph,
@@ -251,7 +251,7 @@ def test_multiple_options_accept_union(self):
             TEST.wf3: Source(A)
         })
 
-        self.assertQuery(lang, workflows, [A], by_penultimate=False,
+        self.assertQuery(lang, workflows, [A], by_penultimate_output=False,
             results={TEST.wf3})
         self.assertQuery(lang, workflows, [B],
             results={TEST.wf1, TEST.wf2})
@@ -417,7 +417,7 @@ def test_multiple_outputs(self):
         graph.add((root, TF.output, B))
         graph.add((A, TF["from"], C))
         graph.add((B, TF["from"], C))
-        query = TransformationQuery(lang, graph, by_penultimate=False, 
+        query = TransformationQuery(lang, graph, by_penultimate_output=False, 
             unfold_tree=False, skip_same_branch_matches=False)
         result = list(query.chronology())
         self.assertIn(result, [
@@ -455,8 +455,9 @@ def test_sensible_order(self):
             graph.add((A, TF["from"], B))
             graph.add((A, TF["from"], C))
             graph.add((B, TF["from"], C))
-            query = TransformationQuery(lang, graph, by_penultimate=False, 
-                unfold_tree=False, skip_same_branch_matches=False)
+            query = TransformationQuery(lang, graph, 
+                by_penultimate_output=False, unfold_tree=False, 
+                                        skip_same_branch_matches=False)
             result = list(query.chronology())
             self.assertIn(result, [
                 ['?workflow :output ?_0.', '?_0 :from* ?_1.',

transforge/query.py

@@ -67,8 +67,9 @@ def __init__(self, lang: Language, graph: Graph,
             root: Node | None = None,
             with_noncanonical_types: bool = False, by_io: bool = True,
             by_types: bool = True, by_operators: bool = True,
-            by_chronology: bool = True, by_penultimate: bool = True,
-            by_second: bool = True,
+            by_chronology: bool = True,
+            by_penultimate_output: bool = True,
+            by_second_input: bool = False,
             # By default, we turn the skip_same_branch_matches feature
             # off because it does not seem to actually improve performance.
             skip_same_branch_matches: bool = False,
@@ -89,8 +90,8 @@ def __init__(self, lang: Language, graph: Graph,
         self.graph.parse_shortcuts()
 
         self.by_io = by_io
-        self.by_penultimate = by_penultimate
-        self.by_second = by_second
+        self.by_penultimate_output = by_penultimate_output
+        self.by_second_input = by_second_input
         self.by_types = by_types
         self.by_operators = by_operators
         self.by_chronology = by_chronology
@@ -289,7 +290,7 @@ def output_nodes(self) -> Iterator[str]:
         Conditions for matching on input and outputs of the query.
         """
         for outputv, output in self.outputs.items():
-            if self.by_penultimate:
+            if self.by_penultimate_output:
                 yield f"?workflow :output/:from? {outputv.n3()}."
             else:
                 yield f"?workflow :output {outputv.n3()}."
@@ -305,7 +306,7 @@ def output_nodes(self) -> Iterator[str]:
 
     def input_nodes(self) -> Iterator[str]:
         for inputv, input in self.inputs.items():
-            if self.by_second:
+            if self.by_second_input:
                 yield f"?workflow :input/^:from? {inputv.n3()}."
             else:
                 yield f"?workflow :input {inputv.n3()}."