support Pydot versions before 3.0

Author: mr-c

cwltool/cwlviewer.py

@@ -7,6 +7,12 @@
 
 import pydot
 import rdflib
+from packaging.version import Version
+
+if Version(pydot.__version__) > Version("3.0"):
+    quote_id_if_necessary = pydot.quote_id_if_necessary
+else:
+    quote_id_if_necessary = pydot.quote_if_necessary  # type: ignore[attr-defined]
 
 
 def _get_inner_edges_query() -> str:
@@ -99,8 +105,8 @@ def _set_inner_edges(self) -> None:
             self._dot_graph.add_node(n)
             self._dot_graph.add_edge(
                 pydot.Edge(
-                    pydot.quote_id_if_necessary(str(inner_edge_row["source_step"])),
-                    pydot.quote_id_if_necessary(str(inner_edge_row["target_step"])),
+                    quote_id_if_necessary(str(inner_edge_row["source_step"])),
+                    quote_id_if_necessary(str(inner_edge_row["target_step"])),
                 )
             )
 
@@ -130,8 +136,8 @@ def _set_input_edges(self) -> None:
             inputs_subgraph.add_node(n)
             self._dot_graph.add_edge(
                 pydot.Edge(
-                    pydot.quote_id_if_necessary(str(input_row["input"])),
-                    pydot.quote_id_if_necessary(str(input_row["step"])),
+                    quote_id_if_necessary(str(input_row["input"])),
+                    quote_id_if_necessary(str(input_row["step"])),
                 )
             )
 
@@ -161,8 +167,8 @@ def _set_output_edges(self) -> None:
             outputs_graph.add_node(n)
             self._dot_graph.add_edge(
                 pydot.Edge(
-                    pydot.quote_id_if_necessary(output_edge_row["step"]),
-                    pydot.quote_id_if_necessary(output_edge_row["output"]),
+                    quote_id_if_necessary(output_edge_row["step"]),
+                    quote_id_if_necessary(output_edge_row["output"]),
                 )
             )
 

mypy-stubs/pydot.pyi

@@ -10,7 +10,8 @@ requires = [
     "cwl-utils>=0.32",
     "toml",
     "argcomplete>=1.12.0",
-    "rich-argparse"
+    "rich-argparse",
+    "pydot >= 1.4.1"
 ]
 build-backend = "setuptools.build_meta"
 

pyproject.toml

@@ -995,8 +995,10 @@ def test_var_spool_cwl_checker3() -> None:
 def test_print_dot() -> None:
     # print Workflow
     cwl_path = get_data("tests/wf/three_step_color.cwl")
-    expected_dot = pydot.graph_from_dot_data(
-        """
+    expected_dot = cast(
+        list[pydot.core.Dot],
+        pydot.graph_from_dot_data(
+            """
     digraph {{
         graph [bgcolor="#eeeeee",
                 clusterrank=local,
@@ -1041,10 +1043,11 @@ def test_print_dot() -> None:
         "command_line_tool" -> "file_output";
 }}
     """.format()
+        ),
     )[0]
     stdout = StringIO()
     assert main(["--debug", "--print-dot", cwl_path], stdout=stdout) == 0
-    computed_dot = pydot.graph_from_dot_data(stdout.getvalue())[0]
+    computed_dot = cast(list[pydot.core.Dot], pydot.graph_from_dot_data(stdout.getvalue()))[0]
     computed_edges = sorted((source, target) for source, target in computed_dot.obj_dict["edges"])
     expected_edges = sorted((source, target) for source, target in expected_dot.obj_dict["edges"])
     assert computed_edges == expected_edges