fix tests

WDL/Tree.py

@@ -1128,7 +1128,7 @@ def typecheck(self, doc: "Document", check_quant: bool) -> None:
         #    conditional section therein
         stdlib = StdLib.Base(self.effective_wdl_version)
         _build_workflow_type_env(doc, stdlib, check_quant)
-        assert self._type_env
+        assert self._type_env is not None
         with Error.multi_context() as errors:
             # 3. typecheck the right-hand side expressions of each declaration
             #    and the inputs to each call (descending into scatter & conditional

tests/test_1doc.py

@@ -53,7 +53,7 @@ def test_wc(self):
         }
         """]
         for task_str in variants:
-            task = WDL.parse_tasks(task_str)[0]
+            task = WDL.parse_tasks(task_str, "1.0")[0]
             self.assertEqual(len(task.inputs), 1)
             self.assertEqual(str(task.inputs[0]), "String in")
 
@@ -92,7 +92,7 @@ def test_errors(self):
                     String in
                 }
                 command {
-                    echo "~{bogus}" | wc
+                    echo "${bogus}" | wc
                 }
             }
             """)[0].typecheck()
@@ -109,7 +109,7 @@ def test_errors(self):
                     String ans = "${bogus}"
                 }
             }
-            """)[0].typecheck()
+            """, "1.0")[0].typecheck()
         with self.assertRaises(WDL.Error.MultipleValidationErrors):
             WDL.parse_tasks("""
             task wc {
@@ -124,7 +124,7 @@ def test_errors(self):
                 output {
                 }
             }
-            """)[0].typecheck()
+            """, "1.0")[0].typecheck()
 
     def test_placeholders(self):
         task = WDL.parse_tasks("""
@@ -136,7 +136,7 @@ def test_placeholders(self):
                     echo "~{true='yes' false='no' b}"
                 >>>
             }
-            """)[0]
+            """, "1.0")[0]
         task.typecheck()
         stdlib = WDL.StdLib.Base("1.0")
         self.assertEqual(task.command.parts[1].eval(WDL.Env.Bindings().bind('b', WDL.Value.Boolean(True)), stdlib).value, 'yes')
@@ -170,7 +170,7 @@ def test_placeholders(self):
                         echo "~{true='yes' false='no' b}"
                     }
                 }
-                """)[0].typecheck()
+                """, "1.0")[0].typecheck()
 
         with self.assertRaises(WDL.Error.StaticTypeMismatch):
             WDL.parse_tasks("""
@@ -179,7 +179,7 @@ def test_placeholders(self):
                         echo "~{true='yes' false='no' 42}"
                     }
                 }
-                """)[0].typecheck()
+                """, "1.0")[0].typecheck()
 
         with self.assertRaises(WDL.Error.StaticTypeMismatch):
             WDL.parse_tasks("""
@@ -191,7 +191,7 @@ def test_placeholders(self):
                         echo "~{false='no' b}"
                     }
                 }
-                """)[0].typecheck()
+                """, "1.0")[0].typecheck()
 
         task = WDL.parse_tasks("""
             task wc {
@@ -202,7 +202,7 @@ def test_placeholders(self):
                     echo "~{sep=', ' s} baz"
                 >>>
             }
-            """)[0]
+            """, "1.0")[0]
         task.typecheck()
         foobar = WDL.Value.Array(WDL.Type.String(), [WDL.Value.String("foo"), WDL.Value.String("bar")])
         self.assertEqual(task.command.parts[1].eval(WDL.Env.Bindings().bind('s', foobar), stdlib).value, 'foo, bar')
@@ -218,7 +218,7 @@ def test_placeholders(self):
                     echo "~{s} baz"
                 >>>
             }
-            """)[0].typecheck()
+            """, "1.0")[0].typecheck()
         with self.assertRaises(WDL.Error.StaticTypeMismatch):
             WDL.parse_tasks("""
             task wc {
@@ -229,7 +229,7 @@ def test_placeholders(self):
                     echo "~{sep=', ' s} baz"
                 >>>
             }
-            """)[0].typecheck()
+            """, "1.0")[0].typecheck()
 
         task = WDL.parse_tasks("""
             task wc {
@@ -325,7 +325,7 @@ def test_meta(self):
                 meta_key: 321
             }
         }
-        """)[0]
+        """, "1.0")[0]
         task.typecheck()
         self.assertIsInstance(task.parameter_meta['b']['help'], str)
         self.assertEqual(task.parameter_meta['b']['help'], "it's a boolean")
@@ -360,7 +360,7 @@ def test_meta(self):
                 cpu: 42
             }
         }
-        """)[0]
+        """, "1.0")[0]
         task.typecheck()
         self.assertIsInstance(task.meta['description'], str)
         self.assertEqual(task.meta['description'], "it's a task")

tests/test_4taskrun.py

@@ -1198,7 +1198,7 @@ def test_mount_tmpdir(self):
         cfg = WDL.runtime.config.Loader(logging.getLogger(self.id()), [])
         cfg.override({"file_io": {"mount_tmpdir_for": ["xyz"]}})
         outputs = self._test_task(txt, cfg=cfg)
-        self.assertEquals(outputs["tmpdir"], "")
+        self.assertEqual(outputs["tmpdir"], "")
         outputs = self._test_task(txt.replace("XXX", "xyz"), cfg=cfg)
         self.assertTrue(outputs["tmpdir"].startswith("/mnt/miniwdl"))
 

tests/test_5stdlib.py

@@ -1035,7 +1035,7 @@ def test_issue538(self):
             }
         }
         """)
-        self.assertEquals(outp["result"], {"map": {"foo":"bar", "fizz":"buzz"}})
+        self.assertEqual(outp["result"], {"map": {"foo":"bar", "fizz":"buzz"}})
 
     def test_issue563(self):
         # still more struct init regression
@@ -1055,7 +1055,7 @@ def test_issue563(self):
             }
         }
         """, {"j": {"x": 0}})
-        self.assertEquals(outp, {"out": [{"x": 0}]})
+        self.assertEqual(outp, {"out": [{"x": 0}]})
 
     def test_issue580(self):
         # error in nested struct

tests/test_6workflowrun.py

@@ -1128,7 +1128,7 @@ def test_retry(self):
         self.assertFalse(outputs["stdout_txt"].endswith("stdout.txt"))
         with open(outputs["stdout_txt"]) as stdout_txt:
             stdout_lines = stdout_txt.read().strip().split("\n")
-            self.assertEquals(len(stdout_lines), 1)
+            self.assertEqual(len(stdout_lines), 1)
         cfg = WDL.runtime.config.Loader(logging.getLogger(self.id()), [])
         cfg.override({"file_io": {"delete_work": "failure"}, "task_runtime": {"_mock_interruptions": 2}})
         outputs = self._test_workflow(txt, cfg=cfg)