try to refine type

acclimatise/cli.py

@@ -108,7 +108,9 @@ def explore(
     for format in formats:
         converter_cls = WrapperGenerator.choose_converter(format)
         converter = converter_cls(
-            generate_names=generate_names, ignore_positionals=not pos, case=case,
+            generate_names=generate_names,
+            ignore_positionals=not pos,
+            case=case,
         )
         list(converter.generate_tree(command, out_dir))
 
@@ -133,7 +135,9 @@ def pipe(cmd, pos, generate_names, case, format):
 
     converter_cls = WrapperGenerator.choose_converter(format)
     converter = converter_cls(
-        generate_names=generate_names, ignore_positionals=not pos, case=case,
+        generate_names=generate_names,
+        ignore_positionals=not pos,
+        case=case,
     )
     output = converter.save_to_string(command)
     print(output)

acclimatise/converter/wdl.py

@@ -36,7 +36,12 @@ def flag_to_command_input(
     if isinstance(named_flag.arg, model.Flag):
         args.update(dict(optional=named_flag.arg.optional))
         if isinstance(named_flag.arg.args, model.EmptyFlagArg):
-            args.update(dict(true=named_flag.arg.longest_synonym, false=""))
+            args.update(
+                dict(
+                    true=named_flag.arg.longest_synonym,
+                    false=""
+                )
+            )
         else:
             args.update(dict(prefix=named_flag.arg.longest_synonym,))
     elif isinstance(named_flag, model.Positional):

acclimatise/model.py

@@ -293,15 +293,21 @@ def _name_from_arg(self) -> typing.Iterable[str]:
 
     def get_type(self) -> cli_types.CliType:
         # Try the argument name, then the flag name, then the description in that order
-        arg_type = self.args.get_type()
-        if arg_type is not None:
-            return arg_type
-
-        flag_type = infer_type(self.full_name())
-        if flag_type is not None:
-            return flag_type
-
-        return infer_type(self.description) or cli_types.CliString()
+        tpe = None
+        tpe_cand = [
+            self.args.get_type(),
+            infer_type(self.full_name()),
+            infer_type(self.description),
+            cli_types.CliString(),
+        ]
+        for c in tpe_cand:
+            if tpe is None:
+                if c is not None:
+                    tpe = c
+            else:
+                if isinstance(type(c), type(tpe)):
+                    tpe = c
+        return tpe
 
     def full_name(self) -> str:
         """

acclimatise/usage_parser/elements.py

@@ -36,7 +36,11 @@ def action(s, loc, toks):
 
 mandatory_element = (
     element_char.copy()
-    .setParseAction(lambda s, loc, toks: UsageElement(text=toks[0],))
+    .setParseAction(
+        lambda s, loc, toks: UsageElement(
+            text=toks[0],
+        )
+    )
     .setName("MandatoryElement")
 )
 """

test/executors/test_docker.py

@@ -7,7 +7,9 @@
 def test_docker(bwamem_help):
     client = docker.from_env()
     container = client.containers.run(
-        "biocontainers/bwa:v0.7.17_cv1", entrypoint=["sleep", "999999999"], detach=True,
+        "biocontainers/bwa:v0.7.17_cv1",
+        entrypoint=["sleep", "999999999"],
+        detach=True,
     )
 
     exec = DockerExecutor(container)
@@ -23,7 +25,9 @@ def test_docker_kill():
     """
     client = docker.from_env(timeout=99999)
     container = client.containers.run(
-        "ubuntu:latest", entrypoint=["sleep", "999999999"], detach=True,
+        "ubuntu:latest",
+        entrypoint=["sleep", "999999999"],
+        detach=True,
     )
 
     exec = DockerExecutor(container)
@@ -54,7 +58,9 @@ def test_infinite_output():
     """
     client = docker.from_env(timeout=99999)
     container = client.containers.run(
-        "ubuntu:latest", entrypoint=["sleep", "999999999"], detach=True,
+        "ubuntu:latest",
+        entrypoint=["sleep", "999999999"],
+        detach=True,
     )
 
     exec = DockerExecutor(container)

test/name_generation/test_single_flag.py

@@ -54,7 +54,11 @@ def test_name_to_words(gen):
     """
     Check that we can get an argument name even if the argument's flag is a symbol
     """
-    arg = Flag(synonyms=["--genomepaths"], description="", args=EmptyFlagArg(),)
+    arg = Flag(
+        synonyms=["--genomepaths"],
+        description="",
+        args=EmptyFlagArg(),
+    )
 
     name = gen.choose_variable_names([arg])[0].name
     assert "genome" in name

test/test_cli.py

@@ -69,7 +69,14 @@ def test_explore_samtools_no_subcommands(runner, caplog):
     caplog.set_level(100000)
     with tempfile.TemporaryDirectory() as tempdir:
         result = runner.invoke(
-            main, ["explore", "samtools", "--no-subcommands", "--out-dir", tempdir,],
+            main,
+            [
+                "explore",
+                "samtools",
+                "--no-subcommands",
+                "--out-dir",
+                tempdir,
+            ],
         )
         cli_worked(result)
         # Since we aren't looking at subcommands, there should be one file for each format