Bump mypy from 1.3.0 to 1.6.0

Makefile

@@ -183,12 +183,6 @@ list-author-emails:
 
 mypy3: mypy
 mypy: $(PYSOURCES)
-	if ! test -f $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
-	then \
-		rm -Rf mypy-stubs/ruamel/yaml ; \
-		ln -s $(shell python -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))') \
-			mypy-stubs/ruamel/ ; \
-	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
 
 mypyc: $(PYSOURCES)

cwltool/context.py

@@ -43,7 +43,7 @@
 
 
 class ContextBase:
-    """Shared kwargs based initilizer for :py:class:`RuntimeContext` and :py:class:`LoadingContext`."""
+    """Shared kwargs based initializer for :py:class:`RuntimeContext` and :py:class:`LoadingContext`."""
 
     def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         """Initialize."""

cwltool/job.py

@@ -190,7 +190,7 @@ def is_streamable(file: str) -> bool:
                 return False
             for inp in self.joborder.values():
                 if isinstance(inp, dict) and inp.get("location", None) == file:
-                    return inp.get("streamable", False)
+                    return cast(bool, inp.get("streamable", False))
             return False
 
         for knownfile in self.pathmapper.files():

lint-requirements.txt

@@ -1,3 +1,3 @@
 flake8-bugbear<23.10
-black~=23.9
+black~=22.0
 codespell

mypy-requirements.txt

@@ -1,4 +1,4 @@
-mypy==1.3.0  # also update pyproject.toml
+mypy==1.6.0  # also update pyproject.toml
 ruamel.yaml>=0.16.0,<0.18
 cwl-utils>=0.22
 types-requests

mypy.ini

@@ -5,6 +5,7 @@ show_column_numbers = true
 show_error_codes = true
 pretty = true
 warn_unreachable = True
+new_type_inference = True
 
 [mypy-galaxy.tool_util.*]
 ignore_missing_imports = True

pyproject.toml

@@ -1,12 +1,13 @@
 [build-system]
 requires = [
     "setuptools>=45",
-    "mypy==1.3.0",  # also update mypy-requirements.txt
+    "mypy==1.6.0",  # also update mypy-requirements.txt
     "types-requests",
     "types-psutil",
     "importlib_resources>=1.4",  # equivalent to Python 3.9
     "ruamel.yaml>=0.16.0,<0.18",
     "schema-salad>=8.4.20230426093816,<9",
+    "packaging<22",
     "cwl-utils>=0.19",
     "toml",
     "argcomplete>=1.12.0",

requirements.txt

@@ -1,6 +1,5 @@
 requests>=2.6.1
-ruamel.yaml>=0.15.0,<0.18
-ruamel.yaml>=0.16;python_version>='3.10'
+ruamel.yaml>=0.16.0,<0.18
 rdflib>=4.2.2,<7.1
 shellescape>=3.4.1,<3.9
 schema-salad>=8.4.20230426093816,<9
@@ -12,4 +11,5 @@ coloredlogs
 pydot>=1.4.1
 argcomplete>=1.12.0
 pyparsing!=3.0.2  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
+packaging<22
 cwl-utils>=0.22

setup.py

@@ -85,7 +85,7 @@
         "cwltool/workflow.py",
     ]
 
-    from mypyc.build import mypycify  # type: ignore[import]
+    from mypyc.build import mypycify  # type: ignore[import-untyped]
 
     opt_level = os.getenv("MYPYC_OPT_LEVEL", "3")
     ext_modules = mypycify(mypyc_targets, opt_level=opt_level)
@@ -112,8 +112,7 @@
         "setuptools",
         "requests >= 2.6.1",  # >= 2.6.1 to workaround
         # https://github.com/ionrock/cachecontrol/issues/137
-        "ruamel.yaml >= 0.15, < 0.18",
-        "ruamel.yaml >= 0.16.0;python_version>='3.10'",
+        "ruamel.yaml >= 0.16, < 0.18",
         "rdflib >= 4.2.2, < 7.1.0",
         "shellescape >= 3.4.1, < 3.9",
         "schema-salad >= 8.4.20230426093816, < 9",
@@ -125,6 +124,7 @@
         "pydot >= 1.4.1",
         "argcomplete",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
+        "packaging<22",
         "cwl-utils >= 0.22",
     ],
     extras_require={

tests/test_toolargparse.py

@@ -180,7 +180,7 @@ def test_dont_require_inputs(tmp_path: Path) -> None:
 
 
 def test_argparser_with_doc() -> None:
-    """The `desription` field is set if `doc` field is provided."""
+    """The `description` field is set if `doc` field is provided."""
     loadingContext = LoadingContext()
     tool = load_tool(get_data("tests/with_doc.cwl"), loadingContext)
     p = argparse.ArgumentParser()
@@ -189,7 +189,7 @@ def test_argparser_with_doc() -> None:
 
 
 def test_argparser_without_doc() -> None:
-    """The `desription` field is None if `doc` field is not provided."""
+    """The `description` field is None if `doc` field is not provided."""
     loadingContext = LoadingContext()
     tool = load_tool(get_data("tests/without_doc.cwl"), loadingContext)
     p = argparse.ArgumentParser()

tests/wf/schemadef-bug-1473.cwl

@@ -449,7 +449,7 @@
                                     "name": "#settings-by-samples__1.0.0.yaml/settings-by-samples/samples"
                                 },
                                 {
-                                    "label": "settings by override cylces",
+                                    "label": "settings by override cycles",
                                     "doc": "Additional bcl convert settings\n",
                                     "type": [
                                         "null",