bonus mypy fixes

Author: mr-c

Makefile

@@ -157,7 +157,7 @@ list-author-emails:
 	@git log --format='%aN,%aE' | sort -u | grep -v 'root'
 
 mypy3: mypy
-mypy: ${PYSOURCES}
+mypy: $(filter-out setup.py gittagger.py,${PYSOURCES})
 	if ! test -f $(shell python3 -c 'import ruamel.yaml; import os.path; print(os.path.dirname(ruamel.yaml.__file__))')/py.typed ; \
 	then \
 		rm -Rf typeshed/2and3/ruamel/yaml ; \
@@ -166,7 +166,7 @@ mypy: ${PYSOURCES}
 	fi  # if minimally required ruamel.yaml version is 0.15.99 or greater, than the above can be removed
 	MYPYPATH=$$MYPYPATH:typeshed/3:typeshed/2and3 mypy --disallow-untyped-calls \
 		 --warn-redundant-casts \
-		 cwltool
+		 $^
 
 mypyc: ${PYSOURCES}
 	MYPYPATH=typeshed/2and3/:typeshed/3 CWLTOOL_USE_MYPYC=1 pip install --verbose -e . && pytest --ignore cwltool/schemas --basetemp ./tmp

tests/test_anon_types.py

@@ -1,6 +1,6 @@
 from typing import cast
 
-import pytest  # type: ignore
+import pytest
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
@@ -112,6 +112,6 @@
 )
 
 
-@pytest.mark.parametrize("snippet", snippet)  # type: ignore
+@pytest.mark.parametrize("snippet", snippet)
 def test_anon_types(snippet: CommentedMap) -> None:
     CommandLineTool(snippet, LoadingContext())

tests/test_check.py

@@ -1,4 +1,4 @@
-import pytest  # type: ignore
+import pytest
 
 from cwltool.main import main
 
@@ -7,7 +7,7 @@
 bad_flows = ["tests/wf/badout1.cwl", "tests/wf/badout2.cwl", "tests/wf/badout3.cwl"]
 
 
-@needs_docker  # type: ignore
-@pytest.mark.parametrize("bad_flow", bad_flows)  # type: ignore
+@needs_docker
+@pytest.mark.parametrize("bad_flow", bad_flows)
 def test_output_checking(bad_flow: str) -> None:
     assert main([get_data(bad_flow)]) == 1

tests/test_context.py

@@ -6,19 +6,19 @@
 
 
 @windows_needs_docker
-def test_replace_default_stdout_stderr():
+def test_replace_default_stdout_stderr() -> None:
     import sys
 
     # break stdout & stderr
     original_stdout = sys.stdout
     original_stderr = sys.stderr
 
-    sys.stdout = ""
-    sys.stderr = ""
+    sys.stdout = ""  # type: ignore
+    sys.stderr = ""  # type: ignore
 
     runtime_context = RuntimeContext()
-    runtime_context.default_stdout = subprocess.DEVNULL
-    runtime_context.default_stderr = subprocess.DEVNULL
+    runtime_context.default_stdout = subprocess.DEVNULL  # type: ignore
+    runtime_context.default_stderr = subprocess.DEVNULL  # type: ignore
     factory = get_windows_safe_factory(runtime_context=runtime_context)
     echo = factory.make(get_data("tests/echo.cwl"))
 

tests/test_dependencies.py

@@ -1,7 +1,7 @@
 import os
 from distutils import spawn
 
-import pytest  # type: ignore
+import pytest
 
 from cwltool.utils import onWindows
 
@@ -13,8 +13,8 @@
     deps = None
 
 
-@needs_docker  # type: ignore
-@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")  # type: ignore
+@needs_docker
+@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
 def test_biocontainers() -> None:
     wflow = get_data("tests/seqtk_seq.cwl")
     job = get_data("tests/seqtk_seq_job.json")
@@ -23,8 +23,8 @@ def test_biocontainers() -> None:
     assert error_code == 0
 
 
-@pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows")  # type: ignore
-@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")  # type: ignore
+@pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows")
+@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
 def test_bioconda() -> None:
     wflow = get_data("tests/seqtk_seq.cwl")
     job = get_data("tests/seqtk_seq_job.json")
@@ -35,7 +35,7 @@ def test_bioconda() -> None:
     assert error_code == 0, stderr
 
 
-@pytest.mark.skipif(  # type: ignore
+@pytest.mark.skipif(
     not spawn.find_executable("modulecmd"), reason="modulecmd not installed"
 )
 def test_modules() -> None:

tests/test_docker.py

@@ -7,7 +7,7 @@
 from .util import get_data, get_main_output, needs_docker
 
 
-@needs_docker  # type: ignore
+@needs_docker
 def test_docker_workflow(tmpdir: py.path.local) -> None:
     result_code, _, stderr = get_main_output(
         [
@@ -42,7 +42,7 @@ def test_docker_iwdr() -> None:
         assert result_code != 0
 
 
-@needs_docker  # type: ignore
+@needs_docker
 def test_docker_incorrect_image_pull() -> None:
     result_code = main(
         [
@@ -56,7 +56,7 @@ def test_docker_incorrect_image_pull() -> None:
     assert result_code != 0
 
 
-@needs_docker  # type: ignore
+@needs_docker
 def test_docker_file_mount() -> None:
     # test for bug in
     # ContainerCommandLineJob.create_file_and_add_volume()

tests/test_docker_info.py

@@ -1,7 +1,7 @@
 from .util import get_data, get_main_output, needs_docker
 
 
-@needs_docker  # type: ignore
+@needs_docker
 def test_docker_mem() -> None:
     error_code, stdout, stderr = get_main_output(
         [

tests/test_docker_warning.py

@@ -1,6 +1,6 @@
 from typing import Any, cast
 
-import pytest  # type: ignore
+import pytest
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 

tests/test_empty_input.py

@@ -5,7 +5,7 @@
 from .util import get_data, temp_dir, windows_needs_docker
 
 
-@windows_needs_docker  # type: ignore
+@windows_needs_docker
 def test_empty_input() -> None:
     empty_json = "{}"
     empty_input = StringIO(empty_json)