Bump mypy from 1.15.0 to 1.17.1

cwlupgrader/main.py

@@ -60,14 +60,14 @@ def parse_args(args: list[str]) -> argparse.Namespace:
 
 
 def main(args: Optional[list[str]] = None) -> int:
-    """Hook to set the args."""
+    """Run with optional arguments override."""
     if not args:
         args = sys.argv[1:]
     return run(parse_args(args))
 
 
 def run(args: argparse.Namespace) -> int:
-    """Main function."""
+    """Run the program using the provided arguments."""
     imports: set[str] = set()
     if args.dir and not os.path.exists(args.dir):
         os.makedirs(args.dir)
@@ -188,7 +188,7 @@ def load_cwl_document(path: str) -> Any:
 
 
 def write_cwl_document(document: Any, name: str, dirname: str) -> None:
-    """
+    r"""
     Serialize the document using the Ruamel YAML round trip dumper.
 
     Will also prepend "#!/usr/bin/env cwl-runner\n" and
@@ -265,7 +265,7 @@ def v1_1_to_v1_2(document: CommentedMap, outdir: str) -> CommentedMap:
 
 
 def draft3_to_v1_0(document: CommentedMap, outdir: str) -> CommentedMap:
-    """Transformation loop."""
+    """Transform a draft3 document to a version 1.0 document."""
     _draft3_to_v1_0(document, outdir)
     if isinstance(document, MutableMapping):
         for key, value in document.items():
@@ -281,12 +281,12 @@ def draft3_to_v1_0(document: CommentedMap, outdir: str) -> CommentedMap:
 
 
 def draft3_to_v1_1(document: CommentedMap, outdir: str) -> CommentedMap:
-    """transformation loop."""
+    """Transform a draft3 document to a version 1.1 document."""
     return v1_0_to_v1_1(draft3_to_v1_0(document, outdir), outdir)
 
 
 def draft3_to_v1_2(document: CommentedMap, outdir: str) -> CommentedMap:
-    """transformation loop."""
+    """Transform a draft3 document to a version 1.2 document."""
     return v1_1_to_v1_2(v1_0_to_v1_1(draft3_to_v1_0(document, outdir), outdir), outdir)
 
 
@@ -556,7 +556,7 @@ def upgrade_v1_0_hints_and_reqs(document: dict[str, Any]) -> None:
 
 
 def has_hint_or_req(document: dict[str, Any], name: str) -> bool:
-    """Detects an existing named hint or requirement."""
+    """Detect an existing named hint or requirement."""
     for extra in ("requirements", "hints"):
         if extra in document:
             with SourceLine(document, extra, Exception):
@@ -572,7 +572,7 @@ def has_hint_or_req(document: dict[str, Any], name: str) -> bool:
 
 
 def workflow_clean(document: dict[str, Any]) -> None:
-    """Transform draft-3 style Workflows to more idiomatic v1.0"""
+    """Transform draft-3 style Workflows to more idiomatic v1.0."""
     input_output_clean(document)
     hints_and_requirements_clean(document)
     outputs = document["outputs"]
@@ -760,7 +760,7 @@ def shorten_type(type_obj: Union[str, list[Any]]) -> Union[str, list[Any]]:
 
 
 def clean_secondary_files(document: dict[str, Any]) -> None:
-    """Cleanup for secondaryFiles"""
+    """Cleanup for secondaryFiles."""
     if "secondaryFiles" in document:
         for i, sfile in enumerate(document["secondaryFiles"]):
             if "$(" in sfile or "${" in sfile:

mypy-requirements.txt

@@ -1,2 +1 @@
-mypy==1.15.0
-types-setuptools
+mypy==1.17.1

tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for cwl-upgrader."""

tests/test_complete.py

@@ -3,14 +3,14 @@
 
 from cwlupgrader.main import load_cwl_document, main, upgrade_document
 
-from .util import get_data
+from .util import get_data, get_path
 
 
 def test_draft3_workflow(tmp_path: Path) -> None:
     """Basic draft3 to CWL v1.1 test."""
     main([f"--dir={tmp_path}", "--v1-only", get_data("testdata/draft-3/wf.cwl")])
     result = filecmp.cmp(
-        get_data("testdata/v1.0/wf.cwl"),
+        get_path("testdata/v1.0/wf.cwl"),
         tmp_path / "wf.cwl",
         shallow=False,
     )
@@ -27,7 +27,7 @@ def test_draft3_tool_long_form_arrays(tmp_path: Path) -> None:
         ]
     )
     result = filecmp.cmp(
-        get_data("testdata/v1.0/attributor-prok-cheetah.cwl"),
+        get_path("testdata/v1.0/attributor-prok-cheetah.cwl"),
         tmp_path / "attributor-prok-cheetah.cwl",
         shallow=False,
     )
@@ -95,7 +95,7 @@ def test_packed_graph(tmp_path: Path) -> None:
         [f"--dir={tmp_path}", "--v1.1-only", get_data("testdata/v1.0/conflict-wf.cwl")]
     )
     assert filecmp.cmp(
-        get_data("testdata/v1.1/conflict-wf.cwl"),
+        get_path("testdata/v1.1/conflict-wf.cwl"),
         tmp_path / "conflict-wf.cwl",
         shallow=False,
     )
@@ -105,12 +105,12 @@ def test_multi_version_upgrade_external_steps(tmp_path: Path) -> None:
     """Test 1.0 to 1.2 upgrade of Workflow with external steps."""
     main([f"--dir={tmp_path}", get_data("testdata/v1.0/1st-workflow.cwl")])
     assert filecmp.cmp(
-        get_data("testdata/v1.2/arguments.cwl"),
+        get_path("testdata/v1.2/arguments.cwl"),
         tmp_path / "arguments.cwl",
         shallow=False,
     )
     assert filecmp.cmp(
-        get_data("testdata/v1.2/tar-param.cwl"),
+        get_path("testdata/v1.2/tar-param.cwl"),
         tmp_path / "tar-param.cwl",
         shallow=False,
     )

tests/test_output_dir.py

@@ -5,15 +5,15 @@
 
 from cwlupgrader.main import main
 
-from .util import get_data
+from .util import get_data, get_path
 
 
 def test_draft3_workflow(tmp_path: Path) -> None:
     """Confirm that --dir works when the directory doesn't exist yet."""
     out_dir = tmp_path / "new"
     main([f"--dir={out_dir}", "--v1-only", get_data("testdata/draft-3/wf.cwl")])
     result = filecmp.cmp(
-        get_data("testdata/v1.0/wf.cwl"),
+        get_path("testdata/v1.0/wf.cwl"),
         out_dir / "wf.cwl",
         shallow=False,
     )

tests/util.py

@@ -1,20 +1,30 @@
-import os
+"""Shared test utility functions."""
 
-from pkg_resources import Requirement, ResolutionError, resource_filename
+import atexit
+import os
+import shutil
+from contextlib import ExitStack
+from importlib.resources import as_file, files
+from pathlib import Path
 
 
-def get_data(filename: str) -> str:
+def get_path(filename: str) -> Path:
+    """Get the file Path for a given test file."""
+    # normalizing path depending on OS or else it will cause problem when joining path
     filename = os.path.normpath(filename)
-    # normalizing path depending on OS or else it will cause problem when
-    # joining path
     filepath = None
     try:
-        filepath = resource_filename(Requirement.parse("cwlupgrader"), filename)
-    except ResolutionError:
+        file_manager = ExitStack()
+        atexit.register(file_manager.close)
+        traversable = files("cwlupgrader") / filename
+        filepath = file_manager.enter_context(as_file(traversable))
+    except ModuleNotFoundError:
         pass
-    if not filepath or not os.path.isfile(filepath):
-        filepath = os.path.join(os.path.dirname(__file__), os.pardir, filename)
-        # warning, __file__ is all lowercase on Windows systems, this can
-        # sometimes conflict with docker toolkit. Workaround: pip install .
-        # and run the tests elsewhere via python -m pytest --pyarg cwltool
-    return filepath
+    if not filepath or not filepath.is_file():
+        filepath = Path(os.path.dirname(__file__), os.pardir, filename)
+    return filepath.resolve()
+
+
+def get_data(filename: str) -> str:
+    """Get the filename as string for a given test file."""
+    return str(get_path(filename))