mypyc fixes

Author: mr-c

cwl_utils/hello.simg

@@ -10,6 +10,7 @@
 import sys
 from contextlib import suppress
 from copy import deepcopy
+from importlib.resources import files
 from pathlib import Path
 from typing import Any, TypeGuard, Union
 from urllib.parse import urlparse
@@ -59,13 +60,6 @@
     "null": "null",
 }
 
-JSON_TEMPLATE_PATH = (
-    Path(__file__)
-    .parent.joinpath("./templates/workflow_input_json_schema_template.json")
-    .absolute()
-    .resolve()
-)
-
 # Some type hinting
 InputType = Union[
     InputArraySchema, InputEnumSchema, InputRecordSchema, str, File, Directory
@@ -343,7 +337,12 @@ def cwl_to_jsonschema(cwl_obj: Workflow | CommandLineTool) -> Any:
 
     """
     # Initialise the schema from the workflow input json schema template
-    with JSON_TEMPLATE_PATH.open() as template_h:
+
+    with (
+        files("cwl-utils")
+        .joinpath("./templates/workflow_input_json_schema_template.json")
+        .open() as template_h
+    ):
         input_json_schema = json.load(template_h)
 
     # Get the complex schema keys

cwl_utils/inputs_schema_gen.py

@@ -25,7 +25,7 @@
 from cwl_utils.types import CWLOutputType
 from cwl_utils.utils import singularity_supports_userns
 
-default_timeout = 20
+default_timeout: float = 20
 """Default number of seconds to wait while running a javascript engine."""
 
 seg_symbol = r"""\w+"""
@@ -66,7 +66,15 @@ def stdfmt(data: str) -> str:
 class JSEngine(ABC):
     @abstractmethod
     def eval(
-        self, scan: str, jslib: str = "", **kwargs: Any
+        self,
+        scan: str,
+        jslib: str = "",
+        timeout: float = default_timeout,
+        force_docker_pull: bool = False,
+        debug: bool = False,
+        js_console: bool = False,
+        container_engine: str = "docker",
+        **kwargs: Any,
     ) -> CWLOutputType | Awaitable[CWLOutputType]: ...
 
     @abstractmethod

cwl_utils/sandboxjs.py

@@ -2,15 +2,17 @@
 """Tests of example Python scripts."""
 import os
 import runpy
+from importlib.resources import as_file, files
 from pathlib import Path
 
 
 def test_load_example() -> None:
     """Test the load_cwl_by_path.py script."""
     cwd = Path.cwd()
-    parent = Path(__file__).resolve().parent
-    os.chdir(parent.parent)
-    result_raw = runpy.run_path(str(parent / "load_cwl_by_path.py"))
-    os.chdir(cwd)
+    target = files("cwl_utils/tests").joinpath("load_cwl_by_path.py")
+    with as_file(target) as target_path:
+        os.chdir(target_path.parent)
+        result_raw = runpy.run_path(str(target_path))
+        os.chdir(cwd)
     result = result_raw["saved_obj"]
     assert result["class"] == "Workflow"

cwl_utils/tests/test_examples.py

@@ -12,16 +12,10 @@ def get_path(filename: str) -> Path:
     """Get the filepath for a given test file."""
     # normalizing path depending on OS or else it will cause problem when joining path
     filename = os.path.normpath(filename)
-    filepath = None
-    try:
-        file_manager = ExitStack()
-        atexit.register(file_manager.close)
-        traversable = files("cwl-utils") / filename
-        filepath = file_manager.enter_context(as_file(traversable))
-    except ModuleNotFoundError:
-        pass
-    if not filepath or not filepath.is_file():
-        filepath = Path(os.path.dirname(__file__), os.pardir, filename)
+    file_manager = ExitStack()
+    atexit.register(file_manager.close)
+    traversable = files("cwl_utils") / filename
+    filepath = file_manager.enter_context(as_file(traversable))
     return filepath.resolve()
 
 

cwl_utils/tests/util.py

@@ -1,6 +1,5 @@
 # SPDX-License-Identifier: Apache-2.0
 """Miscellaneous utility functions."""
-import os
 import pathlib
 import subprocess  # nosec
 import sys
@@ -9,8 +8,8 @@
 import urllib.request
 from collections.abc import MutableMapping, MutableSequence
 from copy import deepcopy
+from importlib.resources import files
 from io import StringIO
-from pathlib import Path
 from typing import Any
 from urllib.parse import urlparse
 
@@ -215,7 +214,7 @@ def singularity_supports_userns() -> bool:
     global _USERNS  # pylint: disable=global-statement
     if _USERNS is None:
         try:
-            hello_image = Path(os.path.dirname(__file__), "hello.simg")
+            hello_image = files("cwl_utils").joinpath("hello.simg")
             result = subprocess.Popen(  # nosec
                 ["singularity", "exec", "--userns", str(hello_image), "true"],
                 stderr=subprocess.PIPE,

cwl_utils/utils.py

@@ -90,6 +90,7 @@ include = [
 "/*requirements.txt",
 "/cwl_utils/**.py",
 "/cwl_utils/*.js",
+"/cwl_utils/parser/*.py",
 "/cwl_utils/tests/**.py",
 "/cwl_utils/templates/*",
 "/cwl_utils/testdata/*.cwl",
@@ -129,6 +130,7 @@ include = [
 "/LICENSE",
 "/cwl_utils/**.py",
 "/cwl_utils/*.js",
+"/cwl_utils/parser/*.py",
 "/cwl_utils/tests/**.py",
 "/cwl_utils/templates/*",
 "/cwl_utils/testdata/*.cwl",
@@ -153,13 +155,20 @@ enable-by-default = false
 dependencies = [
     "hatch-mypyc>=0.16.0",
     "mypy==1.19.0",
+    "types-requests",
+    "types-jsonschema",
+    "types-setuptools>=57.4.0",
 ]
 require-runtime-dependencies = true
 exclude = [
 "/create_cwl_from_objects.py",
 "/load_cwl_by_path.py",
+"/cwl_utils/tests",
+"/cwl_utils/testdata",
+]
+include = [
+"/cwl_utils/parser",
 ]
-
 
 [tool.hatch.envs.test]
 features = ["testing"]