remove last usage of pkg_resources

cwltool/main.py

@@ -34,7 +34,6 @@
 import argcomplete
 import coloredlogs
 import ruamel.yaml
-from importlib_resources import files
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from ruamel.yaml.main import YAML
 from schema_salad.exceptions import ValidationException
@@ -108,6 +107,7 @@
     CWLOutputType,
     HasReqsHints,
     adjustDirObjs,
+    files,
     normalizeFilesDirs,
     processes_to_kill,
     trim_listing,

cwltool/process.py

@@ -33,7 +33,6 @@
 )
 
 from cwl_utils import expression
-from importlib_resources import files
 from mypy_extensions import mypyc_attr
 from rdflib import Graph
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
@@ -70,6 +69,7 @@
     aslist,
     cmp_like_py2,
     ensure_writable,
+    files,
     get_listing,
     normalizeFilesDirs,
     random_outdir,

cwltool/utils.py

@@ -53,12 +53,19 @@
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader
 
+if sys.version_info >= (3, 9):
+    from importlib.resources import as_file, files
+else:
+    from importlib_resources import as_file, files
+
 if TYPE_CHECKING:
     from .command_line_tool import CallbackJob, ExpressionJob
     from .job import CommandLineJob, JobBase
     from .stdfsaccess import StdFsAccess
     from .workflow_job import WorkflowJob
 
+__all__ = ["files", "as_file"]
+
 __random_outdir: Optional[str] = None
 
 CONTENT_LIMIT = 64 * 1024
@@ -368,8 +375,8 @@ def add_writable_flag(p: str) -> None:
     if os.path.isdir(path):
         if include_root:
             add_writable_flag(path)
-        for root, dirs, files in os.walk(path):
-            for name in files:
+        for root, dirs, files_ in os.walk(path):
+            for name in files_:
                 add_writable_flag(os.path.join(root, name))
             for name in dirs:
                 add_writable_flag(os.path.join(root, name))
@@ -380,8 +387,8 @@ def add_writable_flag(p: str) -> None:
 def ensure_non_writable(path: str) -> None:
     """Attempt to change permissions to ensure that a path is not writable."""
     if os.path.isdir(path):
-        for root, dirs, files in os.walk(path):
-            for name in files:
+        for root, dirs, files_ in os.walk(path):
+            for name in files_:
                 j = os.path.join(root, name)
                 st = os.stat(j)
                 mode = stat.S_IMODE(st.st_mode)

cwltool/validate_js.py

@@ -18,7 +18,6 @@
 from cwl_utils.errors import SubstitutionError
 from cwl_utils.expression import scanner as scan_expression
 from cwl_utils.sandboxjs import code_fragment_to_js, exec_js_process
-from importlib_resources import files
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import (
     ArraySchema,
@@ -33,6 +32,7 @@
 
 from .errors import WorkflowException
 from .loghandler import _logger
+from .utils import files
 
 
 def is_expression(tool: Any, schema: Optional[Schema]) -> bool:

docs/requirements.txt

@@ -2,6 +2,5 @@ sphinx >= 2.2
 sphinx-rtd-theme==1.3.0
 sphinx-autoapi
 sphinx-autodoc-typehints
-typed_ast;python_version<'3.8'
 sphinxcontrib-autoprogram
-importlib_resources
+importlib_resources;python_version<'3.9'

pyproject.toml

@@ -5,7 +5,7 @@ requires = [
     "mypy==1.7.1",  # also update mypy-requirements.txt
     "types-requests",
     "types-psutil",
-    "importlib_resources>=1.4",  # equivalent to Python 3.9
+    "importlib_resources>=1.4;python_version<'3.9'",
     "ruamel.yaml>=0.16.0,<0.18",
     "schema-salad>=8.4.20230426093816,<9",
     "cwl-utils>=0.22,!=0.30",

requirements.txt

@@ -6,7 +6,7 @@ schema-salad>=8.4.20230426093816,<9
 prov==1.5.1
 mypy-extensions
 psutil>=5.6.6
-importlib_resources>=1.4  # equivalent to Python 3.9
+importlib_resources>=1.4;python_version<'3.9'
 coloredlogs
 pydot>=1.4.1
 argcomplete>=1.12.0

setup.py

@@ -109,7 +109,7 @@
         "prov == 1.5.1",
         "mypy-extensions",
         "psutil >= 5.6.6",
-        "importlib_resources>=1.4",
+        "importlib_resources>=1.4;python_version<'3.9'",
         "coloredlogs",
         "pydot >= 1.4.1",
         "argcomplete",

tests/test_cuda.py

@@ -284,7 +284,7 @@ def test_cuda_job_setup_check_err_wrong_type_cuda_version(
 
 
 def test_cuda_eval_resource_range() -> None:
-    with open(get_data("cwltool/extensions-v1.1.yml")) as res:
+    with open(get_data("extensions-v1.1.yml")) as res:
         use_custom_schema("v1.2", "http://commonwl.org/cwltool", res.read())
 
     joborder = {}  # type: CWLObjectType
@@ -301,7 +301,7 @@ def test_cuda_eval_resource_range() -> None:
 
 
 def test_cuda_eval_resource_max() -> None:
-    with open(get_data("cwltool/extensions-v1.1.yml")) as res:
+    with open(get_data("extensions-v1.1.yml")) as res:
         use_custom_schema("v1.2", "http://commonwl.org/cwltool", res.read())
 
     joborder = {}  # type: CWLObjectType

tests/test_load_tool.py

@@ -87,7 +87,7 @@ def test_load_graph_fragment_from_packed() -> None:
     loadingContext = LoadingContext()
     uri = Path(get_data("tests/wf/packed-with-loadlisting.cwl")).as_uri() + "#main"
     try:
-        with open(get_data("cwltool/extensions.yml")) as res:
+        with open(get_data("extensions.yml")) as res:
             use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read())
 
         # The updater transforms LoadListingRequirement from an

tests/test_mpi.py

@@ -7,7 +7,6 @@
 from typing import Any, Generator, List, MutableMapping, Optional, Tuple
 
 import pytest
-from importlib_resources import files
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.avro.schema import Names
 from schema_salad.utils import yaml_no_ts
@@ -19,6 +18,7 @@
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.main import main
 from cwltool.mpi import MpiConfig, MPIRequirementName
+from cwltool.utils import files
 
 from .util import get_data, working_directory
 

tests/util.py

@@ -1,19 +1,22 @@
+"""Test functions."""
+import atexit
 import contextlib
 import io
 import json
 import os
 import shutil
 import subprocess
 import sys
+from contextlib import ExitStack
 from pathlib import Path
 from typing import Dict, Generator, List, Mapping, Optional, Tuple, Union
 
 import pytest
-from pkg_resources import Requirement, ResolutionError, resource_filename
 
 from cwltool.env_to_stdout import deserialize_env
 from cwltool.main import main
 from cwltool.singularity import is_version_2_6, is_version_3_or_newer
+from cwltool.utils import as_file, files
 
 
 def force_default_container(default_container_id: str, _: str) -> str:
@@ -25,12 +28,15 @@ def get_data(filename: str) -> str:
     filename = os.path.normpath(filename)
     filepath = None
     try:
-        filepath = resource_filename(Requirement.parse("cwltool"), filename)
-    except ResolutionError:
+        file_manager = ExitStack()
+        atexit.register(file_manager.close)
+        traversable = files("cwltool") / 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)
-    return str(Path(filepath).resolve())
+        filepath = Path(os.path.dirname(__file__)) / ".." / filename
+    return str(filepath.resolve())
 
 
 needs_docker = pytest.mark.skipif(

tox.ini

@@ -48,7 +48,6 @@ deps =
   py3{8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
   py3{8,9,10,11,12}-lint: -rlint-requirements.txt
   py3{8,9,10,11,12}-bandit: bandit
-  py3{8,9,10,11,12}-bandit: importlib_metadata != 4.8.0
   py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
   py312-pydocstyle: pydocstyle
   py312-pydocstyle: diff-cover