Drop Python 3.8 support, explicitly support Python 3.13

Author: mr-c

.github/workflows/ci-tests.yml

@@ -28,11 +28,11 @@ jobs:
   tox:
     name: CI tests via Tox
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12]
+        py-ver-minor: [8, 9, 10, 11, 12, 13]
         step: [lint, unit, mypy]
 
     env:
@@ -80,7 +80,7 @@ jobs:
   tox-style:
     name: CI linters via Tox
 
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     strategy:
       matrix:
@@ -115,7 +115,7 @@ jobs:
 
   conformance_tests:
     name: upgrade & test conformance tests
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4
@@ -131,7 +131,7 @@ jobs:
 
   release_test:
     name: cwl-utils release test
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v4

Makefile

@@ -165,7 +165,7 @@ shellcheck: FORCE
 	shellcheck conformance-test.sh release-test.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py38-plus $^
+	pyupgrade --exit-zero-even-if-changed --py39-plus $^
 	auto-walrus $^
 
 release-test: FORCE

cwlupgrader/__init__.py

@@ -1,3 +1,3 @@
 """Transforms draft-3 CWL documents into v1.0+ as idiomatically as possible."""
 
-__version__ = "1.2.11"
+__version__ = "1.2.12"

cwlupgrader/main.py

@@ -8,9 +8,9 @@
 import os.path
 import stat
 import sys
-from collections.abc import MutableSequence, Sequence
+from collections.abc import MutableMapping, MutableSequence, Sequence
 from pathlib import Path
-from typing import Any, Callable, Dict, List, MutableMapping, Optional, Set, Union
+from typing import Any, Callable, Optional, Union
 
 import ruamel.yaml
 from ruamel.yaml.comments import CommentedMap  # for consistent sort order
@@ -27,7 +27,7 @@
 yaml.default_flow_style = False
 
 
-def parse_args(args: List[str]) -> argparse.Namespace:
+def parse_args(args: list[str]) -> argparse.Namespace:
     """Argument parser."""
     parser = argparse.ArgumentParser(
         description="Tool to upgrade CWL documents from one version to another. "
@@ -59,7 +59,7 @@ def parse_args(args: List[str]) -> argparse.Namespace:
     return parser.parse_args(args)
 
 
-def main(args: Optional[List[str]] = None) -> int:
+def main(args: Optional[list[str]] = None) -> int:
     """Hook to set the args."""
     if not args:
         args = sys.argv[1:]
@@ -68,7 +68,7 @@ def main(args: Optional[List[str]] = None) -> int:
 
 def run(args: argparse.Namespace) -> int:
     """Main function."""
-    imports: Set[str] = set()
+    imports: set[str] = set()
     if args.dir and not os.path.exists(args.dir):
         os.makedirs(args.dir)
     for path in args.inputs:
@@ -107,7 +107,7 @@ def upgrade_document(
     document: Any,
     output_dir: str,
     target_version: Optional[str] = "latest",
-    imports: Optional[Set[str]] = None,
+    imports: Optional[set[str]] = None,
 ) -> Any:
     if imports is None:
         imports = set()
@@ -210,7 +210,7 @@ def write_cwl_document(document: Any, name: str, dirname: str) -> None:
 
 
 def process_imports(
-    document: Any, imports: Set[str], updater: Callable[[Any, str], Any], outdir: str
+    document: Any, imports: set[str], updater: Callable[[Any, str], Any], outdir: str
 ) -> None:
     """Find any '$import's and process them."""
     if isinstance(document, CommentedMap):
@@ -481,10 +481,10 @@ def _v1_1_to_v1_2(document: CommentedMap, outdir: str) -> CommentedMap:
     return document
 
 
-def cleanup_v1_0_input_bindings(document: Dict[str, Any]) -> None:
+def cleanup_v1_0_input_bindings(document: dict[str, Any]) -> None:
     """In v1.1 Workflow or ExpressionTool level inputBindings are deprecated."""
 
-    def cleanup(inp: Dict[str, Any]) -> None:
+    def cleanup(inp: dict[str, Any]) -> None:
         """Serialize non loadContents fields and add that to the doc."""
         if "inputBinding" in inp:
             bindings = inp["inputBinding"]
@@ -505,10 +505,10 @@ def cleanup(inp: Dict[str, Any]) -> None:
             cleanup(inputs[input_name])
 
 
-def move_up_loadcontents(document: Dict[str, Any]) -> None:
+def move_up_loadcontents(document: dict[str, Any]) -> None:
     """Promote 'loadContents' up a level for CWL v1.1."""
 
-    def cleanup(inp: Dict[str, Any]) -> None:
+    def cleanup(inp: dict[str, Any]) -> None:
         """Move loadContents to the preferred location."""
         if "inputBinding" in inp:
             bindings = inp["inputBinding"]
@@ -525,7 +525,7 @@ def cleanup(inp: Dict[str, Any]) -> None:
             cleanup(inputs[input_name])
 
 
-def upgrade_v1_0_hints_and_reqs(document: Dict[str, Any]) -> None:
+def upgrade_v1_0_hints_and_reqs(document: dict[str, Any]) -> None:
     """Rename some pre-v1.1 extensions to their official CWL v1.1 names."""
     for extra in ("requirements", "hints"):
         if extra in document:
@@ -555,7 +555,7 @@ def upgrade_v1_0_hints_and_reqs(document: Dict[str, Any]) -> None:
                     )
 
 
-def has_hint_or_req(document: Dict[str, Any], name: str) -> bool:
+def has_hint_or_req(document: dict[str, Any], name: str) -> bool:
     """Detects an existing named hint or requirement."""
     for extra in ("requirements", "hints"):
         if extra in document:
@@ -571,7 +571,7 @@ def has_hint_or_req(document: Dict[str, Any], name: str) -> bool:
     return False
 
 
-def workflow_clean(document: Dict[str, Any]) -> None:
+def workflow_clean(document: dict[str, Any]) -> None:
     """Transform draft-3 style Workflows to more idiomatic v1.0"""
     input_output_clean(document)
     hints_and_requirements_clean(document)
@@ -652,7 +652,7 @@ def workflow_clean(document: Dict[str, Any]) -> None:
     document["steps"] = new_steps
 
 
-def input_output_clean(document: Dict[str, Any]) -> None:
+def input_output_clean(document: dict[str, Any]) -> None:
     """Transform draft-3 style input/output listings into idiomatic v1.0."""
     for param_type in ["inputs", "outputs"]:
         if param_type not in document:
@@ -701,7 +701,7 @@ def array_type_raise_sf(param: MutableMapping[str, Any]) -> None:
         del typ["secondaryFiles"]
 
 
-def hints_and_requirements_clean(document: Dict[str, Any]) -> None:
+def hints_and_requirements_clean(document: dict[str, Any]) -> None:
     """Transform draft-3 style hints/reqs into idiomatic v1.0 hints/reqs."""
     for section in ["hints", "requirements"]:
         if section in document:
@@ -736,13 +736,13 @@ def hints_and_requirements_clean(document: Dict[str, Any]) -> None:
                 document[section] = new_section
 
 
-def shorten_type(type_obj: Union[str, List[Any]]) -> Union[str, List[Any]]:
+def shorten_type(type_obj: Union[str, list[Any]]) -> Union[str, list[Any]]:
     """Transform draft-3 style type declarations into idiomatic v1.0 types."""
     if isinstance(type_obj, str) or not isinstance(type_obj, Sequence):
         return type_obj
     new_type = []  # type: List[str]
     for entry in type_obj:  # find arrays that we can shorten and do so
-        if isinstance(entry, Dict):
+        if isinstance(entry, dict):
             if entry["type"] == "array" and isinstance(entry["items"], str):
                 entry = entry["items"] + "[]"
             elif entry["type"] == "enum":
@@ -759,7 +759,7 @@ def shorten_type(type_obj: Union[str, List[Any]]) -> Union[str, List[Any]]:
     return new_type
 
 
-def clean_secondary_files(document: Dict[str, Any]) -> None:
+def clean_secondary_files(document: dict[str, Any]) -> None:
     """Cleanup for secondaryFiles"""
     if "secondaryFiles" in document:
         for i, sfile in enumerate(document["secondaryFiles"]):
@@ -769,7 +769,7 @@ def clean_secondary_files(document: Dict[str, Any]) -> None:
                 ).replace(".path", ".location")
 
 
-def sort_v1_0(document: Dict[str, Any]) -> CommentedMap:
+def sort_v1_0(document: dict[str, Any]) -> CommentedMap:
     """Sort the sections of the CWL document in a more meaningful order."""
     keyorder = [
         "cwlVersion",
@@ -800,7 +800,7 @@ def sort_v1_0(document: Dict[str, Any]) -> CommentedMap:
     )
 
 
-def sort_enum(enum: Dict[str, Any]) -> Dict[str, Any]:
+def sort_enum(enum: dict[str, Any]) -> dict[str, Any]:
     """Sort the enum type definitions in a more meaningful order."""
     keyorder = ["type", "name", "label", "symbols", "inputBinding"]
     return CommentedMap(
@@ -811,7 +811,7 @@ def sort_enum(enum: Dict[str, Any]) -> Dict[str, Any]:
     )
 
 
-def sort_input_or_output(io_def: Dict[str, Any]) -> Dict[str, Any]:
+def sort_input_or_output(io_def: dict[str, Any]) -> dict[str, Any]:
     """Sort the input definitions in a more meaningful order."""
     keyorder = [
         "label",

pyproject.toml

@@ -18,16 +18,16 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: File Formats",
     "Topic :: Software Development :: Libraries",
     "Typing :: Typed",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
     "setuptools",
     "ruamel.yaml >= 0.16.0, < 0.19",

tox.ini

@@ -1,9 +1,8 @@
 [tox]
 envlist =
-  py3{8,9,10,11,12}-lint,
-  py3{8,9,10,11,12}-unit,
-
-  py3{8,9,10,11,12}-mypy,
+  py3{9,10,11,12,13}-lint,
+  py3{9,10,11,12,13}-unit,
+  py3{9,10,11,12,13}-mypy,
   py312-lintreadme,
   py312-pydocstyle
 isolated_build = True
@@ -14,47 +13,47 @@ addopts=-n auto
 
 [gh-actions]
 python =
-  3.8: py38
   3.9: py39
   3.10: py310
   3.11: py311
   3.12: py312
+  3.13: py313
 
 [testenv]
 description =
-  py3{8,9,10,11,12}-unit: Run the unit tests
-  py3{8,9,10,11,12}-lint: Lint the Python code
-  py3{8,9,10,11,12}-mypy: Check for type safety
+  py3{9,10,11,12,13}-unit: Run the unit tests
+  py3{9,10,11,12,13}-lint: Lint the Python code
+  py3{9,10,11,12,13}-mypy: Check for type safety
   py312-pydocstyle: docstring style checker
   py312-lintreadme: Lint the README.rst->.md conversion
 
 passenv =
   CI
   GITHUB_*
 deps =
-  py3{8,9,10,11,12}-{unit,mypy}: -rrequirements.txt
-  py3{8,9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
-  py3{8,9,10,11,12}-lint: flake8-bugbear
-  py3{8,9,10,11,12}-lint: black
-  py3{8,9,10,11,12}-mypy: -rmypy-requirements.txt
+  py3{9,10,11,12,13}-{unit,mypy}: -rrequirements.txt
+  py3{9,10,11,12,13}-{unit,mypy}: -rtest-requirements.txt
+  py3{9,10,11,12,13}-lint: flake8-bugbear
+  py3{9,10,11,12,13}-lint: black
+  py3{9,10,11,12,13}-mypy: -rmypy-requirements.txt
 
 setenv =
-  py3{8,9,10,11,12}-unit: LC_ALL = C.UTF-8
+  py3{9,10,11,12,13}-unit: LC_ALL = C.UTF-8
 
 commands =
-  py3{8,9,10,11,12}-unit: python -m pip install -U pip setuptools wheel
-  py3{8,9,10,11,12}-unit: make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
-  py3{8,9,10,11,12}-lint: make flake8
-  py3{8,9,10,11,12}-lint: make format-check
-  py3{8,9,10,11,12}-mypy: make mypy
+  py3{9,10,11,12,13}-unit: python -m pip install -U pip setuptools wheel
+  py3{9,10,11,12,13}-unit: make coverage-report coverage.xml PYTEST_EXTRA="{posargs}"
+  py3{9,10,11,12,13}-lint: make flake8
+  py3{9,10,11,12,13}-lint: make format-check
+  py3{9,10,11,12,13}-mypy: make mypy
 
 allowlist_externals =
-  py3{8,9,10,11,12}-lint: flake8
-  py3{8,9,10,11,12}-lint: black
-  py3{8,9,10,11,12}-{mypy,shellcheck,lint,unit}: make
+  py3{9,10,11,12,13}-lint: flake8
+  py3{9,10,11,12,13}-lint: black
+  py3{9,10,11,12,13}-{mypy,shellcheck,lint,unit}: make
 
 skip_install =
-  py3{8,9,10,11,12}-lint: true
+  py3{9,10,11,12,13}-lint: true
 
 [testenv:py312-pydocstyle]
 allowlist_externals = make