Drop support for Python 3.9

Author: mr-c

.github/workflows/ci-tests.yml

@@ -32,7 +32,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [9, 10, 11, 12, 13, 14]
+        py-ver-minor: [10, 11, 12, 13, 14]
         step: [lint, unit, bandit, mypy]
 
     env:

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 Style guide:
 - PEP-8 (as implemented by the `black` code formatting tool)
-- Python 3.8+ compatible code
+- Python 3.10+ compatible code
 - PEP-484 type hints
 
 The development is done using `git`, we encourage you to get familiar with it.

Makefile

@@ -190,7 +190,7 @@ shellcheck: FORCE
 		cwltool-in-docker.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py39-plus $^
+	pyupgrade --exit-zero-even-if-changed --py310-plus $^
 	auto-walrus $^
 
 release-test: FORCE

README.rst

@@ -842,7 +842,7 @@ executor
   ::
 
     executor(tool, job_order_object, runtimeContext, logger)
-      (Process, Dict[Text, Any], RuntimeContext) -> Tuple[Dict[Text, Any], Text]
+      (Process, Dict[str, Any], RuntimeContext) -> Tuple[Dict[str, Any], str]
 
   An implementation of the top-level workflow execution loop should
   synchronously run a process object to completion and return the
@@ -852,7 +852,7 @@ versionfunc
   ::
 
     ()
-      () -> Text
+      () -> str
 
   Return version string.
 
@@ -879,7 +879,7 @@ resolver
   ::
 
     resolver(document_loader, document)
-      (Loader, Union[Text, dict[Text, Any]]) -> Text
+      (Loader, str | dict[str, Any]) -> str
 
   Resolve a relative document identifier to an absolute one that can be fetched.
 
@@ -890,23 +890,23 @@ construct_tool_object
   ::
 
     construct_tool_object(toolpath_object, loadingContext)
-      (MutableMapping[Text, Any], LoadingContext) -> Process
+      (MutableMapping[str, Any], LoadingContext) -> Process
 
   Hook to construct a Process object (eg CommandLineTool) object from a document.
 
 select_resources
   ::
 
     selectResources(request)
-      (Dict[str, int], RuntimeContext) -> Dict[Text, int]
+      (Dict[str, int], RuntimeContext) -> Dict[str, int]
 
   Take a resource request and turn it into a concrete resource assignment.
 
 make_fs_access
   ::
 
     make_fs_access(basedir)
-      (Text) -> StdFsAccess
+      (str) -> StdFsAccess
 
   Return a file system access object.
 
@@ -924,6 +924,6 @@ Workflow.make_workflow_step
   ::
 
     make_workflow_step(toolpath_object, pos, loadingContext, parentworkflowProv)
-      (Dict[Text, Any], int, LoadingContext, Optional[ProvenanceProfile]) -> WorkflowStep
+      (Dict[str, Any], int, LoadingContext, Optional[ProvenanceProfile]) -> WorkflowStep
 
   Create and return a workflow step object.

cwltool/argparser.py

@@ -3,8 +3,8 @@
 import argparse
 import os
 import urllib
-from collections.abc import MutableMapping, MutableSequence, Sequence
-from typing import Any, Callable, Optional, Union, cast
+from collections.abc import Callable, MutableMapping, MutableSequence, Sequence
+from typing import Any, cast
 
 import rich.markup
 from rich_argparse import HelpPreviewAction, RichHelpFormatter
@@ -732,7 +732,7 @@ def get_default_args() -> dict[str, Any]:
 class FSAction(argparse.Action):
     """Base action for our custom actions."""
 
-    objclass: Optional[str] = None
+    objclass: str | None = None
 
     def __init__(
         self,
@@ -754,8 +754,8 @@ def __call__(
         self,
         parser: argparse.ArgumentParser,
         namespace: argparse.Namespace,
-        values: Union[str, Sequence[Any], None],
-        option_string: Optional[str] = None,
+        values: str | Sequence[Any] | None,
+        option_string: str | None = None,
     ) -> None:
         setattr(
             namespace,
@@ -770,7 +770,7 @@ def __call__(
 class FSAppendAction(argparse.Action):
     """Appending version of the base action for our custom actions."""
 
-    objclass: Optional[str] = None
+    objclass: str | None = None
 
     def __init__(
         self,
@@ -792,8 +792,8 @@ def __call__(
         self,
         parser: argparse.ArgumentParser,
         namespace: argparse.Namespace,
-        values: Union[str, Sequence[Any], None],
-        option_string: Optional[str] = None,
+        values: str | Sequence[Any] | None,
+        option_string: str | None = None,
     ) -> None:
         g = getattr(namespace, self.dest)
         if not g:
@@ -808,19 +808,19 @@ def __call__(
 
 
 class FileAction(FSAction):
-    objclass: Optional[str] = "File"
+    objclass: str | None = "File"
 
 
 class DirectoryAction(FSAction):
-    objclass: Optional[str] = "Directory"
+    objclass: str | None = "Directory"
 
 
 class FileAppendAction(FSAppendAction):
-    objclass: Optional[str] = "File"
+    objclass: str | None = "File"
 
 
 class DirectoryAppendAction(FSAppendAction):
-    objclass: Optional[str] = "Directory"
+    objclass: str | None = "Directory"
 
 
 class AppendAction(argparse.Action):
@@ -844,8 +844,8 @@ def __call__(
         self,
         parser: argparse.ArgumentParser,
         namespace: argparse.Namespace,
-        values: Union[str, Sequence[Any], None],
-        option_string: Optional[str] = None,
+        values: str | Sequence[Any] | None,
+        option_string: str | None = None,
     ) -> None:
         g = getattr(namespace, self.dest, None)
         if g is None:
@@ -893,8 +893,8 @@ def add_argument(
             return None
 
     ahelp = description.replace("%", "%%")
-    action: Optional[Union[type[argparse.Action], str]] = None
-    atype: Optional[Any] = None
+    action: type[argparse.Action] | str | None = None
+    atype: Any | None = None
     typekw: dict[str, Any] = {}
 
     if inptype == "File":

cwltool/builder.py

@@ -3,9 +3,9 @@
 import copy
 import logging
 import math
-from collections.abc import MutableMapping, MutableSequence
+from collections.abc import Callable, MutableMapping, MutableSequence
 from decimal import Decimal
-from typing import IO, TYPE_CHECKING, Any, Callable, Optional, Union, cast
+from typing import IO, TYPE_CHECKING, Any, Optional, cast
 
 from cwl_utils import expression
 from cwl_utils.file_formats import check_format
@@ -101,9 +101,9 @@ def __init__(
         names: Names,
         requirements: list[CWLObjectType],
         hints: list[CWLObjectType],
-        resources: dict[str, Union[int, float]],
-        mutation_manager: Optional[MutationManager],
-        formatgraph: Optional[Graph],
+        resources: dict[str, int | float],
+        mutation_manager: MutationManager | None,
+        formatgraph: Graph | None,
         make_fs_access: type[StdFsAccess],
         fs_access: StdFsAccess,
         job_script_provider: Optional["DependenciesConfiguration"],
@@ -157,10 +157,10 @@ def __init__(
 
         self.pathmapper: Optional["PathMapper"] = None
         self.prov_obj: Optional["ProvenanceProfile"] = None
-        self.find_default_container: Optional[Callable[[], str]] = None
+        self.find_default_container: Callable[[], str] | None = None
         self.container_engine = container_engine
 
-    def build_job_script(self, commands: list[str]) -> Optional[str]:
+    def build_job_script(self, commands: list[str]) -> str | None:
         """Use the job_script_provider to turn the commands into a job script."""
         if self.job_script_provider is not None:
             return self.job_script_provider.build_job_script(self, commands)
@@ -169,11 +169,11 @@ def build_job_script(self, commands: list[str]) -> Optional[str]:
     def bind_input(
         self,
         schema: CWLObjectType,
-        datum: Union[CWLObjectType, list[CWLObjectType]],
+        datum: CWLObjectType | list[CWLObjectType],
         discover_secondaryFiles: bool,
-        lead_pos: Optional[Union[int, list[int]]] = None,
-        tail_pos: Optional[Union[str, list[int]]] = None,
-    ) -> list[MutableMapping[str, Union[str, list[int]]]]:
+        lead_pos: int | list[int] | None = None,
+        tail_pos: str | list[int] | None = None,
+    ) -> list[MutableMapping[str, str | list[int]]]:
         """
         Bind an input object to the command line.
 
@@ -189,8 +189,8 @@ def bind_input(
         if lead_pos is None:
             lead_pos = []
 
-        bindings: list[MutableMapping[str, Union[str, list[int]]]] = []
-        binding: Union[MutableMapping[str, Union[str, list[int]]], CommentedMap] = {}
+        bindings: list[MutableMapping[str, str | list[int]]] = []
+        binding: MutableMapping[str, str | list[int]] | CommentedMap = {}
         value_from_expression = False
         if "inputBinding" in schema and isinstance(schema["inputBinding"], MutableMapping):
             binding = CommentedMap(schema["inputBinding"].items())
@@ -226,7 +226,7 @@ def bind_input(
         if isinstance(schema["type"], MutableSequence):
             bound_input = False
             for t in schema["type"]:
-                avsc: Optional[Schema] = None
+                avsc: Schema | None = None
                 if isinstance(t, str) and self.names.has_name(t, None):
                     avsc = self.names.get_name(t, None)
                 elif (
@@ -360,9 +360,9 @@ def _capture_files(f: CWLObjectType) -> CWLObjectType:
                 datum = cast(CWLObjectType, datum)
                 self.files.append(datum)
 
-                loadContents_sourceline: Union[
-                    None, MutableMapping[str, Union[str, list[int]]], CWLObjectType
-                ] = None
+                loadContents_sourceline: (
+                    None | MutableMapping[str, str | list[int]] | CWLObjectType
+                ) = None
                 if binding and binding.get("loadContents"):
                     loadContents_sourceline = binding
                 elif schema.get("loadContents"):
@@ -502,7 +502,7 @@ def addsf(
                 if "format" in schema:
                     eval_format: Any = self.do_eval(schema["format"])
                     if isinstance(eval_format, str):
-                        evaluated_format: Union[str, list[str]] = eval_format
+                        evaluated_format: str | list[str] = eval_format
                     elif isinstance(eval_format, MutableSequence):
                         for index, entry in enumerate(eval_format):
                             message = None
@@ -582,7 +582,7 @@ def addsf(
 
         return bindings
 
-    def tostr(self, value: Union[MutableMapping[str, str], Any]) -> str:
+    def tostr(self, value: MutableMapping[str, str] | Any) -> str:
         """
         Represent an input parameter as a string.
 
@@ -668,11 +668,11 @@ def generate_arg(self, binding: CWLObjectType) -> list[str]:
 
     def do_eval(
         self,
-        ex: Optional[CWLOutputType],
-        context: Optional[Any] = None,
+        ex: CWLOutputType | None,
+        context: Any | None = None,
         recursive: bool = False,
         strip_whitespace: bool = True,
-    ) -> Optional[CWLOutputType]:
+    ) -> CWLOutputType | None:
         if recursive:
             if isinstance(ex, MutableMapping):
                 return {k: self.do_eval(v, context, recursive) for k, v in ex.items()}

cwltool/checker.py

@@ -23,9 +23,9 @@ def _get_type(tp: Any) -> Any:
 def check_types(
     srctype: SinkType,
     sinktype: SinkType,
-    linkMerge: Optional[str],
-    valueFrom: Optional[str],
-) -> Union[Literal["pass"], Literal["warning"], Literal["exception"]]:
+    linkMerge: str | None,
+    valueFrom: str | None,
+) -> Literal["pass"] | Literal["warning"] | Literal["exception"]:
     """
     Check if the source and sink types are correct.
 
@@ -60,7 +60,7 @@ def merge_flatten_type(src: SinkType) -> CWLOutputType:
     return {"items": src, "type": "array"}
 
 
-def can_assign_src_to_sink(src: SinkType, sink: Optional[SinkType], strict: bool = False) -> bool:
+def can_assign_src_to_sink(src: SinkType, sink: SinkType | None, strict: bool = False) -> bool:
     """
     Check for identical type specifications, ignoring extra keys like inputBinding.
 
@@ -322,14 +322,14 @@ class _SrcSink(NamedTuple):
 
     src: CWLObjectType
     sink: CWLObjectType
-    linkMerge: Optional[str]
-    message: Optional[str]
+    linkMerge: str | None
+    message: str | None
 
 
 def _check_all_types(
     src_dict: dict[str, CWLObjectType],
     sinks: MutableSequence[CWLObjectType],
-    sourceField: Union[Literal["source"], Literal["outputSource"]],
+    sourceField: Literal["source"] | Literal["outputSource"],
     param_to_step: dict[str, CWLObjectType],
 ) -> dict[str, list[_SrcSink]]:
     """
@@ -350,7 +350,7 @@ def _check_all_types(
                 extra_message = "pickValue is: %s" % pickValue
 
             if isinstance(sink[sourceField], MutableSequence):
-                linkMerge: Optional[str] = cast(
+                linkMerge: str | None = cast(
                     Optional[str],
                     sink.get(
                         "linkMerge",
@@ -518,7 +518,7 @@ def is_conditional_step(param_to_step: dict[str, CWLObjectType], parm_id: str) -
 
 def is_all_output_method_loop_step(param_to_step: dict[str, CWLObjectType], parm_id: str) -> bool:
     """Check if a step contains a `loop` directive with `all_iterations` outputMethod."""
-    source_step: Optional[MutableMapping[str, Any]] = param_to_step.get(parm_id)
+    source_step: MutableMapping[str, Any] | None = param_to_step.get(parm_id)
     if source_step is not None:
         if (
             source_step.get("loop") is not None