Drop Python 3.6

Author: mr-c

.github/workflows/ci-tests.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [6, 7, 8, 9, 10]
+        py-ver-minor: [7, 8, 9, 10]
         step: [lint, unit, bandit, mypy]
 
     env:

Makefile

@@ -184,7 +184,7 @@ shellcheck: FORCE
 		cwltool-in-docker.sh
 
 pyupgrade: $(PYSOURCES)
-	pyupgrade --exit-zero-even-if-changed --py36-plus $^
+	pyupgrade --exit-zero-even-if-changed --py37-plus $^
 
 release-test: check-python3 FORCE
 	git diff-index --quiet HEAD -- || ( echo You have uncommited changes, please commit them and try again; false )

README.rst

@@ -694,7 +694,7 @@ List of all environment can be seen using:
 and running a specfic test env using:
 ``tox -e <env name>``
 and additionally run a specific test using this format:
-``tox -e py36-unit -- -v tests/test_examples.py::test_scandeps``
+``tox -e py310-unit -- -v tests/test_examples.py::test_scandeps``
 
 -  Running the entire suite of CWL conformance tests:
 

cwltool/context.py

@@ -3,14 +3,23 @@
 import os
 import tempfile
 import threading
-from typing import IO, Any, Callable, Dict, Iterable, List, Optional, TextIO, Union
+from typing import (
+    IO,
+    TYPE_CHECKING,
+    Any,
+    Callable,
+    Dict,
+    Iterable,
+    List,
+    Optional,
+    TextIO,
+    Union,
+)
 
-# move to a regular typing import when Python 3.3-3.6 is no longer supported
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.avro.schema import Names
 from schema_salad.ref_resolver import Loader
 from schema_salad.utils import FetcherCallableType
-from typing_extensions import TYPE_CHECKING
 
 from .builder import Builder
 from .mpi import MpiConfig

cwltool/cuda.py

@@ -1,10 +1,10 @@
 import subprocess  # nosec
 import xml.dom.minidom  # nosec
+from typing import Tuple, cast
+
 from .loghandler import _logger
 from .utils import CWLObjectType
 
-from typing import Tuple, cast
-
 
 def cuda_version_and_device_count() -> Tuple[str, int]:
     try:

cwltool/job.py

@@ -51,8 +51,8 @@
 from .utils import (
     CWLObjectType,
     CWLOutputType,
-    HasReqsHints,
     DirectoryType,
+    HasReqsHints,
     OutputCallbackType,
     bytes2str_in_dicts,
     create_tmp_dir,

cwltool/provenance.py

@@ -247,24 +247,22 @@ def _valid_orcid(orcid: Optional[str]) -> str:
         "oa:motivatedBy": Dict[str, str],
     },
 )
-Aggregate = TypedDict(
-    "Aggregate",
-    {
-        "uri": Optional[str],
-        "bundledAs": Optional[Dict[str, Any]],
-        "mediatype": Optional[str],
-        "conformsTo": Optional[Union[str, List[str]]],
-        "createdOn": Optional[str],
-        "createdBy": Optional[Dict[str, str]],
-    },
-    total=False,
-)
+
+
+class Aggregate(TypedDict, total=False):
+    uri: Optional[str]
+    bundledAs: Optional[Dict[str, Any]]
+    mediatype: Optional[str]
+    conformsTo: Optional[Union[str, List[str]]]
+    createdOn: Optional[str]
+    createdBy: Optional[Dict[str, str]]
+
+
 # Aggregate.bundledAs is actually type Aggregate, but cyclic definitions are not suported
-AuthoredBy = TypedDict(
-    "AuthoredBy",
-    {"orcid": Optional[str], "name": Optional[str], "uri": Optional[str]},
-    total=False,
-)
+class AuthoredBy(TypedDict, total=False):
+    orcid: Optional[str]
+    name: Optional[str]
+    uri: Optional[str]
 
 
 class ResearchObject:

cwltool/utils.py

@@ -101,14 +101,13 @@
 JSONType = Union[
     Dict[str, JSONAtomType], List[JSONAtomType], str, int, float, bool, None
 ]
-WorkflowStateItem = NamedTuple(
-    "WorkflowStateItem",
-    [
-        ("parameter", CWLObjectType),
-        ("value", Optional[CWLOutputType]),
-        ("success", str),
-    ],
-)
+
+
+class WorkflowStateItem(NamedTuple):
+    parameter: CWLObjectType
+    value: Optional[CWLOutputType]
+    success: str
+
 
 ParametersType = List[CWLObjectType]
 StepType = CWLObjectType  # WorkflowStep

requirements.txt

@@ -12,4 +12,3 @@ coloredlogs
 pydot>=1.4.1
 argcomplete>=1.12.0
 pyparsing != 3.0.2  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
-pyparsing < 3;python_version<='3.6'  # breaks --print-dot

setup.py

@@ -120,13 +120,12 @@
         "coloredlogs",
         "pydot >= 1.4.1",
         "pyparsing != 3.0.2",  # breaks --print-dot (pydot) https://github.com/pyparsing/pyparsing/issues/319
-        "pyparsing < 3 ;python_version<='3.6'",  # breaks --print-dot (pydot)
         "argcomplete",
     ],
     extras_require={
         "deps": ["galaxy-tool-util >= 21.1.0"],
     },
-    python_requires=">=3.6, <4",
+    python_requires=">=3.7, <4",
     setup_requires=PYTEST_RUNNER,
     test_suite="tests",
     tests_require=[
@@ -151,10 +150,10 @@
         "Operating System :: POSIX",
         "Operating System :: POSIX :: Linux",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Scientific/Engineering",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Astronomy",