Drop support for Python 3.8

Author: mr-c

.github/workflows/ci-tests.yml

@@ -30,9 +30,10 @@ jobs:
     name: Tox
     runs-on: ubuntu-22.04
     strategy:
+      fail-fast: false
       matrix:
         py-ver-major: [3]
-        py-ver-minor: [8, 9, 10, 11, 12]
+        py-ver-minor: [9, 10, 11, 12]
         step: [lint, unit, bandit, mypy]
 
     env:

Makefile

@@ -171,7 +171,7 @@ shellcheck: FORCE
 	shellcheck 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

cwl_flask.py

@@ -8,7 +8,8 @@
 import tempfile
 import threading
 import time
-from typing import Any, Dict, Generator, List, Tuple
+from collections.abc import Generator
+from typing import Any
 
 import werkzeug.wrappers.response
 import yaml
@@ -17,7 +18,7 @@
 app = Flask(__name__)
 
 jobs_lock = threading.Lock()
-jobs: List["Job"] = []
+jobs: list["Job"] = []
 
 
 class Job(threading.Thread):
@@ -66,7 +67,7 @@ def run(self) -> None:
             with self.updatelock:
                 self.status["state"] = "Failed"
 
-    def getstatus(self) -> Dict[str, Any]:
+    def getstatus(self) -> dict[str, Any]:
         """Report the current status."""
         with self.updatelock:
             return self.status.copy()
@@ -106,7 +107,7 @@ def runworkflow() -> werkzeug.wrappers.response.Response:
 
 
 @app.route("/jobs/<int:jobid>", methods=["GET", "POST"])
-def jobcontrol(jobid: int) -> Tuple[str, int]:
+def jobcontrol(jobid: int) -> tuple[str, int]:
     """Accept a job related action and report the result."""
     with jobs_lock:
         job = jobs[jobid]
@@ -152,7 +153,7 @@ def getjobs() -> Response:
     with jobs_lock:
         jobscopy = copy.copy(jobs)
 
-    def spool(jc: List[Job]) -> Generator[str, None, None]:
+    def spool(jc: list[Job]) -> Generator[str, None, None]:
         yield "["
         first = True
         for j in jc:

cwltool_stream.py

@@ -5,15 +5,15 @@
 import sys
 import tempfile
 from io import StringIO
-from typing import List, Union
+from typing import Union
 
 import cwltool.main
 
 _logger = logging.getLogger("cwltool")
 _logger.setLevel(logging.ERROR)
 
 
-def main(args: List[str] = sys.argv[1:]) -> int:
+def main(args: list[str] = sys.argv[1:]) -> int:
     """Streaming execution of cwltool."""
     if len(args) == 0:
         print("Workflow must be on command line")

pyproject.toml

@@ -15,13 +15,13 @@ classifiers = [
     "Operating System :: MacOS :: MacOS X",
     "Operating System :: POSIX",
     "Programming Language :: Python",
-    "programming language :: python :: 3.7",
-    "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",
     "Topic :: Software Development :: Libraries :: Python Modules",
 ]
-requires-python = "~=3.7"
+requires-python = ">=3.9"
 dependencies = [
     "connexion[swagger-ui] >= 2.0.2, < 3",
     "ruamel.yaml >= 0.15.78",

test/test_integration.py

@@ -5,7 +5,7 @@
 import subprocess
 import time
 import unittest
-from typing import List, Optional, Tuple, cast
+from typing import Optional, cast
 
 import pytest
 import requests
@@ -21,10 +21,10 @@ class IntegrationTest(unittest.TestCase):
     cwl_dockstore_url: str
     cwl_local_path: str
     cwl_json_input: str
-    cwl_attachments: List[str]
+    cwl_attachments: list[str]
     wdl_local_path: str
     wdl_json_input: str
-    wdl_attachments: List[str]
+    wdl_attachments: list[str]
     client: WESClient
     manual: bool
     wes_server_process: "subprocess.Popen[bytes]"
@@ -168,8 +168,8 @@ def run_md5sum(
         self,
         wf_input: str,
         json_input: str,
-        workflow_attachment: Optional[List[str]] = None,
-    ) -> Tuple[str, str]:
+        workflow_attachment: Optional[list[str]] = None,
+    ) -> tuple[str, str]:
         """
         Pass a local md5sum cwl to the wes-service server.
 
@@ -216,7 +216,7 @@ def check_for_file(self, filepath: str, seconds: int = 120) -> bool:
         return True
 
 
-def get_server_pids() -> Optional[List[bytes]]:
+def get_server_pids() -> Optional[list[bytes]]:
     try:
         pids = (
             subprocess.check_output(["pgrep", "-f", "wes_service_main.py"])

tox.ini

@@ -1,63 +1,62 @@
 [tox]
 envlist =
-  py3{8,9,10,11,12}-lint,
-  py3{8,9,10,11,12}-unit,
-  py3{8,9,10,11,12}-bandit,
-  py3{8,9,10,11,12}-mypy,
+  py3{9,10,11,12}-lint,
+  py3{9,10,11,12}-unit,
+  py3{9,10,11,12}-bandit,
+  py3{9,10,11,12}-mypy,
   py312-lintreadme,
   py312-pydocstyle
 isolated_build = True
 skip_missing_interpreters = True
 
 [gh-actions]
 python =
-  3.8: py38
   3.9: py39
   3.10: py310
   3.11: py311
   3.12: py312
 
 [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}-bandit: Search for common security issues
-  py3{8,9,10,11,12}-mypy: Check for type safety
+  py3{9,10,11,12}-unit: Run the unit tests
+  py3{9,10,11,12}-lint: Lint the Python code
+  py3{9,10,11,12}-bandit: Search for common security issues
+  py3{9,10,11,12}-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}-mypy: -rmypy-requirements.txt
-  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: -rlint-requirements.txt
-  py3{8,9,10,11,12}-bandit: bandit
+  py3{9,10,11,12}-mypy: -rmypy-requirements.txt
+  py3{9,10,11,12}-{unit,mypy}: -rrequirements.txt
+  py3{9,10,11,12}-{unit,mypy}: -rtest-requirements.txt
+  py3{9,10,11,12}-lint: -rlint-requirements.txt
+  py3{9,10,11,12}-bandit: bandit
 
 setenv =
-  py3{8,9,10,11,12}-unit: LC_ALL = C.UTF-8
+  py3{9,10,11,12}-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}-bandit: bandit --recursive wes_client wes_service
-  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}-unit: python -m pip install -U pip setuptools wheel
+  py3{9,10,11,12}-unit: make coverage-report coverage.xml PYTEST_EXTRA={posargs}
+  py3{9,10,11,12}-bandit: bandit --recursive wes_client wes_service
+  py3{9,10,11,12}-lint: make flake8
+  py3{9,10,11,12}-lint: make format-check
+  py3{9,10,11,12}-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,memleak,shellcheck,lint,lintreadme,unit}: make
+  py3{9,10,11,12}-lint: flake8
+  py3{9,10,11,12}-lint: black
+  py3{9,10,11,12}-{mypy,memleak,shellcheck,lint,lintreadme,unit}: make
 
 skip_install =
-  py3{8,9,10,11,12}-lint: true
-  py3{8,9,10,11,12}-bandit: true
+  py3{9,10,11,12}-lint: true
+  py3{9,10,11,12}-bandit: true
 
 extras =
-  py3{8,9,10,11,12}-unit: toil
+  py3{9,10,11,12}-unit: toil
 
 [testenv:py312-pydocstyle]
 allowlist_externals = make

wes_client/util.py

@@ -6,7 +6,7 @@
 import os
 import sys
 from subprocess import DEVNULL, CalledProcessError, check_call  # nosec B404
-from typing import Any, Dict, List, Optional, Set, Tuple, Union, cast
+from typing import Any, Optional, Union, cast
 from urllib.request import pathname2url, urlopen
 
 import requests
@@ -51,7 +51,7 @@ def get_version(extension: str, workflow_file: str) -> str:
             return "draft-2"
 
 
-def wf_info(workflow_path: str) -> Tuple[str, str]:
+def wf_info(workflow_path: str) -> tuple[str, str]:
     """
     Return the version of the file and the file extension.
 
@@ -127,8 +127,8 @@ def fixpaths(d: Any) -> None:
 
 
 def build_wes_request(
-    workflow_file: str, json_path: str, attachments: Optional[List[str]] = None
-) -> List[Tuple[str, Any]]:
+    workflow_file: str, json_path: str, attachments: Optional[list[str]] = None
+) -> list[tuple[str, Any]]:
     """
     :param workflow_file: Path to cwl/wdl file.  Can be http/https/file.
     :param json_path: Path to accompanying json file.
@@ -151,7 +151,7 @@ def build_wes_request(
         wf_params = json_path
     wf_version, wf_type = wf_info(workflow_file)
 
-    parts: List[Tuple[str, Any]] = [
+    parts: list[tuple[str, Any]] = [
         ("workflow_params", wf_params),
         ("workflow_type", wf_type),
         ("workflow_type_version", wf_version),
@@ -187,7 +187,7 @@ def build_wes_request(
     return parts
 
 
-def expand_globs(attachments: Optional[Union[List[str], str]]) -> Set[str]:
+def expand_globs(attachments: Optional[Union[list[str], str]]) -> set[str]:
     """Expand any globs present in the attachment list."""
     expanded_list = []
     if attachments is None:
@@ -204,26 +204,26 @@ def expand_globs(attachments: Optional[Union[List[str], str]]) -> Set[str]:
     return set(expanded_list)
 
 
-def wes_response(postresult: requests.Response) -> Dict[str, Any]:
+def wes_response(postresult: requests.Response) -> dict[str, Any]:
     """Convert a Response object to JSON text."""
     if postresult.status_code != 200:
         error = str(json.loads(postresult.text))
         logging.error(error)
         raise Exception(error)
 
-    return cast(Dict[str, Any], json.loads(postresult.text))
+    return cast(dict[str, Any], json.loads(postresult.text))
 
 
 class WESClient:
     """WES client."""
 
-    def __init__(self, service: Dict[str, Any]):
+    def __init__(self, service: dict[str, Any]):
         """Initialize the cliet with the provided credentials and endpoint."""
         self.auth = service["auth"]
         self.proto = service["proto"]
         self.host = service["host"]
 
-    def get_service_info(self) -> Dict[str, Any]:
+    def get_service_info(self) -> dict[str, Any]:
         """
         Get information about Workflow Execution Service. May
         include information related (but not limited to) the
@@ -242,7 +242,7 @@ def get_service_info(self) -> Dict[str, Any]:
         )
         return wes_response(postresult)
 
-    def list_runs(self) -> Dict[str, Any]:
+    def list_runs(self) -> dict[str, Any]:
         """
         List the workflows, this endpoint will list the workflows
         in order of oldest to newest. There is no guarantee of
@@ -260,8 +260,8 @@ def list_runs(self) -> Dict[str, Any]:
         return wes_response(postresult)
 
     def run(
-        self, wf: str, jsonyaml: str, attachments: Optional[List[str]]
-    ) -> Dict[str, Any]:
+        self, wf: str, jsonyaml: str, attachments: Optional[list[str]]
+    ) -> dict[str, Any]:
         """
         Composes and sends a post request that signals the wes server to run a workflow.
 
@@ -283,7 +283,7 @@ def run(
         )
         return wes_response(postresult)
 
-    def cancel(self, run_id: str) -> Dict[str, Any]:
+    def cancel(self, run_id: str) -> dict[str, Any]:
         """
         Cancel a running workflow.
 
@@ -299,7 +299,7 @@ def cancel(self, run_id: str) -> Dict[str, Any]:
         )
         return wes_response(postresult)
 
-    def get_run_log(self, run_id: str) -> Dict[str, Any]:
+    def get_run_log(self, run_id: str) -> dict[str, Any]:
         """
         Get detailed info about a running workflow.
 
@@ -315,7 +315,7 @@ def get_run_log(self, run_id: str) -> Dict[str, Any]:
         )
         return wes_response(postresult)
 
-    def get_run_status(self, run_id: str) -> Dict[str, Any]:
+    def get_run_status(self, run_id: str) -> dict[str, Any]:
         """
         Get quick status info about a running workflow.
 

wes_client/wes_client_main.py

@@ -6,15 +6,14 @@
 import sys
 import time
 from importlib.metadata import version
-from typing import List
 
 import requests
 from requests.exceptions import InvalidSchema, MissingSchema
 
 from wes_client.util import WESClient, modify_jsonyaml_paths
 
 
-def main(argv: List[str] = sys.argv[1:]) -> int:
+def main(argv: list[str] = sys.argv[1:]) -> int:
     """Run the WES service."""
     parser = argparse.ArgumentParser(description="Workflow Execution Service")
     parser.add_argument(