Drop support for Python 3.9

.github/workflows/lint.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.14']
+        python-version: ['3.10', '3.14']
     steps:
       - uses: actions/checkout@v5
         with:

.github/workflows/test.yaml

@@ -31,86 +31,86 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: dev
             galaxy_python_version: '3.9'
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_25.1
             galaxy_python_version: '3.9'
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_25.0
             galaxy_python_version: '3.9'
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_24.2
             galaxy_python_version: '3.8'
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_24.1
             galaxy_python_version: '3.8'
           - os: ubuntu-latest
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_24.0
             galaxy_python_version: '3.8'
           # Python 3.7 is not available via setup-python on ubuntu >=24.04
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_23.2
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_23.1
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_23.0
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_22.05
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_22.01
             galaxy_python_version: '3.7'
           # The minimum Python supported version by the following releases is
           # 3.6, but it is EOL
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_21.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_21.05
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_21.01
             galaxy_python_version: '3.7'
           # The minimum Python supported version by the following releases is
           # 3.5, but it is EOL
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_20.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_20.05
             galaxy_python_version: '3.7'
           # The minimum Python supported version by the following releases is
           # 2.7, but it is EOL
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_20.01
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_19.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py39
+            tox_env: py310
             galaxy_version: release_19.05
             galaxy_python_version: '3.7'
           - os: ubuntu-latest
@@ -120,7 +120,7 @@ jobs:
           # Cannot test on macOS because service containers are not supported
           # yet: https://github.community/t/github-actions-services-available-on-others-vms/16916
           # - os: macos-latest
-          #   tox_env: py39
+          #   tox_env: py310
           #   galaxy_version: dev
           #   galaxy_python_version: '3.8'
     steps:

ABOUT.rst

@@ -3,7 +3,7 @@ interacting with the `Galaxy`_ API.
 
 BioBlend is supported and tested on:
 
-- Python 3.9 - 3.14
+- Python 3.10 - 3.14
 - Galaxy release 19.05 and later.
 
 BioBlend's goal is to make it easier to script and automate the running of

CHANGELOG.md

@@ -1,3 +1,7 @@
+## BioBlend v
+
+* Dropped support for Python 3.9.
+
 ## BioBlend v1.7.0 - 2025-11-07
 
 * Deprecation: this is the last release to support end-of-life Python 3.9.

CONTRIBUTING.md

@@ -13,7 +13,7 @@ How to run BioBlend tests
 
 1. Clone Galaxy to a directory outside of BioBlend source directory via `git clone https://github.com/galaxyproject/galaxy.git`
 
-2. Change directory to your BioBlend source and run the tests via `./run_bioblend_tests.sh -g GALAXY_PATH [-r GALAXY_REV] [-e TOX_ENV]` where `GALAXY_PATH` is the directory where the galaxy repository was cloned, `GALAXY_REV` is the branch or commit of Galaxy that you would like to test against (if different from the current state of your galaxy clone), and `TOX_ENV` is used to specify the Python version to use for BioBlend, e.g. `py39` for Python 3.9.
+2. Change directory to your BioBlend source and run the tests via `./run_bioblend_tests.sh -g GALAXY_PATH [-r GALAXY_REV] [-e TOX_ENV]` where `GALAXY_PATH` is the directory where the galaxy repository was cloned, `GALAXY_REV` is the branch or commit of Galaxy that you would like to test against (if different from the current state of your galaxy clone), and `TOX_ENV` is used to specify the Python version to use for BioBlend, e.g. `py310` for Python 3.10.
 
    You can also add `2>&1 | tee log.txt` to the command above to contemporarily view the test output and save it to the `log.txt` file.
 

README.rst

@@ -15,7 +15,7 @@ BioBlend is a Python library for interacting with the `Galaxy`_ API.
 
 BioBlend is supported and tested on:
 
-- Python 3.9 - 3.14
+- Python 3.10 - 3.14
 - Galaxy release 19.05 and later.
 
 Full docs are available at https://bioblend.readthedocs.io/ with a quick library

bioblend/__init__.py

@@ -3,11 +3,9 @@
 import logging.config
 import os
 import time
+from collections.abc import Callable
 from typing import (
-    Callable,
-    Optional,
     TypeVar,
-    Union,
 )
 
 from bioblend.config import (
@@ -68,7 +66,7 @@ def emit(self, record: logging.LogRecord) -> None:
 
 
 def set_file_logger(
-    name: str, filepath: str, level: Union[int, str] = logging.INFO, format_string: Optional[str] = None
+    name: str, filepath: str, level: int | str = logging.INFO, format_string: str | None = None
 ) -> None:
     global log
     if not format_string:
@@ -83,7 +81,7 @@ def set_file_logger(
     log = logger
 
 
-def set_stream_logger(name: str, level: Union[int, str] = logging.DEBUG, format_string: Optional[str] = None) -> None:
+def set_stream_logger(name: str, level: int | str = logging.DEBUG, format_string: str | None = None) -> None:
     global log
     if not format_string:
         format_string = default_format_string
@@ -107,7 +105,7 @@ class ConnectionError(Exception):
     """
 
     def __init__(  # noqa: B042  # https://github.com/PyCQA/flake8-bugbear/issues/525
-        self, message: str, body: Optional[Union[bytes, str]] = None, status_code: Optional[int] = None
+        self, message: str, body: bytes | str | None = None, status_code: int | None = None
     ) -> None:
         super().__init__(message)
         self.body = body

bioblend/_tests/TestGalaxyDatasetCollections.py

@@ -4,7 +4,6 @@
 from inspect import signature
 from typing import (
     Any,
-    Union,
 )
 from zipfile import ZipFile
 
@@ -166,7 +165,7 @@ def test_download_dataset_collection(self):
         os.mkdir(extract_dir_path)
 
         if archive_type == "zip":
-            archive: Union[ZipFile, tarfile.TarFile] = ZipFile(archive_path)
+            archive: ZipFile | tarfile.TarFile = ZipFile(archive_path)
         elif archive_type == "tgz":
             archive = tarfile.open(archive_path)
 

bioblend/_tests/TestGalaxyObjects.py

@@ -9,15 +9,14 @@
 import unittest
 import uuid
 from collections.abc import (
+    Callable,
     Collection,
     Iterable,
 )
 from ssl import SSLError
 from typing import (
     Any,
-    Callable,
     Literal,
-    Union,
 )
 from urllib.error import URLError
 from urllib.request import urlopen
@@ -128,7 +127,7 @@ def is_reachable(url: str) -> bool:
     res = None
     try:
         res = urlopen(url, timeout=5)
-    except (SSLError, URLError, socket.timeout):
+    except (SSLError, URLError, TimeoutError):
         return False
     if res is not None:
         res.close()
@@ -990,7 +989,7 @@ def tearDown(self):
     def _test(self, existing_hist: bool = False, pass_params: bool = False) -> None:
         hist_name = f"test_{uuid.uuid4().hex}"
         if existing_hist:
-            hist: Union[str, wrappers.History] = self.gi.histories.create(hist_name)
+            hist: str | wrappers.History = self.gi.histories.create(hist_name)
         else:
             hist = hist_name
         if pass_params:

bioblend/_tests/TestGalaxyWorkflows.py

@@ -6,7 +6,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
 )
 
 import pytest
@@ -155,7 +154,7 @@ def test_import_other_users_published_workflow(self) -> None:
         assert not imported_wf_by_new_user["deleted"]
         assert not imported_wf_by_new_user["published"]
 
-    def _import_export(self, style: Optional[Literal["ga", "format2"]] = None):
+    def _import_export(self, style: Literal["ga", "format2"] | None = None):
         path = test_util.get_abspath(os.path.join("data", "paste_columns.ga"))
         with open(path) as f:
             wf_dict = json.load(f)

bioblend/_tests/TestToolshed.py

@@ -1,7 +1,6 @@
 import os
 import unittest
 
-import bioblend
 import bioblend.toolshed
 from . import test_util
 

bioblend/_tests/pytest_galaxy_test_wrapper.py

@@ -8,7 +8,6 @@
 import sys
 from typing import (
     NoReturn,
-    Optional,
 )
 
 try:
@@ -28,7 +27,7 @@
 ]
 
 
-def main(args: Optional[list[str]] = None) -> NoReturn:
+def main(args: list[str] | None = None) -> NoReturn:
     """Entry point that delegates to pytest.main."""
     if pytest is None:
         raise Exception("pytest is required to use this script.")

bioblend/_tests/test_util.py

@@ -4,11 +4,8 @@
 import random
 import string
 import unittest
-from typing import (
-    Any,
-    Callable,
-    Optional,
-)
+from collections.abc import Callable
+from typing import Any
 
 import requests
 
@@ -43,7 +40,7 @@ def skip_unless_toolshed() -> Callable:
     return lambda f: f
 
 
-def skip_unless_galaxy(min_release: Optional[str] = None) -> Callable:
+def skip_unless_galaxy(min_release: str | None = None) -> Callable:
     """Decorate tests with this to skip the test if Galaxy is not
     configured.
     """

bioblend/config.py

@@ -2,7 +2,6 @@
 import os
 from typing import (
     IO,
-    Optional,
 )
 
 BioBlendConfigPath = "/etc/bioblend.cfg"
@@ -21,7 +20,7 @@ class Config(configparser.ConfigParser):
     * Individual user: ``~/.bioblend`` (which works on both Windows and Unix)
     """
 
-    def __init__(self, path: Optional[str] = None, fp: Optional[IO[str]] = None, do_load: bool = True) -> None:
+    def __init__(self, path: str | None = None, fp: IO[str] | None = None, do_load: bool = True) -> None:
         super().__init__({"working_dir": "/mnt/pyami", "debug": "0"})
         if do_load:
             if path:

bioblend/galaxy/__init__.py

@@ -2,8 +2,6 @@
 A base representation of an instance of Galaxy
 """
 
-from typing import Optional
-
 from bioblend.galaxy import (
     config,
     container_resolution,
@@ -36,13 +34,13 @@ class GalaxyInstance(GalaxyClient):
     def __init__(
         self,
         url: str,
-        key: Optional[str] = None,
-        email: Optional[str] = None,
-        password: Optional[str] = None,
+        key: str | None = None,
+        email: str | None = None,
+        password: str | None = None,
         *,
-        token: Optional[str] = None,
+        token: str | None = None,
         verify: bool = True,
-        user_agent: Optional[str] = None,
+        user_agent: str | None = None,
     ) -> None:
         """
         A base representation of a connection to a Galaxy instance, identified