From 57e97db9ffbcf131f1168cb3e9c9cfff00961fd4 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 5 Nov 2025 00:15:42 +0000
Subject: [PATCH] Drop support for Python 3.9

which has reached end of life on 2025-10-31.
---
 .github/workflows/lint.yaml                   |  2 +-
 .github/workflows/test.yaml                   | 40 ++++----
 ABOUT.rst                                     |  2 +-
 CHANGELOG.md                                  |  4 +
 CONTRIBUTING.md                               |  2 +-
 README.rst                                    |  2 +-
 bioblend/__init__.py                          | 10 +-
 .../_tests/TestGalaxyDatasetCollections.py    |  3 +-
 bioblend/_tests/TestGalaxyObjects.py          |  7 +-
 bioblend/_tests/TestGalaxyWorkflows.py        |  3 +-
 bioblend/_tests/TestToolshed.py               |  1 -
 bioblend/_tests/pytest_galaxy_test_wrapper.py |  3 +-
 bioblend/_tests/test_util.py                  |  9 +-
 bioblend/config.py                            |  3 +-
 bioblend/galaxy/__init__.py                   | 12 +--
 bioblend/galaxy/client.py                     | 51 +++++-----
 .../galaxy/container_resolution/__init__.py   | 24 +++--
 .../galaxy/dataset_collections/__init__.py    |  9 +-
 bioblend/galaxy/datasets/__init__.py          | 40 ++++----
 bioblend/galaxy/folders/__init__.py           | 14 ++-
 bioblend/galaxy/genomes/__init__.py           | 21 ++--
 bioblend/galaxy/groups/__init__.py            |  9 +-
 bioblend/galaxy/histories/__init__.py         | 95 +++++++++----------
 bioblend/galaxy/invocations/__init__.py       | 35 ++++---
 bioblend/galaxy/jobs/__init__.py              | 25 +++--
 bioblend/galaxy/libraries/__init__.py         | 54 +++++------
 bioblend/galaxy/objects/client.py             | 42 ++++----
 bioblend/galaxy/objects/galaxy_instance.py    | 11 +--
 bioblend/galaxy/objects/wrappers.py           | 38 ++++----
 bioblend/galaxy/quotas/__init__.py            | 23 +++--
 bioblend/galaxy/roles/__init__.py             |  5 +-
 bioblend/galaxy/tool_dependencies/__init__.py |  9 +-
 bioblend/galaxy/tools/__init__.py             | 28 +++---
 bioblend/galaxy/tools/inputs.py               |  6 +-
 bioblend/galaxy/toolshed/__init__.py          |  8 +-
 bioblend/galaxy/users/__init__.py             |  9 +-
 bioblend/galaxy/workflows/__init__.py         | 41 ++++----
 bioblend/galaxyclient.py                      | 36 ++++---
 bioblend/toolshed/__init__.py                 | 10 +-
 bioblend/toolshed/repositories/__init__.py    | 38 ++++----
 bioblend/util/__init__.py                     |  3 +-
 pyproject.toml                                |  7 +-
 run_bioblend_tests.sh                         |  4 +-
 tox.ini                                       |  2 +-
 44 files changed, 375 insertions(+), 425 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index c192f9027..d9152a79e 100644
--- a/.github/workflows/lint.yaml
+++ b/.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:
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 18405ab90..b3107ad95 100644
--- a/.github/workflows/test.yaml
+++ b/.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:
diff --git a/ABOUT.rst b/ABOUT.rst
index da11a4ebe..78619dde6 100644
--- a/ABOUT.rst
+++ b/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
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 52b787206..d1408ef91 100644
--- a/CHANGELOG.md
+++ b/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.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 9210ecf48..2a54493a5 100644
--- a/CONTRIBUTING.md
+++ b/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.
 
diff --git a/README.rst b/README.rst
index e402bc53c..8d6686fdd 100644
--- a/README.rst
+++ b/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
diff --git a/bioblend/__init__.py b/bioblend/__init__.py
index 63ee26e6b..9b75a83c4 100644
--- a/bioblend/__init__.py
+++ b/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
diff --git a/bioblend/_tests/TestGalaxyDatasetCollections.py b/bioblend/_tests/TestGalaxyDatasetCollections.py
index 2f54b01fe..1b32a1973 100644
--- a/bioblend/_tests/TestGalaxyDatasetCollections.py
+++ b/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)
 
diff --git a/bioblend/_tests/TestGalaxyObjects.py b/bioblend/_tests/TestGalaxyObjects.py
index 0739d8949..7cb73a73e 100644
--- a/bioblend/_tests/TestGalaxyObjects.py
+++ b/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:
diff --git a/bioblend/_tests/TestGalaxyWorkflows.py b/bioblend/_tests/TestGalaxyWorkflows.py
index 3a581d101..565b9f742 100644
--- a/bioblend/_tests/TestGalaxyWorkflows.py
+++ b/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)
diff --git a/bioblend/_tests/TestToolshed.py b/bioblend/_tests/TestToolshed.py
index 97cc2bb0f..f8b8602f1 100644
--- a/bioblend/_tests/TestToolshed.py
+++ b/bioblend/_tests/TestToolshed.py
@@ -1,7 +1,6 @@
 import os
 import unittest
 
-import bioblend
 import bioblend.toolshed
 from . import test_util
 
diff --git a/bioblend/_tests/pytest_galaxy_test_wrapper.py b/bioblend/_tests/pytest_galaxy_test_wrapper.py
index 0af83a1e9..a7c56ab36 100755
--- a/bioblend/_tests/pytest_galaxy_test_wrapper.py
+++ b/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.")
diff --git a/bioblend/_tests/test_util.py b/bioblend/_tests/test_util.py
index 879c58489..19805a50b 100644
--- a/bioblend/_tests/test_util.py
+++ b/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.
     """
diff --git a/bioblend/config.py b/bioblend/config.py
index c77aa3dcc..d37a13872 100644
--- a/bioblend/config.py
+++ b/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:
diff --git a/bioblend/galaxy/__init__.py b/bioblend/galaxy/__init__.py
index b04911b5c..b2dd16a8b 100644
--- a/bioblend/galaxy/__init__.py
+++ b/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
diff --git a/bioblend/galaxy/client.py b/bioblend/galaxy/client.py
index 36e781a12..66f0521e1 100644
--- a/bioblend/galaxy/client.py
+++ b/bioblend/galaxy/client.py
@@ -9,7 +9,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     overload,
     TYPE_CHECKING,
 )
@@ -58,7 +57,7 @@ def __init__(self, galaxy_instance: "GalaxyClient") -> None:
         """
         self.gi = galaxy_instance
 
-    def _make_url(self, module_id: Optional[str] = None, deleted: bool = False, contents: bool = False) -> str:
+    def _make_url(self, module_id: str | None = None, deleted: bool = False, contents: bool = False) -> str:
         """
         Compose a URL based on the provided arguments.
 
@@ -85,11 +84,11 @@ def _make_url(self, module_id: Optional[str] = None, deleted: bool = False, cont
     @overload
     def _get(
         self,
-        id: Optional[str] = None,
+        id: str | None = None,
         deleted: bool = False,
         contents: bool = False,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        url: str | None = None,
+        params: dict | None = None,
         *,
         json: Literal[False],
         stream: bool = False,
@@ -98,22 +97,22 @@ def _get(
     @overload
     def _get(
         self,
-        id: Optional[str] = None,
+        id: str | None = None,
         deleted: bool = False,
         contents: bool = False,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        url: str | None = None,
+        params: dict | None = None,
         json: bool = True,
         stream: bool = False,
     ) -> Any: ...
 
     def _get(
         self,
-        id: Optional[str] = None,
+        id: str | None = None,
         deleted: bool = False,
         contents: bool = False,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        url: str | None = None,
+        params: dict | None = None,
         json: bool = True,
         stream: bool = False,
     ) -> Any:
@@ -170,11 +169,11 @@ def _get(
 
     def _post(
         self,
-        payload: Optional[dict] = None,
-        id: Optional[str] = None,
+        payload: dict | None = None,
+        id: str | None = None,
         deleted: bool = False,
         contents: bool = False,
-        url: Optional[str] = None,
+        url: str | None = None,
         files_attached: bool = False,
     ) -> Any:
         """
@@ -198,10 +197,10 @@ def _post(
 
     def _put(
         self,
-        payload: Optional[dict] = None,
-        id: Optional[str] = None,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        payload: dict | None = None,
+        id: str | None = None,
+        url: str | None = None,
+        params: dict | None = None,
     ) -> Any:
         """
         Do a generic PUT request, composing the url from the contents of the
@@ -219,10 +218,10 @@ def _put(
 
     def _patch(
         self,
-        payload: Optional[dict] = None,
-        id: Optional[str] = None,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        payload: dict | None = None,
+        id: str | None = None,
+        url: str | None = None,
+        params: dict | None = None,
     ) -> Any:
         """
         Do a generic PATCH request, composing the url from the contents of the
@@ -240,12 +239,12 @@ def _patch(
 
     def _delete(
         self,
-        payload: Optional[dict] = None,
-        id: Optional[str] = None,
+        payload: dict | None = None,
+        id: str | None = None,
         deleted: bool = False,
         contents: bool = False,
-        url: Optional[str] = None,
-        params: Optional[dict] = None,
+        url: str | None = None,
+        params: dict | None = None,
     ) -> Any:
         """
         Do a generic DELETE request, composing the url from the contents of the
diff --git a/bioblend/galaxy/container_resolution/__init__.py b/bioblend/galaxy/container_resolution/__init__.py
index 29a32995d..cd6cbe4b6 100644
--- a/bioblend/galaxy/container_resolution/__init__.py
+++ b/bioblend/galaxy/container_resolution/__init__.py
@@ -3,8 +3,6 @@
 Works only with Galaxy > 22.01
 """
 
-from typing import Optional
-
 from bioblend.galaxy.client import Client
 
 
@@ -57,9 +55,9 @@ def show_container_resolver(self, index: int) -> dict:
     def resolve(
         self,
         tool_id: str,
-        index: Optional[int] = None,
-        resolver_type: Optional[str] = None,
-        container_type: Optional[str] = None,
+        index: int | None = None,
+        resolver_type: str | None = None,
+        container_type: str | None = None,
         requirements_only: bool = False,
         install: bool = False,
     ) -> dict:
@@ -117,10 +115,10 @@ def resolve(
 
     def resolve_toolbox(
         self,
-        index: Optional[int] = None,
-        tool_ids: Optional[list[str]] = None,
-        resolver_type: Optional[str] = None,
-        container_type: Optional[str] = None,
+        index: int | None = None,
+        tool_ids: list[str] | None = None,
+        resolver_type: str | None = None,
+        container_type: str | None = None,
         requirements_only: bool = False,
         install: bool = False,
     ) -> list:
@@ -169,10 +167,10 @@ def resolve_toolbox(
 
     def resolve_toolbox_with_install(
         self,
-        index: Optional[int] = None,
-        tool_ids: Optional[list[str]] = None,
-        resolver_type: Optional[str] = None,
-        container_type: Optional[str] = None,
+        index: int | None = None,
+        tool_ids: list[str] | None = None,
+        resolver_type: str | None = None,
+        container_type: str | None = None,
         requirements_only: bool = False,
     ) -> list:
         """
diff --git a/bioblend/galaxy/dataset_collections/__init__.py b/bioblend/galaxy/dataset_collections/__init__.py
index 31f8fa96d..a4e550b46 100644
--- a/bioblend/galaxy/dataset_collections/__init__.py
+++ b/bioblend/galaxy/dataset_collections/__init__.py
@@ -1,7 +1,6 @@
 import logging
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
     Union,
 )
@@ -26,12 +25,12 @@ def __init__(
         self,
         name: str,
         type: str = "list",
-        elements: Optional[Union[list[Union["CollectionElement", "SimpleElement"]], dict[str, Any]]] = None,
+        elements: list[Union["CollectionElement", "SimpleElement"]] | dict[str, Any] | None = None,
     ) -> None:
         self.name = name
         self.type = type
         if isinstance(elements, dict):
-            self.elements: list[Union[CollectionElement, SimpleElement]] = [
+            self.elements: list[CollectionElement | SimpleElement] = [
                 HistoryDatasetElement(name=key, id=value) for key, value in elements.values()
             ]
         elif elements:
@@ -43,7 +42,7 @@ def add(self, element: Union["CollectionElement", "SimpleElement"]) -> "HasEleme
 
 
 class CollectionDescription(HasElements):
-    def to_dict(self) -> dict[str, Union[str, list]]:
+    def to_dict(self) -> dict[str, str | list]:
         return {
             "name": self.name,
             "collection_type": self.type,
@@ -52,7 +51,7 @@ def to_dict(self) -> dict[str, Union[str, list]]:
 
 
 class CollectionElement(HasElements):
-    def to_dict(self) -> dict[str, Union[str, list]]:
+    def to_dict(self) -> dict[str, str | list]:
         return {
             "src": "new_collection",
             "name": self.name,
diff --git a/bioblend/galaxy/datasets/__init__.py b/bioblend/galaxy/datasets/__init__.py
index 9fc8460c8..124221aa6 100644
--- a/bioblend/galaxy/datasets/__init__.py
+++ b/bioblend/galaxy/datasets/__init__.py
@@ -9,10 +9,8 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     overload,
     TYPE_CHECKING,
-    Union,
 )
 
 from requests import Response
@@ -112,11 +110,11 @@ def download_dataset(
     def download_dataset(
         self,
         dataset_id: str,
-        file_path: Optional[str] = None,
+        file_path: str | None = None,
         use_default_filename: bool = True,
         require_ok_state: bool = True,
         maxwait: float = 12000,
-    ) -> Union[bytes, str]:
+    ) -> bytes | str:
         """
         Download a dataset to file or in memory. If the dataset state is not
         'ok', a ``DatasetStateException`` will be thrown, unless ``require_ok_state=False``.
@@ -191,19 +189,19 @@ def get_datasets(
         self,
         limit: int = 500,
         offset: int = 0,
-        name: Optional[str] = None,
-        extension: Optional[Union[str, list[str]]] = None,
-        state: Optional[Union[str, list[str]]] = None,
-        visible: Optional[bool] = None,
-        deleted: Optional[bool] = None,
-        purged: Optional[bool] = None,
-        tool_id: Optional[str] = None,
-        tag: Optional[str] = None,
-        history_id: Optional[str] = None,
-        create_time_min: Optional[str] = None,
-        create_time_max: Optional[str] = None,
-        update_time_min: Optional[str] = None,
-        update_time_max: Optional[str] = None,
+        name: str | None = None,
+        extension: str | list[str] | None = None,
+        state: str | list[str] | None = None,
+        visible: bool | None = None,
+        deleted: bool | None = None,
+        purged: bool | None = None,
+        tool_id: str | None = None,
+        tag: str | None = None,
+        history_id: str | None = None,
+        create_time_min: str | None = None,
+        create_time_max: str | None = None,
+        update_time_min: str | None = None,
+        update_time_max: str | None = None,
         order: str = "create_time-dsc",
     ) -> list[dict[str, Any]]:
         """
@@ -331,7 +329,7 @@ def get_datasets(
 
         return self._get(params=params)
 
-    def _param_to_filter(self, param: Union[str, list[str]]) -> tuple[str, str]:
+    def _param_to_filter(self, param: str | list[str]) -> tuple[str, str]:
         if isinstance(param, str):
             return "eq", param
         if isinstance(param, list):
@@ -364,9 +362,9 @@ def publish_dataset(self, dataset_id: str, published: bool = False) -> dict[str,
     def update_permissions(
         self,
         dataset_id: str,
-        access_ids: Optional[list] = None,
-        manage_ids: Optional[list] = None,
-        modify_ids: Optional[list] = None,
+        access_ids: list | None = None,
+        manage_ids: list | None = None,
+        modify_ids: list | None = None,
     ) -> dict:
         """
         Set access, manage or modify permissions for a dataset to a list of roles.
diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 08d67c4a5..076871027 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -7,10 +7,8 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     overload,
     TYPE_CHECKING,
-    Union,
 )
 
 from bioblend.galaxy.client import Client
@@ -25,7 +23,7 @@ class FoldersClient(Client):
     def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
         super().__init__(galaxy_instance)
 
-    def create_folder(self, parent_folder_id: str, name: str, description: Optional[str] = None) -> dict[str, Any]:
+    def create_folder(self, parent_folder_id: str, name: str, description: str | None = None) -> dict[str, Any]:
         """
         Create a folder.
 
@@ -157,7 +155,7 @@ def delete_folder(self, folder_id: str, undelete: bool = False) -> dict[str, Any
         payload = {"undelete": undelete}
         return self._delete(payload=payload, id=folder_id)
 
-    def update_folder(self, folder_id: str, name: str, description: Optional[str] = None) -> dict[str, Any]:
+    def update_folder(self, folder_id: str, name: str, description: str | None = None) -> dict[str, Any]:
         """
         Update folder information.
 
@@ -198,9 +196,9 @@ def set_permissions(
         self,
         folder_id: str,
         action: Literal["set_permissions"] = "set_permissions",
-        add_ids: Optional[list[str]] = None,
-        manage_ids: Optional[list[str]] = None,
-        modify_ids: Optional[list[str]] = None,
+        add_ids: list[str] | None = None,
+        manage_ids: list[str] | None = None,
+        modify_ids: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Set the permissions of a folder.
@@ -224,7 +222,7 @@ def set_permissions(
         :return: dictionary including details of the folder
         """
         url = self._make_url(folder_id) + "/permissions"
-        payload: dict[str, Union[str, list[str]]] = {"action": action}
+        payload: dict[str, str | list[str]] = {"action": action}
         if add_ids:
             payload["add_ids[]"] = add_ids
         if manage_ids:
diff --git a/bioblend/galaxy/genomes/__init__.py b/bioblend/galaxy/genomes/__init__.py
index dcef315aa..9e254ce9a 100644
--- a/bioblend/galaxy/genomes/__init__.py
+++ b/bioblend/galaxy/genomes/__init__.py
@@ -5,7 +5,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -34,10 +33,10 @@ def get_genomes(self) -> list:
     def show_genome(
         self,
         id: str,
-        num: Optional[str] = None,
-        chrom: Optional[str] = None,
-        low: Optional[str] = None,
-        high: Optional[str] = None,
+        num: str | None = None,
+        chrom: str | None = None,
+        low: str | None = None,
+        high: str | None = None,
     ) -> dict[str, Any]:
         """
         Returns information about build <id>
@@ -74,12 +73,12 @@ def show_genome(
     def install_genome(
         self,
         func: Literal["download", "index"] = "download",
-        source: Optional[str] = None,
-        dbkey: Optional[str] = None,
-        ncbi_name: Optional[str] = None,
-        ensembl_dbkey: Optional[str] = None,
-        url_dbkey: Optional[str] = None,
-        indexers: Optional[list] = None,
+        source: str | None = None,
+        dbkey: str | None = None,
+        ncbi_name: str | None = None,
+        ensembl_dbkey: str | None = None,
+        url_dbkey: str | None = None,
+        indexers: list | None = None,
     ) -> dict[str, Any]:
         """
         Download and/or index a genome.
diff --git a/bioblend/galaxy/groups/__init__.py b/bioblend/galaxy/groups/__init__.py
index 281066320..eaaee1f1a 100644
--- a/bioblend/galaxy/groups/__init__.py
+++ b/bioblend/galaxy/groups/__init__.py
@@ -4,7 +4,6 @@
 
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -60,7 +59,7 @@ def show_group(self, group_id: str) -> dict[str, Any]:
         return self._get(id=group_id)
 
     def create_group(
-        self, group_name: str, user_ids: Optional[list[str]] = None, role_ids: Optional[list[str]] = None
+        self, group_name: str, user_ids: list[str] | None = None, role_ids: list[str] | None = None
     ) -> list[dict[str, Any]]:
         """
         Create a new group.
@@ -93,9 +92,9 @@ def create_group(
     def update_group(
         self,
         group_id: str,
-        group_name: Optional[str] = None,
-        user_ids: Optional[list[str]] = None,
-        role_ids: Optional[list[str]] = None,
+        group_name: str | None = None,
+        user_ids: list[str] | None = None,
+        role_ids: list[str] | None = None,
     ) -> None:
         """
         Update a group.
diff --git a/bioblend/galaxy/histories/__init__.py b/bioblend/galaxy/histories/__init__.py
index 6bbeb035b..ef6e03340 100644
--- a/bioblend/galaxy/histories/__init__.py
+++ b/bioblend/galaxy/histories/__init__.py
@@ -13,7 +13,6 @@
     Any,
     IO,
     Literal,
-    Optional,
     overload,
     Union,
 )
@@ -41,7 +40,7 @@ class HistoryClient(Client):
     def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
         super().__init__(galaxy_instance)
 
-    def create_history(self, name: Optional[str] = None) -> dict[str, Any]:
+    def create_history(self, name: str | None = None) -> dict[str, Any]:
         """
         Create a new history, optionally setting the ``name``.
 
@@ -56,7 +55,7 @@ def create_history(self, name: Optional[str] = None) -> dict[str, Any]:
             payload["name"] = name
         return self._post(payload)
 
-    def import_history(self, file_path: Optional[str] = None, url: Optional[str] = None) -> dict[str, Any]:
+    def import_history(self, file_path: str | None = None, url: str | None = None) -> dict[str, Any]:
         """
         Import a history from an archive on disk or a URL.
 
@@ -86,20 +85,20 @@ def import_history(self, file_path: Optional[str] = None, url: Optional[str] = N
 
     def _get_histories(
         self,
-        name: Optional[str] = None,
+        name: str | None = None,
         deleted: bool = False,
-        filter_user_published: Optional[bool] = None,
+        filter_user_published: bool | None = None,
         get_all_published: bool = False,
-        slug: Optional[str] = None,
-        all: Optional[bool] = False,
-        create_time_min: Optional[str] = None,
-        create_time_max: Optional[str] = None,
-        update_time_min: Optional[str] = None,
-        update_time_max: Optional[str] = None,
-        view: Optional[Literal["summary", "detailed"]] = None,
-        keys: Optional[list[str]] = None,
-        limit: Optional[int] = None,
-        offset: Optional[int] = None,
+        slug: str | None = None,
+        all: bool | None = False,
+        create_time_min: str | None = None,
+        create_time_max: str | None = None,
+        update_time_min: str | None = None,
+        update_time_max: str | None = None,
+        view: Literal["summary", "detailed"] | None = None,
+        keys: list[str] | None = None,
+        limit: int | None = None,
+        offset: int | None = None,
     ) -> list[dict[str, Any]]:
         """
         Hidden method to be used by both get_histories() and get_published_histories()
@@ -148,20 +147,20 @@ def _get_histories(
 
     def get_histories(
         self,
-        history_id: Optional[str] = None,
-        name: Optional[str] = None,
+        history_id: str | None = None,
+        name: str | None = None,
         deleted: bool = False,
-        published: Optional[bool] = None,
-        slug: Optional[str] = None,
-        all: Optional[bool] = False,
-        create_time_min: Optional[str] = None,
-        create_time_max: Optional[str] = None,
-        update_time_min: Optional[str] = None,
-        update_time_max: Optional[str] = None,
-        view: Optional[Literal["summary", "detailed"]] = None,
-        keys: Optional[list[str]] = None,
-        limit: Optional[int] = None,
-        offset: Optional[int] = None,
+        published: bool | None = None,
+        slug: str | None = None,
+        all: bool | None = False,
+        create_time_min: str | None = None,
+        create_time_max: str | None = None,
+        update_time_min: str | None = None,
+        update_time_max: str | None = None,
+        view: Literal["summary", "detailed"] | None = None,
+        keys: list[str] | None = None,
+        limit: int | None = None,
+        offset: int | None = None,
     ) -> list[dict[str, Any]]:
         """
         Get all histories, or select a subset by specifying optional arguments
@@ -249,13 +248,13 @@ def get_histories(
 
     def get_published_histories(
         self,
-        name: Optional[str] = None,
+        name: str | None = None,
         deleted: bool = False,
-        slug: Optional[str] = None,
-        create_time_min: Optional[str] = None,
-        create_time_max: Optional[str] = None,
-        update_time_min: Optional[str] = None,
-        update_time_max: Optional[str] = None,
+        slug: str | None = None,
+        create_time_min: str | None = None,
+        create_time_max: str | None = None,
+        update_time_min: str | None = None,
+        update_time_max: str | None = None,
     ) -> list[dict[str, Any]]:
         """
         Get all published histories (by any user), or select a subset by
@@ -314,23 +313,23 @@ def show_history(
         self,
         history_id: str,
         contents: Literal[True],
-        deleted: Optional[bool] = None,
-        visible: Optional[bool] = None,
-        details: Optional[str] = None,
-        types: Optional[list[str]] = None,
-        keys: Optional[list[str]] = None,
+        deleted: bool | None = None,
+        visible: bool | None = None,
+        details: str | None = None,
+        types: list[str] | None = None,
+        keys: list[str] | None = None,
     ) -> list[dict[str, Any]]: ...
 
     def show_history(
         self,
         history_id: str,
         contents: bool = False,
-        deleted: Optional[bool] = None,
-        visible: Optional[bool] = None,
-        details: Optional[str] = None,
-        types: Optional[list[str]] = None,
-        keys: Optional[list[str]] = None,
-    ) -> Union[dict[str, Any], list[dict[str, Any]]]:
+        deleted: bool | None = None,
+        visible: bool | None = None,
+        details: str | None = None,
+        types: list[str] | None = None,
+        keys: list[str] | None = None,
+    ) -> dict[str, Any] | list[dict[str, Any]]:
         """
         Get details of a given history. By default, just get the history meta
         information.
@@ -377,7 +376,7 @@ def show_history(
             more extensive functionality for filtering and ordering the results.
 
         """
-        params: dict[str, Union[bool, list, str]] = {}
+        params: dict[str, bool | list | str] = {}
         if contents:
             if details:
                 params["details"] = details
@@ -477,7 +476,7 @@ def show_dataset_collection(self, history_id: str, dataset_collection_id: str) -
         return self._get(url=url)
 
     def show_matching_datasets(
-        self, history_id: str, name_filter: Optional[Union[str, Pattern[str]]] = None
+        self, history_id: str, name_filter: str | Pattern[str] | None = None
     ) -> list[dict[str, Any]]:
         """
         Get dataset details for matching datasets within a history.
@@ -826,7 +825,7 @@ def export_history(
         include_hidden: bool = False,
         include_deleted: bool = False,
         wait: bool = False,
-        maxwait: Optional[float] = None,
+        maxwait: float | None = None,
     ) -> str:
         """
         Start a job to create an export archive for the given history.
diff --git a/bioblend/galaxy/invocations/__init__.py b/bioblend/galaxy/invocations/__init__.py
index 241897ddd..e33e9a69e 100644
--- a/bioblend/galaxy/invocations/__init__.py
+++ b/bioblend/galaxy/invocations/__init__.py
@@ -5,7 +5,6 @@
 import logging
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -38,16 +37,16 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
 
     def get_invocations(
         self,
-        workflow_id: Optional[str] = None,
-        history_id: Optional[str] = None,
-        user_id: Optional[str] = None,
+        workflow_id: str | None = None,
+        history_id: str | None = None,
+        user_id: str | None = None,
         include_terminal: bool = True,
-        limit: Optional[int] = None,
+        limit: int | None = None,
         *,
-        offset: Optional[int] = None,
+        offset: int | None = None,
         view: str = "collection",
         step_details: bool = False,
-        job_id: Optional[int] = None,
+        job_id: int | None = None,
     ) -> list[dict[str, Any]]:
         """
         Get all workflow invocations, or select a subset by specifying optional
@@ -163,16 +162,16 @@ def show_invocation(self, invocation_id: str) -> dict[str, Any]:
     def rerun_invocation(
         self,
         invocation_id: str,
-        inputs_update: Optional[dict] = None,
-        params_update: Optional[dict] = None,
-        history_id: Optional[str] = None,
-        history_name: Optional[str] = None,
+        inputs_update: dict | None = None,
+        params_update: dict | None = None,
+        history_id: str | None = None,
+        history_name: str | None = None,
         import_inputs_to_history: bool = False,
-        replacement_params: Optional[dict] = None,
+        replacement_params: dict | None = None,
         allow_tool_state_corrections: bool = False,
-        inputs_by: Optional[InputsBy] = None,
+        inputs_by: InputsBy | None = None,
         parameters_normalized: bool = False,
-        resource_params: Optional[dict[str, Any]] = None,
+        resource_params: dict[str, Any] | None = None,
         use_cached_job: bool = True,
     ) -> dict[str, Any]:
         """
@@ -504,10 +503,10 @@ def get_invocation_archive(
         include_deleted: bool = False,
         include_hidden: bool = False,
         bco_merge_history_metadata: bool = False,
-        bco_override_environment_variables: Optional[dict[str, Any]] = None,
-        bco_override_empirical_error: Optional[dict[str, Any]] = None,
-        bco_override_algorithmic_error: Optional[dict[str, Any]] = None,
-        bco_override_xref: Optional[dict[str, Any]] = None,
+        bco_override_environment_variables: dict[str, Any] | None = None,
+        bco_override_empirical_error: dict[str, Any] | None = None,
+        bco_override_algorithmic_error: dict[str, Any] | None = None,
+        bco_override_xref: dict[str, Any] | None = None,
         maxwait: float = 1200,
     ) -> requests.Response:
         """
diff --git a/bioblend/galaxy/jobs/__init__.py b/bioblend/galaxy/jobs/__init__.py
index df0d45d89..3bbbce325 100644
--- a/bioblend/galaxy/jobs/__init__.py
+++ b/bioblend/galaxy/jobs/__init__.py
@@ -6,7 +6,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -34,14 +33,14 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
 
     def get_jobs(
         self,
-        state: Optional[str] = None,
-        history_id: Optional[str] = None,
-        invocation_id: Optional[str] = None,
-        tool_id: Optional[str] = None,
-        workflow_id: Optional[str] = None,
-        user_id: Optional[str] = None,
-        date_range_min: Optional[str] = None,
-        date_range_max: Optional[str] = None,
+        state: str | None = None,
+        history_id: str | None = None,
+        invocation_id: str | None = None,
+        tool_id: str | None = None,
+        workflow_id: str | None = None,
+        user_id: str | None = None,
+        date_range_min: str | None = None,
+        date_range_max: str | None = None,
         limit: int = 500,
         offset: int = 0,
         user_details: bool = False,
@@ -195,8 +194,8 @@ def rerun_job(
         self,
         job_id: str,
         remap: bool = False,
-        tool_inputs_update: Optional[dict[str, Any]] = None,
-        history_id: Optional[str] = None,
+        tool_inputs_update: dict[str, Any] | None = None,
+        history_id: str | None = None,
     ) -> dict[str, Any]:
         """
         Rerun a job.
@@ -272,7 +271,7 @@ def get_state(self, job_id: str) -> str:
         """
         return self.show_job(job_id).get("state", "")
 
-    def search_jobs(self, tool_id: str, inputs: dict[str, Any], state: Optional[str] = None) -> list[dict[str, Any]]:
+    def search_jobs(self, tool_id: str, inputs: dict[str, Any], state: str | None = None) -> list[dict[str, Any]]:
         """
         Return jobs matching input parameters.
 
@@ -339,7 +338,7 @@ def cancel_job(self, job_id: str) -> bool:
         """
         return self._delete(id=job_id)
 
-    def report_error(self, job_id: str, dataset_id: str, message: str, email: Optional[str] = None) -> dict[str, Any]:
+    def report_error(self, job_id: str, dataset_id: str, message: str, email: str | None = None) -> dict[str, Any]:
         """
         Report an error for a given job and dataset to the server administrators.
 
diff --git a/bioblend/galaxy/libraries/__init__.py b/bioblend/galaxy/libraries/__init__.py
index ce3927eb7..610c1ab19 100644
--- a/bioblend/galaxy/libraries/__init__.py
+++ b/bioblend/galaxy/libraries/__init__.py
@@ -6,10 +6,8 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     overload,
     TYPE_CHECKING,
-    Union,
 )
 
 from bioblend import (
@@ -34,9 +32,7 @@ class LibraryClient(Client):
     def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
         super().__init__(galaxy_instance)
 
-    def create_library(
-        self, name: str, description: Optional[str] = None, synopsis: Optional[str] = None
-    ) -> dict[str, Any]:
+    def create_library(self, name: str, description: str | None = None, synopsis: str | None = None) -> dict[str, Any]:
         """
         Create a data library with the properties defined in the arguments.
 
@@ -221,7 +217,7 @@ def _get_root_folder_id(self, library_id: str) -> str:
         return library_dict["root_folder_id"]
 
     def create_folder(
-        self, library_id: str, folder_name: str, description: Optional[str] = None, base_folder_id: Optional[str] = None
+        self, library_id: str, folder_name: str, description: str | None = None, base_folder_id: str | None = None
     ) -> list[dict[str, Any]]:
         """
         Create a folder in a library.
@@ -256,7 +252,7 @@ def create_folder(
         return self._post(payload, id=library_id, contents=True)
 
     def get_folders(
-        self, library_id: str, folder_id: Optional[str] = None, name: Optional[str] = None
+        self, library_id: str, folder_id: str | None = None, name: str | None = None
     ) -> list[dict[str, Any]]:
         """
         Get all the folders in a library, or select a subset by specifying a
@@ -289,7 +285,7 @@ def get_folders(
         return folders
 
     def get_libraries(
-        self, library_id: Optional[str] = None, name: Optional[str] = None, deleted: Optional[bool] = False
+        self, library_id: str | None = None, name: str | None = None, deleted: bool | None = False
     ) -> list[dict[str, Any]]:
         """
         Get all libraries, or select a subset by specifying optional arguments
@@ -325,7 +321,7 @@ def show_library(self, library_id: str, contents: Literal[False] = False) -> dic
     @overload
     def show_library(self, library_id: str, contents: Literal[True]) -> list[dict[str, Any]]: ...
 
-    def show_library(self, library_id: str, contents: bool = False) -> Union[dict[str, Any], list[dict[str, Any]]]:
+    def show_library(self, library_id: str, contents: bool = False) -> dict[str, Any] | list[dict[str, Any]]:
         """
         Get information about a library.
 
@@ -394,10 +390,10 @@ def upload_file_from_url(
         self,
         library_id: str,
         file_url: str,
-        folder_id: Optional[str] = None,
+        folder_id: str | None = None,
         file_type: str = "auto",
         dbkey: str = "?",
-        tags: Optional[list[str]] = None,
+        tags: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """
         Upload a file to a library from a URL.
@@ -432,10 +428,10 @@ def upload_file_contents(
         self,
         library_id: str,
         pasted_content: str,
-        folder_id: Optional[str] = None,
+        folder_id: str | None = None,
         file_type: str = "auto",
         dbkey: str = "?",
-        tags: Optional[list[str]] = None,
+        tags: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """
         Upload pasted_content to a data library as a new file.
@@ -470,10 +466,10 @@ def upload_file_from_local_path(
         self,
         library_id: str,
         file_local_path: str,
-        folder_id: Optional[str] = None,
+        folder_id: str | None = None,
         file_type: str = "auto",
         dbkey: str = "?",
-        tags: Optional[list[str]] = None,
+        tags: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """
         Read local file contents from file_local_path and upload data to a
@@ -514,14 +510,14 @@ def upload_file_from_server(
         self,
         library_id: str,
         server_dir: str,
-        folder_id: Optional[str] = None,
+        folder_id: str | None = None,
         file_type: str = "auto",
         dbkey: str = "?",
-        link_data_only: Optional[LinkDataOnly] = None,
+        link_data_only: LinkDataOnly | None = None,
         roles: str = "",
         preserve_dirs: bool = False,
         tag_using_filenames: bool = False,
-        tags: Optional[list[str]] = None,
+        tags: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """
         Upload all files in the specified subdirectory of the Galaxy library
@@ -592,14 +588,14 @@ def upload_from_galaxy_filesystem(
         self,
         library_id: str,
         filesystem_paths: str,
-        folder_id: Optional[str] = None,
+        folder_id: str | None = None,
         file_type: str = "auto",
         dbkey: str = "?",
-        link_data_only: Optional[LinkDataOnly] = None,
+        link_data_only: LinkDataOnly | None = None,
         roles: str = "",
         preserve_dirs: bool = False,
         tag_using_filenames: bool = False,
-        tags: Optional[list[str]] = None,
+        tags: list[str] | None = None,
     ) -> list[dict[str, Any]]:
         """
         Upload a set of files already present on the filesystem of the Galaxy
@@ -666,7 +662,7 @@ def upload_from_galaxy_filesystem(
         )
 
     def copy_from_dataset(
-        self, library_id: str, dataset_id: str, folder_id: Optional[str] = None, message: str = ""
+        self, library_id: str, dataset_id: str, folder_id: str | None = None, message: str = ""
     ) -> dict[str, Any]:
         """
         Copy a Galaxy dataset into a library.
@@ -726,10 +722,10 @@ def get_dataset_permissions(self, dataset_id: str) -> dict[str, Any]:
     def set_library_permissions(
         self,
         library_id: str,
-        access_in: Optional[list[str]] = None,
-        modify_in: Optional[list[str]] = None,
-        add_in: Optional[list[str]] = None,
-        manage_in: Optional[list[str]] = None,
+        access_in: list[str] | None = None,
+        modify_in: list[str] | None = None,
+        add_in: list[str] | None = None,
+        manage_in: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Set the permissions for a library. Note: it will override all security
@@ -768,9 +764,9 @@ def set_library_permissions(
     def set_dataset_permissions(
         self,
         dataset_id: str,
-        access_in: Optional[list[str]] = None,
-        modify_in: Optional[list[str]] = None,
-        manage_in: Optional[list[str]] = None,
+        access_in: list[str] | None = None,
+        modify_in: list[str] | None = None,
+        manage_in: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Set the permissions for a dataset. Note: it will override all security
diff --git a/bioblend/galaxy/objects/client.py b/bioblend/galaxy/objects/client.py
index 8f053bee4..378633da8 100644
--- a/bioblend/galaxy/objects/client.py
+++ b/bioblend/galaxy/objects/client.py
@@ -14,10 +14,8 @@
     cast,
     Generic,
     Literal,
-    Optional,
     overload,
     TYPE_CHECKING,
-    Union,
 )
 
 import bioblend
@@ -66,7 +64,7 @@ def list(self) -> list:
         :return: a list of objects
         """
 
-    def _select_id(self, id_: Optional[str] = None, name: Optional[str] = None) -> str:
+    def _select_id(self, id_: str | None = None, name: str | None = None) -> str:
         """
         Return the id that corresponds to the given id or name info.
         """
@@ -84,9 +82,7 @@ def _select_id(self, id_: Optional[str] = None, name: Optional[str] = None) -> s
         else:
             return id_
 
-    def _get_dict(
-        self, meth_name: str, reply: Optional[Union[dict[str, Any], builtins.list[dict[str, Any]]]]
-    ) -> dict[str, Any]:
+    def _get_dict(self, meth_name: str, reply: dict[str, Any] | builtins.list[dict[str, Any]] | None) -> dict[str, Any]:
         if reply is None:
             raise RuntimeError(f"{meth_name}: no reply")
         elif isinstance(reply, dict):
@@ -112,7 +108,7 @@ def __init__(self, obj_gi: "GalaxyInstance") -> None:
         self._show_f = getattr(gi_client, show_fname)
 
     def get_previews(
-        self, name: Optional[str] = None, deleted: bool = False, **kwargs: Any
+        self, name: str | None = None, deleted: bool = False, **kwargs: Any
     ) -> list[wrappers.DatasetContainerPreviewSubtype]:
         dicts = self._get_f(name=name, deleted=deleted, **kwargs)
         return [
@@ -139,7 +135,7 @@ class ObjLibraryClient(ObjDatasetContainerClient[wrappers.Library, wrappers.Libr
     CONTAINER_TYPE = wrappers.Library
     CONTAINER_PREVIEW_TYPE = wrappers.LibraryPreview
 
-    def create(self, name: str, description: Optional[str] = None, synopsis: Optional[str] = None) -> wrappers.Library:
+    def create(self, name: str, description: str | None = None, synopsis: str | None = None) -> wrappers.Library:
         """
         Create a data library with the properties defined in the arguments.
 
@@ -150,7 +146,7 @@ def create(self, name: str, description: Optional[str] = None, synopsis: Optiona
         lib_info = self._get_dict("create_library", res)
         return self.get(lib_info["id"])
 
-    def list(self, name: Optional[str] = None, deleted: bool = False) -> list[wrappers.Library]:
+    def list(self, name: str | None = None, deleted: bool = False) -> list[wrappers.Library]:
         """
         Get libraries owned by the user of this Galaxy instance.
 
@@ -170,7 +166,7 @@ def list(self, name: Optional[str] = None, deleted: bool = False) -> list[wrappe
         else:
             return [self.get(_["id"]) for _ in dicts]
 
-    def delete(self, id_: Optional[str] = None, name: Optional[str] = None) -> None:
+    def delete(self, id_: str | None = None, name: str | None = None) -> None:
         """
         Delete the library with the given id or name.
 
@@ -194,7 +190,7 @@ class ObjHistoryClient(ObjDatasetContainerClient[wrappers.History, wrappers.Hist
     CONTAINER_TYPE = wrappers.History
     CONTAINER_PREVIEW_TYPE = wrappers.HistoryPreview
 
-    def create(self, name: Optional[str] = None) -> wrappers.History:
+    def create(self, name: str | None = None) -> wrappers.History:
         """
         Create a new Galaxy history, optionally setting its name.
 
@@ -205,7 +201,7 @@ def create(self, name: Optional[str] = None) -> wrappers.History:
         hist_info = self._get_dict("create_history", res)
         return self.get(hist_info["id"])
 
-    def list(self, name: Optional[str] = None, deleted: bool = False) -> list[wrappers.History]:
+    def list(self, name: str | None = None, deleted: bool = False) -> list[wrappers.History]:
         """
         Get histories owned by the user of this Galaxy instance.
 
@@ -219,7 +215,7 @@ def list(self, name: Optional[str] = None, deleted: bool = False) -> list[wrappe
         dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
         return [self.get(_["id"]) for _ in dicts]
 
-    def delete(self, id_: Optional[str] = None, name: Optional[str] = None, purge: bool = False) -> None:
+    def delete(self, id_: str | None = None, name: str | None = None, purge: bool = False) -> None:
         """
         Delete the history with the given id or name.
 
@@ -244,7 +240,7 @@ class ObjWorkflowClient(ObjClient):
     Interacts with Galaxy workflows.
     """
 
-    def import_new(self, src: Union[str, dict[str, Any]], publish: bool = False) -> wrappers.Workflow:
+    def import_new(self, src: str | dict[str, Any], publish: bool = False) -> wrappers.Workflow:
         """
         Imports a new workflow into Galaxy.
 
@@ -296,13 +292,13 @@ def get(self, id_: str) -> wrappers.Workflow:
 
     # the 'deleted' option is not available for workflows
     def get_previews(
-        self, name: Optional[str] = None, published: bool = False, **kwargs: Any
+        self, name: str | None = None, published: bool = False, **kwargs: Any
     ) -> list[wrappers.WorkflowPreview]:
         dicts = self.gi.workflows.get_workflows(name=name, published=published, **kwargs)
         return [wrappers.WorkflowPreview(_, gi=self.obj_gi) for _ in dicts]
 
     # the 'deleted' option is not available for workflows
-    def list(self, name: Optional[str] = None, published: bool = False) -> list[wrappers.Workflow]:
+    def list(self, name: str | None = None, published: bool = False) -> list[wrappers.Workflow]:
         """
         Get workflows owned by the user of this Galaxy instance.
 
@@ -316,7 +312,7 @@ def list(self, name: Optional[str] = None, published: bool = False) -> list[wrap
         dicts = self.gi.workflows.get_workflows(name=name, published=published)
         return [self.get(_["id"]) for _ in dicts]
 
-    def delete(self, id_: Optional[str] = None, name: Optional[str] = None) -> None:
+    def delete(self, id_: str | None = None, name: str | None = None) -> None:
         """
         Delete the workflow with the given id or name.
 
@@ -357,11 +353,11 @@ def get_previews(self, **kwargs: Any) -> list[wrappers.InvocationPreview]:
 
     def list(
         self,
-        workflow: Optional[wrappers.Workflow] = None,
-        history: Optional[wrappers.History] = None,
+        workflow: wrappers.Workflow | None = None,
+        history: wrappers.History | None = None,
         include_terminal: bool = True,
-        limit: Optional[int] = None,
-        offset: Optional[int] = None,
+        limit: int | None = None,
+        offset: int | None = None,
     ) -> list[wrappers.Invocation]:
         """
         Get full listing of workflow invocations, or select a subset
@@ -422,7 +418,7 @@ def get(self, id_: str, io_details: bool = False, link_details: bool = False) ->
         tool_dict = self._get_dict("show_tool", res)
         return wrappers.Tool(tool_dict, gi=self.obj_gi)
 
-    def get_previews(self, name: Optional[str] = None, trackster: bool = False, **kwargs: Any) -> list[wrappers.Tool]:
+    def get_previews(self, name: str | None = None, trackster: bool = False, **kwargs: Any) -> list[wrappers.Tool]:
         """
         Get the list of tools installed on the Galaxy instance.
 
@@ -439,7 +435,7 @@ def get_previews(self, name: Optional[str] = None, trackster: bool = False, **kw
         return [wrappers.Tool(_, gi=self.obj_gi) for _ in dicts]
 
     # the 'deleted' option is not available for tools
-    def list(self, name: Optional[str] = None, trackster: bool = False) -> list[wrappers.Tool]:
+    def list(self, name: str | None = None, trackster: bool = False) -> list[wrappers.Tool]:
         """
         Get the list of tools installed on the Galaxy instance.
 
diff --git a/bioblend/galaxy/objects/galaxy_instance.py b/bioblend/galaxy/objects/galaxy_instance.py
index e06bb4ae5..59f9c92ff 100644
--- a/bioblend/galaxy/objects/galaxy_instance.py
+++ b/bioblend/galaxy/objects/galaxy_instance.py
@@ -4,7 +4,6 @@
 
 import time
 from collections.abc import Iterable
-from typing import Optional
 
 import bioblend
 import bioblend.galaxy
@@ -50,13 +49,13 @@ class GalaxyInstance:
     def __init__(
         self,
         url: str,
-        api_key: Optional[str] = None,
-        email: Optional[str] = None,
-        password: Optional[str] = None,
+        api_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:
         self.gi = bioblend.galaxy.GalaxyInstance(
             url, key=api_key, email=email, password=password, token=token, verify=verify, user_agent=user_agent
diff --git a/bioblend/galaxy/objects/wrappers.py b/bioblend/galaxy/objects/wrappers.py
index 35504363a..5669a71b3 100644
--- a/bioblend/galaxy/objects/wrappers.py
+++ b/bioblend/galaxy/objects/wrappers.py
@@ -7,6 +7,7 @@
 import abc
 import json
 from collections.abc import (
+    Callable,
     Iterable,
     Iterator,
     Mapping,
@@ -14,7 +15,6 @@
 )
 from typing import (
     Any,
-    Callable,
     cast,
     ClassVar,
     Generic,
@@ -189,9 +189,9 @@ class Step(Wrapper):
     input_steps: dict[str, dict]
     name: str
     type: str
-    tool_id: Optional[str]
+    tool_id: str | None
     tool_inputs: dict
-    tool_version: Optional[str]
+    tool_version: str | None
 
     def __init__(self, step_dict: dict[str, Any], parent: Wrapper) -> None:
         super().__init__(step_dict, parent=parent, gi=parent.gi)
@@ -218,7 +218,7 @@ class InvocationStep(Wrapper):
         "workflow_step_label",
         "workflow_step_uuid",
     )
-    action: Optional[object]
+    action: object | None
     gi: "GalaxyInstance"
     job_id: str
     order_index: int
@@ -492,13 +492,13 @@ def delete(self) -> None:
 
     def invoke(
         self,
-        inputs: Optional[dict[str, Any]] = None,
-        params: Optional[dict[str, Any]] = None,
-        history: Optional[Union[str, "History"]] = None,
+        inputs: dict[str, Any] | None = None,
+        params: dict[str, Any] | None = None,
+        history: Union[str, "History"] | None = None,
         import_inputs_to_history: bool = False,
-        replacement_params: Optional[dict[str, Any]] = None,
+        replacement_params: dict[str, Any] | None = None,
         allow_tool_state_corrections: bool = True,
-        inputs_by: Optional[InputsBy] = None,
+        inputs_by: InputsBy | None = None,
         parameters_normalized: bool = False,
     ) -> "Invocation":
         """
@@ -708,9 +708,9 @@ def number_of_steps(self) -> int:
 
     def sorted_steps_by(
         self,
-        indices: Optional[Iterable[int]] = None,
-        states: Optional[Iterable[Union[str, None]]] = None,
-        step_ids: Optional[Iterable[str]] = None,
+        indices: Iterable[int] | None = None,
+        states: Iterable[str | None] | None = None,
+        step_ids: Iterable[str] | None = None,
     ) -> list[InvocationStep]:
         """
         Get steps for this invocation, or get a subset by specifying
@@ -728,7 +728,7 @@ def sorted_steps_by(
         :rtype: list of InvocationStep
         :return: invocation steps
         """
-        steps: Union[list[InvocationStep], filter] = self.steps
+        steps: list[InvocationStep] | filter = self.steps
         if indices is not None:
             steps = filter(lambda step: step.order_index in indices, steps)
         if states is not None:
@@ -1218,7 +1218,7 @@ class DatasetContainer(Wrapper, Generic[DatasetSubtype], metaclass=abc.ABCMeta):
     def __init__(
         self,
         c_dict: dict[str, Any],
-        content_infos: Optional[list[ContentInfo]] = None,
+        content_infos: list[ContentInfo] | None = None,
         gi: Optional["GalaxyInstance"] = None,
     ) -> None:
         """
@@ -1277,7 +1277,7 @@ def get_dataset(self, ds_id: str) -> DatasetSubtype:
         ds_dict = gi_client.show_dataset(self.id, ds_id)
         return self.DS_TYPE(ds_dict, self, gi=self.gi)
 
-    def get_datasets(self, name: Optional[str] = None) -> list[DatasetSubtype]:
+    def get_datasets(self, name: str | None = None) -> list[DatasetSubtype]:
         """
         Get all datasets contained inside this dataset container.
 
@@ -1458,7 +1458,7 @@ def export(
         include_hidden: bool = False,
         include_deleted: bool = False,
         wait: bool = False,
-        maxwait: Optional[int] = None,
+        maxwait: int | None = None,
     ) -> str:
         """
         Start a job to create an export archive for this history.  See
@@ -1548,7 +1548,7 @@ def delete(self) -> None:
         self.refresh()
         self.unmap()
 
-    def _pre_upload(self, folder: Optional["Folder"]) -> Optional[str]:
+    def _pre_upload(self, folder: Optional["Folder"]) -> str | None:
         """
         Return the id of the given folder, after sanity checking.
         """
@@ -1606,7 +1606,7 @@ def upload_from_local(self, path: str, folder: Optional["Folder"] = None, **kwar
 
     def upload_from_galaxy_fs(
         self,
-        paths: Union[str, Iterable[str]],
+        paths: str | Iterable[str],
         folder: Optional["Folder"] = None,
         link_data_only: Literal["copy_files", "link_to_files"] = "copy_files",
         **kwargs: Any,
@@ -1663,7 +1663,7 @@ def copy_from_dataset(
         return self.get_dataset(res["library_dataset_id"])
 
     def create_folder(
-        self, name: str, description: Optional[str] = None, base_folder: Optional["Folder"] = None
+        self, name: str, description: str | None = None, base_folder: Optional["Folder"] = None
     ) -> "Folder":
         """
         Create a folder in this library.
diff --git a/bioblend/galaxy/quotas/__init__.py b/bioblend/galaxy/quotas/__init__.py
index 30bd990f8..6c449c403 100644
--- a/bioblend/galaxy/quotas/__init__.py
+++ b/bioblend/galaxy/quotas/__init__.py
@@ -5,7 +5,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -79,10 +78,10 @@ def create_quota(
         description: str,
         amount: str,
         operation: QuotaOperations,
-        default: Optional[DefaultQuotaValues] = "no",
-        in_users: Optional[list[str]] = None,
-        in_groups: Optional[list[str]] = None,
-        quota_source_label: Optional[str] = None,
+        default: DefaultQuotaValues | None = "no",
+        in_users: list[str] | None = None,
+        in_groups: list[str] | None = None,
+        quota_source_label: str | None = None,
     ) -> dict[str, Any]:
         """
         Create a new quota
@@ -143,13 +142,13 @@ def create_quota(
     def update_quota(
         self,
         quota_id: str,
-        name: Optional[str] = None,
-        description: Optional[str] = None,
-        amount: Optional[str] = None,
-        operation: Optional[QuotaOperations] = "=",
-        default: Optional[DefaultQuotaValues] = None,
-        in_users: Optional[list[str]] = None,
-        in_groups: Optional[list[str]] = None,
+        name: str | None = None,
+        description: str | None = None,
+        amount: str | None = None,
+        operation: QuotaOperations | None = "=",
+        default: DefaultQuotaValues | None = None,
+        in_users: list[str] | None = None,
+        in_groups: list[str] | None = None,
     ) -> str:
         """
         Update an existing quota
diff --git a/bioblend/galaxy/roles/__init__.py b/bioblend/galaxy/roles/__init__.py
index c6c449928..303e2f6e7 100644
--- a/bioblend/galaxy/roles/__init__.py
+++ b/bioblend/galaxy/roles/__init__.py
@@ -4,7 +4,6 @@
 
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -63,8 +62,8 @@ def create_role(
         self,
         role_name: str,
         description: str,
-        user_ids: Optional[list[str]] = None,
-        group_ids: Optional[list[str]] = None,
+        user_ids: list[str] | None = None,
+        group_ids: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Create a new role.
diff --git a/bioblend/galaxy/tool_dependencies/__init__.py b/bioblend/galaxy/tool_dependencies/__init__.py
index 0b2f689af..927f9aa63 100644
--- a/bioblend/galaxy/tool_dependencies/__init__.py
+++ b/bioblend/galaxy/tool_dependencies/__init__.py
@@ -5,7 +5,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -23,11 +22,11 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
 
     def summarize_toolbox(
         self,
-        index: Optional[int] = None,
-        tool_ids: Optional[list[str]] = None,
-        resolver_type: Optional[str] = None,
+        index: int | None = None,
+        tool_ids: list[str] | None = None,
+        resolver_type: str | None = None,
         include_containers: bool = False,
-        container_type: Optional[str] = None,
+        container_type: str | None = None,
         index_by: Literal["requirements", "tools"] = "requirements",
     ) -> list:
         """
diff --git a/bioblend/galaxy/tools/__init__.py b/bioblend/galaxy/tools/__init__.py
index 78f16c7a2..71935b411 100644
--- a/bioblend/galaxy/tools/__init__.py
+++ b/bioblend/galaxy/tools/__init__.py
@@ -6,9 +6,7 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
-    Union,
 )
 
 from bioblend.galaxy.client import Client
@@ -28,7 +26,7 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
         super().__init__(galaxy_instance)
 
     def get_tools(
-        self, tool_id: Optional[str] = None, name: Optional[str] = None, trackster: Optional[bool] = None
+        self, tool_id: str | None = None, name: str | None = None, trackster: bool | None = None
     ) -> list[dict[str, Any]]:
         """
         Get all tools, or select a subset by specifying optional arguments for
@@ -71,7 +69,7 @@ def get_tool_panel(self) -> list[dict[str, Any]]:
         """
         return self._raw_get_tool(in_panel=True)
 
-    def _raw_get_tool(self, in_panel: Optional[bool] = None, trackster: Optional[bool] = None) -> list[dict[str, Any]]:
+    def _raw_get_tool(self, in_panel: bool | None = None, trackster: bool | None = None) -> list[dict[str, Any]]:
         params = {
             "in_panel": in_panel,
             "trackster": trackster,
@@ -206,7 +204,7 @@ def show_tool(self, tool_id: str, io_details: bool = False, link_details: bool =
         }
         return self._get(id=tool_id, params=params)
 
-    def get_tool_tests(self, tool_id: str, tool_version: Optional[str] = None) -> list[dict[str, Any]]:
+    def get_tool_tests(self, tool_id: str, tool_version: str | None = None) -> list[dict[str, Any]]:
         """
         Fetch the test case definitions configured for a tool.
 
@@ -241,9 +239,9 @@ def get_tool_tests(self, tool_id: str, tool_version: Optional[str] = None) -> li
     def build(
         self,
         tool_id: str,
-        inputs: Optional[dict[str, Any]] = None,
-        tool_version: Optional[str] = None,
-        history_id: Optional[str] = None,
+        inputs: dict[str, Any] | None = None,
+        tool_version: str | None = None,
+        history_id: str | None = None,
     ) -> dict[str, Any]:
         """
         This method returns the tool model, which includes an updated input parameter array for the given tool,
@@ -342,7 +340,7 @@ def build(
             }
 
         """
-        params: dict[str, Union[str, dict]] = {}
+        params: dict[str, str | dict] = {}
 
         if inputs:
             params["inputs"] = inputs
@@ -361,9 +359,9 @@ def run_tool(
         self,
         history_id: str,
         tool_id: str,
-        tool_inputs: Union[InputsBuilder, dict],
+        tool_inputs: InputsBuilder | dict,
         input_format: Literal["21.01", "legacy"] = "legacy",
-        data_manager_mode: Optional[Literal["populate", "dry_run", "bundle"]] = None,
+        data_manager_mode: Literal["populate", "dry_run", "bundle"] | None = None,
     ) -> dict[str, Any]:
         """
         Runs tool specified by ``tool_id`` in history indicated
@@ -447,7 +445,7 @@ def run_tool(
         You can also check the examples in `Galaxy's API test suite
         <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy_test/api/test_tools.py>`_.
         """
-        payload: dict[str, Union[str, dict]] = {
+        payload: dict[str, str | dict] = {
             "history_id": history_id,
             "tool_id": tool_id,
             "input_format": input_format,
@@ -467,9 +465,9 @@ def upload_file(
         self,
         path: str,
         history_id: str,
-        storage: Optional[str] = None,
-        metadata: Optional[dict] = None,
-        chunk_size: Optional[int] = UPLOAD_CHUNK_SIZE,
+        storage: str | None = None,
+        metadata: dict | None = None,
+        chunk_size: int | None = UPLOAD_CHUNK_SIZE,
         **kwargs: Any,
     ) -> dict[str, Any]:
         """
diff --git a/bioblend/galaxy/tools/inputs.py b/bioblend/galaxy/tools/inputs.py
index bfab60992..c50573bd5 100644
--- a/bioblend/galaxy/tools/inputs.py
+++ b/bioblend/galaxy/tools/inputs.py
@@ -1,8 +1,6 @@
 from collections.abc import Iterator
 from typing import (
     Any,
-    Optional,
-    Union,
 )
 
 
@@ -30,7 +28,7 @@ def to_dict(self) -> dict[str, Any]:
             values[key] = value
         return values
 
-    def flat_iter(self, prefix: Optional[str] = None) -> Iterator[tuple[str, Any]]:
+    def flat_iter(self, prefix: str | None = None) -> Iterator[tuple[str, Any]]:
         for key, value in self._input_dict.items():
             effective_key = key if prefix is None else f"{prefix}|{key}"
             if hasattr(value, "flat_iter"):
@@ -59,7 +57,7 @@ def __init__(self, value: Any) -> None:
 
 
 class DatasetParam(Param):
-    def __init__(self, value: Union[dict[str, str], str], src: str = "hda") -> None:
+    def __init__(self, value: dict[str, str] | str, src: str = "hda") -> None:
         if not isinstance(value, dict):
             value = {"src": src, "id": value}
         super().__init__(value)
diff --git a/bioblend/galaxy/toolshed/__init__.py b/bioblend/galaxy/toolshed/__init__.py
index 38d807783..96fdf8477 100644
--- a/bioblend/galaxy/toolshed/__init__.py
+++ b/bioblend/galaxy/toolshed/__init__.py
@@ -4,9 +4,7 @@
 
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
-    Union,
 )
 
 from bioblend.galaxy.client import Client
@@ -79,9 +77,9 @@ def install_repository_revision(
         install_tool_dependencies: bool = False,
         install_repository_dependencies: bool = False,
         install_resolver_dependencies: bool = False,
-        tool_panel_section_id: Optional[str] = None,
-        new_tool_panel_section_label: Optional[str] = None,
-    ) -> Union[list[dict[str, Any]], dict[str, str]]:
+        tool_panel_section_id: str | None = None,
+        new_tool_panel_section_label: str | None = None,
+    ) -> list[dict[str, Any]] | dict[str, str]:
         """
         Install a specified repository revision from a specified Tool Shed into
         this Galaxy instance. This example demonstrates installation of a repository
diff --git a/bioblend/galaxy/users/__init__.py b/bioblend/galaxy/users/__init__.py
index 040f987af..0c6fe56fa 100644
--- a/bioblend/galaxy/users/__init__.py
+++ b/bioblend/galaxy/users/__init__.py
@@ -6,7 +6,6 @@
 
 from typing import (
     Any,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -26,9 +25,9 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
     def get_users(
         self,
         deleted: bool = False,
-        f_email: Optional[str] = None,
-        f_name: Optional[str] = None,
-        f_any: Optional[str] = None,
+        f_email: str | None = None,
+        f_name: str | None = None,
+        f_any: str | None = None,
     ) -> list[dict[str, Any]]:
         """
         Get a list of all registered users. If ``deleted`` is set to ``True``,
@@ -230,7 +229,7 @@ def get_or_create_user_apikey(self, user_id: str) -> str:
         url = self._make_url(user_id) + "/api_key"
         return self._get(url=url)
 
-    def update_user(self, user_id: str, user_data: Optional[dict] = None, **kwargs: Any) -> dict[str, Any]:
+    def update_user(self, user_id: str, user_data: dict | None = None, **kwargs: Any) -> dict[str, Any]:
         """
         Update user information. You can either pass the attributes you want to
         change in the user_data dictionary, or provide them separately as
diff --git a/bioblend/galaxy/workflows/__init__.py b/bioblend/galaxy/workflows/__init__.py
index 9daed5577..bcbf75631 100644
--- a/bioblend/galaxy/workflows/__init__.py
+++ b/bioblend/galaxy/workflows/__init__.py
@@ -7,7 +7,6 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
 )
 
@@ -29,7 +28,7 @@ def __init__(self, galaxy_instance: "GalaxyInstance") -> None:
 
     # the 'deleted' option is not available for workflows
     def get_workflows(
-        self, workflow_id: Optional[str] = None, name: Optional[str] = None, published: bool = False
+        self, workflow_id: str | None = None, name: str | None = None, published: bool = False
     ) -> list[dict[str, Any]]:
         """
         Get all workflows, or select a subset by specifying optional arguments
@@ -68,9 +67,9 @@ def get_workflows(
     def show_workflow(
         self,
         workflow_id: str,
-        version: Optional[int] = None,
-        instance: Optional[bool] = None,
-        legacy: Optional[bool] = None,
+        version: int | None = None,
+        instance: bool | None = None,
+        legacy: bool | None = None,
     ) -> dict[str, Any]:
         """
         Display information needed to run a workflow.
@@ -217,7 +216,7 @@ def import_shared_workflow(self, workflow_id: str) -> dict[str, Any]:
         return self._post(url=url, payload=payload)
 
     def export_workflow_dict(
-        self, workflow_id: str, version: Optional[int] = None, style: Optional[Literal["ga", "format2"]] = None
+        self, workflow_id: str, version: int | None = None, style: Literal["ga", "format2"] | None = None
     ) -> dict[str, Any]:
         """
         Exports a workflow.
@@ -311,24 +310,24 @@ def update_workflow(self, workflow_id: str, **kwargs: Any) -> dict[str, Any]:
     def invoke_workflow(
         self,
         workflow_id: str,
-        inputs: Optional[dict] = None,
-        params: Optional[dict] = None,
-        history_id: Optional[str] = None,
-        history_name: Optional[str] = None,
+        inputs: dict | None = None,
+        params: dict | None = None,
+        history_id: str | None = None,
+        history_name: str | None = None,
         import_inputs_to_history: bool = False,
-        replacement_params: Optional[dict] = None,
+        replacement_params: dict | None = None,
         allow_tool_state_corrections: bool = False,
-        inputs_by: Optional[InputsBy] = None,
+        inputs_by: InputsBy | None = None,
         parameters_normalized: bool = False,
         require_exact_tool_versions: bool = True,
-        version: Optional[int] = None,
+        version: int | None = None,
         use_cached_job: bool = False,
-        parameters: Optional[dict] = None,
+        parameters: dict | None = None,
         instance: bool = False,
-        resource_params: Optional[dict[str, Any]] = None,
-        preferred_object_store_id: Optional[str] = None,
-        preferred_intermediate_object_store_id: Optional[str] = None,
-        preferred_outputs_object_store_id: Optional[str] = None,
+        resource_params: dict[str, Any] | None = None,
+        preferred_object_store_id: str | None = None,
+        preferred_intermediate_object_store_id: str | None = None,
+        preferred_outputs_object_store_id: str | None = None,
     ) -> dict[str, Any]:
         """
         Invoke the workflow identified by ``workflow_id``. This will
@@ -804,9 +803,9 @@ def extract_workflow_from_history(
         self,
         history_id: str,
         workflow_name: str,
-        job_ids: Optional[list[str]] = None,
-        dataset_hids: Optional[list[str]] = None,
-        dataset_collection_hids: Optional[list[str]] = None,
+        job_ids: list[str] | None = None,
+        dataset_hids: list[str] | None = None,
+        dataset_collection_hids: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Extract a workflow from a history.
diff --git a/bioblend/galaxyclient.py b/bioblend/galaxyclient.py
index 049aff35f..13d3b806c 100644
--- a/bioblend/galaxyclient.py
+++ b/bioblend/galaxyclient.py
@@ -12,8 +12,6 @@
 import logging
 from typing import (
     Any,
-    Optional,
-    Union,
 )
 
 import requests
@@ -35,14 +33,14 @@ class 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,
-        timeout: Optional[float] = None,
-        user_agent: Optional[str] = None,
+        timeout: float | None = None,
+        user_agent: str | None = None,
     ) -> None:
         """
         :param verify: Whether to verify the server's TLS certificate
@@ -76,14 +74,14 @@ def __init__(
         # If key has been supplied, use it; otherwise just set email and
         # password and grab user's key before first request.
         if key:
-            self._key: Optional[str] = key
+            self._key: str | None = key
         elif token:
-            self.token: Optional[str] = token
+            self.token: str | None = token
         else:
             self._key = None
             self.email = email
             self.password = password
-        self.json_headers: dict[str, Union[str, bytes, None]] = {"Content-Type": "application/json"}
+        self.json_headers: dict[str, str | bytes | None] = {"Content-Type": "application/json"}
         if user_agent:
             self.json_headers["User-Agent"] = user_agent
         # json_headers needs to be set before key can be defined, otherwise authentication with email/password causes an error
@@ -149,7 +147,7 @@ def make_get_request(self, url: str, **kwargs: Any) -> requests.Response:
         return r
 
     def make_post_request(
-        self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None, files_attached: bool = False
+        self, url: str, payload: dict | None = None, params: dict | None = None, files_attached: bool = False
     ) -> Any:
         """
         Make a POST request using the provided ``url`` and ``payload``.
@@ -212,7 +210,7 @@ def my_dumps(d: dict) -> dict:
         )
 
     def make_delete_request(
-        self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None
+        self, url: str, payload: dict | None = None, params: dict | None = None
     ) -> requests.Response:
         """
         Make a DELETE request using the provided ``url`` and the optional
@@ -237,7 +235,7 @@ def make_delete_request(
         )
         return r
 
-    def make_put_request(self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None) -> Any:
+    def make_put_request(self, url: str, payload: dict | None = None, params: dict | None = None) -> Any:
         """
         Make a PUT request using the provided ``url`` with required payload.
 
@@ -273,7 +271,7 @@ def make_put_request(self, url: str, payload: Optional[dict] = None, params: Opt
             status_code=r.status_code,
         )
 
-    def make_patch_request(self, url: str, payload: Optional[dict] = None, params: Optional[dict] = None) -> Any:
+    def make_patch_request(self, url: str, payload: dict | None = None, params: dict | None = None) -> Any:
         """
         Make a PATCH request using the provided ``url`` with required payload.
 
@@ -313,9 +311,9 @@ def get_tus_uploader(
         self,
         path: str,
         url: str = "/upload/resumable_upload",
-        storage: Optional[str] = None,
-        metadata: Optional[dict] = None,
-        chunk_size: Optional[int] = UPLOAD_CHUNK_SIZE,
+        storage: str | None = None,
+        metadata: dict | None = None,
+        chunk_size: int | None = UPLOAD_CHUNK_SIZE,
     ) -> tusclient.uploader.Uploader:
         """
         Return the tus client uploader object for uploading to the Galaxy tus endpoint
@@ -357,7 +355,7 @@ def get_tus_uploader(
             )
 
     @property
-    def key(self) -> Optional[str]:
+    def key(self) -> str | None:
         if not self._key and self.email is not None and self.password is not None:
             unencoded_credentials = f"{self.email}:{self.password}"
             authorization = base64.b64encode(unencoded_credentials.encode())
diff --git a/bioblend/toolshed/__init__.py b/bioblend/toolshed/__init__.py
index 4644babde..05477f931 100644
--- a/bioblend/toolshed/__init__.py
+++ b/bioblend/toolshed/__init__.py
@@ -2,8 +2,6 @@
 A base representation of an instance of Tool Shed
 """
 
-from typing import Optional
-
 from bioblend.galaxyclient import GalaxyClient
 from bioblend.toolshed import (
     categories,
@@ -16,12 +14,12 @@ class ToolShedInstance(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,
         *,
         verify: bool = True,
-        user_agent: Optional[str] = None,
+        user_agent: str | None = None,
     ) -> None:
         """
         A base representation of a connection to a ToolShed instance, identified
diff --git a/bioblend/toolshed/repositories/__init__.py b/bioblend/toolshed/repositories/__init__.py
index 06ab081c7..9deefd76b 100644
--- a/bioblend/toolshed/repositories/__init__.py
+++ b/bioblend/toolshed/repositories/__init__.py
@@ -5,9 +5,7 @@
 from typing import (
     Any,
     Literal,
-    Optional,
     TYPE_CHECKING,
-    Union,
 )
 
 from bioblend.galaxy.client import Client
@@ -23,7 +21,7 @@ class ToolShedRepositoryClient(Client):
     def __init__(self, toolshed_instance: "ToolShedInstance") -> None:
         super().__init__(toolshed_instance)
 
-    def get_repositories(self, name: Optional[str] = None, owner: Optional[str] = None) -> list[dict[str, Any]]:
+    def get_repositories(self, name: str | None = None, owner: str | None = None) -> list[dict[str, Any]]:
         """
         Get all repositories in a Galaxy Tool Shed, or select a subset by
         specifying optional arguments for filtering (e.g. a repository name).
@@ -299,10 +297,10 @@ def get_repository_revision_install_info(
 
     def repository_revisions(
         self,
-        downloadable: Optional[bool] = None,
-        malicious: Optional[bool] = None,
-        missing_test_components: Optional[bool] = None,
-        includes_tools: Optional[bool] = None,
+        downloadable: bool | None = None,
+        malicious: bool | None = None,
+        missing_test_components: bool | None = None,
+        includes_tools: bool | None = None,
     ) -> list[dict[str, Any]]:
         """
         Returns a (possibly filtered) list of dictionaries that include
@@ -410,7 +408,7 @@ def show_repository_revision(
         url = "/".join((self.gi.url, "repository_revisions", metadata_id))
         return self._get(url=url)
 
-    def update_repository(self, id: str, tar_ball_path: str, commit_message: Optional[str] = None) -> dict[str, Any]:
+    def update_repository(self, id: str, tar_ball_path: str, commit_message: str | None = None) -> dict[str, Any]:
         """
         Update the contents of a Tool Shed repository with specified tar ball.
 
@@ -448,11 +446,11 @@ def create_repository(
         self,
         name: str,
         synopsis: str,
-        description: Optional[str] = None,
+        description: str | None = None,
         type: Literal["unrestricted", "repository_suite_definition", "tool_dependency_definition"] = "unrestricted",
-        remote_repository_url: Optional[str] = None,
-        homepage_url: Optional[str] = None,
-        category_ids: Optional[list[str]] = None,
+        remote_repository_url: str | None = None,
+        homepage_url: str | None = None,
+        category_ids: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Create a new repository in a Tool Shed.
@@ -499,7 +497,7 @@ def create_repository(
              "type": "unrestricted",
              "user_id": "adb5f5c93f827949"}
         """
-        payload: dict[str, Union[str, list[str]]] = {
+        payload: dict[str, str | list[str]] = {
             "name": name,
             "synopsis": synopsis,
         }
@@ -520,12 +518,12 @@ def create_repository(
     def update_repository_metadata(
         self,
         toolShed_id: str,
-        name: Optional[str] = None,
-        synopsis: Optional[str] = None,
-        description: Optional[str] = None,
-        remote_repository_url: Optional[str] = None,
-        homepage_url: Optional[str] = None,
-        category_ids: Optional[list[str]] = None,
+        name: str | None = None,
+        synopsis: str | None = None,
+        description: str | None = None,
+        remote_repository_url: str | None = None,
+        homepage_url: str | None = None,
+        category_ids: list[str] | None = None,
     ) -> dict[str, Any]:
         """
         Update metadata of a Tool Shed repository.
@@ -555,7 +553,7 @@ def update_repository_metadata(
         :rtype: dict
         :return: a dictionary containing information about the updated repository.
         """
-        payload: dict[str, Union[str, list[str]]] = {}
+        payload: dict[str, str | list[str]] = {}
         if name:
             payload["name"] = name
         if synopsis:
diff --git a/bioblend/util/__init__.py b/bioblend/util/__init__.py
index fd05b9299..fd3cd3c8f 100644
--- a/bioblend/util/__init__.py
+++ b/bioblend/util/__init__.py
@@ -3,7 +3,6 @@
     Any,
     IO,
     NamedTuple,
-    Optional,
     TypeVar,
 )
 
@@ -16,7 +15,7 @@ def close(self) -> None:
         self.fd.close()
 
 
-def attach_file(path: str, name: Optional[str] = None) -> FileStream:
+def attach_file(path: str, name: str | None = None) -> FileStream:
     """
     Attach a path to a request payload object.
 
diff --git a/pyproject.toml b/pyproject.toml
index 48583af37..15b492f5b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,6 @@ classifiers = [
     "Intended Audience :: Developers",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -31,7 +30,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Typing :: Typed",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "PyYAML",
     "requests>=2.20.0",
@@ -56,13 +55,13 @@ Documentation = "https://bioblend.readthedocs.io/"
 [tool.black]
 include = '\.pyi?$'
 line-length = 120
-target-version = ['py39']
+target-version = ['py310']
 
 [tool.darker]
 isort = true
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = ["E", "F", "B", "C4", "G", "ISC", "UP"]
diff --git a/run_bioblend_tests.sh b/run_bioblend_tests.sh
index d9e641cb6..050b4e896 100755
--- a/run_bioblend_tests.sh
+++ b/run_bioblend_tests.sh
@@ -14,7 +14,7 @@ Options:
   -p PORT
       Port to use for the Galaxy server. Defaults to 8080.
   -e TOX_ENV
-      Work against specified tox environments. Defaults to py39.
+      Work against specified tox environments. Defaults to py310.
   -t BIOBLEND_TESTS
       Subset of tests to run, e.g.
       'tests/TestGalaxyObjects.py::TestHistory::test_create_delete' . Defaults
@@ -33,7 +33,7 @@ get_abs_dirname () {
     cd "$1" && pwd
 }
 
-e_val=py39
+e_val=py310
 GALAXY_PORT=8080
 while getopts 'hcg:e:p:t:r:v:' option; do
     case $option in
diff --git a/tox.ini b/tox.ini
index f5a8f9b6b..fe50d188d 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = lint, py39
+envlist = lint, py310
 
 [testenv]
 commands =