Drop support for Python 3.8

which has reached end of life on 2024-10-07.

Author: nsoranzo

.github/workflows/lint.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.13']
+        python-version: ['3.9', '3.13']
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5

.github/workflows/test.yaml

@@ -31,78 +31,78 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            tox_env: py38
+            tox_env: py39
             galaxy_version: dev
             galaxy_python_version: '3.9'
           - os: ubuntu-latest
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_24.2
             galaxy_python_version: '3.8'
           - os: ubuntu-latest
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_24.1
             galaxy_python_version: '3.8'
           - os: ubuntu-latest
-            tox_env: py38
+            tox_env: py39
             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: py38
+            tox_env: py39
             galaxy_version: release_23.2
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_23.1
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_23.0
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_22.05
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             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: py38
+            tox_env: py39
             galaxy_version: release_21.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_21.05
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             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: py38
+            tox_env: py39
             galaxy_version: release_20.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             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: py38
+            tox_env: py39
             galaxy_version: release_20.01
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_19.09
             galaxy_python_version: '3.7'
           - os: ubuntu-22.04
-            tox_env: py38
+            tox_env: py39
             galaxy_version: release_19.05
             galaxy_python_version: '3.7'
           - os: ubuntu-latest
@@ -112,7 +112,7 @@ 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: py38
+          #   tox_env: py39
           #   galaxy_version: dev
           #   galaxy_python_version: '3.8'
     steps:

ABOUT.rst

@@ -3,7 +3,7 @@ interacting with the `Galaxy`_ API.
 
 BioBlend is supported and tested on:
 
-- Python 3.8 - 3.13
+- Python 3.9 - 3.13
 - Galaxy release 19.05 and later.
 
 BioBlend's goal is to make it easier to script and automate the running of

CHANGELOG.md

@@ -1,6 +1,6 @@
 ### BioBlend v
 
-* Added support for Galaxy release 24.2.
+* Dropped support for Python 3.8. Added support for Galaxy release 24.2.
 
 * Added ``offset`` parameter to ``InvocationClient.get_invocations()`` and
   BioBlend.objects ``ObjInvocationClient.list()`` methods.

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. `py38` for Python 3.8.
+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.
 
    You can also add `2>&1 | tee log.txt` to the command above to contemporarily view the test output and save it to the `log.txt` file.
 

README.rst

@@ -15,7 +15,7 @@ BioBlend is a Python library for interacting with the `Galaxy`_ API.
 
 BioBlend is supported and tested on:
 
-- Python 3.8 - 3.13
+- Python 3.9 - 3.13
 - Galaxy release 19.05 and later.
 
 Full docs are available at https://bioblend.readthedocs.io/ with a quick library

bioblend/_tests/GalaxyTestBase.py

@@ -2,7 +2,6 @@
 import unittest
 from typing import (
     Any,
-    Dict,
     Literal,
 )
 
@@ -37,7 +36,7 @@ def _wait_and_verify_dataset(
 
     def _run_random_lines1(
         self, history_id: str, dataset_id: str, input_format: Literal["21.01", "legacy"] = "legacy"
-    ) -> Dict[str, Any]:
+    ) -> dict[str, Any]:
         tool_inputs = {
             "num_lines": "1",
             "input": {"src": "hda", "id": dataset_id},

bioblend/_tests/TestGalaxyDatasetCollections.py

@@ -4,7 +4,6 @@
 from inspect import signature
 from typing import (
     Any,
-    Dict,
     Union,
 )
 from zipfile import ZipFile
@@ -186,7 +185,7 @@ def test_wait_for_dataset_collection(self):
         for element in dataset_collection["elements"]:
             assert element["object"]["state"] == "ok"
 
-    def _create_pair_in_history(self, history_id: str) -> Dict[str, Any]:
+    def _create_pair_in_history(self, history_id: str) -> dict[str, Any]:
         dataset1_id = self._test_dataset(history_id)
         dataset2_id = self._test_dataset(history_id)
         collection_response = self.gi.histories.create_dataset_collection(

bioblend/_tests/TestGalaxyFolders.py

@@ -1,8 +1,3 @@
-from typing import (
-    Dict,
-    List,
-)
-
 from . import (
     GalaxyTestBase,
     test_util,
@@ -112,7 +107,7 @@ def test_update_folder(self):
         assert self.folder["description"] == "new-description"
 
     def test_get_set_permissions(self):
-        empty_permission: Dict[str, List] = {
+        empty_permission: dict[str, list] = {
             "add_library_item_role_list": [],
             "modify_folder_role_list": [],
             "manage_folder_role_list": [],

bioblend/_tests/TestGalaxyInvocations.py

@@ -1,10 +1,7 @@
 import contextlib
 import os
 import time
-from typing import (
-    Any,
-    Dict,
-)
+from typing import Any
 
 from . import (
     GalaxyTestBase,
@@ -123,7 +120,7 @@ def test_workflow_scheduling(self):
         invocation = self._invoke_pause_workflow()
         invocation_id = invocation["id"]
 
-        def invocation_steps_by_order_index() -> Dict[int, Dict[str, Any]]:
+        def invocation_steps_by_order_index() -> dict[int, dict[str, Any]]:
             invocation = self.gi.invocations.show_invocation(invocation_id)
             return {s["order_index"]: s for s in invocation["steps"]}
 
@@ -147,7 +144,7 @@ def test_rerun_invocation(self):
         history = self.gi.histories.show_history(rerun_invocation["history_id"], contents=True)
         assert len(history) == 3
 
-    def _invoke_workflow(self) -> Dict[str, Any]:
+    def _invoke_workflow(self) -> dict[str, Any]:
         dataset = {"src": "hda", "id": self.dataset_id}
 
         return self.gi.workflows.invoke_workflow(
@@ -157,7 +154,7 @@ def _invoke_workflow(self) -> Dict[str, Any]:
             inputs_by="name",
         )
 
-    def _invoke_pause_workflow(self) -> Dict[str, Any]:
+    def _invoke_pause_workflow(self) -> dict[str, Any]:
         return self.gi.workflows.invoke_workflow(
             self.pause_workflow_id,
             inputs={"0": {"src": "hda", "id": self.dataset_id}},