Merge pull request #477 from nsoranzo/drop_py37

Drop support for Python 3.7

.github/workflows/lint.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4

.github/workflows/test.yaml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        tox_env: [py37]
+        tox_env: [py38]
         galaxy_version:
           - dev
           - release_23.1
@@ -52,7 +52,7 @@ 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: py37
+          #   tox_env: py38
           #   galaxy_version: dev
     steps:
       - uses: actions/checkout@v3

ABOUT.rst

@@ -3,7 +3,7 @@ interacting with the `Galaxy`_ API.
 
 BioBlend is supported and tested on:
 
-- Python 3.7 - 3.11
+- Python 3.8 - 3.11
 - Galaxy release 19.05 and later.
 
 BioBlend's goal is to make it easier to script and automate the running of

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. `py37` for Python 3.7.
+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.
 
    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 3.7 - 3.11
+- Python 3.8 - 3.11
 - Galaxy release 19.05 and later.
 
 Full docs are available at https://bioblend.readthedocs.io/ with a quick library

bioblend/_tests/GalaxyTestBase.py

@@ -3,10 +3,9 @@
 from typing import (
     Any,
     Dict,
+    Literal,
 )
 
-from typing_extensions import Literal
-
 import bioblend
 from bioblend.galaxy import GalaxyInstance
 from . import test_util

bioblend/_tests/TestGalaxyJobs.py

@@ -4,8 +4,7 @@
     timedelta,
 )
 from operator import itemgetter
-
-from typing_extensions import Literal
+from typing import Literal
 
 from bioblend.galaxy.tools.inputs import (
     dataset,

bioblend/_tests/TestGalaxyObjects.py

@@ -16,6 +16,7 @@
     Dict,
     Iterable,
     List,
+    Literal,
     Set,
     Tuple,
     Union,
@@ -24,7 +25,6 @@
 from urllib.request import urlopen
 
 import pytest
-from typing_extensions import Literal
 
 import bioblend
 from bioblend.galaxy import dataset_collections

bioblend/galaxy/datasets/__init__.py

@@ -10,6 +10,7 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     overload,
     Tuple,
@@ -18,7 +19,6 @@
 )
 
 from requests import Response
-from typing_extensions import Literal
 
 import bioblend
 from bioblend import TimeoutException

bioblend/galaxy/folders/__init__.py

@@ -5,13 +5,12 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
     Union,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/galaxy/genomes/__init__.py

@@ -4,12 +4,11 @@
 from typing import (
     Any,
     Dict,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/galaxy/histories/__init__.py

@@ -12,14 +12,13 @@
     Dict,
     IO,
     List,
+    Literal,
     Optional,
     overload,
     Pattern,
     Union,
 )
 
-from typing_extensions import Literal
-
 import bioblend
 from bioblend import ConnectionError
 from bioblend.galaxy.client import Client

bioblend/galaxy/jobs/__init__.py

@@ -7,12 +7,11 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend import TimeoutException
 from bioblend.galaxy.client import Client
 

bioblend/galaxy/libraries/__init__.py

@@ -7,12 +7,11 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 from bioblend.galaxy.datasets import (
     DatasetTimeoutException,

bioblend/galaxy/objects/client.py

@@ -13,15 +13,14 @@
     Dict,
     Generic,
     List,
+    Literal,
     Optional,
     overload,
     Type,
     TYPE_CHECKING,
     Union,
 )
 
-from typing_extensions import Literal
-
 import bioblend
 from bioblend.galaxy.datasets import HdaLdda
 from . import wrappers

bioblend/galaxy/objects/wrappers.py

@@ -21,6 +21,7 @@
     Iterable,
     Iterator,
     List,
+    Literal,
     Optional,
     Set,
     Tuple,
@@ -30,8 +31,6 @@
     Union,
 )
 
-from typing_extensions import Literal
-
 import bioblend
 from bioblend.galaxy.workflows import InputsBy
 from bioblend.util import abstractclass

bioblend/galaxy/quotas/__init__.py

@@ -6,12 +6,11 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/galaxy/tool_dependencies/__init__.py

@@ -5,12 +5,11 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/galaxy/tools/__init__.py

@@ -6,13 +6,12 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
     Union,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 from bioblend.galaxyclient import UPLOAD_CHUNK_SIZE
 from bioblend.util import attach_file

bioblend/galaxy/workflows/__init__.py

@@ -7,12 +7,11 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/toolshed/categories/__init__.py

@@ -5,11 +5,10 @@
     Any,
     Dict,
     List,
+    Literal,
     TYPE_CHECKING,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 
 if TYPE_CHECKING:

bioblend/toolshed/repositories/__init__.py

@@ -5,13 +5,12 @@
     Any,
     Dict,
     List,
+    Literal,
     Optional,
     TYPE_CHECKING,
     Union,
 )
 
-from typing_extensions import Literal
-
 from bioblend.galaxy.client import Client
 from bioblend.util import attach_file
 

pyproject.toml

@@ -5,14 +5,14 @@ build-backend = "setuptools.build_meta"
 [tool.black]
 include = '\.pyi?$'
 line-length = 120
-target-version = ['py37']
+target-version = ['py38']
 
 [tool.darker]
 isort = true
 
 [tool.ruff]
 select = ["E", "F", "B", "UP"]
-target-version = "py37"
+target-version = "py38"
 # Exceptions:
 # B9 flake8-bugbear opinionated warnings
 # E501 is line length (delegated to black)

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 py37.
+      Work against specified tox environments. Defaults to py38.
   -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=py37
+e_val=py38
 GALAXY_PORT=8080
 while getopts 'hcg:e:p:t:r:v:' option; do
     case $option in

setup.cfg

@@ -22,7 +22,6 @@ classifiers =
         License :: OSI Approved :: MIT License
         Operating System :: OS Independent
         Programming Language :: Python :: 3
-        Programming Language :: Python :: 3.7
         Programming Language :: Python :: 3.8
         Programming Language :: Python :: 3.9
         Programming Language :: Python :: 3.10
@@ -71,9 +70,8 @@ install_requires =
     requests>=2.20.0
     requests-toolbelt>=0.5.1,!=0.9.0
     tuspy
-    typing-extensions
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 
 [options.entry_points]
 console_scripts =

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = lint, py37
+envlist = lint, py38
 
 [testenv]
 commands =