Python 3.8 as new minimum version

Fixes: https://github.com/galaxyproject/galaxy/issues/16394 Also upgrade code to Python 3.8 syntax with: ``` ack --type=python -f | grep -v '^lib/galaxy/schema/bco/\|^lib/galaxy/schema/drs/\|lib/tool_shed_client/schema/trs.*.py\|^tools/\|^.venv/\|^.tox/' | grep -v '^lib/galaxy/files/sources/\|^lib/galaxy/job_metrics/\|^lib/galaxy/objectstore/\|^lib/galaxy/tool_util/\|^lib/galaxy/util/' | xargs pyupgrade --py38-plus ```
2026-09-01 15:37:32 +08:00 · 2023-10-31 18:51:06 +01:00
parent d31a812a43
commit c00967cca4
72 changed files with 101 additions and 143 deletions
@@ -15,7 +15,7 @@ variables:
 jobs:
  get_code:
    docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
    <<: *set_workdir
    steps:
      # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs:
            - ~/repo
  validate_test_tools:
    docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
    <<: *set_workdir
    steps:
      - *restore_repo_cache
@@ -28,7 +28,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
        chunk: [0, 1]
    services:
      postgres:
@@ -11,7 +11,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
@@ -22,7 +22,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - if: github.event_name == 'schedule'
        run: |
@@ -22,7 +22,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
        marker: ['green', 'red and required', 'red and not required']
        conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
    services:
@@ -24,11 +24,11 @@ jobs:
      matrix:
        db: ['postgresql', 'sqlite']
        postgresql-version: ['13']
-        python-version: ['3.7']
+        python-version: ['3.8']
        include:
          - db: postgresql
            postgresql-version: '9.6'
-            python-version: '3.7'
+            python-version: '3.8'
    services:
      postgres:
        image: postgres:${{ matrix.postgresql-version }}
@@ -9,17 +9,12 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
-          # poetry requires Python >=3.8, but lint requirements currently need
-          # to be generated with `pip freeze`` on the oldest Python version
-          # supported by Galaxy.
-          python-version: |
-            ${{ matrix.python-version }}
-            3.8
+          python-version: ${{ matrix.python-version }}
      - name: Update dependencies
        run: | 
          python -m venv .venv
@@ -33,7 +33,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - uses: actions/checkout@v3
        with:
@@ -16,7 +16,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - name: Get target branch name (push)
        if: github.event_name == 'push'
@@ -21,7 +21,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    defaults:
      run:
        shell: bash -l {0}
@@ -25,7 +25,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    services:
      postgres:
        image: postgres:13
@@ -29,7 +29,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
        chunk: ['0', '1', '2', '3']
    services:
      postgres:
@@ -29,7 +29,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    services:
      postgres:
        image: postgres:13
@@ -22,7 +22,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    env:
      LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
      TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
@@ -20,7 +20,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    steps:
      - uses: actions/checkout@v3
        with:
@@ -20,7 +20,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    steps:
      - uses: actions/checkout@v3
        with:
@@ -18,7 +18,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    defaults:
      run:
        shell: bash -l {0}
@@ -24,7 +24,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    services:
      postgres:
        image: postgres:13
@@ -9,7 +9,7 @@ jobs:
    runs-on: ubuntu-latest
    strategy:
        matrix:
-            python-version: ['3.7']
+            python-version: ['3.8']
    steps:
      - uses: actions/setup-python@v4
        with:
@@ -18,7 +18,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    defaults:
      run:
        shell: bash -l {0}
@@ -30,7 +30,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
        chunk: [0, 1, 2]
    services:
      postgres:
@@ -18,7 +18,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    steps:
      - uses: actions/checkout@v3
        with:
@@ -20,7 +20,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.7']  # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
    steps:
      - uses: actions/checkout@v3
        with:
@@ -21,7 +21,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
        shed-api: ['v1', 'v2']
        test-install-client: ['galaxy_api', 'standalone']
    services:
@@ -22,7 +22,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
    services:
      postgres:
        image: postgres:13
@@ -20,7 +20,7 @@ jobs:
    strategy:
      fail-fast: false
      matrix:
-        python-version: ['3.7', '3.11']
+        python-version: ['3.8', '3.11']
    steps:
      - uses: actions/checkout@v3
        with:
@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================

-Galaxy requires Python 3.7 . To check your Python version, run:
+Galaxy requires Python 3.8 . To check your Python version, run:

 .. code:: console

    $ python -V
-    Python 3.7.6
+    Python 3.8.18

 Start Galaxy:

@@ -1,6 +1,6 @@
 # Supported Python versions

-Galaxy's core functionality is currently supported on Python **>=3.7** .
+Galaxy's core functionality is currently supported on Python **>=3.8** .

 If Galaxy complains about the version of Python you are using:

@@ -52,7 +52,7 @@ index 6647588dfb..c8d82957a1 100644
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
-         python-version: ['3.7']
+         python-version: ['3.8']
 -        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
 +        subset: ['not (upload_datatype or extended_metadata or kubernetes)']
     services:
@@ -123,7 +123,7 @@ class MockContext:
    def __init__(self, model_objects=None):
        self.expunged_all = False
        self.flushed = False
-        self.model_objects = model_objects or defaultdict(lambda: {})
+        self.model_objects = model_objects or defaultdict(dict)
        self.created_objects = []
        self.current = self

@@ -68,12 +68,12 @@ from galaxy.web.short_term_storage import ShortTermStorageMonitor
 log = get_logger(__name__)


-@lru_cache()
+@lru_cache
 def setup_data_table_manager(app):
    app._configure_tool_data_tables(from_shed_config=False)


-@lru_cache()
+@lru_cache
 def cached_create_tool_from_representation(app, raw_tool_source):
    return create_tool_from_representation(
        app=app, raw_tool_source=raw_tool_source, tool_dir="", tool_source_class="XmlToolSource"
@@ -6,6 +6,7 @@ import json
 import logging
 import os
 import re
+import shlex
 import subprocess
 import tempfile
 from typing import (
@@ -38,7 +39,6 @@ from galaxy.datatypes.sniff import (
 )
 from galaxy.util import (
    nice_size,
-    shlex_join,
    string_as_bool,
    unicodify,
 )
@@ -242,7 +242,7 @@ class Ipynb(Json):
                ofilename = dataset.get_file_name()
                log.exception(
                    'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.',
-                    shlex_join(cmd),
+                    shlex.join(cmd),
                )
            return open(ofilename, mode="rb"), headers

@@ -658,9 +658,6 @@ def get_starts_ends_fields_from_gene_bed(line):
    if len(fields) < 12:
        raise Exception(f"Not a proper 12 column BED line ({line}).")
    tx_start = int(fields[1])
-    strand = fields[5]
-    if strand != "-":
-        strand = "+"  # Default strand is +
    cds_start = int(fields[6])
    cds_end = int(fields[7])

@@ -6,7 +6,7 @@

 set -e

-SUPPORTED_PYTHON_VERSIONS="3.7 3.8 3.9 3.10 3.11"
+SUPPORTED_PYTHON_VERSIONS="3.8 3.9 3.10 3.11"
 NOT_SUPPORTED_NEXT_PYTHON_VERSION="3.12"

 this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
@@ -11,7 +11,7 @@ THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"

 update_pinned_reqs() {
    VENV=$(mktemp -d "${TMPDIR:-/tmp}/$1_venv.XXXXXXXXXX")
-    python3.7 -m venv "${VENV}"
+    python3.8 -m venv "${VENV}"
    . "${VENV}/bin/activate"
    pip install --upgrade pip setuptools
    pip install -r "${THIS_DIRECTORY}/$1-requirements.txt"
@@ -409,7 +409,7 @@ class DefaultStrategy(NotificationRecipientResolverStrategy):
        user_ids_from_roles_stmt = self._get_all_user_ids_from_roles_query(all_role_ids)

        union_stmt = union(user_ids_from_groups_stmt, user_ids_from_roles_stmt)
-        user_ids_from_groups_and_roles = set([id for id, in self.sa_session.execute(union_stmt)])
+        user_ids_from_groups_and_roles = {id for id, in self.sa_session.execute(union_stmt)}
        unique_user_ids.update(user_ids_from_groups_and_roles)

        stmt = select(User).where(User.id.in_(unique_user_ids))
@@ -448,7 +448,7 @@ class DefaultStrategy(NotificationRecipientResolverStrategy):
                .where(GroupRoleAssociation.role_id.in_(role_ids))
                .distinct()
            )
-            group_ids_from_roles = set([id for id, in self.sa_session.execute(stmt) if id is not None])
+            group_ids_from_roles = {id for id, in self.sa_session.execute(stmt) if id is not None}
            new_group_ids = group_ids_from_roles - processed_group_ids

            # Get role IDs associated with any of the given group IDs
@@ -458,7 +458,7 @@ class DefaultStrategy(NotificationRecipientResolverStrategy):
                .where(GroupRoleAssociation.group_id.in_(group_ids))
                .distinct()
            )
-            role_ids_from_groups = set([id for id, in self.sa_session.execute(stmt) if id is not None])
+            role_ids_from_groups = {id for id, in self.sa_session.execute(stmt) if id is not None}
            new_role_ids = role_ids_from_groups - processed_role_ids

            # Stop if there are no new group or role IDs to process
@@ -5,6 +5,7 @@ import logging
 import os
 import platform
 import re
+import shlex
 import shutil
 import sys
 import tempfile
@@ -28,7 +29,6 @@ from galaxy.util import (
    commands,
    download_to_file,
    listify,
-    shlex_join,
    smart_str,
    which,
 )
@@ -253,7 +253,7 @@ class CondaContext(installable.InstallableContext):
        env = {}
        if self.condarc_override:
            env["CONDARC"] = self.condarc_override
-        cmd_string = shlex_join(cmd)
+        cmd_string = shlex.join(cmd)
        kwds = dict()
        try:
            if stdout_path:
@@ -12,6 +12,7 @@ Build a mulled image with:
 import json
 import logging
 import os
+import shlex
 import shutil
 import stat
 import string
@@ -38,7 +39,6 @@ from galaxy.util import (
    commands,
    download_to_file,
    safe_makedirs,
-    shlex_join,
    unicodify,
 )
 from ._cli import arg_parser
@@ -335,7 +335,7 @@ def mull_targets(
            involucro_args.insert(6, "-set")
            involucro_args.insert(7, f"TEST_BINDS={','.join(test_bind)}")
    cmd = involucro_context.build_command(involucro_args)
-    print(f"Executing: {shlex_join(cmd)}")
+    print(f"Executing: {shlex.join(cmd)}")
    if dry_run:
        return 0
    ensure_installed(involucro_context, True)
@@ -40,9 +40,6 @@ def main(argv=None):
    )
    parser.add_option("--file-sources", type=str, help="file sources json")
    (options, args) = parser.parse_args(argv)
-    galaxy_version = options.galaxy_version
-    if galaxy_version is None:
-        galaxy_version = "19.05"

    gzip = bool(options.gzip)
    assert len(args) >= 2
@@ -13,7 +13,6 @@ import json
 import os
 import random
 import re
-import shlex
 import shutil
 import smtplib
 import stat
@@ -96,14 +95,6 @@ from .path import (  # noqa: F401
 )
 from .rst_to_html import rst_to_html  # noqa: F401

-try:
-    shlex_join = shlex.join  # type: ignore[attr-defined]
-except AttributeError:
-    # Python < 3.8
-    def shlex_join(split_command):
-        return " ".join(map(shlex.quote, split_command))
-
-
 inflector = Inflector()

 log = get_logger(__name__)
@@ -388,7 +388,7 @@ def external_chown(path, pwent, external_chown_script, description="file"):

        cmd = shlex.split(external_chown_script)
        cmd.extend([path, pwent[0], str(pwent[3])])
-        log.debug(f"Changing ownership of {path} with: '{galaxy.util.shlex_join(cmd)}'")
+        log.debug(f"Changing ownership of {path} with: '{shlex.join(cmd)}'")
        galaxy.util.commands.execute(cmd)
        return True
    except galaxy.util.commands.CommandLineException as e:
@@ -134,7 +134,7 @@ class NotificationService(ServiceBase):
    ):
        """Updates a single notification received by the user with the requested values."""
        self.notification_manager.ensure_notifications_enabled()
-        updated_response = self.update_user_notifications(user_context, set([notification_id]), request)
+        updated_response = self.update_user_notifications(user_context, {notification_id}, request)
        if not updated_response.updated_count:
            self._raise_notification_not_found(notification_id)

@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -77,7 +76,7 @@ install_requires =
    WebOb
    Whoosh
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -35,8 +34,8 @@ install_requires =
    galaxy-data
    galaxy-util
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -38,7 +37,7 @@ install_requires =
    pykwalify
    PyYAML
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -46,4 +45,4 @@ console_scripts =

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -61,7 +60,7 @@ install_requires =
    typing-extensions
    WebOb
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -36,7 +35,7 @@ install_requires =
    fs
    typing-extensions
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -40,7 +39,7 @@ install_requires =
    MarkupSafe
    SQLAlchemy>=1.4.25,<2
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -49,4 +48,4 @@ console_scripts =

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -34,8 +33,8 @@ include_package_data = True
 install_requires =
    galaxy-util
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -10,7 +10,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -34,7 +33,7 @@ version = 22.5.0.dev0
 [options]
 include_package_data = True
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.extras_require]
 postgresql =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -35,8 +34,8 @@ install_requires =
    galaxy-util
    PyYAML
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -36,8 +35,8 @@ install_requires =
    pydantic<2
    PyYAML
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -34,7 +33,7 @@ install_requires =
    galaxy-util
    pydantic[email]
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -39,7 +38,7 @@ install_requires =
    requests
    selenium!=4.11.0,!=4.11.1,!=4.11.2
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -47,4 +46,4 @@ console_scripts =

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -38,7 +37,7 @@ install_requires =
    requests
    tuspy
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.extras_require]
 driver =
@@ -46,4 +45,4 @@ driver =

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -41,8 +40,8 @@ install_requires =
    PyYAML
    requests
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -43,8 +42,8 @@ install_requires =
    graphene-sqlalchemy==3.0.0b3  # these are only needed by tool shed - which we've split out but the test driver loads
    starlette-graphene3
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -43,7 +42,7 @@ install_requires =
    requests
    selenium!=4.11.0,!=4.11.1,!=4.11.2
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.extras_require]
 driver =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -34,7 +33,7 @@ install_requires =
    galaxy-web-stack
    galaxy-web-apps
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -43,7 +42,7 @@ install_requires =
    sortedcontainers
    typing-extensions
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -36,7 +35,7 @@ install_requires =
    pydantic<2
    PyYAML
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.entry_points]
 console_scripts =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -44,7 +43,7 @@ install_requires =
    typing-extensions
    zipstream-new
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.extras_require]
 jstree =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -70,7 +69,7 @@ install_requires =
    WebOb
    Whoosh
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -44,7 +43,7 @@ install_requires =
    WebOb

 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
@@ -9,7 +9,6 @@ classifiers =
    Natural Language :: English
    Operating System :: POSIX
    Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
@@ -36,8 +35,8 @@ install_requires =
    galaxy-util
    SQLAlchemy>=1.4.25,<2
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8

 [options.packages.find]
 exclude =
-    tests*
+    tests*
@@ -1,6 +1,6 @@
 [tool.black]
 line-length = 120
-target-version = ['py37']
+target-version = ['py38']
 include = '\.pyi?$'
 extend-exclude = '''
 ^/(
@@ -50,7 +50,7 @@ Cheetah3 = "!=3.2.6.post2"  # yanked release, https://github.com/python-poetry/p
 cloudauthz = "==0.6.0"
 cloudbridge = "*"
 circus = "*"
-cwltool = "==3.1.20221109155812"
+cwltool = ">=3.1.20221109155812"  # TODO: pin to a newer working version
 conda-package-streaming = "*"
 dictobj = "*"
 dnspython = "*"
@@ -93,9 +93,9 @@ pydantic = {version = "<2", extras = ["email"]}
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"
-pyparsing = "<3.1"  # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152
+pyparsing = "*"
 pysam = ">=0.21"  # for Python 3.11 support on macOS
-python = ">=3.7,<3.12"  # Keep maximum version strict to appease numpy and scipy
+python = ">=3.8,<3.12"  # Keep maximum version strict to appease numpy and scipy
 python-dateutil = "*"
 python-magic = "*"
 python-multipart = "*"  # required to support form parsing in FastAPI/Starlette
@@ -155,6 +155,7 @@ pytest-postgresql = "!=3.0.0"  # https://github.com/ClearcodeHQ/pytest-postgresq
 pytest-shard = "*"
 responses = "*"
 selenium = "*"
+urllib3 = "<2"  # Necessary for poetry for resolve deps for Python 3.8+
 seletools = "*"
 Sphinx = ">=4.0"  # support docutils 0.17
 sphinx-rtd-theme = ">=1.0.0,<2"  # https://github.com/python-poetry/poetry/issues/8194
@@ -184,7 +185,7 @@ types-six = "*"
 # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
 # flake8-logging-format (G) and pyupgrade (UP)
 select = ["E", "F", "B", "G", "UP"]
-target-version = "py37"
+target-version = "py38"
 # Exceptions:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # B9 flake8-bugbear opinionated warnings
@@ -7,7 +7,7 @@ import sys


 def check_python():
-    if sys.version_info[:2] >= (3, 7):  # noqa: UP036
+    if sys.version_info[:2] >= (3, 8):  # noqa: UP036
        # supported
        return
    else:
@@ -15,7 +15,7 @@ def check_python():
        msg = (
            """\
 ERROR: Your Python version is: %s
-Galaxy is currently supported on Python >=3.7 .
+Galaxy is currently supported on Python >=3.8 .
 To run Galaxy, please install a supported Python version.
 If a supported version is already installed but is not your default,
 https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
@@ -14,7 +14,7 @@ SKIP_NODE=${GALAXY_SKIP_NODE:-0}
 INSTALL_PREBUILT_CLIENT=${GALAXY_INSTALL_PREBUILT_CLIENT:-0}
 NODE_VERSION=${GALAXY_NODE_VERSION:-"$(cat client/.node_version)"}
 : "${YARN_INSTALL_OPTS:=--network-timeout 300000 --check-files}"
-: "${GALAXY_CONDA_PYTHON_VERSION:=3.7}"
+: "${GALAXY_CONDA_PYTHON_VERSION:=3.8}"

 for arg in "$@"; do
    if [ "$arg" = "--skip-venv" ]; then
@@ -41,7 +41,7 @@ RMFILES="
    lib/pkg_resources.pyc
 "

-MIN_PYTHON_VERSION=3.7
+MIN_PYTHON_VERSION=3.8
 MIN_PIP_VERSION=20.3

 # return true if $1 is in $2 else false
@@ -24,7 +24,7 @@ def mock_user_id_task(task_user_id: int):
    return task_user_id


-@lru_cache()
+@lru_cache
 def sqlite_url():
    path = tempfile.NamedTemporaryFile().name
    dburl = f"sqlite:///{path}"
@@ -32,7 +32,7 @@ def sqlite_url():
    return dburl


-@lru_cache()
+@lru_cache
 def setup_users(dburl: str, num_users: int = 2):
    """
    Setup test users in galaxy_user table with user id's starting from 2.
@@ -4,6 +4,7 @@
 import collections
 import json
 import os
+import shlex
 import string
 import subprocess
 import tempfile
@@ -18,10 +19,7 @@ import pytest
 from typing_extensions import Literal

 from galaxy.tool_util.verify.wait import timeout_type
-from galaxy.util import (
-    shlex_join,
-    unicodify,
-)
+from galaxy.util import unicodify
 from galaxy_test.base.populators import (
    DatasetPopulator,
    DEFAULT_TIMEOUT,
@@ -361,7 +359,7 @@ class TestKubernetesIntegration(BaseJobEnvironmentIntegrationTestCase, MulledJob
                if allow_wait and "is waiting to start" in p.stderr:
                    return None
                raise Exception(
-                    f"Command '{shlex_join(log_cmd)}' failed with exit code: {p.returncode}.\nstdout: {p.stdout}\nstderr: {p.stderr}"
+                    f"Command '{shlex.join(log_cmd)}' failed with exit code: {p.returncode}.\nstdout: {p.stdout}\nstderr: {p.stderr}"
                )
            return p.stdout

@@ -276,7 +276,7 @@ class TestUserNotifications(NotificationManagerBaseTestCase):
        assert user_notification.seen_time is None
        assert user_notification.deleted is False
        request = UserNotificationUpdateRequest(seen=True)
-        self.notification_manager.update_user_notifications(user, set([notification.id]), request)
+        self.notification_manager.update_user_notifications(user, {notification.id}, request)
        user_notification = self.notification_manager.get_user_notification(user, notification.id)
        assert user_notification.seen_time is not None
        assert user_notification.deleted is False
@@ -39,6 +39,8 @@ passenv =
    GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
    APP_WEBSERVER
    TERM
+    TEST_PYTHON
+    TZ
 setenv =
    coverage: GALAXY_TEST_COVERAGE=1
    first_startup: GALAXY_CONFIG_DATABASE_AUTO_MIGRATE=true