diff --git a/.circleci/config.yml b/.circleci/config.yml index 9c27be38c17..02cead37092 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -15,7 +15,7 @@ variables: jobs: get_code: docker: - - image: cimg/python:3.9 + - image: cimg/python:3.10 <<: *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:3.9 + - image: cimg/python:3.10 <<: *set_workdir steps: - *restore_repo_cache diff --git a/.github/workflows/api.yaml b/.github/workflows/api.yaml index 30b926eb4bc..a8085d198de 100644 --- a/.github/workflows/api.yaml +++ b/.github/workflows/api.yaml @@ -31,7 +31,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] chunk: [0, 1] services: postgres: diff --git a/.github/workflows/bioblend.yaml b/.github/workflows/bioblend.yaml index 4e23a6d0e6c..ea88b832ade 100644 --- a/.github/workflows/bioblend.yaml +++ b/.github/workflows/bioblend.yaml @@ -32,7 +32,7 @@ jobs: fail-fast: false matrix: tox_env: [py314] - galaxy_python_version: ['3.9'] + galaxy_python_version: ['3.10'] steps: - name: Checkout Galaxy uses: actions/checkout@v6 diff --git a/.github/workflows/check_test_class_names.yaml b/.github/workflows/check_test_class_names.yaml index 5c1e61ad01d..5f966e10930 100644 --- a/.github/workflows/check_test_class_names.yaml +++ b/.github/workflows/check_test_class_names.yaml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/converter_tests.yaml b/.github/workflows/converter_tests.yaml index 73eddcea628..f157ae93d9f 100644 --- a/.github/workflows/converter_tests.yaml +++ b/.github/workflows/converter_tests.yaml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - if: github.event_name == 'schedule' run: | diff --git a/.github/workflows/cwl_conformance.yaml b/.github/workflows/cwl_conformance.yaml index 48565879cea..21bdd3d4d8f 100644 --- a/.github/workflows/cwl_conformance.yaml +++ b/.github/workflows/cwl_conformance.yaml @@ -26,7 +26,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] marker: ['green', 'red and required', 'red and not required'] conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2'] services: diff --git a/.github/workflows/db_indexes.yaml b/.github/workflows/db_indexes.yaml index 1fe2c705b38..a2b1788e495 100644 --- a/.github/workflows/db_indexes.yaml +++ b/.github/workflows/db_indexes.yaml @@ -26,11 +26,11 @@ jobs: matrix: db: ['postgresql', 'sqlite'] postgresql-version: ['17'] - python-version: ['3.9'] + python-version: ['3.10'] include: - db: postgresql postgresql-version: '9.6' - python-version: '3.9' + python-version: '3.10' services: postgres: image: postgres:${{ matrix.postgresql-version }} diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml index e3fc0126417..1a8fe78dba5 100644 --- a/.github/workflows/dependencies.yaml +++ b/.github/workflows/dependencies.yaml @@ -14,7 +14,7 @@ jobs: persist-credentials: false - uses: actions/setup-python@v6 with: - python-version: '3.9' + python-version: '3.10' - name: Install uv uses: astral-sh/setup-uv@v7 - name: Update dependencies diff --git a/.github/workflows/deployment.yaml b/.github/workflows/deployment.yaml index f1b1287e6a9..28fa966e8b0 100644 --- a/.github/workflows/deployment.yaml +++ b/.github/workflows/deployment.yaml @@ -29,7 +29,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 018f6e9082b..af666fc3163 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -18,7 +18,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - name: Get target branch name (push) if: github.event_name == 'push' diff --git a/.github/workflows/first_startup.yaml b/.github/workflows/first_startup.yaml index 2fb478fa8bb..0f66fe2ae1f 100644 --- a/.github/workflows/first_startup.yaml +++ b/.github/workflows/first_startup.yaml @@ -25,7 +25,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] defaults: run: shell: bash -l {0} @@ -47,6 +47,7 @@ jobs: - name: Restore client cache uses: actions/cache@v5 with: + fail-on-cache-miss: true key: galaxy-static-${{ needs.build-client.outputs.commit-id }} path: 'galaxy root/static' - name: Install tox diff --git a/.github/workflows/framework_tools.yaml b/.github/workflows/framework_tools.yaml index afc2d4e7b13..1b921215d34 100644 --- a/.github/workflows/framework_tools.yaml +++ b/.github/workflows/framework_tools.yaml @@ -27,7 +27,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] use-legacy-api: ['if_needed', 'always'] services: postgres: diff --git a/.github/workflows/framework_workflows.yaml b/.github/workflows/framework_workflows.yaml index f89793c2ed5..b8a733bd961 100644 --- a/.github/workflows/framework_workflows.yaml +++ b/.github/workflows/framework_workflows.yaml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] services: postgres: image: postgres:17 diff --git a/.github/workflows/integration.yaml b/.github/workflows/integration.yaml index a80fc12f16c..776fe4bdce9 100644 --- a/.github/workflows/integration.yaml +++ b/.github/workflows/integration.yaml @@ -29,7 +29,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] chunk: ['0', '1', '2', '3'] steps: - if: github.event_name == 'schedule' diff --git a/.github/workflows/integration_selenium.yaml b/.github/workflows/integration_selenium.yaml index 468a1792ae5..17159e91ec3 100644 --- a/.github/workflows/integration_selenium.yaml +++ b/.github/workflows/integration_selenium.yaml @@ -33,7 +33,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] services: postgres: image: postgres:17 @@ -71,6 +71,7 @@ jobs: - name: Restore client cache uses: actions/cache@v5 with: + fail-on-cache-miss: true key: galaxy-static-${{ needs.build-client.outputs.commit-id }} path: 'galaxy root/static' - name: Run tests diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index e0b32647bed..9d13c3a3016 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -22,7 +22,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] env: LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt' TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt' diff --git a/.github/workflows/lint_openapi_schema.yml b/.github/workflows/lint_openapi_schema.yml index 34db45a6424..d211bc42a24 100644 --- a/.github/workflows/lint_openapi_schema.yml +++ b/.github/workflows/lint_openapi_schema.yml @@ -22,7 +22,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/main_tools.yaml b/.github/workflows/main_tools.yaml index ce04df8e37a..dd0973843bf 100644 --- a/.github/workflows/main_tools.yaml +++ b/.github/workflows/main_tools.yaml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] services: postgres: image: postgres:17 diff --git a/.github/workflows/mulled.yaml b/.github/workflows/mulled.yaml index 0f89d157780..625c23fb519 100644 --- a/.github/workflows/mulled.yaml +++ b/.github/workflows/mulled.yaml @@ -22,7 +22,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/osx_startup.yaml b/.github/workflows/osx_startup.yaml index 259f91e972d..2e94dfbb65f 100644 --- a/.github/workflows/osx_startup.yaml +++ b/.github/workflows/osx_startup.yaml @@ -23,7 +23,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] defaults: run: shell: bash -l {0} @@ -40,6 +40,7 @@ jobs: - name: Restore client cache uses: actions/cache@v5 with: + fail-on-cache-miss: true key: galaxy-static-${{ needs.build-client.outputs.commit-id }} path: 'galaxy root/static' - name: Install uv diff --git a/.github/workflows/performance.yaml b/.github/workflows/performance.yaml index f025b4d8e19..d97f6399053 100644 --- a/.github/workflows/performance.yaml +++ b/.github/workflows/performance.yaml @@ -26,7 +26,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] services: postgres: image: postgres:17 diff --git a/.github/workflows/playwright.yaml b/.github/workflows/playwright.yaml index 2d1f246b131..b4f0405d871 100644 --- a/.github/workflows/playwright.yaml +++ b/.github/workflows/playwright.yaml @@ -33,7 +33,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] chunk: [0, 1, 2] services: postgres: @@ -78,6 +78,7 @@ jobs: - name: Restore client cache uses: actions/cache@v5 with: + fail-on-cache-miss: true key: galaxy-static-${{ needs.build-client.outputs.commit-id }} path: 'galaxy root/static' - name: Run tests diff --git a/.github/workflows/publish_artifacts.yaml b/.github/workflows/publish_artifacts.yaml index 582cc6f6a61..027042e043f 100644 --- a/.github/workflows/publish_artifacts.yaml +++ b/.github/workflows/publish_artifacts.yaml @@ -41,7 +41,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/selenium.yaml b/.github/workflows/selenium.yaml index 7820aad9110..0d9bbed4beb 100644 --- a/.github/workflows/selenium.yaml +++ b/.github/workflows/selenium.yaml @@ -34,7 +34,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] chunk: [0, 1, 2] services: postgres: @@ -71,6 +71,7 @@ jobs: - name: Restore client cache uses: actions/cache@v5 with: + fail-on-cache-miss: true key: galaxy-static-${{ needs.build-client.outputs.commit-id }} path: 'galaxy root/static' - name: Run tests diff --git a/.github/workflows/test_galaxy_packages.yaml b/.github/workflows/test_galaxy_packages.yaml index fc82284bfe9..1b57dd07d11 100644 --- a/.github/workflows/test_galaxy_packages.yaml +++ b/.github/workflows/test_galaxy_packages.yaml @@ -18,7 +18,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] steps: - uses: actions/checkout@v6 with: diff --git a/.github/workflows/toolshed.yaml b/.github/workflows/toolshed.yaml index 11af6203643..e9355b9b51c 100644 --- a/.github/workflows/toolshed.yaml +++ b/.github/workflows/toolshed.yaml @@ -23,7 +23,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] shed-api: ['v1', 'v2'] test-install-client: ['galaxy_api', 'standalone'] services: diff --git a/.github/workflows/unit-postgres.yaml b/.github/workflows/unit-postgres.yaml index bb324e61f32..6815d2d8a35 100644 --- a/.github/workflows/unit-postgres.yaml +++ b/.github/workflows/unit-postgres.yaml @@ -24,7 +24,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9'] + python-version: ['3.10'] services: postgres: image: postgres:17 diff --git a/.github/workflows/unit.yaml b/.github/workflows/unit.yaml index 6bb9ff3ab95..825aaf74221 100644 --- a/.github/workflows/unit.yaml +++ b/.github/workflows/unit.yaml @@ -22,7 +22,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.14'] + python-version: ['3.10', '3.14'] steps: - uses: actions/checkout@v6 with: diff --git a/Makefile b/Makefile index e1616f388c5..4e5db97eff2 100644 --- a/Makefile +++ b/Makefile @@ -62,8 +62,8 @@ format: ## Format Python code base remove-unused-imports: ## Remove unused imports in Python code base $(IN_VENV) autoflake --in-place --remove-all-unused-imports --recursive --verbose lib/ test/ -pyupgrade: ## Convert older code patterns to Python 3.8/3.9 idiomatic ones - ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs pyupgrade --py39-plus +pyupgrade: ## Convert older code patterns to Python 3.8/3.10 idiomatic ones + ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs pyupgrade --py310-plus ack --type=python -f | grep -v '^$(subst $(SPACE),\|^,$(NEVER_PYUPGRADE_PATHS) $(PY38_PYUPGRADE_PATHS))' | xargs auto-walrus ack --type=python -f $(PY38_PYUPGRADE_PATHS) | xargs pyupgrade --py38-plus diff --git a/README.rst b/README.rst index a2ae0f9125d..fa9f3e7c969 100644 --- a/README.rst +++ b/README.rst @@ -24,12 +24,12 @@ Community support is available at `Galaxy Help Galaxy Quickstart ================= -Galaxy requires Python 3.9 or higher. To check your Python version, run: +Galaxy requires Python 3.10 or higher. To check your Python version, run: .. code:: console $ python -V - Python 3.9.21 + Python 3.10.12 Start Galaxy: diff --git a/client/src/components/Form/Elements/FormDirectory.test.js b/client/src/components/Form/Elements/FormDirectory.test.js index cbff6c9ffe3..3aba1fb14d3 100644 --- a/client/src/components/Form/Elements/FormDirectory.test.js +++ b/client/src/components/Form/Elements/FormDirectory.test.js @@ -23,7 +23,7 @@ async function init(wrapper, data) { expect(filesDialogComponent.exists()).toBe(true); filesDialogComponent.vm.callback({ url: data.url }); // HACK: URL implementation in test environment is not the same as global node - wrapper.vm.pathChunks = data.pathChunks; + wrapper.vm.pathChunks = [...data.pathChunks]; await flushPromises(); await validateLatestEmittedPath(wrapper, data.url); } @@ -175,4 +175,20 @@ describe("DirectoryPathEditableBreadcrumb", () => { // retain special characters in the url await init(wrapper, testingDataWithSpecialChars); }); + + it("should save on blur", async () => { + await init(wrapper, testingData); + // enter a new path chunk + const input = wrapper.find("#path-input-breadcrumb"); + await input.setValue(validPath); + expect(input.element.value).toBe(validPath); + + await input.trigger("blur"); + await flushPromises(); + + expect(spyOnAddPath).toHaveBeenCalled(); + expect(input.element.value).toBe(""); + expect(wrapper.findAll("li.breadcrumb-item").length).toBe(testingData.expectedNumberOfPaths + 1); + await validateLatestEmittedPath(wrapper, `${testingData.url}/${validPath}`); + }); }); diff --git a/client/src/components/Form/Elements/FormDirectory.vue b/client/src/components/Form/Elements/FormDirectory.vue index 4040d5d5241..a57ab446ddc 100644 --- a/client/src/components/Form/Elements/FormDirectory.vue +++ b/client/src/components/Form/Elements/FormDirectory.vue @@ -35,7 +35,8 @@ trim @keyup.enter="addPath" @keydown.191.capture.prevent.stop="addPath" - @keydown.8.capture="removeLastPath" /> + @keydown.8.capture="removeLastPath" + @blur="handleBlur" /> @@ -139,12 +140,23 @@ export default { }, addPath({ key }) { if ((key === "Enter" || key === "/") && this.isValidName) { - const newFolder = this.currentDirectoryName; - this.pathChunks.push({ pathChunk: newFolder, editable: true }); - this.currentDirectoryName = ""; + this.addDirectoryToPath(); + } + }, + handleBlur() { + if (this.currentDirectoryName && this.isValidName) { + this.addDirectoryToPath(); + } else { + // If the input was touched let's propagate the change either way. this.updateURL(); } }, + addDirectoryToPath() { + const newFolder = this.currentDirectoryName; + this.pathChunks.push({ pathChunk: newFolder, editable: true }); + this.currentDirectoryName = ""; + this.updateURL(); + }, updateURL(isReset = false) { let url = undefined; if (!isReset) { diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 60b91c44a99..8f922c5526c 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -3816,9 +3816,9 @@ :Type: bool -~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ ``prefer_oidc_login`` -~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~ :Description: Controls the order of the login page to prefer OIDC-based login @@ -3834,7 +3834,7 @@ :Description: Allow unregistered users to create new local (non-OIDC) accounts (otherwise, they will have to be created by an admin). This option - will be overridden to false in case disable_local_accounts is set + will be overridden to false in case disable_local_accounts is set to true. :Default: ``true`` :Type: bool @@ -3846,7 +3846,7 @@ :Description: Disable local accounts. If this option is set to true, at least - one OIDC provider needs to be configured and will serve as the + one OIDC provider needs to be configured and will serve as the account provider. If this option is set to true, allow_local_account creation will be overridden with false. :Default: ``false`` diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md index 6cdcf6ed491..98ce8f12a85 100644 --- a/doc/source/admin/python.md +++ b/doc/source/admin/python.md @@ -1,6 +1,6 @@ # Supported Python versions -Galaxy's core functionality is currently supported on Python **>=3.9** . +Galaxy's core functionality is currently supported on Python **>=3.10** . If Galaxy complains about the version of Python you are using: diff --git a/lib/galaxy/agents/base.py b/lib/galaxy/agents/base.py index 6c213396847..5bbb7048380 100644 --- a/lib/galaxy/agents/base.py +++ b/lib/galaxy/agents/base.py @@ -8,10 +8,10 @@ from abc import ( ABC, abstractmethod, ) +from collections.abc import Callable from dataclasses import dataclass from typing import ( Any, - Callable, Optional, TYPE_CHECKING, Union, diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index e1552cae0c3..3a48b2ee207 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -6,9 +6,9 @@ import signal import sys import threading import time +from collections.abc import Callable from typing import ( Any, - Callable, Optional, ) diff --git a/lib/galaxy/authnz/psa_authnz.py b/lib/galaxy/authnz/psa_authnz.py index 07f90377b2d..5037ba86c2a 100644 --- a/lib/galaxy/authnz/psa_authnz.py +++ b/lib/galaxy/authnz/psa_authnz.py @@ -1,6 +1,5 @@ import json import logging -import sys import time from typing import TYPE_CHECKING from urllib.parse import quote @@ -47,14 +46,7 @@ from ..config import GalaxyAppConfiguration if TYPE_CHECKING: from social_core.backends.oauth import BaseOAuth2 - - if sys.version_info >= (3, 10): - from social_core.strategy import HttpResponseProtocol - else: - from typing import Protocol - - class HttpResponseProtocol(Protocol): - url: str + from social_core.strategy import HttpResponseProtocol log = logging.getLogger(__name__) diff --git a/lib/galaxy/celery/__init__.py b/lib/galaxy/celery/__init__.py index 8b04929e5eb..a15939cbd8a 100644 --- a/lib/galaxy/celery/__init__.py +++ b/lib/galaxy/celery/__init__.py @@ -1,5 +1,6 @@ import os import uuid +from collections.abc import Callable from functools import ( lru_cache, wraps, @@ -8,7 +9,6 @@ from multiprocessing import get_context from threading import local from typing import ( Any, - Callable, ) import pebble diff --git a/lib/galaxy/celery/tasks.py b/lib/galaxy/celery/tasks.py index 88c30bcef8f..8f7ffe87f15 100644 --- a/lib/galaxy/celery/tasks.py +++ b/lib/galaxy/celery/tasks.py @@ -1,12 +1,12 @@ import datetime import json import shutil +from collections.abc import Callable from concurrent.futures import TimeoutError from functools import lru_cache from pathlib import Path from typing import ( Any, - Callable, Optional, ) diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py index 2a0d20835df..4b1d46c6df0 100644 --- a/lib/galaxy/config/__init__.py +++ b/lib/galaxy/config/__init__.py @@ -16,10 +16,10 @@ import string import sys import tempfile import threading +from collections.abc import Callable from datetime import timedelta from typing import ( Any, - Callable, cast, Optional, SupportsInt, diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py index 144cb38a199..e9f93f91be0 100644 --- a/lib/galaxy/config/config_manage.py +++ b/lib/galaxy/config/config_manage.py @@ -6,11 +6,11 @@ from argparse import ( ArgumentParser, Namespace, ) +from collections.abc import Callable from io import StringIO from textwrap import TextWrapper from typing import ( Any, - Callable, NamedTuple, Optional, ) @@ -19,7 +19,7 @@ import yaml from boltons.iterutils import remap try: - from gravity.util import settings_to_sample + from gravity.settings import settings_to_sample except ImportError: settings_to_sample = None diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 30a3eb9763b..df7c57d9a77 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -47,6 +47,11 @@ gravity: # is ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB), processes exceeding the limit are throttled and put under heavy reclaim pressure. + # If set, this is the default value for all services. Setting ``memory_high`` on an individual service overrides this + # value. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Specify Galaxy config file (galaxy.yml), if the Gravity config is separate from the Galaxy config. Assumed to be the # same file as the Gravity config if a ``galaxy`` key exists at the root level, otherwise, this option is required. # galaxy_config_file: @@ -67,6 +72,11 @@ gravity: # If not specified defaults to ``/gravity/log``. # log_dir: + # Run Galaxy processes in the specified journal namespace (sets the value of ``LogNamespace=`` in the systemd service + # units). This allows you to keep Galaxy log messages separate in the system journal from other log messages. Ignored if + # ``process_manager`` is not ``systemd``. See ``systemd.exec(5)`` for details. + # log_namespace: + # Set to Galaxy's virtualenv directory. # If not specified, Gravity assumes all processes are on PATH. This option is required in most circumstances when using # the ``systemd`` process manager. @@ -74,9 +84,7 @@ gravity: # Select the application server. # ``gunicorn`` is the default application server. - # ``unicornherder`` is a production-oriented manager for (G)unicorn servers that automates zero-downtime Galaxy server restarts, - # similar to uWSGI Zerg Mode used in the past. - # Valid options are: gunicorn, unicornherder + # Valid options are: gunicorn # app_server: gunicorn # Override the default instance name. @@ -107,8 +115,8 @@ gravity: # extra_args: # Use Gunicorn's --preload option to fork workers after loading the Galaxy Application. - # Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``. - # preload: + # Consumes less memory when multiple processes are configured. + # preload: true # umask under which service should be executed # umask: @@ -127,6 +135,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -171,6 +184,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -224,6 +242,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -286,6 +309,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -338,6 +366,11 @@ gravity: # ``supervisor``. # memory_limit: + # Memory usage throttle limit (in GB). If the service exceeds the limit, processes are throttled and put under heavy + # reclaim pressure. Default is no limit or the value of the ``memory_high`` setting at the top level of the Gravity + # configuration, if set. Ignored if ``process_manager`` is ``supervisor``. + # memory_high: + # Extra environment variables and their values to set when running the service. A dictionary where keys are the variable # names. # environment: {} @@ -2111,19 +2144,19 @@ galaxy: # page (even if require_login is true). #show_welcome_with_login: false - # Controls the order of the login page to prefer OIDC-based login - # and registration. + # Controls the order of the login page to prefer OIDC-based login and + # registration. #prefer_oidc_login: false # Allow unregistered users to create new local (non-OIDC) accounts # (otherwise, they will have to be created by an admin). This option - # will be overridden to false in case disable_local_accounts is set - # to true. + # will be overridden to false in case disable_local_accounts is set to + # true. #allow_local_account_creation: true # Disable local accounts. If this option is set to true, at least one - # OIDC provider needs to be configured and will serve as the account - # provider. If this option is set to true, allow_local_account + # OIDC provider needs to be configured and will serve as the account + # provider. If this option is set to true, allow_local_account # creation will be overridden with false. #disable_local_accounts: false diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample index f7e2ac55872..9a4b9a26aab 100644 --- a/lib/galaxy/config/sample/tool_shed.yml.sample +++ b/lib/galaxy/config/sample/tool_shed.yml.sample @@ -23,6 +23,12 @@ tool_shed: # without authentication. #config_hg_for_dev: null + # The base URL of the Tool Shed server used for generating clone URLs + # and repository hostnames. If set, this value will be used instead of + # deriving the URL from the incoming request. + # Example: https://toolshed.g2.bx.psu.edu + #tool_shed_url: null + # Where Tool Shed repositories are stored. #file_path: database/community_files diff --git a/lib/galaxy/datatypes/blast.py b/lib/galaxy/datatypes/blast.py index 1d8a879dd3a..fbcf447f559 100644 --- a/lib/galaxy/datatypes/blast.py +++ b/lib/galaxy/datatypes/blast.py @@ -32,9 +32,9 @@ Covers the ``blastxml`` format and the BLAST databases. """ import logging import os +from collections.abc import Callable from time import sleep from typing import ( - Callable, Optional, ) diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index ce16a8e7422..c88607e4f45 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -6,21 +6,21 @@ import shutil import string import tempfile from collections.abc import ( + Callable, Generator, Iterable, ) from inspect import isclass from typing import ( Any, - Callable, IO, + Literal, Optional, TYPE_CHECKING, Union, ) from markupsafe import escape -from typing_extensions import Literal from galaxy import util from galaxy.datatypes.metadata import ( diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py index f34b4065085..c5f2a4f74ee 100644 --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -1,8 +1,8 @@ # Contains parameters that are used in Display Applications import mimetypes +from collections.abc import Callable from dataclasses import dataclass from typing import ( - Callable, Optional, TYPE_CHECKING, Union, diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index acabffea568..cb9567ea85f 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -11,6 +11,7 @@ import struct from collections.abc import Iterator from typing import ( Any, + Literal, Optional, Union, ) @@ -20,7 +21,6 @@ import numpy as np import png import pydicom import tifffile -from typing_extensions import Literal try: import PIL diff --git a/lib/galaxy/datatypes/molecules.py b/lib/galaxy/datatypes/molecules.py index 610d4421e25..d0246294d69 100644 --- a/lib/galaxy/datatypes/molecules.py +++ b/lib/galaxy/datatypes/molecules.py @@ -1,8 +1,8 @@ import logging import os import re +from collections.abc import Callable from typing import ( - Callable, Optional, ) diff --git a/lib/galaxy/datatypes/msa.py b/lib/galaxy/datatypes/msa.py index 18c0f2655b6..43d09e47c4f 100644 --- a/lib/galaxy/datatypes/msa.py +++ b/lib/galaxy/datatypes/msa.py @@ -2,8 +2,8 @@ import abc import logging import os import re +from collections.abc import Callable from typing import ( - Callable, Optional, ) diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py index 339f22b1665..8fccd58e066 100644 --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -9,11 +9,13 @@ import os import re import string import subprocess -from collections.abc import Iterable +from collections.abc import ( + Callable, + Iterable, +) from itertools import islice from typing import ( Any, - Callable, Optional, ) diff --git a/lib/galaxy/datatypes/sniff.py b/lib/galaxy/datatypes/sniff.py index fa990a0b00b..0b1b4cb5d23 100644 --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -12,10 +12,12 @@ import shutil import struct import tempfile import zipfile -from collections.abc import Iterable +from collections.abc import ( + Callable, + Iterable, +) from functools import partial from typing import ( - Callable, IO, NamedTuple, Optional, diff --git a/lib/galaxy/datatypes/spaln.py b/lib/galaxy/datatypes/spaln.py index e5d6aeea703..a2c477048b1 100644 --- a/lib/galaxy/datatypes/spaln.py +++ b/lib/galaxy/datatypes/spaln.py @@ -4,8 +4,8 @@ spaln Composite Dataset import logging import os.path +from collections.abc import Callable from typing import ( - Callable, Optional, ) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index a5fcd8d28a9..49b1aaf9c13 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -3,44 +3,35 @@ aiohappyeyeballs==2.6.1 aiohttp==3.13.3 aiosignal==1.4.0 -alabaster==0.7.16 ; python_full_version < '3.10' -alabaster==1.0.0 ; python_full_version >= '3.10' +alabaster==1.0.0 anyio==4.12.1 -ase==3.26.0 ; python_full_version < '3.10' -ase==3.27.0 ; python_full_version >= '3.10' +ase==3.27.0 +async-generator==1.10 async-timeout==5.0.1 ; python_full_version < '3.11' attrs==25.4.0 axe-selenium-python==2.1.6 babel==2.17.0 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11' backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x' -black==25.11.0 ; python_full_version < '3.10' -black==25.12.0 ; python_full_version >= '3.10' -boto3==1.41.5 ; python_full_version < '3.10' -boto3==1.42.19 ; python_full_version >= '3.10' -botocore==1.41.5 ; python_full_version < '3.10' -botocore==1.42.19 ; python_full_version >= '3.10' +black==25.12.0 +boto3==1.42.19 +botocore==1.42.19 build==1.4.0 -cachecontrol==0.14.3 ; python_full_version < '3.10' -cachecontrol==0.14.4 ; python_full_version >= '3.10' +cachecontrol==0.14.4 cachetools==6.2.4 cattrs==25.3.0 certifi==2026.1.4 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy' charset-normalizer==3.4.4 -click==8.1.8 ; python_full_version < '3.10' -click==8.3.1 ; python_full_version >= '3.10' +click==8.3.1 codespell==2.4.1 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32' colorlog==6.10.1 -contourpy==1.3.0 ; python_full_version < '3.10' -contourpy==1.3.2 ; python_full_version == '3.10.*' +contourpy==1.3.2 ; python_full_version < '3.11' contourpy==1.3.3 ; python_full_version >= '3.11' -coverage==7.10.7 ; python_full_version < '3.10' -coverage==7.13.1 ; python_full_version >= '3.10' +coverage==7.13.1 cryptography==46.0.3 -cwltest==2.6.20250818005349 ; python_full_version < '3.10' -cwltest==2.6.20251216093331 ; python_full_version >= '3.10' +cwltest==2.6.20251216093331 cycler==0.12.1 darker==3.0.0 darkgraylib==2.4.1 @@ -48,35 +39,41 @@ decorator==5.2.1 defusedxml==0.7.1 docutils==0.21.2 ; python_full_version < '3.11' docutils==0.22.4 ; python_full_version >= '3.11' -dogpile-cache==1.4.1 ; python_full_version < '3.10' -dogpile-cache==1.5.0 ; python_full_version >= '3.10' -enum-tools==0.12.0 ; python_full_version >= '3.10' +dogpile-cache==1.5.0 +enum-tools==0.12.0 exceptiongroup==1.3.1 ; python_full_version < '3.11' -filelock==3.19.1 ; python_full_version < '3.10' -filelock==3.20.3 ; python_full_version >= '3.10' +filelock==3.20.3 fluent-logger==0.11.1 -fonttools==4.60.2 ; python_full_version < '3.10' -fonttools==4.61.1 ; python_full_version >= '3.10' +fonttools==4.61.1 frozenlist==1.8.0 +fsspec==2026.1.0 galaxy-release-util==0.3.1 -greenlet==3.2.4 ; python_full_version < '3.10' -greenlet==3.3.0 ; python_full_version >= '3.10' +gcsfs==2026.1.0 +google-api-core==2.29.0 +google-auth==2.47.0 +google-auth-oauthlib==1.2.4 +google-cloud-core==2.5.0 +google-cloud-storage==3.8.0 +google-cloud-storage-control==1.9.0 +google-crc32c==1.8.0 +google-resumable-media==2.8.0 +googleapis-common-protos==1.72.0 +greenlet==3.3.0 +grpc-google-iam-v1==0.14.3 +grpcio==1.76.0 +grpcio-status==1.76.0 h11==0.16.0 -html5lib==1.1 ; python_full_version < '3.10' -html5rdf==1.2.1 ; python_full_version >= '3.10' +html5rdf==1.2.1 httpcore==1.0.9 httpx==0.28.1 id==1.5.0 idna==3.11 imagesize==1.4.1 -importlib-metadata==8.7.1 ; python_full_version < '3.12' -importlib-resources==6.5.2 ; python_full_version < '3.10' -iniconfig==2.1.0 ; python_full_version < '3.10' -iniconfig==2.3.0 ; python_full_version >= '3.10' +importlib-metadata==8.7.1 +iniconfig==2.3.0 inquirerpy==0.3.4 isodate==0.7.2 ; python_full_version < '3.11' -isort==6.1.0 ; python_full_version < '3.10' -isort==7.0.0 ; python_full_version >= '3.10' +isort==7.0.0 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' jaraco-context==6.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' jaraco-functools==4.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' @@ -85,63 +82,54 @@ jinja2==3.1.6 jmespath==1.0.1 jsonpatch==1.33 jsonpointer==3.0.0 -jsonschema==4.25.1 ; python_full_version < '3.10' -jsonschema==4.26.0 ; python_full_version >= '3.10' +jsonschema==4.26.0 jsonschema-specifications==2025.9.1 junit-xml==1.9 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' -kiwisolver==1.4.7 ; python_full_version < '3.10' -kiwisolver==1.4.9 ; python_full_version >= '3.10' +kiwisolver==1.4.9 librt==0.7.8 ; platform_python_implementation != 'PyPy' lxml==6.0.2 markdown-it-py==3.0.0 ; python_full_version < '3.11' markdown-it-py==4.0.0 ; python_full_version >= '3.11' markdown-it-reporter==0.0.2 markupsafe==3.0.3 -matplotlib==3.9.4 ; python_full_version < '3.10' -matplotlib==3.10.8 ; python_full_version >= '3.10' -mdit-py-plugins==0.4.2 ; python_full_version < '3.10' -mdit-py-plugins==0.5.0 ; python_full_version >= '3.10' +matplotlib==3.10.8 +mdit-py-plugins==0.5.0 mdurl==0.1.2 -mirakuru==2.6.1 ; python_full_version < '3.10' -mirakuru==3.0.1 ; python_full_version >= '3.10' +mirakuru==3.0.1 mistune==3.1.4 more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' msgpack==1.1.2 multidict==6.7.0 mypy==1.19.1 mypy-extensions==1.1.0 -myst-parser==3.0.1 ; python_full_version < '3.10' -myst-parser==4.0.1 ; python_full_version == '3.10.*' +myst-parser==4.0.1 ; python_full_version < '3.11' myst-parser==5.0.0 ; python_full_version >= '3.11' nh3==0.3.2 -numpy==2.0.2 ; python_full_version < '3.10' -numpy==2.2.6 ; python_full_version == '3.10.*' +numpy==2.2.6 ; python_full_version < '3.11' numpy==2.4.1 ; python_full_version >= '3.11' +oauthlib==3.3.1 onedatafilerestclient==21.2.5.2 outcome==1.3.0.post0 -owlrl==6.0.2 ; python_full_version < '3.10' -owlrl==7.1.4 ; python_full_version >= '3.10' -packaging==24.2 ; python_full_version < '3.10' -packaging==25.0 ; python_full_version >= '3.10' +owlrl==7.1.4 +packaging==25.0 pathspec==1.0.3 pfzy==0.3.4 -pillow==11.3.0 ; python_full_version < '3.10' -pillow==12.1.0 ; python_full_version >= '3.10' +pillow==12.1.0 pkce==1.0.3 -platformdirs==4.4.0 ; python_full_version < '3.10' -platformdirs==4.5.1 ; python_full_version >= '3.10' +platformdirs==4.5.1 playwright==1.57.0 pluggy==1.6.0 -port-for==0.7.4 ; python_full_version < '3.10' -port-for==1.0.0 ; python_full_version >= '3.10' -prettytable==3.16.0 ; python_full_version < '3.10' -prettytable==3.17.0 ; python_full_version >= '3.10' +port-for==1.0.0 +prettytable==3.17.0 prompt-toolkit==3.0.52 propcache==0.4.1 +proto-plus==1.27.0 +protobuf==6.33.4 psutil==7.2.1 ; sys_platform != 'cygwin' -psycopg==3.2.13 ; python_full_version < '3.10' -psycopg==3.3.2 ; python_full_version >= '3.10' +psycopg==3.3.2 +pyasn1==0.6.2 +pyasn1-modules==0.4.2 pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') pyee==13.0.0 pygithub==2.8.1 @@ -150,67 +138,56 @@ pyjwt==2.10.1 pynacl==1.6.2 pyparsing==3.3.1 pyproject-hooks==1.2.0 -pyshacl==0.26.0 ; python_full_version < '3.10' -pyshacl==0.30.1 ; python_full_version >= '3.10' +pyshacl==0.30.1 pysocks==1.7.1 -pytest==8.4.2 ; python_full_version < '3.10' -pytest==9.0.2 ; python_full_version >= '3.10' -pytest-asyncio==1.2.0 ; python_full_version < '3.10' -pytest-asyncio==1.3.0 ; python_full_version >= '3.10' +pytest==9.0.2 +pytest-asyncio==1.3.0 pytest-base-url==2.1.0 pytest-cov==7.0.0 -pytest-html==4.1.1 +pytest-html==4.2.0 pytest-httpserver==1.1.3 pytest-json-report==1.5.0 pytest-metadata==3.1.1 pytest-mock==3.15.1 -pytest-playwright==0.7.1 ; python_full_version < '3.10' -pytest-playwright==0.7.2 ; python_full_version >= '3.10' +pytest-playwright==0.7.2 pytest-postgresql==7.0.2 pytest-shard==0.1.2 python-dateutil==2.9.0.post0 python-irodsclient==3.2.0 python-slugify==8.0.4 -pytokens==0.3.0 +pytokens==0.4.0 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32' pyyaml==6.0.3 -rdflib==7.4.0 ; python_full_version < '3.10' -rdflib==7.5.0 ; python_full_version >= '3.10' +rdflib==7.5.0 readme-renderer==44.0 referencing==0.36.2 requests==2.32.5 requests-cache==1.2.1 +requests-oauthlib==2.0.0 requests-toolbelt==1.0.0 responses==0.25.8 rfc3986==2.0.0 rich==13.9.4 rich-click==1.9.5 -roc-validator==0.4.2 ; python_full_version < '3.9.20' -roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10' -roc-validator==0.8.0 ; python_full_version >= '3.10' +roc-validator==0.8.0 roman-numerals==4.1.0 ; python_full_version >= '3.11' -rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.30.0 ; python_full_version >= '3.10' +rpds-py==0.30.0 +rsa==4.9.1 ruamel-yaml==0.18.17 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython' rucio-clients==39.0.0 -s3transfer==0.15.0 ; python_full_version < '3.10' -s3transfer==0.16.0 ; python_full_version >= '3.10' +s3transfer==0.16.0 schema-salad==8.9.20251102115403 -scipy==1.13.1 ; python_full_version < '3.10' -scipy==1.15.3 ; python_full_version == '3.10.*' +scipy==1.15.3 ; python_full_version < '3.11' scipy==1.17.0 ; python_full_version >= '3.11' -secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' -secretstorage==3.5.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' -selenium==4.32.0 ; python_full_version < '3.10' -selenium==4.39.0 ; python_full_version >= '3.10' +secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' +selenium==4.40.0 seletools==1.5.0 six==1.17.0 sniffio==1.3.1 snowballstemmer==3.0.1 sortedcontainers==2.4.0 -sphinx==7.4.7 ; python_full_version < '3.10' -sphinx==8.1.3 ; python_full_version == '3.10.*' +sphinx==8.1.3 ; python_full_version < '3.11' sphinx==9.0.4 ; python_full_version == '3.11.*' sphinx==9.1.0 ; python_full_version >= '3.12' sphinx-rtd-theme==3.1.0 @@ -222,8 +199,7 @@ sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==2.0.0 sphinxcontrib-serializinghtml==2.0.0 statsd==4.0.1 -stevedore==5.5.0 ; python_full_version < '3.10' -stevedore==5.6.0 ; python_full_version >= '3.10' +stevedore==5.6.0 tabulate==0.9.0 testfixtures==8.3.0 ; python_full_version < '3.11' testfixtures==10.0.0 ; python_full_version >= '3.11' @@ -232,28 +208,25 @@ tinydb==4.8.2 toml==0.10.2 tomli==2.4.0 ; python_full_version <= '3.11' total-perspective-vortex==3.1.3 -trio==0.31.0 ; python_full_version < '3.10' -trio==0.32.0 ; python_full_version >= '3.10' +trio==0.32.0 +trio-typing==0.10.0 trio-websocket==0.12.2 tuspy==1.1.0 twill==3.3.1 twine==6.2.0 types-cachetools==6.2.0.20251022 -types-requests==2.31.0.6 ; python_full_version < '3.10' -types-requests==2.32.4.20260107 ; python_full_version >= '3.10' -types-urllib3==1.26.25.14 ; python_full_version < '3.10' +types-certifi==2021.10.8.3 +types-requests==2.32.4.20260107 +types-urllib3==1.26.25.14 typing-extensions==4.15.0 -typos==1.42.0 ; python_full_version >= '3.10' +typos==1.42.1 tzdata==2025.3 ; sys_platform == 'win32' url-normalize==2.2.1 -urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.3 ; python_full_version >= '3.10' +urllib3==2.6.3 watchdog==6.0.0 wcwidth==0.2.14 -webencodings==0.5.1 ; python_full_version < '3.10' websocket-client==1.9.0 werkzeug==3.1.5 -wsproto==1.2.0 ; python_full_version < '3.10' -wsproto==1.3.2 ; python_full_version >= '3.10' +wsproto==1.3.2 yarl==1.22.0 -zipp==3.23.0 ; python_full_version < '3.12' +zipp==3.23.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3a40934f059..97350202d1b 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -3,84 +3,73 @@ a2wsgi==1.10.10 adal==1.2.7 ag-ui-protocol==0.1.10 -aiobotocore==2.26.0 ; python_full_version < '3.10' -aiobotocore==3.1.0 ; python_full_version >= '3.10' +aiobotocore==3.1.0 aiofiles==25.1.0 aiohappyeyeballs==2.6.1 aiohttp==3.13.3 aioitertools==0.13.0 aiosignal==1.4.0 -alembic==1.16.5 ; python_full_version < '3.10' -alembic==1.18.1 ; python_full_version >= '3.10' +alembic==1.18.1 amqp==5.3.1 annotated-doc==0.0.4 annotated-types==0.7.0 anthropic==0.76.0 anyio==4.12.1 -apispec==6.8.4 ; python_full_version < '3.10' -apispec==6.9.0 ; python_full_version >= '3.10' +apispec==6.9.0 appdirs==1.4.4 arcp==0.2.1 argcomplete==3.6.3 async-timeout==5.0.1 ; python_full_version < '3.11.3' attmap==0.13.2 attrs==25.4.0 -authlib==1.6.6 ; python_full_version >= '3.10' +authlib==1.6.6 babel==2.17.0 -backports-tarfile==1.2.0 ; python_full_version >= '3.10' and python_full_version < '3.12' +backports-tarfile==1.2.0 ; python_full_version < '3.12' bagit==1.9.0 bagit-profile==1.3.1 bcrypt==5.0.0 bdbag==1.8.0 beaker==1.13.0 -beartype==0.22.9 ; python_full_version >= '3.10' +beartype==0.22.9 billiard==4.2.4 bioblend==1.7.0 -bleach==6.2.0 ; python_full_version < '3.10' -bleach==6.3.0 ; python_full_version >= '3.10' +bleach==6.3.0 boltons==25.0.0 boto==2.49.0 -boto3==1.41.5 ; python_full_version < '3.10' -boto3==1.42.19 ; python_full_version >= '3.10' -botocore==1.41.5 ; python_full_version < '3.10' -botocore==1.42.19 ; python_full_version >= '3.10' +boto3==1.42.19 +botocore==1.42.19 bx-python==0.14.0 -cachecontrol==0.14.3 ; python_full_version < '3.10' -cachecontrol==0.14.4 ; python_full_version >= '3.10' -cachetools==6.2.4 ; python_full_version >= '3.10' +cachecontrol==0.14.4 +cachetools==6.2.4 celery==5.6.2 certifi==2026.1.4 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy' charset-normalizer==3.4.4 circus==0.19.0 -click==8.1.8 ; python_full_version < '3.10' -click==8.3.1 ; python_full_version >= '3.10' +click==8.3.1 click-didyoumean==0.3.1 click-plugins==1.1.1.2 click-repl==0.3.0 cloudauthz==0.6.0 cloudbridge==3.2.0 -cloudpickle==3.1.2 ; python_full_version >= '3.10' +cloudpickle==3.1.2 cohere==5.20.1 ; sys_platform != 'emscripten' colorama==0.4.6 coloredlogs==15.0.1 conda-package-streaming==0.12.0 cryptography==46.0.3 ct3==3.4.0.post5 -cwl-upgrader==1.2.12 ; python_full_version < '3.10' -cwl-upgrader==1.2.14 ; python_full_version >= '3.10' +cwl-upgrader==1.2.14 cwl-utils==0.40 -cwltool==3.1.20251031082601 ; python_full_version < '3.10' -cwltool==3.1.20260108082145 ; python_full_version >= '3.10' -cyclopts==4.5.0 ; python_full_version >= '3.10' +cwltool==3.1.20260108082145 +cyclopts==4.5.0 defusedxml==0.7.1 deprecated==1.3.1 deprecation==2.1.0 dictobj==0.4 -diskcache==5.6.3 ; python_full_version >= '3.10' +diskcache==5.6.3 distro==1.9.0 -dnspython==2.7.0 ; python_full_version < '3.10' -dnspython==2.8.0 ; python_full_version >= '3.10' +dnspython==2.8.0 docopt==0.6.2 docstring-parser==0.17.0 docutils==0.21.2 ; python_full_version < '3.11' @@ -91,45 +80,38 @@ email-validator==2.3.0 et-xmlfile==2.0.0 eval-type-backport==0.3.1 exceptiongroup==1.3.1 -executing==2.2.1 ; python_full_version >= '3.10' -fakeredis==2.33.0 ; python_full_version >= '3.10' +executing==2.2.1 +fakeredis==2.33.0 fastapi==0.128.0 fastavro==1.12.1 ; sys_platform != 'emscripten' -fastmcp==2.14.3 ; python_full_version >= '3.10' -filelock==3.19.1 ; python_full_version < '3.10' -filelock==3.20.3 ; python_full_version >= '3.10' +fastmcp==2.14.3 +filelock==3.20.3 fissix==24.4.24 frozenlist==1.8.0 fs==2.4.16 -fsspec==2025.10.0 ; python_full_version < '3.10' -fsspec==2026.1.0 ; python_full_version >= '3.10' +fsspec==2026.1.0 future==1.0.0 genai-prices==0.0.51 google-api-core==2.29.0 google-auth==2.47.0 google-cloud-batch==0.20.0 -google-genai==1.47.0 ; python_full_version < '3.10' -google-genai==1.59.0 ; python_full_version >= '3.10' +google-genai==1.59.0 googleapis-common-protos==1.72.0 -gravity @ git+https://github.com/nsoranzo/gravity.git@7c5f457424658ee904694f5566e61b562bce7ed6 -greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64') -greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64') -griffe==1.14.0 ; python_full_version < '3.10' -griffe==1.15.0 ; python_full_version >= '3.10' +gravity==1.2.0 +greenlet==3.3.0 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64' +griffe==1.15.0 groq==1.0.0 grpcio==1.76.0 -grpcio-status==1.71.2 ; python_full_version < '3.10' -grpcio-status==1.76.0 ; python_full_version >= '3.10' +grpcio-status==1.76.0 gunicorn==23.0.0 gxformat2==0.21.0 h11==0.16.0 h5grove==2.3.0 -h5py==3.14.0 ; python_full_version < '3.10' -h5py==3.15.1 ; python_full_version >= '3.10' +h5py==3.15.1 hf-xet==1.2.0 ; platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64' httpcore==1.0.9 httpx==0.28.1 -httpx-sse==0.4.3 ; python_full_version >= '3.10' +httpx-sse==0.4.3 huggingface-hub==0.36.0 humanfriendly==10.0 idna==3.11 @@ -140,37 +122,35 @@ invoke==2.2.1 isa-rwval==0.10.11 isal==1.8.0 isodate==0.7.2 ; python_full_version < '3.11' -jaraco-classes==3.4.0 ; python_full_version >= '3.10' -jaraco-context==6.1.0 ; python_full_version >= '3.10' -jaraco-functools==4.4.0 ; python_full_version >= '3.10' -jeepney==0.9.0 ; python_full_version >= '3.10' and sys_platform == 'linux' +jaraco-classes==3.4.0 +jaraco-context==6.1.0 +jaraco-functools==4.4.0 +jeepney==0.9.0 ; sys_platform == 'linux' jinja2==3.1.6 jiter==0.12.0 jmespath==1.0.1 jsonref==1.1.0 -jsonschema==4.25.1 ; python_full_version < '3.10' -jsonschema==4.26.0 ; python_full_version >= '3.10' -jsonschema-path==0.3.4 ; python_full_version >= '3.10' +jsonschema==4.26.0 +jsonschema-path==0.3.4 jsonschema-specifications==2025.9.1 -keyring==25.7.0 ; python_full_version >= '3.10' +keyring==25.7.0 kombu==5.6.2 lagom==2.7.7 legacy-cgi==2.6.4 ; python_full_version >= '3.13' -limits==4.2 ; python_full_version < '3.10' -limits==5.6.0 ; python_full_version >= '3.10' -logfire==4.19.0 ; python_full_version >= '3.10' +limits==5.6.0 +logfire==4.19.0 logfire-api==4.19.0 -lupa==2.6 ; python_full_version >= '3.10' +lupa==2.6 lxml==6.0.2 mako==1.3.10 -markdown==3.9 ; python_full_version < '3.10' -markdown==3.10 ; python_full_version >= '3.10' +markdown==3.10 markdown-it-py==3.0.0 ; python_full_version < '3.11' markdown-it-py==4.0.0 ; python_full_version >= '3.11' markupsafe==3.0.3 -mcp==1.25.0 ; python_full_version >= '3.10' +mcp==1.25.0 mdurl==0.1.2 -mercurial==7.1.2 +mercurial==7.1.2 ; python_version < '3.14' +mercurial==7.2rc0 ; python_version >= '3.14' mistralai==1.9.11 mistune==3.1.4 more-itertools==10.8.0 @@ -179,73 +159,62 @@ msal==1.34.0 msgpack==1.1.2 multidict==6.7.0 mypy-extensions==1.1.0 -networkx==3.2.1 ; python_full_version < '3.10' -networkx==3.4.2 ; python_full_version == '3.10.*' +networkx==3.4.2 ; python_full_version < '3.11' networkx==3.6.1 ; python_full_version >= '3.11' -nexus-rpc==1.1.0 ; python_full_version < '3.10' -nexus-rpc==1.2.0 ; python_full_version >= '3.10' +nexus-rpc==1.2.0 nodejs-wheel==22.20.0 nodejs-wheel-binaries==22.20.0 -numpy==2.0.2 ; python_full_version < '3.10' -numpy==2.2.6 ; python_full_version == '3.10.*' +numpy==2.2.6 ; python_full_version < '3.11' numpy==2.4.1 ; python_full_version >= '3.11' oauthlib==3.3.1 openai==2.15.0 -openapi-pydantic==0.5.1 ; python_full_version >= '3.10' +openapi-pydantic==0.5.1 openpyxl==3.1.5 opentelemetry-api==1.39.1 -opentelemetry-exporter-otlp-proto-common==1.39.1 ; python_full_version >= '3.10' -opentelemetry-exporter-otlp-proto-http==1.39.1 ; python_full_version >= '3.10' -opentelemetry-exporter-prometheus==0.60b1 ; python_full_version >= '3.10' -opentelemetry-instrumentation==0.60b1 ; python_full_version >= '3.10' -opentelemetry-instrumentation-httpx==0.60b1 ; python_full_version >= '3.10' -opentelemetry-proto==1.39.1 ; python_full_version >= '3.10' -opentelemetry-sdk==1.39.1 ; python_full_version >= '3.10' -opentelemetry-semantic-conventions==0.60b1 ; python_full_version >= '3.10' -opentelemetry-util-http==0.60b1 ; python_full_version >= '3.10' +opentelemetry-exporter-otlp-proto-common==1.39.1 +opentelemetry-exporter-otlp-proto-http==1.39.1 +opentelemetry-exporter-prometheus==0.60b1 +opentelemetry-instrumentation==0.60b1 +opentelemetry-instrumentation-httpx==0.60b1 +opentelemetry-proto==1.39.1 +opentelemetry-sdk==1.39.1 +opentelemetry-semantic-conventions==0.60b1 +opentelemetry-util-http==0.60b1 orjson==3.11.5 oyaml==1.0 -packaging==24.2 ; python_full_version < '3.10' -packaging==25.0 ; python_full_version >= '3.10' +packaging==25.0 paramiko==4.0.0 parsley==1.3 paste==3.10.1 pastedeploy==3.1.0 -pathable==0.4.4 ; python_full_version >= '3.10' -pathvalidate==3.3.1 ; python_full_version >= '3.10' +pathable==0.4.4 +pathvalidate==3.3.1 pebble==5.1.3 -pillow==11.3.0 ; python_full_version < '3.10' -pillow==12.1.0 ; python_full_version >= '3.10' -platformdirs==4.5.1 ; python_full_version >= '3.10' -prometheus-client==0.24.1 ; python_full_version >= '3.10' +pillow==12.1.0 +platformdirs==4.5.1 +prometheus-client==0.24.1 prompt-toolkit==3.0.52 propcache==0.4.1 proto-plus==1.27.0 -protobuf==5.29.5 ; python_full_version < '3.10' -protobuf==6.33.4 ; python_full_version >= '3.10' +protobuf==6.33.4 prov==1.5.1 psutil==7.2.1 pulsar-galaxy-lib==0.15.13 -py-key-value-aio==0.3.0 ; python_full_version >= '3.10' -py-key-value-shared==0.3.0 ; python_full_version >= '3.10' +py-key-value-aio==0.3.0 +py-key-value-shared==0.3.0 pyasn1==0.6.2 pyasn1-modules==0.4.2 pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy') pycryptodome==3.23.0 pydantic==2.12.5 -pydantic-ai==0.8.1 ; python_full_version < '3.10' -pydantic-ai==1.44.0 ; python_full_version >= '3.10' -pydantic-ai-slim==0.8.1 ; python_full_version < '3.10' -pydantic-ai-slim==1.44.0 ; python_full_version >= '3.10' +pydantic-ai==1.44.0 +pydantic-ai-slim==1.44.0 pydantic-core==2.41.5 -pydantic-evals==0.8.1 ; python_full_version < '3.10' -pydantic-evals==1.44.0 ; python_full_version >= '3.10' -pydantic-graph==0.8.1 ; python_full_version < '3.10' -pydantic-graph==1.44.0 ; python_full_version >= '3.10' -pydantic-settings==2.11.0 ; python_full_version < '3.10' -pydantic-settings==2.12.0 ; python_full_version >= '3.10' +pydantic-evals==1.44.0 +pydantic-graph==1.44.0 +pydantic-settings==2.12.0 pydantic-tes==0.2.0 -pydocket==0.16.6 ; python_full_version >= '3.10' +pydocket==0.16.6 pydicom==2.4.4 ; python_full_version < '3.10' pydicom==3.0.1 ; python_full_version >= '3.10' pydot==4.0.1 @@ -263,20 +232,18 @@ pyreadline3==3.5.4 ; sys_platform == 'win32' pysam==0.23.3 python-dateutil==2.9.0.post0 python-dotenv==1.2.1 -python-json-logger==4.0.0 ; python_full_version >= '3.10' +python-json-logger==4.0.0 python-magic==0.4.27 -python-multipart==0.0.20 ; python_full_version < '3.10' -python-multipart==0.0.21 ; python_full_version >= '3.10' +python-multipart==0.0.21 python-slugify==8.0.4 python3-openid==3.2.0 pytz==2025.2 -pywin32==311 ; python_full_version >= '3.10' and sys_platform == 'win32' -pywin32-ctypes==0.2.3 ; python_full_version >= '3.10' and sys_platform == 'win32' +pywin32==311 ; sys_platform == 'win32' +pywin32-ctypes==0.2.3 ; sys_platform == 'win32' pyyaml==6.0.3 pyzmq==27.1.0 -rdflib==7.4.0 ; python_full_version < '3.10' -rdflib==7.5.0 ; python_full_version >= '3.10' -redis==7.1.0 ; python_full_version >= '3.10' +rdflib==7.5.0 +redis==7.1.0 referencing==0.36.2 refgenconf==0.12.2 regex==2026.1.15 @@ -287,45 +254,38 @@ requests-toolbelt==1.0.0 requests-unixsocket==0.4.1 rich==13.9.4 rich-argparse==1.7.2 -rich-rst==1.3.2 ; python_full_version >= '3.10' +rich-rst==1.3.2 rocrate==0.14.2 routes==2.5.1 -rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.30.0 ; python_full_version >= '3.10' +rpds-py==0.30.0 rsa==4.9.1 ruamel-yaml==0.18.17 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython' -s3fs==2025.10.0 ; python_full_version < '3.10' -s3fs==2026.1.0 ; python_full_version >= '3.10' -s3transfer==0.15.0 ; python_full_version < '3.10' -s3transfer==0.16.0 ; python_full_version >= '3.10' +s3fs==2026.1.0 +s3transfer==0.16.0 schema-salad==8.9.20251102115403 -secretstorage==3.5.0 ; python_full_version >= '3.10' and sys_platform == 'linux' +secretstorage==3.5.0 ; sys_platform == 'linux' setuptools==80.9.0 -shellingham==1.5.4 ; python_full_version >= '3.10' +shellingham==1.5.4 six==1.17.0 slowapi==0.1.9 sniffio==1.3.1 -social-auth-core==4.7.0 ; python_full_version < '3.10' -social-auth-core==4.8.3 ; python_full_version >= '3.10' +social-auth-core==4.8.3 sortedcontainers==2.4.0 spython==0.3.14 sqlalchemy==2.0.45 sqlparse==0.5.5 -sse-starlette==3.1.2 ; python_full_version >= '3.10' -starlette==0.49.3 ; python_full_version < '3.10' -starlette==0.50.0 ; python_full_version >= '3.10' +sse-starlette==3.2.0 +starlette==0.50.0 starlette-context==0.4.0 supervisor==4.3.0 svgwrite==1.4.3 -temporalio==1.16.0 ; python_full_version < '3.10' -temporalio==1.20.0 ; python_full_version >= '3.10' +temporalio==1.20.0 tenacity==9.1.2 text-unidecode==1.3 -tifffile==2024.8.30 ; python_full_version < '3.10' -tifffile==2025.5.10 ; python_full_version == '3.10.*' +tifffile==2025.5.10 ; python_full_version < '3.11' tifffile==2026.1.14 ; python_full_version >= '3.11' -tiktoken==0.12.0 ; python_full_version >= '3.10' +tiktoken==0.12.0 tinydb==4.8.2 tokenizers==0.22.2 ; sys_platform != 'emscripten' tomli==2.4.0 ; python_full_version < '3.11' @@ -333,20 +293,16 @@ tornado==6.5.4 tqdm==4.67.1 tuspy==1.1.0 tuspyserver==4.2.3 -typer==0.21.1 ; python_full_version >= '3.10' +typer==0.21.1 types-protobuf==6.32.1.20251210 -types-requests==2.31.0.6 ; python_full_version < '3.10' and sys_platform != 'emscripten' -types-requests==2.32.4.20260107 ; python_full_version >= '3.10' and sys_platform != 'emscripten' -types-urllib3==1.26.25.14 ; python_full_version < '3.10' and sys_platform != 'emscripten' +types-requests==2.32.4.20260107 ; sys_platform != 'emscripten' typing-extensions==4.15.0 typing-inspection==0.4.2 tzdata==2025.3 tzlocal==5.3.1 ubiquerg==0.8.2 -urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.3 ; python_full_version >= '3.10' -uvicorn==0.39.0 ; python_full_version < '3.10' -uvicorn==0.40.0 ; python_full_version >= '3.10' +urllib3==2.6.3 +uvicorn==0.40.0 uvloop==0.22.1 vine==5.1.0 wcwidth==0.2.14 diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt index fa5eae9337a..2d85f414e2c 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -4,170 +4,153 @@ aiohappyeyeballs==2.6.1 aiohttp==3.13.3 aiosignal==1.4.0 anyio==4.12.1 -ase==3.26.0 ; python_full_version < '3.10' -ase==3.27.0 ; python_full_version >= '3.10' +ase==3.27.0 +async-generator==1.10 async-timeout==5.0.1 ; python_full_version < '3.11' attrs==25.4.0 axe-selenium-python==2.1.6 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11' -boto3==1.41.5 ; python_full_version < '3.10' -boto3==1.42.19 ; python_full_version >= '3.10' -botocore==1.41.5 ; python_full_version < '3.10' -botocore==1.42.19 ; python_full_version >= '3.10' -cachecontrol==0.14.3 ; python_full_version < '3.10' -cachecontrol==0.14.4 ; python_full_version >= '3.10' +boto3==1.42.19 +botocore==1.42.19 +cachecontrol==0.14.4 cachetools==6.2.4 cattrs==25.3.0 certifi==2026.1.4 cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt' charset-normalizer==3.4.4 -click==8.1.8 ; python_full_version < '3.10' -click==8.3.1 ; python_full_version >= '3.10' +click==8.3.1 colorama==0.4.6 ; sys_platform == 'win32' colorlog==6.10.1 -contourpy==1.3.0 ; python_full_version < '3.10' -contourpy==1.3.2 ; python_full_version == '3.10.*' +contourpy==1.3.2 ; python_full_version < '3.11' contourpy==1.3.3 ; python_full_version >= '3.11' -coverage==7.10.7 ; python_full_version < '3.10' -coverage==7.13.1 ; python_full_version >= '3.10' -cwltest==2.6.20250818005349 ; python_full_version < '3.10' -cwltest==2.6.20251216093331 ; python_full_version >= '3.10' +coverage==7.13.1 +cwltest==2.6.20251216093331 cycler==0.12.1 decorator==5.2.1 defusedxml==0.7.1 -dogpile-cache==1.4.1 ; python_full_version < '3.10' -dogpile-cache==1.5.0 ; python_full_version >= '3.10' -enum-tools==0.12.0 ; python_full_version >= '3.10' +dogpile-cache==1.5.0 +enum-tools==0.12.0 exceptiongroup==1.3.1 ; python_full_version < '3.11' -filelock==3.19.1 ; python_full_version < '3.10' -filelock==3.20.3 ; python_full_version >= '3.10' +filelock==3.20.3 fluent-logger==0.11.1 -fonttools==4.60.2 ; python_full_version < '3.10' -fonttools==4.61.1 ; python_full_version >= '3.10' +fonttools==4.61.1 frozenlist==1.8.0 -greenlet==3.2.4 ; python_full_version < '3.10' -greenlet==3.3.0 ; python_full_version >= '3.10' +fsspec==2026.1.0 +gcsfs==2026.1.0 +google-api-core==2.29.0 +google-auth==2.47.0 +google-auth-oauthlib==1.2.4 +google-cloud-core==2.5.0 +google-cloud-storage==3.8.0 +google-cloud-storage-control==1.9.0 +google-crc32c==1.8.0 +google-resumable-media==2.8.0 +googleapis-common-protos==1.72.0 +greenlet==3.3.0 +grpc-google-iam-v1==0.14.3 +grpcio==1.76.0 +grpcio-status==1.76.0 h11==0.16.0 -html5lib==1.1 ; python_full_version < '3.10' -html5rdf==1.2.1 ; python_full_version >= '3.10' +html5rdf==1.2.1 httpcore==1.0.9 httpx==0.28.1 idna==3.11 -importlib-metadata==8.7.1 ; python_full_version < '3.12' -importlib-resources==6.5.2 ; python_full_version < '3.10' -iniconfig==2.1.0 ; python_full_version < '3.10' -iniconfig==2.3.0 ; python_full_version >= '3.10' +importlib-metadata==8.7.1 +iniconfig==2.3.0 inquirerpy==0.3.4 isodate==0.7.2 ; python_full_version < '3.11' jinja2==3.1.6 jmespath==1.0.1 jsonpatch==1.33 jsonpointer==3.0.0 -jsonschema==4.25.1 ; python_full_version < '3.10' -jsonschema==4.26.0 ; python_full_version >= '3.10' +jsonschema==4.26.0 jsonschema-specifications==2025.9.1 junit-xml==1.9 -kiwisolver==1.4.7 ; python_full_version < '3.10' -kiwisolver==1.4.9 ; python_full_version >= '3.10' +kiwisolver==1.4.9 librt==0.7.8 ; platform_python_implementation != 'PyPy' lxml==6.0.2 markdown-it-py==3.0.0 ; python_full_version < '3.11' markdown-it-py==4.0.0 ; python_full_version >= '3.11' markupsafe==3.0.3 -matplotlib==3.9.4 ; python_full_version < '3.10' -matplotlib==3.10.8 ; python_full_version >= '3.10' +matplotlib==3.10.8 mdurl==0.1.2 -mirakuru==2.6.1 ; python_full_version < '3.10' -mirakuru==3.0.1 ; python_full_version >= '3.10' +mirakuru==3.0.1 mistune==3.1.4 msgpack==1.1.2 multidict==6.7.0 mypy==1.19.1 mypy-extensions==1.1.0 -numpy==2.0.2 ; python_full_version < '3.10' -numpy==2.2.6 ; python_full_version == '3.10.*' +numpy==2.2.6 ; python_full_version < '3.11' numpy==2.4.1 ; python_full_version >= '3.11' +oauthlib==3.3.1 onedatafilerestclient==21.2.5.2 outcome==1.3.0.post0 -owlrl==6.0.2 ; python_full_version < '3.10' -owlrl==7.1.4 ; python_full_version >= '3.10' -packaging==24.2 ; python_full_version < '3.10' -packaging==25.0 ; python_full_version >= '3.10' +owlrl==7.1.4 +packaging==25.0 pathspec==1.0.3 pfzy==0.3.4 -pillow==11.3.0 ; python_full_version < '3.10' -pillow==12.1.0 ; python_full_version >= '3.10' +pillow==12.1.0 pkce==1.0.3 -platformdirs==4.4.0 ; python_full_version < '3.10' -platformdirs==4.5.1 ; python_full_version >= '3.10' +platformdirs==4.5.1 playwright==1.57.0 pluggy==1.6.0 -port-for==0.7.4 ; python_full_version < '3.10' -port-for==1.0.0 ; python_full_version >= '3.10' -prettytable==3.16.0 ; python_full_version < '3.10' -prettytable==3.17.0 ; python_full_version >= '3.10' +port-for==1.0.0 +prettytable==3.17.0 prompt-toolkit==3.0.52 propcache==0.4.1 +proto-plus==1.27.0 +protobuf==6.33.4 psutil==7.2.1 ; sys_platform != 'cygwin' -psycopg==3.2.13 ; python_full_version < '3.10' -psycopg==3.3.2 ; python_full_version >= '3.10' +psycopg==3.3.2 +pyasn1==0.6.2 +pyasn1-modules==0.4.2 pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt' pyee==13.0.0 pygments==2.19.2 pyparsing==3.3.1 -pyshacl==0.26.0 ; python_full_version < '3.10' -pyshacl==0.30.1 ; python_full_version >= '3.10' +pyshacl==0.30.1 pysocks==1.7.1 -pytest==8.4.2 ; python_full_version < '3.10' -pytest==9.0.2 ; python_full_version >= '3.10' -pytest-asyncio==1.2.0 ; python_full_version < '3.10' -pytest-asyncio==1.3.0 ; python_full_version >= '3.10' +pytest==9.0.2 +pytest-asyncio==1.3.0 pytest-base-url==2.1.0 pytest-cov==7.0.0 -pytest-html==4.1.1 +pytest-html==4.2.0 pytest-httpserver==1.1.3 pytest-json-report==1.5.0 pytest-metadata==3.1.1 pytest-mock==3.15.1 -pytest-playwright==0.7.1 ; python_full_version < '3.10' -pytest-playwright==0.7.2 ; python_full_version >= '3.10' +pytest-playwright==0.7.2 pytest-postgresql==7.0.2 pytest-shard==0.1.2 python-dateutil==2.9.0.post0 python-irodsclient==3.2.0 python-slugify==8.0.4 pyyaml==6.0.3 -rdflib==7.4.0 ; python_full_version < '3.10' -rdflib==7.5.0 ; python_full_version >= '3.10' +rdflib==7.5.0 referencing==0.36.2 requests==2.32.5 requests-cache==1.2.1 +requests-oauthlib==2.0.0 responses==0.25.8 rich==13.9.4 rich-click==1.9.5 -roc-validator==0.4.2 ; python_full_version < '3.9.20' -roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10' -roc-validator==0.8.0 ; python_full_version >= '3.10' -rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.30.0 ; python_full_version >= '3.10' +roc-validator==0.8.0 +rpds-py==0.30.0 +rsa==4.9.1 ruamel-yaml==0.18.17 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython' rucio-clients==39.0.0 -s3transfer==0.15.0 ; python_full_version < '3.10' -s3transfer==0.16.0 ; python_full_version >= '3.10' +s3transfer==0.16.0 schema-salad==8.9.20251102115403 -scipy==1.13.1 ; python_full_version < '3.10' -scipy==1.15.3 ; python_full_version == '3.10.*' +scipy==1.15.3 ; python_full_version < '3.11' scipy==1.17.0 ; python_full_version >= '3.11' -selenium==4.32.0 ; python_full_version < '3.10' -selenium==4.39.0 ; python_full_version >= '3.10' +selenium==4.40.0 seletools==1.5.0 six==1.17.0 sniffio==1.3.1 sortedcontainers==2.4.0 statsd==4.0.1 -stevedore==5.5.0 ; python_full_version < '3.10' -stevedore==5.6.0 ; python_full_version >= '3.10' +stevedore==5.6.0 tabulate==0.9.0 testfixtures==8.3.0 ; python_full_version < '3.11' testfixtures==10.0.0 ; python_full_version >= '3.11' @@ -176,27 +159,24 @@ tinydb==4.8.2 toml==0.10.2 tomli==2.4.0 ; python_full_version <= '3.11' total-perspective-vortex==3.1.3 -trio==0.31.0 ; python_full_version < '3.10' -trio==0.32.0 ; python_full_version >= '3.10' +trio==0.32.0 +trio-typing==0.10.0 trio-websocket==0.12.2 tuspy==1.1.0 twill==3.3.1 types-cachetools==6.2.0.20251022 -types-requests==2.31.0.6 ; python_full_version < '3.10' -types-requests==2.32.4.20260107 ; python_full_version >= '3.10' -types-urllib3==1.26.25.14 ; python_full_version < '3.10' +types-certifi==2021.10.8.3 +types-requests==2.32.4.20260107 +types-urllib3==1.26.25.14 typing-extensions==4.15.0 -typos==1.42.0 ; python_full_version >= '3.10' +typos==1.42.1 tzdata==2025.3 ; sys_platform == 'win32' url-normalize==2.2.1 -urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.3 ; python_full_version >= '3.10' +urllib3==2.6.3 watchdog==6.0.0 wcwidth==0.2.14 -webencodings==0.5.1 ; python_full_version < '3.10' websocket-client==1.9.0 werkzeug==3.1.5 -wsproto==1.2.0 ; python_full_version < '3.10' -wsproto==1.3.2 ; python_full_version >= '3.10' +wsproto==1.3.2 yarl==1.22.0 -zipp==3.23.0 ; python_full_version < '3.12' +zipp==3.23.0 diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index f2a936e6ec3..745cd5ddb46 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -27,13 +27,11 @@ types-paramiko==4.0.0.20250822 types-python-dateutil==2.9.0.20251115 types-python-slugify==8.0.2.20240310 types-pyyaml==6.0.12.20250915 -types-requests==2.31.0.6 ; python_full_version < '3.10' -types-requests==2.32.4.20260107 ; python_full_version >= '3.10' +types-requests==2.32.4.20260107 types-s3transfer==0.16.0 types-setuptools==80.9.0.20251223 types-six==1.17.0.20251009 -types-urllib3==1.26.25.14 ; python_full_version < '3.10' types-webencodings==0.5.0.20251108 typing-extensions==4.15.0 typing-inspection==0.4.2 -urllib3==2.6.3 ; python_full_version >= '3.10' +urllib3==2.6.3 diff --git a/lib/galaxy/files/__init__.py b/lib/galaxy/files/__init__.py index bd41e42f9ae..cf21e294c03 100644 --- a/lib/galaxy/files/__init__.py +++ b/lib/galaxy/files/__init__.py @@ -1,9 +1,9 @@ import logging import os from collections import defaultdict +from collections.abc import Callable from typing import ( Any, - Callable, NamedTuple, Optional, Protocol, diff --git a/lib/galaxy/files/sources/azure.py b/lib/galaxy/files/sources/azure.py index 25fc06fbaca..f90d794a5e0 100644 --- a/lib/galaxy/files/sources/azure.py +++ b/lib/galaxy/files/sources/azure.py @@ -1,4 +1,4 @@ -from typing_extensions import Literal +from typing import Literal try: from fs.azblob.blob_fs import BlobFS diff --git a/lib/galaxy/files/sources/invenio.py b/lib/galaxy/files/sources/invenio.py index 8d1cbe846f0..e78e182e89d 100644 --- a/lib/galaxy/files/sources/invenio.py +++ b/lib/galaxy/files/sources/invenio.py @@ -5,13 +5,13 @@ import urllib.request from typing import ( Any, cast, + Literal, Optional, ) from urllib.error import HTTPError from urllib.parse import quote from typing_extensions import ( - Literal, TypedDict, ) diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py index 1114a9be9ad..ed9adc73f2d 100644 --- a/lib/galaxy/files/templates/models.py +++ b/lib/galaxy/files/templates/models.py @@ -1,6 +1,7 @@ from typing import ( Annotated, Any, + Literal, Optional, Union, ) @@ -9,7 +10,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal from galaxy.util.config_templates import ( ConfiguredOAuth2Sources, diff --git a/lib/galaxy/job_execution/container_monitor.py b/lib/galaxy/job_execution/container_monitor.py index 0590ce715db..52302ccad79 100644 --- a/lib/galaxy/job_execution/container_monitor.py +++ b/lib/galaxy/job_execution/container_monitor.py @@ -6,8 +6,8 @@ import sys import tempfile import time import traceback +from collections.abc import Callable from functools import partial -from typing import Callable from galaxy.tool_util.deps import docker_util from galaxy.util import ( diff --git a/lib/galaxy/job_execution/output_collect.py b/lib/galaxy/job_execution/output_collect.py index 728e6298990..063dd1996f7 100644 --- a/lib/galaxy/job_execution/output_collect.py +++ b/lib/galaxy/job_execution/output_collect.py @@ -5,10 +5,10 @@ import logging import operator import os import re +from collections.abc import Callable from tempfile import NamedTemporaryFile from typing import ( Any, - Callable, Optional, TYPE_CHECKING, Union, diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index c70a4f5bc2a..40b706cbd5c 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -15,7 +15,10 @@ import shutil import sys import time import traceback -from collections.abc import Iterable +from collections.abc import ( + Callable, + Iterable, +) from dataclasses import ( dataclass, field, @@ -23,7 +26,6 @@ from dataclasses import ( from json import loads from typing import ( Any, - Callable, cast, Optional, TYPE_CHECKING, diff --git a/lib/galaxy/jobs/job_destination.py b/lib/galaxy/jobs/job_destination.py index db6c615ac27..1a9fc0701df 100644 --- a/lib/galaxy/jobs/job_destination.py +++ b/lib/galaxy/jobs/job_destination.py @@ -1,4 +1,3 @@ -import sys from dataclasses import ( dataclass, field, @@ -14,10 +13,8 @@ if TYPE_CHECKING: from galaxy.jobs import ResubmitConfigDict from galaxy.model import Job -dataclass_kwargs = {"kw_only": True} if sys.version_info >= (3, 10) else {} - -@dataclass(**dataclass_kwargs, eq=False) +@dataclass(kw_only=True, eq=False) class JobDestination: """ Provides details about where a job runs diff --git a/lib/galaxy/jobs/mapper.py b/lib/galaxy/jobs/mapper.py index a4401b999c2..2684b0da492 100644 --- a/lib/galaxy/jobs/mapper.py +++ b/lib/galaxy/jobs/mapper.py @@ -1,9 +1,9 @@ import importlib import logging +from collections.abc import Callable from inspect import getfullargspec from types import ModuleType from typing import ( - Callable, TYPE_CHECKING, Union, ) diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index cda9b6ea780..e6242cca853 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -10,11 +10,10 @@ import string import time from typing import ( TYPE_CHECKING, + TypeAlias, Union, ) -from typing_extensions import TypeAlias - from galaxy import model from galaxy.jobs.handler import DEFAULT_JOB_RUNNER_FAILURE_MESSAGE from galaxy.jobs.job_destination import JobDestination diff --git a/lib/galaxy/jobs/runners/util/cli/job/__init__.py b/lib/galaxy/jobs/runners/util/cli/job/__init__.py index 26076407ca5..957953b78a4 100644 --- a/lib/galaxy/jobs/runners/util/cli/job/__init__.py +++ b/lib/galaxy/jobs/runners/util/cli/job/__init__.py @@ -7,8 +7,7 @@ from abc import ( abstractmethod, ) from enum import Enum - -from typing_extensions import TypeAlias +from typing import TypeAlias try: from galaxy.model import Job diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py index 0e231f3ad32..9c82de31dc0 100644 --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -30,10 +30,10 @@ import builtins import datetime import logging import re +from collections.abc import Callable from functools import partial from typing import ( Any, - Callable, Generic, NamedTuple, Optional, diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py index 4f0a834fd9a..26ab331775b 100644 --- a/lib/galaxy/managers/collections.py +++ b/lib/galaxy/managers/collections.py @@ -1,6 +1,7 @@ import logging from typing import ( Any, + Literal, Optional, overload, TYPE_CHECKING, @@ -12,7 +13,6 @@ from sqlalchemy.orm import ( joinedload, Query, ) -from typing_extensions import Literal from galaxy import model from galaxy.datatypes.registry import Registry diff --git a/lib/galaxy/managers/context.py b/lib/galaxy/managers/context.py index c6ec8eff247..00a169d8439 100644 --- a/lib/galaxy/managers/context.py +++ b/lib/galaxy/managers/context.py @@ -37,10 +37,10 @@ A method that requires a user but not a history should declare its # more checks against this issue. import abc import string +from collections.abc import Callable from json import dumps from typing import ( Any, - Callable, cast, Literal, Optional, diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py index e68ad5c0515..5845e1405b5 100644 --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -9,6 +9,7 @@ import logging from typing import ( Any, cast, + Literal, Optional, TYPE_CHECKING, Union, @@ -25,7 +26,6 @@ from sqlalchemy import ( true, ) from sqlalchemy.orm import aliased -from typing_extensions import Literal from galaxy import model from galaxy.exceptions import ( diff --git a/lib/galaxy/managers/pages.py b/lib/galaxy/managers/pages.py index 88eb9685328..77ec6655d11 100644 --- a/lib/galaxy/managers/pages.py +++ b/lib/galaxy/managers/pages.py @@ -8,10 +8,10 @@ from within Galaxy. import logging import re +from collections.abc import Callable from html.entities import name2codepoint from html.parser import HTMLParser from typing import ( - Callable, Optional, TYPE_CHECKING, Union, diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 344128c3145..0582c2c9236 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -9,6 +9,7 @@ from typing import ( NamedTuple, Optional, TYPE_CHECKING, + TypeAlias, Union, ) @@ -41,9 +42,6 @@ from sqlalchemy.orm import ( joinedload, subqueryload, ) -from typing_extensions import ( - TypeAlias, -) from galaxy import ( exceptions, diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 101f8881f2a..c70972861e5 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -32,10 +32,12 @@ from typing import ( cast, ClassVar, Generic, + Literal, NamedTuple, Optional, overload, TYPE_CHECKING, + TypeAlias, TypeVar, Union, ) @@ -132,10 +134,8 @@ from sqlalchemy.orm.session import Session from sqlalchemy.sql.expression import FromClause from typing_extensions import ( deprecated, - Literal, NotRequired, Protocol, - TypeAlias, TypedDict, ) @@ -7221,6 +7221,12 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable): def expire_populated_state(self): required_object_session(self).expire(self, ("populated_state",)) + # Clear the cached populated_optimized value so it will be recomputed + # on the next access with fresh database state. This prevents a race + # condition where the cached value becomes stale while nested + # collections are being populated. + if hasattr(self, "_populated_optimized"): + delattr(self, "_populated_optimized") @property def allow_implicit_mapping(self): diff --git a/lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py b/lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py index 1037ea0c2de..3bbb83dc62b 100644 --- a/lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py +++ b/lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py @@ -1,6 +1,7 @@ from dataclasses import dataclass from typing import ( cast, + Literal, Optional, Protocol, TYPE_CHECKING, @@ -15,7 +16,6 @@ from pydantic import ( BaseModel, Field, ) -from typing_extensions import Literal from galaxy.exceptions import RequestParameterInvalidException from galaxy.model.dataset_collections.rule_target_columns import ( diff --git a/lib/galaxy/model/migrations/alembic/env.py b/lib/galaxy/model/migrations/alembic/env.py index 98091912b80..c9db41cc84d 100644 --- a/lib/galaxy/model/migrations/alembic/env.py +++ b/lib/galaxy/model/migrations/alembic/env.py @@ -1,7 +1,7 @@ import logging import re +from collections.abc import Callable from typing import ( - Callable, cast, ) diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py index 00441b3ce38..08eedd509ae 100644 --- a/lib/galaxy/model/store/__init__.py +++ b/lib/galaxy/model/store/__init__.py @@ -8,6 +8,7 @@ import tarfile import tempfile from collections import defaultdict from collections.abc import ( + Callable, Iterable, Iterator, ) @@ -22,7 +23,6 @@ from tempfile import mkdtemp from types import TracebackType from typing import ( Any, - Callable, cast, Literal, Optional, diff --git a/lib/galaxy/model/store/discover.py b/lib/galaxy/model/store/discover.py index ccd0c7960ef..50e6125a113 100644 --- a/lib/galaxy/model/store/discover.py +++ b/lib/galaxy/model/store/discover.py @@ -9,10 +9,12 @@ corresponding to files in other contexts. import abc import logging import os -from collections.abc import Iterable +from collections.abc import ( + Callable, + Iterable, +) from typing import ( Any, - Callable, NamedTuple, Optional, TYPE_CHECKING, diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py index 4df58cf2150..4fa03b74647 100644 --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -1,10 +1,10 @@ import logging import os +from collections.abc import Callable from datetime import datetime from enum import Enum from typing import ( Any, - Callable, Optional, ) diff --git a/lib/galaxy/model/unittest_utils/model_testing_utils.py b/lib/galaxy/model/unittest_utils/model_testing_utils.py index dacbde037a4..a1af8dd23ba 100644 --- a/lib/galaxy/model/unittest_utils/model_testing_utils.py +++ b/lib/galaxy/model/unittest_utils/model_testing_utils.py @@ -1,9 +1,11 @@ import os import uuid -from collections.abc import Iterator +from collections.abc import ( + Callable, + Iterator, +) from contextlib import contextmanager from typing import ( - Callable, Optional, ) diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py index fe97e604c1b..0e3d0f719b0 100644 --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -135,7 +135,7 @@ class ControlTask: while self.response is self._response: self.connection.drain_events(timeout=timeout) return self.response - except socket.timeout: + except TimeoutError: log.exception("Error waiting for task: '%s' sent with routing key '%s'", payload, routing_key) except Exception: log.exception("Error queueing async task: '%s'. for %s", payload, routing_key) diff --git a/lib/galaxy/quota/_schema.py b/lib/galaxy/quota/_schema.py index faf9c3cc85e..e0fee00f1d0 100644 --- a/lib/galaxy/quota/_schema.py +++ b/lib/galaxy/quota/_schema.py @@ -1,5 +1,6 @@ from enum import Enum from typing import ( + Literal, Optional, ) @@ -7,7 +8,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal from galaxy.schema.fields import ( EncodedDatabaseIdField, diff --git a/lib/galaxy/schema/fetch_data.py b/lib/galaxy/schema/fetch_data.py index e9f236603aa..91cfe8348e6 100644 --- a/lib/galaxy/schema/fetch_data.py +++ b/lib/galaxy/schema/fetch_data.py @@ -3,6 +3,7 @@ from enum import Enum from typing import ( Annotated, Any, + Literal, Optional, Union, ) @@ -17,7 +18,6 @@ from pydantic import ( TypeAdapter, UUID4, ) -from typing_extensions import Literal from galaxy.schema.fields import DecodedDatabaseIdField from galaxy.schema.schema import Model diff --git a/lib/galaxy/schema/fields.py b/lib/galaxy/schema/fields.py index 180e463d877..75428e18038 100644 --- a/lib/galaxy/schema/fields.py +++ b/lib/galaxy/schema/fields.py @@ -1,7 +1,8 @@ import re +from collections.abc import Callable from typing import ( Annotated, - Callable, + get_args, get_origin, TYPE_CHECKING, Union, @@ -14,9 +15,6 @@ from pydantic import ( WithJsonSchema, ) from pydantic_core import PydanticCustomError -from typing_extensions import ( - get_args, -) from galaxy.exceptions import MessageException diff --git a/lib/galaxy/schema/groups.py b/lib/galaxy/schema/groups.py index 867841bce92..3998096f81b 100644 --- a/lib/galaxy/schema/groups.py +++ b/lib/galaxy/schema/groups.py @@ -1,10 +1,12 @@ -from typing import Optional +from typing import ( + Literal, + Optional, +) from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/history.py b/lib/galaxy/schema/history.py index b0978dc6716..9b9a5c4985f 100644 --- a/lib/galaxy/schema/history.py +++ b/lib/galaxy/schema/history.py @@ -1,5 +1,6 @@ from datetime import datetime from typing import ( + Literal, Optional, ) @@ -8,7 +9,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal from galaxy.schema.fields import EncodedDatabaseIdField from galaxy.schema.schema import ( diff --git a/lib/galaxy/schema/invocation.py b/lib/galaxy/schema/invocation.py index 6797700f0d1..25e77fe9dfa 100644 --- a/lib/galaxy/schema/invocation.py +++ b/lib/galaxy/schema/invocation.py @@ -4,6 +4,7 @@ from typing import ( Annotated, Any, Generic, + Literal, Optional, Union, ) @@ -17,7 +18,6 @@ from pydantic import ( UUID4, ) from typing_extensions import ( - Literal, TypeAliasType, ) diff --git a/lib/galaxy/schema/jobs.py b/lib/galaxy/schema/jobs.py index 39e3ee33cf2..a1f76797049 100644 --- a/lib/galaxy/schema/jobs.py +++ b/lib/galaxy/schema/jobs.py @@ -1,6 +1,7 @@ import json from typing import ( Any, + Literal, Optional, Union, ) @@ -11,7 +12,6 @@ from pydantic import ( field_validator, UUID4, ) -from typing_extensions import Literal from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/library_contents.py b/lib/galaxy/schema/library_contents.py index 1e0d1f05b65..66b3593cf98 100644 --- a/lib/galaxy/schema/library_contents.py +++ b/lib/galaxy/schema/library_contents.py @@ -3,6 +3,7 @@ from enum import Enum from typing import ( Annotated, Any, + Literal, Optional, Union, ) @@ -13,9 +14,6 @@ from pydantic import ( RootModel, ) from pydantic.functional_validators import field_validator -from typing_extensions import ( - Literal, -) from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/notifications.py b/lib/galaxy/schema/notifications.py index a7f59906924..885240d16f7 100644 --- a/lib/galaxy/schema/notifications.py +++ b/lib/galaxy/schema/notifications.py @@ -4,6 +4,7 @@ from typing import ( Annotated, Any, Generic, + Literal, Optional, Union, ) @@ -13,9 +14,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import ( - Literal, -) from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py index 540b1a765fa..073c36b6836 100644 --- a/lib/galaxy/schema/schema.py +++ b/lib/galaxy/schema/schema.py @@ -9,7 +9,9 @@ from enum import Enum from typing import ( Annotated, Any, + Literal, Optional, + TypeAlias, Union, ) from uuid import UUID @@ -29,9 +31,7 @@ from pydantic import ( ) from pydantic_core import core_schema from typing_extensions import ( - Literal, NotRequired, - TypeAlias, TypedDict, ) diff --git a/lib/galaxy/schema/storage_cleaner.py b/lib/galaxy/schema/storage_cleaner.py index d34f2a61b0c..a7de24ca60c 100644 --- a/lib/galaxy/schema/storage_cleaner.py +++ b/lib/galaxy/schema/storage_cleaner.py @@ -1,11 +1,11 @@ from datetime import datetime from enum import Enum from typing import ( + Literal, Union, ) from pydantic import Field -from typing_extensions import Literal from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/types.py b/lib/galaxy/schema/types.py index 7a8dae0b28a..8cfce956ba1 100644 --- a/lib/galaxy/schema/types.py +++ b/lib/galaxy/schema/types.py @@ -1,14 +1,12 @@ from datetime import datetime from typing import ( Annotated, + Literal, Union, ) from pydantic import ValidationInfo from pydantic.functional_validators import AfterValidator -from typing_extensions import ( - Literal, -) # Relative URLs cannot be validated with AnyUrl, they need a scheme. # Making them an alias of `str` for now diff --git a/lib/galaxy/schema/visualization.py b/lib/galaxy/schema/visualization.py index d769623f408..9471301256f 100644 --- a/lib/galaxy/schema/visualization.py +++ b/lib/galaxy/schema/visualization.py @@ -1,5 +1,6 @@ from datetime import datetime from typing import ( + Literal, Optional, Union, ) @@ -9,7 +10,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal from galaxy.schema.fields import ( DecodedDatabaseIdField, diff --git a/lib/galaxy/schema/workflow/comments.py b/lib/galaxy/schema/workflow/comments.py index 0565c60b5b8..e41763d383b 100644 --- a/lib/galaxy/schema/workflow/comments.py +++ b/lib/galaxy/schema/workflow/comments.py @@ -1,4 +1,5 @@ from typing import ( + Literal, Optional, Union, ) @@ -8,7 +9,6 @@ from pydantic import ( Field, RootModel, ) -from typing_extensions import Literal class BaseComment(BaseModel): diff --git a/lib/galaxy/security/__init__.py b/lib/galaxy/security/__init__.py index 9cd98a972d1..401b3d535b7 100644 --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -4,11 +4,10 @@ Galaxy Security """ from typing import ( + Literal, Optional, ) -from typing_extensions import Literal - from galaxy.util.bunch import Bunch ActionModel = Literal["grant", "restrict"] diff --git a/lib/galaxy/selenium/axe_results.py b/lib/galaxy/selenium/axe_results.py index a0d67e5edfb..a43e1d61c6a 100644 --- a/lib/galaxy/selenium/axe_results.py +++ b/lib/galaxy/selenium/axe_results.py @@ -1,10 +1,10 @@ from typing import ( Any, + Literal, Optional, ) from typing_extensions import ( - Literal, Protocol, ) diff --git a/lib/galaxy/selenium/has_driver_protocol.py b/lib/galaxy/selenium/has_driver_protocol.py index 62fccb1047b..ef0ef09af88 100644 --- a/lib/galaxy/selenium/has_driver_protocol.py +++ b/lib/galaxy/selenium/has_driver_protocol.py @@ -5,10 +5,10 @@ allowing NavigatesGalaxy to work with either backend via composition. """ from abc import abstractmethod +from collections.abc import Callable from contextlib import AbstractContextManager from typing import ( Any, - Callable, Generic, Literal, Optional, diff --git a/lib/galaxy/tool_shed/metadata/metadata_generator.py b/lib/galaxy/tool_shed/metadata/metadata_generator.py index b0b7a6123a8..6422639bc3f 100644 --- a/lib/galaxy/tool_shed/metadata/metadata_generator.py +++ b/lib/galaxy/tool_shed/metadata/metadata_generator.py @@ -392,7 +392,9 @@ class BaseMetadataGenerator: if invalid_tool_configs: metadata_dict["invalid_tools"] = invalid_tool_configs self.metadata_dict = metadata_dict - remove_dir(work_dir) + # Only remove work_dir if not resetting all metadata - in that case the caller handles cleanup + if not self.resetting_all_metadata_on_repository: + remove_dir(work_dir) def generate_package_dependency_metadata(self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict): """ diff --git a/lib/galaxy/tools/_types.py b/lib/galaxy/tools/_types.py index dd6057a11a1..8ee3648aff7 100644 --- a/lib/galaxy/tools/_types.py +++ b/lib/galaxy/tools/_types.py @@ -22,11 +22,10 @@ provide strong traditional typing semantics. from typing import ( Any, + Literal, Union, ) -from typing_extensions import Literal - # Input dictionary from the API, may include map/reduce instructions. Objects are referenced by "src" # dictionaries and encoded IDS. ToolRequestT = dict[str, Any] diff --git a/lib/galaxy/tools/evaluation.py b/lib/galaxy/tools/evaluation.py index 12dec5410c4..bf6d106a08e 100644 --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -5,10 +5,10 @@ import re import shlex import string import tempfile +from collections.abc import Callable from datetime import datetime from typing import ( Any, - Callable, Literal, Optional, TYPE_CHECKING, diff --git a/lib/galaxy/tools/execute.py b/lib/galaxy/tools/execute.py index f445e5fe0d5..8a0e9ae9796 100644 --- a/lib/galaxy/tools/execute.py +++ b/lib/galaxy/tools/execute.py @@ -8,17 +8,17 @@ import collections import logging import typing from abc import abstractmethod +from collections.abc import Callable from typing import ( Any, - Callable, NamedTuple, Optional, + TypeAlias, Union, ) from boltons.iterutils import remap from packaging.version import Version -from typing_extensions import TypeAlias from galaxy import model from galaxy.exceptions import ToolInputsNotOKException diff --git a/lib/galaxy/tools/fetch/workbooks.py b/lib/galaxy/tools/fetch/workbooks.py index 52d44c1f36f..1e509b152bf 100644 --- a/lib/galaxy/tools/fetch/workbooks.py +++ b/lib/galaxy/tools/fetch/workbooks.py @@ -1,5 +1,6 @@ from dataclasses import dataclass from typing import ( + Literal, Optional, Union, ) @@ -9,7 +10,6 @@ from pydantic import ( BaseModel, Field, ) -from typing_extensions import Literal from galaxy.exceptions import RequestParameterInvalidException from galaxy.model.dataset_collections.auto_identifiers import ( diff --git a/lib/galaxy/tools/parameters/cancelable_request.py b/lib/galaxy/tools/parameters/cancelable_request.py index 38566237964..635760e0449 100644 --- a/lib/galaxy/tools/parameters/cancelable_request.py +++ b/lib/galaxy/tools/parameters/cancelable_request.py @@ -2,11 +2,11 @@ import asyncio import logging from typing import ( Any, + Literal, Optional, ) import aiohttp -from typing_extensions import Literal log = logging.getLogger() diff --git a/lib/galaxy/tools/parameters/dynamic_options.py b/lib/galaxy/tools/parameters/dynamic_options.py index ba4e7d15e3f..69ee4431744 100644 --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -15,11 +15,10 @@ from typing import ( Any, cast, get_args, + Literal, Optional, ) -from typing_extensions import Literal - from galaxy.model import ( DatasetCollectionElement, HistoryDatasetAssociation, diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index b69ae48bde4..eb525a8c848 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -6,11 +6,13 @@ import io import logging import os import unicodedata -from collections.abc import Mapping +from collections.abc import ( + Callable, + Mapping, +) from math import inf from typing import ( Any, - Callable, Optional, TYPE_CHECKING, ) diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py index 2d6064c5496..6cde4936535 100644 --- a/lib/galaxy/tools/remote_tool_eval.py +++ b/lib/galaxy/tools/remote_tool_eval.py @@ -3,8 +3,8 @@ import os import shutil import tempfile import traceback +from collections.abc import Callable from typing import ( - Callable, NamedTuple, ) diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py index c303a694ea1..9b276694b36 100644 --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -15,12 +15,12 @@ from typing import ( cast, Optional, TYPE_CHECKING, + TypeAlias, Union, ) from typing_extensions import ( Self, - TypeAlias, ) from galaxy.model import ( diff --git a/lib/galaxy/visualization/data_providers/registry.py b/lib/galaxy/visualization/data_providers/registry.py index ba802629d3c..ba03f8f08b8 100644 --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -1,10 +1,9 @@ from typing import ( + Literal, Optional, Union, ) -from typing_extensions import Literal - from galaxy.datatypes.data import ( Data, Newick, diff --git a/lib/galaxy/visualization/plugins/resource_parser.py b/lib/galaxy/visualization/plugins/resource_parser.py index 173da37e281..af24e3c8e01 100644 --- a/lib/galaxy/visualization/plugins/resource_parser.py +++ b/lib/galaxy/visualization/plugins/resource_parser.py @@ -6,8 +6,8 @@ a dictionary of string data/ids (often from a query string). import json import logging import weakref +from collections.abc import Callable from typing import ( - Callable, Optional, Union, ) diff --git a/lib/galaxy/web/framework/middleware/remoteuser.py b/lib/galaxy/web/framework/middleware/remoteuser.py index 8e150917e43..7139311d491 100644 --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -67,7 +67,7 @@ class RemoteUser: if self.display_servers and "REMOTE_ADDR" in environ: try: host = socket.gethostbyaddr(environ["REMOTE_ADDR"])[0] - except (OSError, socket.herror, socket.gaierror, socket.timeout): + except (OSError, socket.herror, socket.gaierror): # in the event of a lookup failure, deny access host = None if host in self.display_servers: diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py index b2c74d3c500..44accd7ba68 100644 --- a/lib/galaxy/web_stack/__init__.py +++ b/lib/galaxy/web_stack/__init__.py @@ -5,8 +5,8 @@ import multiprocessing import os import sys import threading +from collections.abc import Callable from typing import ( - Callable, Optional, TYPE_CHECKING, ) diff --git a/lib/galaxy/web_stack/handlers.py b/lib/galaxy/web_stack/handlers.py index debe0e1ffde..0ee037dbf0f 100644 --- a/lib/galaxy/web_stack/handlers.py +++ b/lib/galaxy/web_stack/handlers.py @@ -8,13 +8,15 @@ import logging import os import random from collections.abc import ( + Callable, Iterable, Sequence, ) from enum import Enum from typing import ( Any, - Callable, + Concatenate, + Literal, Protocol, TYPE_CHECKING, TypeVar, @@ -22,10 +24,6 @@ from typing import ( ) from sqlalchemy.orm import object_session -from typing_extensions import ( - Concatenate, - Literal, -) from galaxy.exceptions import HandlerAssignmentError from galaxy.util import ( diff --git a/lib/galaxy/webapps/base/controller.py b/lib/galaxy/webapps/base/controller.py index 215f63c6b5f..ac7a605b1cc 100644 --- a/lib/galaxy/webapps/base/controller.py +++ b/lib/galaxy/webapps/base/controller.py @@ -3,9 +3,9 @@ Contains functionality needed in every web interface """ import logging +from collections.abc import Callable from typing import ( Any, - Callable, ) from webob.exc import ( diff --git a/lib/galaxy/webapps/base/webapp.py b/lib/galaxy/webapps/base/webapp.py index 9fdd44724f3..70276f05b26 100644 --- a/lib/galaxy/webapps/base/webapp.py +++ b/lib/galaxy/webapps/base/webapp.py @@ -721,7 +721,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction, context.ProvidesHistoryCo if self.app.datatypes_registry.get_display_sites("ucsc") and self.request.path == display_as: try: host = socket.gethostbyaddr(self.environ["REMOTE_ADDR"])[0] - except (OSError, socket.herror, socket.gaierror, socket.timeout): + except (OSError, socket.herror, socket.gaierror): host = None if host in UCSC_SERVERS: return diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py index f3a57ee407c..fcc32ac9650 100644 --- a/lib/galaxy/webapps/galaxy/api/__init__.py +++ b/lib/galaxy/webapps/galaxy/api/__init__.py @@ -3,13 +3,16 @@ This module *does not* contain API routes. It exclusively contains dependencies """ import inspect -from collections.abc import AsyncGenerator +from collections.abc import ( + AsyncGenerator, + Callable, +) from enum import Enum from string import Template from typing import ( Any, - Callable, cast, + Literal, NamedTuple, Optional, TypeVar, @@ -56,7 +59,6 @@ from starlette.routing import ( NoMatchFound, ) from starlette.types import Scope -from typing_extensions import Literal try: from starlette_context import context as request_context diff --git a/lib/galaxy/webapps/galaxy/services/credentials.py b/lib/galaxy/webapps/galaxy/services/credentials.py index 619ab4cbdb1..9b7977c75db 100644 --- a/lib/galaxy/webapps/galaxy/services/credentials.py +++ b/lib/galaxy/webapps/galaxy/services/credentials.py @@ -1,6 +1,6 @@ +from collections.abc import Callable from typing import ( Any, - Callable, cast, Optional, Union, diff --git a/lib/galaxy/webapps/galaxy/services/dataset_collections.py b/lib/galaxy/webapps/galaxy/services/dataset_collections.py index ec3d927bdb6..243ddd2c1e5 100644 --- a/lib/galaxy/webapps/galaxy/services/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/services/dataset_collections.py @@ -1,6 +1,7 @@ from io import BytesIO from logging import getLogger from typing import ( + Literal, Optional, TYPE_CHECKING, Union, @@ -13,7 +14,6 @@ from pydantic import ( RootModel, ValidationError, ) -from typing_extensions import Literal from galaxy import exceptions from galaxy.datatypes.registry import Registry diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py index 8b80da54e22..dec28c6a815 100644 --- a/lib/galaxy/webapps/galaxy/services/history_contents.py +++ b/lib/galaxy/webapps/galaxy/services/history_contents.py @@ -5,6 +5,7 @@ from collections.abc import Iterable from typing import ( Any, cast, + Literal, Optional, TYPE_CHECKING, Union, @@ -16,7 +17,6 @@ from pydantic import ( Field, ) from typing_extensions import ( - Literal, Protocol, ) diff --git a/lib/galaxy/webapps/openapi/_compat/v2.py b/lib/galaxy/webapps/openapi/_compat/v2.py index ad6c5ea57ca..7327e4ca440 100644 --- a/lib/galaxy/webapps/openapi/_compat/v2.py +++ b/lib/galaxy/webapps/openapi/_compat/v2.py @@ -2,6 +2,7 @@ from collections.abc import Sequence from typing import ( Any, cast, + Literal, Union, ) @@ -18,7 +19,6 @@ from pydantic.json_schema import ( GenerateJsonSchema as GenerateJsonSchema, JsonSchemaValue as JsonSchemaValue, ) -from typing_extensions import Literal def get_definitions( diff --git a/lib/galaxy/work/context.py b/lib/galaxy/work/context.py index 67aae7c9f2f..5ea9805d781 100644 --- a/lib/galaxy/work/context.py +++ b/lib/galaxy/work/context.py @@ -1,12 +1,11 @@ import abc from typing import ( Any, + Literal, Optional, TYPE_CHECKING, ) -from typing_extensions import Literal - from galaxy.managers.context import ProvidesHistoryContext if TYPE_CHECKING: diff --git a/lib/galaxy/workflow/refactor/schema.py b/lib/galaxy/workflow/refactor/schema.py index 1ed82e902ec..edef0d8b8b5 100644 --- a/lib/galaxy/workflow/refactor/schema.py +++ b/lib/galaxy/workflow/refactor/schema.py @@ -2,6 +2,7 @@ from enum import Enum from typing import ( Annotated, Any, + Literal, Optional, Union, ) @@ -10,9 +11,6 @@ from pydantic import ( BaseModel, Field, ) -from typing_extensions import ( - Literal, -) LABEL_DESCRIPTION = "The unique label of the step being referenced." INPUT_NAME_DESCRIPTION = "The input name as defined by the workflow module corresponding to the step being referenced. For Galaxy tool steps these inputs should be normalized using '|' (e.g. 'cond|repeat_0|input')." diff --git a/lib/galaxy_test/api/test_drs.py b/lib/galaxy_test/api/test_drs.py index 5859e2ecbe0..757bc5a691e 100644 --- a/lib/galaxy_test/api/test_drs.py +++ b/lib/galaxy_test/api/test_drs.py @@ -1,7 +1,5 @@ import tempfile -from typing import ( - Callable, -) +from collections.abc import Callable from unittest import SkipTest from urllib.parse import ( urljoin, diff --git a/lib/galaxy_test/base/decorators.py b/lib/galaxy_test/base/decorators.py index 95ea1a18ab2..1bf4555014c 100644 --- a/lib/galaxy_test/base/decorators.py +++ b/lib/galaxy_test/base/decorators.py @@ -12,10 +12,12 @@ histories, libraries, etc... should be annotated ideally. import os import unittest from functools import wraps -from typing import Union +from typing import ( + Literal, + Union, +) import pytest -from typing_extensions import Literal KnownRequirementT = Union[ Literal["admin"], diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py index 429d6bd91cb..392bc1f59bc 100644 --- a/lib/galaxy_test/base/populators.py +++ b/lib/galaxy_test/base/populators.py @@ -52,14 +52,17 @@ from abc import ( ABCMeta, abstractmethod, ) -from collections.abc import Generator +from collections.abc import ( + Callable, + Generator, +) from functools import wraps from io import StringIO from operator import itemgetter from typing import ( Any, - Callable, cast, + Literal, NamedTuple, Optional, Union, @@ -82,7 +85,6 @@ from pydantic import ( from requests import Response from rocrate.rocrate import ROCrate from typing_extensions import ( - Literal, Self, TypedDict, ) diff --git a/lib/galaxy_test/base/uses_shed_api.py b/lib/galaxy_test/base/uses_shed_api.py index 597920cb5fd..e53ac075b4d 100644 --- a/lib/galaxy_test/base/uses_shed_api.py +++ b/lib/galaxy_test/base/uses_shed_api.py @@ -1,7 +1,7 @@ import abc +from collections.abc import Callable from typing import ( Any, - Callable, Optional, ) from unittest import SkipTest diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py index 793c26051b6..31334e166ad 100644 --- a/lib/galaxy_test/selenium/test_workflow_run.py +++ b/lib/galaxy_test/selenium/test_workflow_run.py @@ -1,10 +1,10 @@ import json +from typing import Literal from uuid import uuid4 import yaml from selenium.webdriver.common.by import By from selenium.webdriver.common.keys import Keys -from typing_extensions import Literal from galaxy_test.base import rules_test_data from galaxy_test.base.workflow_fixtures import ( diff --git a/lib/tool_shed/managers/categories.py b/lib/tool_shed/managers/categories.py index 6b62c91fea9..a2b84135c4d 100644 --- a/lib/tool_shed/managers/categories.py +++ b/lib/tool_shed/managers/categories.py @@ -1,6 +1,6 @@ +from collections.abc import Callable from typing import ( Any, - Callable, ) from sqlalchemy import select diff --git a/lib/tool_shed/managers/repositories.py b/lib/tool_shed/managers/repositories.py index 0cdc2d50ec1..e92f5e0d85a 100644 --- a/lib/tool_shed/managers/repositories.py +++ b/lib/tool_shed/managers/repositories.py @@ -5,10 +5,10 @@ Manager and Serializer for TS repositories. import json import logging from collections import namedtuple +from collections.abc import Callable from time import strftime from typing import ( Any, - Callable, cast, Optional, Union, diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py index 13031959ff7..5c26eb70f10 100644 --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -799,14 +799,24 @@ class RepositoryMetadataManager(ToolShedMetadataGenerator): metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - for changeset in self.repository.get_changesets_for_setting_metadata(self.app): - work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-ramorits") - ctx = repo[changeset] - log.debug("Cloning repository changeset revision: %s", str(ctx.rev())) - assert self.repository_clone_url - repository_clone_url = repository_clone_url or self.repository_clone_url - cloned_ok, error_message = hg_util.clone_repository(repository_clone_url, work_dir, str(ctx.rev())) - if cloned_ok: + + # Clone repository once, then update for each changeset revision. + work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-ramorits") + assert self.repository_clone_url + repository_clone_url = repository_clone_url or self.repository_clone_url + log.debug("Cloning repository for metadata reset") + cloned_ok, error_message = hg_util.clone_repository(repository_clone_url, work_dir) + if not cloned_ok: + log.error(f"Failed to clone repository: {error_message}") + basic_util.remove_dir(work_dir) + self._clean_repository_metadata(changeset_revisions) + return + + try: + for changeset in self.repository.get_changesets_for_setting_metadata(self.app): + ctx = repo[changeset] + log.debug("Updating to changeset revision: %s", str(ctx.rev())) + hg_util.update_repository(work_dir, str(ctx.rev())) log.debug("Generating metadata for changeset revision: %s", str(ctx.rev())) self.set_changeset_revision(str(ctx)) self.set_repository_files_dir(work_dir) @@ -823,11 +833,11 @@ class RepositoryMetadataManager(ToolShedMetadataGenerator): # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - log.info(f"amd {ancestor_metadata_dict}") + log.debug(f"amd {ancestor_metadata_dict}") comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) - log.info(f"comparison {comparison}") + log.debug(f"comparison {comparison}") if comparison in [self.NO_METADATA, self.EQUAL, self.SUBSET]: ancestor_changeset_revision = self.changeset_revision ancestor_metadata_dict = self.metadata_dict @@ -858,6 +868,7 @@ class RepositoryMetadataManager(ToolShedMetadataGenerator): changeset_revisions.append(metadata_changeset_revision) ancestor_changeset_revision = None ancestor_metadata_dict = None + finally: basic_util.remove_dir(work_dir) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. diff --git a/lib/tool_shed/test/base/api_util.py b/lib/tool_shed/test/base/api_util.py index 30df5c37033..ae84e29e96c 100644 --- a/lib/tool_shed/test/base/api_util.py +++ b/lib/tool_shed/test/base/api_util.py @@ -1,15 +1,15 @@ import os import re +from collections.abc import Callable from functools import wraps from typing import ( Any, - Callable, + Literal, Optional, ) from urllib.parse import urljoin import requests -from typing_extensions import Literal from galaxy_test.base.api_asserts import ( assert_has_keys, diff --git a/lib/tool_shed/test/functional/conftest.py b/lib/tool_shed/test/functional/conftest.py index d0bcaf78508..c35efde18f3 100644 --- a/lib/tool_shed/test/functional/conftest.py +++ b/lib/tool_shed/test/functional/conftest.py @@ -1,7 +1,7 @@ import os -from collections.abc import Generator -from typing import ( +from collections.abc import ( Callable, + Generator, ) import pytest diff --git a/lib/tool_shed/webapp/api/groups.py b/lib/tool_shed/webapp/api/groups.py index ea5b88e657d..aa89e3ba2e4 100644 --- a/lib/tool_shed/webapp/api/groups.py +++ b/lib/tool_shed/webapp/api/groups.py @@ -1,7 +1,5 @@ import logging -from typing import ( - Callable, -) +from collections.abc import Callable from sqlalchemy import select diff --git a/lib/tool_shed/webapp/api/repositories.py b/lib/tool_shed/webapp/api/repositories.py index 1534d34b6a5..1d3256c69cb 100644 --- a/lib/tool_shed/webapp/api/repositories.py +++ b/lib/tool_shed/webapp/api/repositories.py @@ -1,11 +1,9 @@ import json import logging import os +from collections.abc import Callable from io import StringIO from time import strftime -from typing import ( - Callable, -) from webob.compat import cgi_FieldStorage diff --git a/lib/tool_shed/webapp/api/repository_revisions.py b/lib/tool_shed/webapp/api/repository_revisions.py index aee7c1076d0..9aed99467bb 100644 --- a/lib/tool_shed/webapp/api/repository_revisions.py +++ b/lib/tool_shed/webapp/api/repository_revisions.py @@ -1,7 +1,5 @@ import logging -from typing import ( - Callable, -) +from collections.abc import Callable from sqlalchemy import select diff --git a/lib/tool_shed/webapp/controllers/repository.py b/lib/tool_shed/webapp/controllers/repository.py index 4d8f2a4c612..c4bbb712266 100644 --- a/lib/tool_shed/webapp/controllers/repository.py +++ b/lib/tool_shed/webapp/controllers/repository.py @@ -4,10 +4,9 @@ import os import string import tempfile from datetime import date +from typing import Any from mercurial import ( - cmdutil, - commands, mdiff, patch, ) @@ -74,15 +73,15 @@ malicious_error = " This changeset cannot be downloaded because it potentially malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." -def get_mercurial_default_options_dict(command): - """Borrowed from repoman - get default parameters for a mercurial command.""" - possible = cmdutil.findpossible(command, commands.table) - # Mercurial >= 3.4 returns a tuple whose first element is the old return dict - if type(possible) is tuple: - possible = possible[0] - if len(possible) != 1: - raise Exception(f'unable to find mercurial command "{command}"') - return {r[1].replace(b"-", b"_"): r[2] for r in next(iter(possible.values()))[1][1]} +def get_mercurial_default_options_dict(command: str) -> dict[str, Any]: + """Get default parameters for a mercurial command.""" + # Use mdiff.diffopts defaults directly instead of introspecting command table + # (the old cmdutil.findpossible API was removed in Mercurial 7.2) + if command == "diff": + # Convert byte keys to strings but preserve value types (int, bool) + # as mdiff.diffopts expects properly typed values + return {(k.decode("utf-8") if isinstance(k, bytes) else k): v for k, v in mdiff.diffopts.defaults.items()} + raise Exception(f'unable to find mercurial command "{command}"') class RepositoryController(BaseUIController, ratings_util.ItemRatings): @@ -2366,10 +2365,8 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings): else: ctx_child = None diffs = [] - options_dict = get_mercurial_default_options_dict(b"diff") - # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each - # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed. - options_dict = {util.unicodify(k): util.unicodify(v) for k, v in options_dict.items()} + # Get default diff options with string keys and properly typed values + options_dict = get_mercurial_default_options_dict("diff") options_dict["maxfile"] = basic_util.MAXDIFFSIZE options_dict["maxtotal"] = basic_util.MAXDIFFSIZE diffopts = mdiff.diffopts(**options_dict) diff --git a/lib/tool_shed/webapp/framework/middleware/remoteuser.py b/lib/tool_shed/webapp/framework/middleware/remoteuser.py index fff7395b228..73b4a033a44 100644 --- a/lib/tool_shed/webapp/framework/middleware/remoteuser.py +++ b/lib/tool_shed/webapp/framework/middleware/remoteuser.py @@ -52,7 +52,7 @@ class RemoteUser: if self.display_servers and "REMOTE_ADDR" in environ: try: host = socket.gethostbyaddr(environ["REMOTE_ADDR"])[0] - except (OSError, socket.herror, socket.gaierror, socket.timeout): + except (OSError, socket.herror, socket.gaierror): # in the event of a lookup failure, deny access host = None if host in self.display_servers: diff --git a/lib/tool_shed/webapp/model/migrations/alembic/env.py b/lib/tool_shed/webapp/model/migrations/alembic/env.py index 04f4769df4c..1245260b50e 100644 --- a/lib/tool_shed/webapp/model/migrations/alembic/env.py +++ b/lib/tool_shed/webapp/model/migrations/alembic/env.py @@ -1,6 +1,6 @@ import logging +from collections.abc import Callable from typing import ( - Callable, cast, ) diff --git a/lib/tool_shed_client/schema/__init__.py b/lib/tool_shed_client/schema/__init__.py index 1fe5e92890e..62cd8582b74 100644 --- a/lib/tool_shed_client/schema/__init__.py +++ b/lib/tool_shed_client/schema/__init__.py @@ -1,5 +1,6 @@ from typing import ( Any, + Literal, Optional, Union, ) @@ -11,7 +12,6 @@ from pydantic import ( RootModel, ) from typing_extensions import ( - Literal, TypedDict, ) diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index a8d1aab0bc4..e5463ab0e2c 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -83,8 +82,7 @@ install_requires = WebOb>=1.8.9 Whoosh packages = find: -python_requires = >=3.9 - +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 8de84944002..50be0e6d7cc 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -36,8 +35,7 @@ install_requires = galaxy-data galaxy-util packages = find: -python_requires = >=3.9 - +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index b14aa426151..64c32e32a49 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -39,12 +38,12 @@ install_requires = pykwalify PyYAML packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = pytest - gravity @ git+https://github.com/nsoranzo/gravity.git@python3.14 + gravity>=1.2.0 [options.entry_points] console_scripts = diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 7688f40af7d..dd66573c4e3 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -67,8 +66,7 @@ install_requires = tifffile typing-extensions packages = find: -python_requires = >=3.9 - +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 8be26ed4ffa..00aeea918b0 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -39,7 +38,7 @@ install_requires = typing-extensions fsspec packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index a5f6b3cc879..184fefcb320 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -41,7 +40,7 @@ install_requires = MarkupSafe SQLAlchemy>=2.0.37,<2.1,!=2.0.41 packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg index 76920ecaece..cf3c7ffc0cf 100644 --- a/packages/meta/setup.cfg +++ b/packages/meta/setup.cfg @@ -10,7 +10,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -35,7 +34,7 @@ version = 25.1.dev0 [options] include_package_data = True packages = find: -python_requires = >=3.9 +python_requires = >=3.10 install_requires = file: requirements.txt [options.extras_require] diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 34272a9810c..2f98ba69c62 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -41,7 +40,7 @@ install_requires = PyYAML seletools packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.packages.find] exclude = diff --git a/packages/pyproject.toml b/packages/pyproject.toml index c88224144d2..b715463b6a4 100644 --- a/packages/pyproject.toml +++ b/packages/pyproject.toml @@ -2,7 +2,7 @@ name = "galaxy-meta-package" version = "0.0.0" description = "Meta package stub (not a real package)" -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [] [tool.uv] diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index 321e3b5d8f0..a7a34374f5d 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -36,7 +35,7 @@ install_requires = galaxy-util pydantic[email]>=2.7.4 packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index c827528df7a..9b43f67eaea 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -41,7 +40,7 @@ install_requires = selenium!=4.11.0,!=4.11.1,!=4.11.2 playwright packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index e155e793e76..8344f74656e 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -39,7 +38,7 @@ install_requires = requests tuspy packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] driver = diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 07aa7e5fc85..b8592f53237 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -44,7 +43,7 @@ install_requires = requests jsonschema packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index b8928e3d232..3f4d57a8b90 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -42,7 +41,7 @@ install_requires = galaxy-web-apps pytest packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg index 4513e653046..1a9d0c7703d 100644 --- a/packages/test_selenium/setup.cfg +++ b/packages/test_selenium/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -44,7 +43,7 @@ install_requires = requests selenium!=4.11.0,!=4.11.1,!=4.11.2 packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] driver = diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index ce03b3d453d..1b1e45dc9bb 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -58,7 +57,7 @@ install_requires = WebOb Whoosh packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/tool_shed_schema/setup.cfg b/packages/tool_shed_schema/setup.cfg index 0037fccb48d..cf223a9d157 100644 --- a/packages/tool_shed_schema/setup.cfg +++ b/packages/tool_shed_schema/setup.cfg @@ -9,8 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.8 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -38,7 +36,7 @@ install_requires = pydantic>=2.7.4 typing-extensions packages = find: -python_requires = >=3.8 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 743c8c464c4..ee0552b54bb 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -37,7 +36,7 @@ install_requires = pydantic>=2.7.4 PyYAML packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.entry_points] console_scripts = diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 06e8f0849f6..76625ee1ea5 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -68,7 +67,7 @@ install_requires = uvloop>=0.21.0 WebOb>=1.8.9 packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/web_client/setup.cfg b/packages/web_client/setup.cfg index d96f6eeca27..b1ad9d9709c 100644 --- a/packages/web_client/setup.cfg +++ b/packages/web_client/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -33,7 +32,7 @@ version = 25.1.dev0 [options] include_package_data = True packages = galaxy.web_client -python_requires = >=3.9 +python_requires = >=3.10 [options.entry_points] console_scripts = diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index f5c15567349..97a95a06966 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -45,7 +44,7 @@ install_requires = WebOb packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 17bbf6008d4..7532c6d525c 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -9,7 +9,6 @@ classifiers = Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 - Programming Language :: Python :: 3.9 Programming Language :: Python :: 3.10 Programming Language :: Python :: 3.11 Programming Language :: Python :: 3.12 @@ -37,7 +36,7 @@ install_requires = galaxy-util SQLAlchemy>=2.0.37,<2.1,!=2.0.41 packages = find: -python_requires = >=3.9 +python_requires = >=3.10 [options.extras_require] test = diff --git a/pyproject.toml b/pyproject.toml index 2fadca4969e..45107f67afa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -10,7 +10,7 @@ maintainers = [ ] license = {file = "LICENSE.txt"} readme = "README.rst" -requires-python = ">=3.9" +requires-python = ">=3.10" dependencies = [ "a2wsgi", "aiofiles", @@ -41,7 +41,7 @@ dependencies = [ "fissix", "fs", "future>=1.0.0", # Python 3.12 support - "gravity @ git+https://github.com/nsoranzo/gravity.git@python3.14", # Python 3.14 support + "gravity>=1.2.0", # Python 3.14 support "gunicorn", "gxformat2>=0.21.0", "h5grove>=1.2.1", @@ -57,7 +57,8 @@ dependencies = [ "Mako", "Markdown", "MarkupSafe", - "mercurial>=6.8.2", # Python 3.13 support + "mercurial>=6.8.2 ; python_version<'3.14'", # Python 3.13 support + "mercurial>=7.2rc0 ; python_version>='3.14'", # Python 3.14 support "mrcfile", "more-itertools", "msal", @@ -190,7 +191,6 @@ typecheck = [ [tool.black] line-length = 120 -target-version = ['py39'] include = '\.pyi?$' extend-exclude = ''' ^/( @@ -203,7 +203,6 @@ extend-exclude = ''' isort = true [tool.ruff] -target-version = "py39" exclude = [ "lib/tool_shed/test/test_data/repos" ] @@ -219,7 +218,8 @@ select = ["E", "F", "B", "C4", "G", "ISC", "NPY", "UP"] # E402 module level import not at top of file # TODO, we would like to improve this. # E501 is line length (delegated to black) # G* are TODOs -ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"] +# UP007, UP045: Python >=3.10 type annotation improvements, to be revisited later +ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004", "UP007", "UP045"] [tool.ruff.lint.flake8-comprehensions] allow-dict-calls-with-keyword-arguments = true diff --git a/scripts/check_python.py b/scripts/check_python.py index b3fec2eb98f..79f4d2d7241 100644 --- a/scripts/check_python.py +++ b/scripts/check_python.py @@ -7,7 +7,7 @@ from __future__ import print_function import sys -MIN_VERSION_TUPLE = (3, 9) +MIN_VERSION_TUPLE = (3, 10) def check_python(): diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh index 1f3359391e1..10b6b351327 100755 --- a/scripts/common_startup.sh +++ b/scripts/common_startup.sh @@ -12,7 +12,7 @@ SET_VENV=1 SKIP_CLIENT_BUILD=${GALAXY_SKIP_CLIENT_BUILD:-0} INSTALL_PREBUILT_CLIENT=${GALAXY_INSTALL_PREBUILT_CLIENT:-0} : "${PNPM_INSTALL_OPTS:=--frozen-lockfile}" -: "${GALAXY_CONDA_PYTHON_VERSION:=3.9}" +: "${GALAXY_CONDA_PYTHON_VERSION:=3.10}" for arg in "$@"; do if [ "$arg" = "--skip-venv" ]; then @@ -37,7 +37,7 @@ RMFILES=" lib/pkg_resources.pyc " -MIN_PYTHON_VERSION=3.9 +MIN_PYTHON_VERSION=3.10 MIN_PIP_VERSION=20.3 # return true if $1 is in $2 else false diff --git a/test/functional/tools/output_filter.xml b/test/functional/tools/output_filter.xml index 584f2f43cf3..d54c3f8ae93 100644 --- a/test/functional/tools/output_filter.xml +++ b/test/functional/tools/output_filter.xml @@ -9,13 +9,54 @@ echo '5' > 5 && echo 'p1.forward' > p1.forward && echo 'p1.reverse' > p1.reverse && echo 'p2.forward' > p2.forward && -echo 'p2.reverse' > p2.reverse +echo 'p2.reverse' > p2.reverse +#for $r in $repeat + #if $r.cond.select == "a" and $r.cond.inner_cond.inner_select == "2" + && echo "$r.cond.inner_cond.text" >> repeat_cond.txt + #end if +#end for ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -34,6 +75,9 @@ echo 'p2.reverse' > p2.reverse produce_paired_collection is True + + any( [ r["cond"]["select"] == "a" and r["cond"]["inner_cond"]["inner_select"] == "2" for r in repeat ] ) + @@ -98,6 +142,15 @@ echo 'p2.reverse' > p2.reverse + + + + + + + + + @@ -147,5 +200,21 @@ echo 'p2.reverse' > p2.reverse + + + + + + + + + + + + + + + + diff --git a/test/integration/test_container_resolvers.py b/test/integration/test_container_resolvers.py index a92d00d64bc..4e3fdcfb4ca 100644 --- a/test/integration/test_container_resolvers.py +++ b/test/integration/test_container_resolvers.py @@ -4,12 +4,12 @@ import re from typing import ( Any, ClassVar, + Literal, Optional, TYPE_CHECKING, ) from typing_extensions import ( - Literal, Protocol, ) diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py index 8e64168d7f4..43507c45545 100644 --- a/test/integration/test_kubernetes_runner.py +++ b/test/integration/test_kubernetes_runner.py @@ -11,12 +11,12 @@ import subprocess import tempfile import time from typing import ( + Literal, Optional, overload, ) import pytest -from typing_extensions import Literal from galaxy.model import Job from galaxy.tool_util.verify.wait import timeout_type diff --git a/test/integration/test_purge_datasets.py b/test/integration/test_purge_datasets.py index 8fb165e8954..363245397c1 100644 --- a/test/integration/test_purge_datasets.py +++ b/test/integration/test_purge_datasets.py @@ -1,6 +1,6 @@ import os +from collections.abc import Callable from typing import ( - Callable, Optional, ) diff --git a/test/unit/app/managers/test_user_file_sources.py b/test/unit/app/managers/test_user_file_sources.py index cc849865360..f817ab5ec39 100644 --- a/test/unit/app/managers/test_user_file_sources.py +++ b/test/unit/app/managers/test_user_file_sources.py @@ -884,4 +884,4 @@ class MockExceptionResponse: self._exception_msg = exception_msg def raise_for_status(self): - raise HTTPError(self._exception_msg, self._exception_msg, response=None) # type: ignore[arg-type,unused-ignore] # Fixed in types-requests 2.31.0.9 , which requires Python >=3.9 via urllib3 >=2 + raise HTTPError(self._exception_msg, self._exception_msg, response=None) diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py index f6fea192def..56ff5e6e0b9 100644 --- a/test/unit/data/model/test_model_store.py +++ b/test/unit/data/model/test_model_store.py @@ -660,23 +660,12 @@ def validate_invocation_collection_crate_directory(crate_directory): def validate_with_roc_validator(crate_directory, profile): - # roc-validator changed the ValidationSettings argument data_path to rocrate_uri in - # v5.0.0+, but also dropped support for Python 3.9 - if sys.version_info >= (3, 10): - settings = services.ValidationSettings( - rocrate_uri=crate_directory, - profile_identifier=profile, - requirement_severity=models.Severity.REQUIRED, - abort_on_first=False, # do not stop on first issue - ) - else: - settings = services.ValidationSettings( - data_path=crate_directory, - profile_identifier=profile, - requirement_severity=models.Severity.REQUIRED, - abort_on_first=False, # do not stop on first issue - http_cache_timeout=0, # do not use cache - ) + settings = services.ValidationSettings( + rocrate_uri=crate_directory, + profile_identifier=profile, + requirement_severity=models.Severity.REQUIRED, + abort_on_first=False, # do not stop on first issue + ) result = services.validate(settings) diff --git a/test/unit/files/_base.py b/test/unit/files/_base.py index bd5c55e979f..13336570382 100644 --- a/test/unit/files/_base.py +++ b/test/unit/files/_base.py @@ -14,9 +14,9 @@ from abc import ( ABC, abstractmethod, ) +from collections.abc import Callable from typing import ( Any, - Callable, Optional, ) diff --git a/test/unit/selenium/util.py b/test/unit/selenium/util.py index fa7f13dbe2f..20142ac9b2e 100644 --- a/test/unit/selenium/util.py +++ b/test/unit/selenium/util.py @@ -1,7 +1,7 @@ """Pytest-specific utility functions and decorators for selenium unit tests.""" +from collections.abc import Callable from typing import ( - Callable, TypeVar, Union, )