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Merge branch 'dev' into feat/dicom

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This commit is contained in:
Leonid Kostrykin
2026-01-20 11:30:52 +01:00
committed by GitHub
parent 26bece8b6b 5aded9505f
commit 1d7a944b31
172 changed files with 667 additions and 659 deletions
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.circleci/config.yml
+2 -2
View File
@@ -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
.github/workflows/api.yaml
+1 -1
View File
@@ -31,7 +31,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9']
python-version: ['3.10']
chunk: [0, 1]
services:
postgres:
.github/workflows/bioblend.yaml
+1 -1
View File
@@ -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
.github/workflows/check_test_class_names.yaml
+1 -1
View File
@@ -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:
.github/workflows/converter_tests.yaml
+1 -1
View File
@@ -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: |
.github/workflows/cwl_conformance.yaml
+1 -1
View File
@@ -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:
.github/workflows/db_indexes.yaml
+2 -2
View File
@@ -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:${{ matrix.postgresql-version }}
.github/workflows/dependencies.yaml
+1 -1
View File
@@ -14,7 +14,7 @@ jobs:
persist-credentials: false
- uses: actions/setup-python@v6
with:
python-version: '3.9'
python-version: '3.10'
- name: Install uv
uses: astral-sh/setup-uv@v7
- name: Update dependencies
.github/workflows/deployment.yaml
+1 -1
View File
@@ -29,7 +29,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
steps:
- uses: actions/checkout@v6
with:
.github/workflows/docs.yaml
+1 -1
View File
@@ -18,7 +18,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
steps:
- name: Get target branch name (push)
if: github.event_name == 'push'
.github/workflows/first_startup.yaml
+2 -1
View File
@@ -25,7 +25,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9', '3.14']
python-version: ['3.10', '3.14']
defaults:
run:
shell: bash -l {0}
@@ -47,6 +47,7 @@ jobs:
- name: Restore client cache
uses: actions/cache@v5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Install tox
.github/workflows/framework_tools.yaml
+1 -1
View File
@@ -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:
.github/workflows/framework_workflows.yaml
+1 -1
View File
@@ -28,7 +28,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
services:
postgres:
image: postgres:17
.github/workflows/integration.yaml
+1 -1
View File
@@ -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'
.github/workflows/integration_selenium.yaml
+2 -1
View File
@@ -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-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Run tests
.github/workflows/lint.yaml
+1 -1
View File
@@ -22,7 +22,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9', '3.14']
python-version: ['3.10', '3.14']
env:
LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
.github/workflows/lint_openapi_schema.yml
+1 -1
View File
@@ -22,7 +22,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9', '3.14']
python-version: ['3.10', '3.14']
steps:
- uses: actions/checkout@v6
with:
.github/workflows/main_tools.yaml
+1 -1
View File
@@ -24,7 +24,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
services:
postgres:
image: postgres:17
.github/workflows/mulled.yaml
+1 -1
View File
@@ -22,7 +22,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9']
python-version: ['3.10']
steps:
- uses: actions/checkout@v6
with:
.github/workflows/osx_startup.yaml
+2 -1
View File
@@ -23,7 +23,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9', '3.14']
python-version: ['3.10', '3.14']
defaults:
run:
shell: bash -l {0}
@@ -40,6 +40,7 @@ jobs:
- name: Restore client cache
uses: actions/cache@v5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Install uv
.github/workflows/performance.yaml
+1 -1
View File
@@ -26,7 +26,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
services:
postgres:
image: postgres:17
.github/workflows/playwright.yaml
+2 -1
View File
@@ -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-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Run tests
.github/workflows/publish_artifacts.yaml
+1 -1
View File
@@ -41,7 +41,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.9']
python-version: ['3.10']
steps:
- uses: actions/checkout@v6
with:
.github/workflows/selenium.yaml
+2 -1
View File
@@ -34,7 +34,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9']
python-version: ['3.10']
chunk: [0, 1, 2]
services:
postgres:
@@ -71,6 +71,7 @@ jobs:
- name: Restore client cache
uses: actions/cache@v5
with:
fail-on-cache-miss: true
key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
path: 'galaxy root/static'
- name: Run tests
.github/workflows/test_galaxy_packages.yaml
+1 -1
View File
@@ -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:
.github/workflows/toolshed.yaml
+1 -1
View File
@@ -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:
.github/workflows/unit-postgres.yaml
+1 -1
View File
@@ -24,7 +24,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ['3.9']
python-version: ['3.10']
services:
postgres:
image: postgres:17
.github/workflows/unit.yaml
+1 -1
View File
@@ -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:
Makefile
+2 -2
View File
@@ -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
README.rst
+2 -2
View File
@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
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:
client/src/components/Form/Elements/FormDirectory.test.js
+17 -1
View File
@@ -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}`);
});
});
client/src/components/Form/Elements/FormDirectory.vue
+16 -4
View File
@@ -35,7 +35,8 @@
trim
@keyup.enter="addPath"
@keydown.191.capture.prevent.stop="addPath"
@keydown.8.capture="removeLastPath" />
@keydown.8.capture="removeLastPath"
@blur="handleBlur" />
</b-breadcrumb-item>
</b-breadcrumb>
@@ -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) {
doc/source/admin/galaxy_options.rst
+4 -4
View File
@@ -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``
doc/source/admin/python.md
+1 -1
View File
@@ -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:
lib/galaxy/agents/base.py
+1 -1
View File
@@ -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,
lib/galaxy/app.py
+1 -1
View File
@@ -6,9 +6,9 @@ import signal
import sys
import threading
import time
from collections.abc import Callable
from typing import (
Any,
Callable,
Optional,
)
lib/galaxy/authnz/psa_authnz.py
+1 -9
View File
@@ -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__)
lib/galaxy/celery/__init__.py
+1 -1
View File
@@ -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
lib/galaxy/celery/tasks.py
+1 -1
View File
@@ -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,
)
lib/galaxy/config/__init__.py
+1 -1
View File
@@ -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,
lib/galaxy/config/config_manage.py
+2 -2
View File
@@ -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
lib/galaxy/config/sample/galaxy.yml.sample
+44 -11
View File
@@ -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 ``<galaxy_data_dir>/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
lib/galaxy/config/sample/tool_shed.yml.sample
+6
View File
@@ -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
lib/galaxy/datatypes/blast.py
+1 -1
View File
@@ -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,
)
lib/galaxy/datatypes/data.py
+2 -2
View File
@@ -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 (
lib/galaxy/datatypes/display_applications/parameters.py
+1 -1
View File
@@ -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,
lib/galaxy/datatypes/images.py
+1 -1
View File
@@ -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
lib/galaxy/datatypes/molecules.py
+1 -1
View File
@@ -1,8 +1,8 @@
import logging
import os
import re
from collections.abc import Callable
from typing import (
Callable,
Optional,
)
lib/galaxy/datatypes/msa.py
+1 -1
View File
@@ -2,8 +2,8 @@ import abc
import logging
import os
import re
from collections.abc import Callable
from typing import (
Callable,
Optional,
)
lib/galaxy/datatypes/sequence.py
+4 -2
View File
@@ -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,
)
lib/galaxy/datatypes/sniff.py
+4 -2
View File
@@ -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,
lib/galaxy/datatypes/spaln.py
+1 -1
View File
@@ -4,8 +4,8 @@ spaln Composite Dataset
import logging
import os.path
from collections.abc import Callable
from typing import (
Callable,
Optional,
)
lib/galaxy/dependencies/dev-requirements.txt
+79 -106
View File
@@ -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
lib/galaxy/dependencies/pinned-requirements.txt
+94 -138
View File
@@ -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
lib/galaxy/dependencies/pinned-test-requirements.txt
+71 -91
View File
@@ -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
lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+2 -4
View File
@@ -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
lib/galaxy/files/__init__.py
+1 -1
View File
@@ -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,
lib/galaxy/files/sources/azure.py
+1 -1
View File
@@ -1,4 +1,4 @@
from typing_extensions import Literal
from typing import Literal
try:
from fs.azblob.blob_fs import BlobFS
lib/galaxy/files/sources/invenio.py
+1 -1
View File
@@ -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,
)
lib/galaxy/files/templates/models.py
+1 -1
View File
@@ -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,
lib/galaxy/job_execution/container_monitor.py
+1 -1
View File
@@ -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 (
lib/galaxy/job_execution/output_collect.py
+1 -1
View File
@@ -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,
lib/galaxy/jobs/__init__.py
+4 -2
View File
@@ -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,
lib/galaxy/jobs/job_destination.py
+1 -4
View File
@@ -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
lib/galaxy/jobs/mapper.py
+1 -1
View File
@@ -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,
)
lib/galaxy/jobs/runners/drmaa.py
+1 -2
View File
@@ -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
lib/galaxy/jobs/runners/util/cli/job/__init__.py
+1 -2
View File
@@ -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
lib/galaxy/managers/base.py
+1 -1
View File
@@ -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,
lib/galaxy/managers/collections.py
+1 -1
View File
@@ -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
lib/galaxy/managers/context.py
+1 -1
View File
@@ -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,
lib/galaxy/managers/histories.py
+1 -1
View File
@@ -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 (
lib/galaxy/managers/pages.py
+1 -1
View File
@@ -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,
lib/galaxy/managers/workflows.py
+1 -3
View File
@@ -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,
lib/galaxy/model/__init__.py
+8 -2
View File
@@ -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):
lib/galaxy/model/dataset_collections/types/sample_sheet_workbook.py
+1 -1
View File
@@ -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 (
lib/galaxy/model/migrations/alembic/env.py
+1 -1
View File
@@ -1,7 +1,7 @@
import logging
import re
from collections.abc import Callable
from typing import (
Callable,
cast,
)
lib/galaxy/model/store/__init__.py
+1 -1
View File
@@ -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,
lib/galaxy/model/store/discover.py
+4 -2
View File
@@ -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,
lib/galaxy/model/tool_shed_install/__init__.py
+1 -1
View File
@@ -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,
)
lib/galaxy/model/unittest_utils/model_testing_utils.py
+4 -2
View File
@@ -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,
)
lib/galaxy/queue_worker.py
+1 -1
View File
@@ -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)
lib/galaxy/quota/_schema.py
+1 -1
View File
@@ -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,
lib/galaxy/schema/fetch_data.py
+1 -1
View File
@@ -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
lib/galaxy/schema/fields.py
+2 -4
View File
@@ -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
lib/galaxy/schema/groups.py
+4 -2
View File
@@ -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,
lib/galaxy/schema/history.py
+1 -1
View File
@@ -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 (
lib/galaxy/schema/invocation.py
+1 -1
View File
@@ -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,
)
lib/galaxy/schema/jobs.py
+1 -1
View File
@@ -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,
lib/galaxy/schema/library_contents.py
+1 -3
View File
@@ -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,
lib/galaxy/schema/notifications.py
+1 -3
View File
@@ -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,
lib/galaxy/schema/schema.py
+2 -2
View File
@@ -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,
)
lib/galaxy/schema/storage_cleaner.py
+1 -1
View File
@@ -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,
lib/galaxy/schema/types.py
+1 -3
View File
@@ -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
lib/galaxy/schema/visualization.py
+1 -1
View File
@@ -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,
lib/galaxy/schema/workflow/comments.py
+1 -1
View File
@@ -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):
lib/galaxy/security/__init__.py
+1 -2
View File
@@ -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"]
lib/galaxy/selenium/axe_results.py
+1 -1
View File
@@ -1,10 +1,10 @@
from typing import (
Any,
Literal,
Optional,
)
from typing_extensions import (
Literal,
Protocol,
)
lib/galaxy/selenium/has_driver_protocol.py
+1 -1
View File
@@ -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,
lib/galaxy/tool_shed/metadata/metadata_generator.py
+3 -1
View File
@@ -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):
"""
lib/galaxy/tools/_types.py
+1 -2
View File
@@ -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]

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