From 5bbdef365a7aea41bbef8a0941bdc24bd3d24671 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 3 Jul 2026 15:50:18 +0200 Subject: [PATCH] style: apply isort/black (tox -e format) --- lib/galaxy/tool_source_store/database.py | 4 +--- lib/galaxy/tool_source_store/populator.py | 20 ++++++++--------- .../tool_util/toolbox/lineages/factory.py | 5 ++++- lib/galaxy/tools/lazy_toolbox.py | 22 ++++++++----------- lib/galaxy/tools/special_tools.py | 3 +-- 5 files changed, 25 insertions(+), 29 deletions(-) diff --git a/lib/galaxy/tool_source_store/database.py b/lib/galaxy/tool_source_store/database.py index 7bf14ea5073..2ff3b428582 100644 --- a/lib/galaxy/tool_source_store/database.py +++ b/lib/galaxy/tool_source_store/database.py @@ -113,9 +113,7 @@ class DatabaseToolSourceStore(ToolSourceStore): def get(self, hash: str) -> StoredToolSource | None: """Retrieve a tool source by hash.""" with self._read_session() as session: - model = session.execute( - select(ToolSourceRecord).where(ToolSourceRecord.hash == hash) - ).scalar_one_or_none() + model = session.execute(select(ToolSourceRecord).where(ToolSourceRecord.hash == hash)).scalar_one_or_none() if not model: return None return self._model_to_stored(model) diff --git a/lib/galaxy/tool_source_store/populator.py b/lib/galaxy/tool_source_store/populator.py index 9d151bde2c0..c93ef100779 100644 --- a/lib/galaxy/tool_source_store/populator.py +++ b/lib/galaxy/tool_source_store/populator.py @@ -44,9 +44,19 @@ from typing import ( cast, ) +from kombu import Connection +from kombu.pools import producers + +from galaxy.config import GalaxyAppConfiguration +from galaxy.datatypes.registry import Registry +from galaxy.model import set_datatypes_registry +from galaxy.model.mapping import init_models_from_config +from galaxy.model.scoped_session import galaxy_scoped_session +from galaxy.queues import galaxy_exchange from galaxy.tool_source_store import ( _build_default_store, build_named_store, + build_tool_source_store, ReadOnlyStoreError, StoredToolSource, ToolSourceStore, @@ -59,16 +69,6 @@ from galaxy.tool_source_store.index import ( ToolIndex, ToolIndexEntry, ) -from kombu import Connection -from kombu.pools import producers - -from galaxy.config import GalaxyAppConfiguration -from galaxy.datatypes.registry import Registry -from galaxy.model import set_datatypes_registry -from galaxy.model.mapping import init_models_from_config -from galaxy.model.scoped_session import galaxy_scoped_session -from galaxy.queues import galaxy_exchange -from galaxy.tool_source_store import build_tool_source_store from galaxy.tool_source_store.search import ( ToolSearchTuning, ToolWhooshIndex, diff --git a/lib/galaxy/tool_util/toolbox/lineages/factory.py b/lib/galaxy/tool_util/toolbox/lineages/factory.py index 507bd0c059f..44fa27c7a44 100644 --- a/lib/galaxy/tool_util/toolbox/lineages/factory.py +++ b/lib/galaxy/tool_util/toolbox/lineages/factory.py @@ -1,7 +1,10 @@ +from collections.abc import ( + Callable, + Iterable, +) from typing import ( TYPE_CHECKING, ) -from collections.abc import Callable, Iterable from galaxy.util.tool_version import remove_version_from_guid from .interface import ToolLineage diff --git a/lib/galaxy/tools/lazy_toolbox.py b/lib/galaxy/tools/lazy_toolbox.py index 60b330ca037..f4338749c12 100644 --- a/lib/galaxy/tools/lazy_toolbox.py +++ b/lib/galaxy/tools/lazy_toolbox.py @@ -19,8 +19,11 @@ from typing import ( from uuid import UUID from cachetools import LRUCache -from galaxy.tool_util.version import parse_version +from galaxy.exceptions import ( + ObjectNotFound, + RequestParameterInvalidException, +) from galaxy.tool_source_store import ( StoredToolSource, ToolSourceStore, @@ -31,16 +34,13 @@ from galaxy.tool_source_store.index import ( ToolIndexEntry, ) from galaxy.tool_source_store.populator import populate_store_inline -from galaxy.exceptions import ( - ObjectNotFound, - RequestParameterInvalidException, -) from galaxy.tool_util.id_util import extract_short_id_from_guid -from galaxy.tool_util.toolbox.base import ToolConfRepository -from galaxy.util.tool_version import remove_version_from_guid from galaxy.tool_util.parser import get_tool_source +from galaxy.tool_util.toolbox.base import ToolConfRepository from galaxy.tool_util.toolbox.lineages.interface import ToolLineage from galaxy.tool_util.toolbox.panel import ToolSection +from galaxy.tool_util.version import parse_version +from galaxy.util.tool_version import remove_version_from_guid from . import ( create_tool_from_source, ToolBox, @@ -327,9 +327,7 @@ class LazyTool: from ``_tools_by_id``. """ try: - return self._materialize().to_dict( - trans, link_details=link_details, tool_help=tool_help, **kw - ) + return self._materialize().to_dict(trans, link_details=link_details, tool_help=tool_help, **kw) except Exception as e: log.warning("LazyTool.to_dict: materialise failed for %s, falling back to entry: %s", self.id, e) return self.to_panel_entry(trans) @@ -864,9 +862,7 @@ class LazyToolBox(ToolBox): return tool - def _create_tool_from_stored_source( - self, stored: StoredToolSource, entry: ToolIndexEntry | None = None - ) -> "Tool": + def _create_tool_from_stored_source(self, stored: StoredToolSource, entry: ToolIndexEntry | None = None) -> "Tool": """Create a Tool object from stored source.""" tool_source = get_tool_source( raw_tool_source=stored.raw_source, diff --git a/lib/galaxy/tools/special_tools.py b/lib/galaxy/tools/special_tools.py index 7c55c53c303..7e474149cae 100644 --- a/lib/galaxy/tools/special_tools.py +++ b/lib/galaxy/tools/special_tools.py @@ -33,8 +33,7 @@ def hidden_lib_tool_paths() -> list[str]: """ base = os.path.dirname(__file__) return [ - os.path.abspath(os.path.join(base, p)) - for p in (*SPECIAL_TOOLS.values(), *_EXTRA_HIDDEN_LIB_TOOLS.values()) + os.path.abspath(os.path.join(base, p)) for p in (*SPECIAL_TOOLS.values(), *_EXTRA_HIDDEN_LIB_TOOLS.values()) ]