mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_26.0' into dev
# Conflicts: # lib/galaxy/version.py # packages/app/HISTORY.rst # packages/auth/HISTORY.rst # packages/config/HISTORY.rst # packages/data/HISTORY.rst # packages/files/HISTORY.rst # packages/job_execution/HISTORY.rst # packages/job_metrics/HISTORY.rst # packages/meta/HISTORY.rst # packages/navigation/HISTORY.rst # packages/objectstore/HISTORY.rst # packages/schema/HISTORY.rst # packages/selenium/HISTORY.rst # packages/test_api/HISTORY.rst # packages/test_base/HISTORY.rst # packages/test_driver/HISTORY.rst # packages/tool_shed/HISTORY.rst # packages/tool_shed_schema/HISTORY.rst # packages/tool_util/HISTORY.rst # packages/tool_util_models/HISTORY.rst # packages/tours/HISTORY.rst # packages/util/HISTORY.rst # packages/web_apps/HISTORY.rst # packages/web_client/HISTORY.rst # packages/web_framework/HISTORY.rst # packages/web_stack/HISTORY.rst
This commit is contained in:
guerler
@@ -363,7 +363,13 @@ export default {
|
||||
this.disabled = true;
|
||||
this.loading = true;
|
||||
|
||||
return getToolFormData(this.id || this.toolUuid, this.currentVersion, this.job_id, this.history_id)
|
||||
return getToolFormData(
|
||||
this.id || this.toolUuid,
|
||||
this.currentVersion,
|
||||
this.job_id,
|
||||
this.history_id,
|
||||
this.toolUuid,
|
||||
)
|
||||
.then((data) => {
|
||||
this.currentVersion = data.version;
|
||||
this.formConfig = data;
|
||||
|
||||
@@ -13,7 +13,7 @@ export async function updateToolFormData(tool_id, tool_uuid, tool_version, histo
|
||||
inputs: inputs,
|
||||
history_id: history_id,
|
||||
};
|
||||
const url = `${getAppRoot()}api/tools/${tool_uuid || tool_id}/build`;
|
||||
const url = `${getAppRoot()}api/tools/${tool_id || tool_uuid}/build`;
|
||||
try {
|
||||
const { data } = await axios.post(url, current_state);
|
||||
return data;
|
||||
@@ -23,7 +23,7 @@ export async function updateToolFormData(tool_id, tool_uuid, tool_version, histo
|
||||
}
|
||||
|
||||
/** Tools data request helper **/
|
||||
export async function getToolFormData(tool_id, tool_version, job_id, history_id) {
|
||||
export async function getToolFormData(tool_id, tool_version, job_id, history_id, tool_uuid) {
|
||||
let url = "";
|
||||
const data = {};
|
||||
|
||||
@@ -42,6 +42,7 @@ export async function getToolFormData(tool_id, tool_version, job_id, history_id)
|
||||
}
|
||||
history_id && (data["history_id"] = history_id);
|
||||
tool_version && (data["tool_version"] = tool_version);
|
||||
tool_uuid && (data["tool_uuid"] = tool_uuid);
|
||||
|
||||
// attach data to request url
|
||||
if (Object.entries(data).length != 0) {
|
||||
|
||||
@@ -7,7 +7,10 @@ import { getAppRoot } from "@/onload/loadConfig";
|
||||
import { rethrowSimple } from "@/utils/simple-error";
|
||||
|
||||
async function toolSource({ id, uuid }) {
|
||||
const url = `${getAppRoot()}api/tools/${uuid || id}/raw_tool_source`;
|
||||
let url = `${getAppRoot()}api/tools/${id || uuid}/raw_tool_source`;
|
||||
if (uuid) {
|
||||
url += `?tool_uuid=${uuid}`;
|
||||
}
|
||||
try {
|
||||
const { data, headers } = await axios.get(url);
|
||||
const result = {};
|
||||
|
||||
@@ -539,7 +539,8 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
io_details = util.string_as_bool(kwd.get("io_details", False))
|
||||
link_details = util.string_as_bool(kwd.get("link_details", False))
|
||||
tool_version = kwd.get("tool_version")
|
||||
tool = self.service._get_tool(trans, id, user=trans.user, tool_version=tool_version, tool_uuid=id)
|
||||
tool_uuid = kwd.get("tool_uuid")
|
||||
tool = self.service._get_tool(trans, id, user=trans.user, tool_version=tool_version, tool_uuid=tool_uuid)
|
||||
return tool.to_dict(trans, io_details=io_details, link_details=link_details)
|
||||
|
||||
@expose_api_anonymous
|
||||
@@ -870,7 +871,10 @@ class ToolsController(BaseGalaxyAPIController, UsesVisualizationMixin):
|
||||
raise exceptions.InsufficientPermissionsException(
|
||||
"Only administrators may display tool sources on this Galaxy server."
|
||||
)
|
||||
tool = self.service._get_tool(trans, id, user=trans.user, tool_version=kwds.get("tool_version"), tool_uuid=id)
|
||||
tool_uuid = kwds.get("tool_uuid")
|
||||
tool = self.service._get_tool(
|
||||
trans, id, user=trans.user, tool_version=kwds.get("tool_version"), tool_uuid=tool_uuid
|
||||
)
|
||||
trans.response.headers["language"] = tool.tool_source.language
|
||||
if dynamic_tool := getattr(tool, "dynamic_tool", None):
|
||||
if dynamic_tool.value.get("class") == "GalaxyUserTool":
|
||||
|
||||
@@ -10,6 +10,7 @@ from typing import (
|
||||
Optional,
|
||||
Union,
|
||||
)
|
||||
from uuid import UUID
|
||||
|
||||
from starlette.datastructures import UploadFile
|
||||
|
||||
@@ -482,12 +483,14 @@ class ToolsService(ServiceBase):
|
||||
def _get_tool(
|
||||
self, trans: ProvidesUserContext, id, tool_version=None, tool_uuid=None, user: Optional[User] = None
|
||||
) -> Tool:
|
||||
if tool_uuid:
|
||||
try:
|
||||
UUID(tool_uuid)
|
||||
except ValueError:
|
||||
raise exceptions.RequestParameterInvalidException(f"Invalid tool_uuid '{tool_uuid}'.")
|
||||
tool = trans.app.toolbox.get_tool(id, tool_version)
|
||||
if not tool:
|
||||
if user:
|
||||
# FIXME: id as tool_uuid is for raw_tool_source endpoint, port to fastapi and fix
|
||||
if id == tool_uuid:
|
||||
id = None
|
||||
if user and (id or tool_uuid):
|
||||
tool = trans.app.toolbox.get_tool(user=user, tool_id=id, tool_uuid=tool_uuid)
|
||||
if tool:
|
||||
return tool
|
||||
|
||||
@@ -9,6 +9,166 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix workflow report time handling by `@dannon <https://github.com/dannon>`_ in `#19292 <https://github.com/galaxyproject/galaxy/pull/19292>`_
|
||||
* Bump python-ldap from 3.4.0 to 3.4.5 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21042 <https://github.com/galaxyproject/galaxy/pull/21042>`_
|
||||
* Cross product tools: Fix typos in help section by `@RZ9082 <https://github.com/RZ9082>`_ in `#21061 <https://github.com/galaxyproject/galaxy/pull/21061>`_
|
||||
* Bump urllib3 from 2.5.0 to 2.6.0 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21399 <https://github.com/galaxyproject/galaxy/pull/21399>`_
|
||||
* Don't set OAUTHLIB_INSECURE_TRANSPORT setting in user_data by `@nuwang <https://github.com/nuwang>`_ in `#21451 <https://github.com/galaxyproject/galaxy/pull/21451>`_
|
||||
* Bump filelock from 3.20.0 to 3.20.1 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21476 <https://github.com/galaxyproject/galaxy/pull/21476>`_
|
||||
* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
|
||||
* Restrict collection of dynamic working dir output to specified directory in pulsar by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21515 <https://github.com/galaxyproject/galaxy/pull/21515>`_
|
||||
* Fix input tags not being copied when using copy_inputs_to_history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21529 <https://github.com/galaxyproject/galaxy/pull/21529>`_
|
||||
* Bump aiohttp from 3.13.2 to 3.13.3 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21538 <https://github.com/galaxyproject/galaxy/pull/21538>`_
|
||||
* Bump urllib3 from 2.6.2 to 2.6.3 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21546 <https://github.com/galaxyproject/galaxy/pull/21546>`_
|
||||
* Bump werkzeug from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21549 <https://github.com/galaxyproject/galaxy/pull/21549>`_
|
||||
* Overhaul ChatGXY Routing approach by `@dannon <https://github.com/dannon>`_ in `#21580 <https://github.com/galaxyproject/galaxy/pull/21580>`_
|
||||
* Bump pyasn1 from 0.6.1 to 0.6.2 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21605 <https://github.com/galaxyproject/galaxy/pull/21605>`_
|
||||
* Fix toolshed tests on Python 3.14 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21617 <https://github.com/galaxyproject/galaxy/pull/21617>`_
|
||||
* Bump python-multipart from 0.0.21 to 0.0.22 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21663 <https://github.com/galaxyproject/galaxy/pull/21663>`_
|
||||
* Fix storing origin for workflow landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21696 <https://github.com/galaxyproject/galaxy/pull/21696>`_
|
||||
* Handle TPV floating point memory values by `@ksuderman <https://github.com/ksuderman>`_ in `#21763 <https://github.com/galaxyproject/galaxy/pull/21763>`_
|
||||
* Deserialize json string for export_metadata from old records by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21772 <https://github.com/galaxyproject/galaxy/pull/21772>`_
|
||||
* Fix passing invalid job_destination dict to JobState constructor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21798 <https://github.com/galaxyproject/galaxy/pull/21798>`_
|
||||
* Update ``get_definitions()`` to FastAPI 0.128.8 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21834 <https://github.com/galaxyproject/galaxy/pull/21834>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix dict leaking to process_dataset() during workflow execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21982 <https://github.com/galaxyproject/galaxy/pull/21982>`_
|
||||
* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
|
||||
* Restore file doesn't match sniffed datatype message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21988 <https://github.com/galaxyproject/galaxy/pull/21988>`_
|
||||
* Fix uncaught `ImplicitConversionRequired` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22027 <https://github.com/galaxyproject/galaxy/pull/22027>`_
|
||||
* Fix AttributeError when fetching citations for missing tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22029 <https://github.com/galaxyproject/galaxy/pull/22029>`_
|
||||
* AttributeError when history is None during tool execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22031 <https://github.com/galaxyproject/galaxy/pull/22031>`_
|
||||
* Fix AttributeError when export_metadata is a string instead of dict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22033 <https://github.com/galaxyproject/galaxy/pull/22033>`_
|
||||
* Fix TypeError when column_names metadata is None by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22057 <https://github.com/galaxyproject/galaxy/pull/22057>`_
|
||||
* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
|
||||
* Fix FileNotFoundError when workflow references purged HDA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22060 <https://github.com/galaxyproject/galaxy/pull/22060>`_
|
||||
* Add check_database_connection to workflow scheduling path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22063 <https://github.com/galaxyproject/galaxy/pull/22063>`_
|
||||
* Model hidden_data params as optional data in tool meta-models. by `@jmchilton <https://github.com/jmchilton>`_ in `#22116 <https://github.com/galaxyproject/galaxy/pull/22116>`_
|
||||
* Fix unhandled exceptions in tool form model population by `@guerler <https://github.com/guerler>`_ in `#22129 <https://github.com/galaxyproject/galaxy/pull/22129>`_
|
||||
* Backport transient CI fixes from #22102 to release_26.0 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22135 <https://github.com/galaxyproject/galaxy/pull/22135>`_
|
||||
* Do not queue paused jobs by `@martenson <https://github.com/martenson>`_ in `#22156 <https://github.com/galaxyproject/galaxy/pull/22156>`_
|
||||
* Fix AmbiguousColumn error in job search for tools with long input names by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22167 <https://github.com/galaxyproject/galaxy/pull/22167>`_
|
||||
* Fixes for gxformat2 by `@jmchilton <https://github.com/jmchilton>`_ in `#22179 <https://github.com/galaxyproject/galaxy/pull/22179>`_
|
||||
* Add batch celery task for history dataset purging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22180 <https://github.com/galaxyproject/galaxy/pull/22180>`_
|
||||
* Include missing tools in stock_tool_paths. by `@jmchilton <https://github.com/jmchilton>`_ in `#22181 <https://github.com/galaxyproject/galaxy/pull/22181>`_
|
||||
* Throw ParameterValueError instead of generic error by `@guerler <https://github.com/guerler>`_ in `#22188 <https://github.com/galaxyproject/galaxy/pull/22188>`_
|
||||
* Fix event loop blocking in async API routes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22202 <https://github.com/galaxyproject/galaxy/pull/22202>`_
|
||||
* Update fastmcp requirement to 3.0.2 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22221 <https://github.com/galaxyproject/galaxy/pull/22221>`_
|
||||
* Add optional dataset collection mode to harmonize tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22236 <https://github.com/galaxyproject/galaxy/pull/22236>`_
|
||||
* Fix batch history purge not updating user's update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22238 <https://github.com/galaxyproject/galaxy/pull/22238>`_
|
||||
* Fix file source removal by `@davelopez <https://github.com/davelopez>`_ in `#22246 <https://github.com/galaxyproject/galaxy/pull/22246>`_
|
||||
* Validate replacement_params values are strings before storing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22250 <https://github.com/galaxyproject/galaxy/pull/22250>`_
|
||||
* Fix N+1 queries in fetch_job_states for jobs_summary endpoints by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22251 <https://github.com/galaxyproject/galaxy/pull/22251>`_
|
||||
* Fix oauth2 template validation by `@davelopez <https://github.com/davelopez>`_ in `#22253 <https://github.com/galaxyproject/galaxy/pull/22253>`_
|
||||
* Drop stored workflow menu entries from user serialization by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22254 <https://github.com/galaxyproject/galaxy/pull/22254>`_
|
||||
* Batch-prefetch HDCA job_state_summary in history contents listing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22256 <https://github.com/galaxyproject/galaxy/pull/22256>`_
|
||||
* Fix HDCA lost in tool form on rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22258 <https://github.com/galaxyproject/galaxy/pull/22258>`_
|
||||
* Fix purge for anon histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22275 <https://github.com/galaxyproject/galaxy/pull/22275>`_
|
||||
* Raise error when API client sends invalid parameter keys by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22277 <https://github.com/galaxyproject/galaxy/pull/22277>`_
|
||||
* Raise MessageException instead of generic Exception in rules_dsl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22285 <https://github.com/galaxyproject/galaxy/pull/22285>`_
|
||||
* Fix toolshed static image url encoding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22286 <https://github.com/galaxyproject/galaxy/pull/22286>`_
|
||||
* Fix nested DatasetCollectionElement in dynamic options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22287 <https://github.com/galaxyproject/galaxy/pull/22287>`_
|
||||
* Fix flaky job search for HDCA inputs on PostgreSQL by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22290 <https://github.com/galaxyproject/galaxy/pull/22290>`_
|
||||
* Fix HDCA shown as unavailable on tool form rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22291 <https://github.com/galaxyproject/galaxy/pull/22291>`_
|
||||
* Fix AttributeError when anonymous user searches workflows with ``is:bookmarked`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22296 <https://github.com/galaxyproject/galaxy/pull/22296>`_
|
||||
* Downgrade authnz OAuth callback errors from ERROR/EXCEPTION to WARNING by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22300 <https://github.com/galaxyproject/galaxy/pull/22300>`_
|
||||
* Delay workflow scheduling when collection has unresolved 'auto' extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22303 <https://github.com/galaxyproject/galaxy/pull/22303>`_
|
||||
* Fix slow get_private_role_user_emails_dict query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22307 <https://github.com/galaxyproject/galaxy/pull/22307>`_
|
||||
* Mark dataset collections as deleted when purging a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22315 <https://github.com/galaxyproject/galaxy/pull/22315>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
* Remove broken serialize_urls from HDASerializer by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22358 <https://github.com/galaxyproject/galaxy/pull/22358>`_
|
||||
* Fix HideDatasetAction not applied for cached workflow jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22360 <https://github.com/galaxyproject/galaxy/pull/22360>`_
|
||||
* Don't retry JobNotReadyException in job destination mapping by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22377 <https://github.com/galaxyproject/galaxy/pull/22377>`_
|
||||
* Fix workflow extract NoneType on LDDA leaf in implicit collection by `@jmchilton <https://github.com/jmchilton>`_ in `#22381 <https://github.com/galaxyproject/galaxy/pull/22381>`_
|
||||
* Serialize data provider errors as MessageException subclasses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22398 <https://github.com/galaxyproject/galaxy/pull/22398>`_
|
||||
* Handle ``MaxDiscoveredFilesExceededError`` for dynamic collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22402 <https://github.com/galaxyproject/galaxy/pull/22402>`_
|
||||
* Unwrap HDCAs/DCEs nested in multi data input lists by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22405 <https://github.com/galaxyproject/galaxy/pull/22405>`_
|
||||
* Reject HDCA submitted to single data parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22406 <https://github.com/galaxyproject/galaxy/pull/22406>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
|
||||
* Replace Copy Dataset Mako with Vue Component by `@guerler <https://github.com/guerler>`_ in `#17507 <https://github.com/galaxyproject/galaxy/pull/17507>`_
|
||||
* Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by `@davelopez <https://github.com/davelopez>`_ in `#20924 <https://github.com/galaxyproject/galaxy/pull/20924>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Integrate 'uv' for enhanced package management by `@arash77 <https://github.com/arash77>`_ in `#21002 <https://github.com/galaxyproject/galaxy/pull/21002>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Improve type annotation of job runners by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21050 <https://github.com/galaxyproject/galaxy/pull/21050>`_
|
||||
* Remove Job.params by `@jdavcs <https://github.com/jdavcs>`_ in `#21075 <https://github.com/galaxyproject/galaxy/pull/21075>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21104 <https://github.com/galaxyproject/galaxy/pull/21104>`_
|
||||
* Pulsar relay implementation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21118 <https://github.com/galaxyproject/galaxy/pull/21118>`_
|
||||
* Remove legacy Visualization Mako and Controllers by `@guerler <https://github.com/guerler>`_ in `#21133 <https://github.com/galaxyproject/galaxy/pull/21133>`_
|
||||
* Fix various bugs/hacks with tool_data_table handling. by `@jmchilton <https://github.com/jmchilton>`_ in `#21163 <https://github.com/galaxyproject/galaxy/pull/21163>`_
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Replace tuswsgi with tuspyserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21201 <https://github.com/galaxyproject/galaxy/pull/21201>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21229 <https://github.com/galaxyproject/galaxy/pull/21229>`_
|
||||
* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
|
||||
* Allow filtering job searches by history ID by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21257 <https://github.com/galaxyproject/galaxy/pull/21257>`_
|
||||
* Move js-client bootstrapping to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21264 <https://github.com/galaxyproject/galaxy/pull/21264>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21301 <https://github.com/galaxyproject/galaxy/pull/21301>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21345 <https://github.com/galaxyproject/galaxy/pull/21345>`_
|
||||
* Link to an external profile when user accounts are managed by a single OIDC provider by `@marius-mather <https://github.com/marius-mather>`_ in `#21356 <https://github.com/galaxyproject/galaxy/pull/21356>`_
|
||||
* Add OMERO File Source Plugin by `@davelopez <https://github.com/davelopez>`_ in `#21367 <https://github.com/galaxyproject/galaxy/pull/21367>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21368 <https://github.com/galaxyproject/galaxy/pull/21368>`_
|
||||
* Fix: tool execution typing improvements/fixes by `@jmchilton <https://github.com/jmchilton>`_ in `#21374 <https://github.com/galaxyproject/galaxy/pull/21374>`_
|
||||
* Update fastapi to 0.123.4 and ``get_openapi()`` fork by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21384 <https://github.com/galaxyproject/galaxy/pull/21384>`_
|
||||
* Add initial support for the DICOM format by `@kostrykin <https://github.com/kostrykin>`_ in `#21385 <https://github.com/galaxyproject/galaxy/pull/21385>`_
|
||||
* Add new Azure Flat object store file source by `@guerler <https://github.com/guerler>`_ in `#21398 <https://github.com/galaxyproject/galaxy/pull/21398>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21400 <https://github.com/galaxyproject/galaxy/pull/21400>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Add Google Batch job runner by `@ksuderman <https://github.com/ksuderman>`_ in `#21443 <https://github.com/galaxyproject/galaxy/pull/21443>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21449 <https://github.com/galaxyproject/galaxy/pull/21449>`_
|
||||
* Add Jupyternaut adapter for JupyterLite integration by `@guerler <https://github.com/guerler>`_ in `#21463 <https://github.com/galaxyproject/galaxy/pull/21463>`_
|
||||
* Add support for Python 3.14 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21486 <https://github.com/galaxyproject/galaxy/pull/21486>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21500 <https://github.com/galaxyproject/galaxy/pull/21500>`_
|
||||
* Raise ConfigurationError instead etree.ParseError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21509 <https://github.com/galaxyproject/galaxy/pull/21509>`_
|
||||
* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21513 <https://github.com/galaxyproject/galaxy/pull/21513>`_
|
||||
* Add support for workflow landing requests using simple URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21525 <https://github.com/galaxyproject/galaxy/pull/21525>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21526 <https://github.com/galaxyproject/galaxy/pull/21526>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21552 <https://github.com/galaxyproject/galaxy/pull/21552>`_
|
||||
* Add discarded_data option to model store import API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21582 <https://github.com/galaxyproject/galaxy/pull/21582>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Switch Google Cloud Storage file source from fs-gcsfs to gcsfs (fsspec) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21590 <https://github.com/galaxyproject/galaxy/pull/21590>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21606 <https://github.com/galaxyproject/galaxy/pull/21606>`_
|
||||
* Update to gravity 1.2.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21608 <https://github.com/galaxyproject/galaxy/pull/21608>`_
|
||||
* Move legacy Visualization Plugins API to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21612 <https://github.com/galaxyproject/galaxy/pull/21612>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21653 <https://github.com/galaxyproject/galaxy/pull/21653>`_
|
||||
* Add agent based AI tool recommendation by `@dannon <https://github.com/dannon>`_ in `#21661 <https://github.com/galaxyproject/galaxy/pull/21661>`_
|
||||
* Type annotations and refactorings by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21673 <https://github.com/galaxyproject/galaxy/pull/21673>`_
|
||||
* Check file source template config files for determining conditional dependencies + add constraint for zero-ice by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21688 <https://github.com/galaxyproject/galaxy/pull/21688>`_
|
||||
* Standardize agent API schemas and response metadata by `@dannon <https://github.com/dannon>`_ in `#21692 <https://github.com/galaxyproject/galaxy/pull/21692>`_
|
||||
* Backport chat API improvements by `@dannon <https://github.com/dannon>`_ in `#21973 <https://github.com/galaxyproject/galaxy/pull/21973>`_
|
||||
* Use ParameterValueError for dataset count validation to reduce Sentry noise by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22058 <https://github.com/galaxyproject/galaxy/pull/22058>`_
|
||||
* Use mock test server when tests don't target external galaxy server by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22103 <https://github.com/galaxyproject/galaxy/pull/22103>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Merge 25.1 into dev, fix openapi schema generation for TypedDict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21168 <https://github.com/galaxyproject/galaxy/pull/21168>`_
|
||||
* Don't return 404 when file name can't be serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21577 <https://github.com/galaxyproject/galaxy/pull/21577>`_
|
||||
* Reduce completion monitor logging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21674 <https://github.com/galaxyproject/galaxy/pull/21674>`_
|
||||
* Backport: Fix dbkey filter returning no options when dbkey unset by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21945 <https://github.com/galaxyproject/galaxy/pull/21945>`_
|
||||
* Show invalid tool error reasons in Tool Shed UI by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22040 <https://github.com/galaxyproject/galaxy/pull/22040>`_
|
||||
* Backport of 21939 by `@jdavcs <https://github.com/jdavcs>`_ in `#22265 <https://github.com/galaxyproject/galaxy/pull/22265>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,17 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,48 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Infer type from extension for mzml by `@bgruening <https://github.com/bgruening>`_ in `#21033 <https://github.com/galaxyproject/galaxy/pull/21033>`_
|
||||
* Update config samples from schema by `@davelopez <https://github.com/davelopez>`_ in `#21053 <https://github.com/galaxyproject/galaxy/pull/21053>`_
|
||||
* remove a tool from sample that is no longer included in dist by `@martenson <https://github.com/martenson>`_ in `#21371 <https://github.com/galaxyproject/galaxy/pull/21371>`_
|
||||
* Various fixes around ascp file source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21372 <https://github.com/galaxyproject/galaxy/pull/21372>`_
|
||||
* Add tool_shed_url config for explicit hostname setting by `@jmchilton <https://github.com/jmchilton>`_ in `#21499 <https://github.com/galaxyproject/galaxy/pull/21499>`_
|
||||
* Use inference_services config for plugin chat proxy by `@dannon <https://github.com/dannon>`_ in `#21986 <https://github.com/galaxyproject/galaxy/pull/21986>`_
|
||||
* Silence social_core's noisy handle_http_errors logging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22403 <https://github.com/galaxyproject/galaxy/pull/22403>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Improve docs for `invalidjobexception_state` and `_retry` of DRMAA runners by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20612 <https://github.com/galaxyproject/galaxy/pull/20612>`_
|
||||
* Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by `@davelopez <https://github.com/davelopez>`_ in `#20924 <https://github.com/galaxyproject/galaxy/pull/20924>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Remove legacy Visualization Mako and Controllers by `@guerler <https://github.com/guerler>`_ in `#21133 <https://github.com/galaxyproject/galaxy/pull/21133>`_
|
||||
* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
|
||||
* Slight improvement of mztab2 datatype by `@nguilhot <https://github.com/nguilhot>`_ in `#21258 <https://github.com/galaxyproject/galaxy/pull/21258>`_
|
||||
* Link to an external profile when user accounts are managed by a single OIDC provider by `@marius-mather <https://github.com/marius-mather>`_ in `#21356 <https://github.com/galaxyproject/galaxy/pull/21356>`_
|
||||
* Ascp plugin by `@d-callan <https://github.com/d-callan>`_ in `#21357 <https://github.com/galaxyproject/galaxy/pull/21357>`_
|
||||
* Add initial support for the DICOM format by `@kostrykin <https://github.com/kostrykin>`_ in `#21385 <https://github.com/galaxyproject/galaxy/pull/21385>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Update to gravity 1.2.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21608 <https://github.com/galaxyproject/galaxy/pull/21608>`_
|
||||
* Add new datatypes: .taf and .taf.gz by `@Maed0x <https://github.com/Maed0x>`_ in `#22242 <https://github.com/galaxyproject/galaxy/pull/22242>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Backport of 21939 by `@jdavcs <https://github.com/jdavcs>`_ in `#22265 <https://github.com/galaxyproject/galaxy/pull/22265>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,80 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Drop down revision for drop_job_params migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21122 <https://github.com/galaxyproject/galaxy/pull/21122>`_
|
||||
* Create alembic merge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21447 <https://github.com/galaxyproject/galaxy/pull/21447>`_
|
||||
* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
|
||||
* Fix width and height assignment for image metadata using Pillow by `@kostrykin <https://github.com/kostrykin>`_ in `#21554 <https://github.com/galaxyproject/galaxy/pull/21554>`_
|
||||
* Avoid slash duplication in display application urls by `@guerler <https://github.com/guerler>`_ in `#21809 <https://github.com/galaxyproject/galaxy/pull/21809>`_
|
||||
* Fix redirect upon impersonation by `@guerler <https://github.com/guerler>`_ in `#21810 <https://github.com/galaxyproject/galaxy/pull/21810>`_
|
||||
* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
|
||||
* Fix AttributeError serializing implicit output collections during job prep by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22034 <https://github.com/galaxyproject/galaxy/pull/22034>`_
|
||||
* Fix ``preferred_object_store_id`` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
|
||||
* Fix TypeError when column_names metadata is None by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22057 <https://github.com/galaxyproject/galaxy/pull/22057>`_
|
||||
* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
|
||||
* Fix nested collection query performance by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22119 <https://github.com/galaxyproject/galaxy/pull/22119>`_
|
||||
* Fix CardinalityViolation in nested collection ARRAY walk scalar subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22123 <https://github.com/galaxyproject/galaxy/pull/22123>`_
|
||||
* Use skip_locked also when updating collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22133 <https://github.com/galaxyproject/galaxy/pull/22133>`_
|
||||
* Fix redundant empty collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22154 <https://github.com/galaxyproject/galaxy/pull/22154>`_
|
||||
* Don't fail on probable delete race by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22183 <https://github.com/galaxyproject/galaxy/pull/22183>`_
|
||||
* Back port collection fixes from #22170. by `@jmchilton <https://github.com/jmchilton>`_ in `#22193 <https://github.com/galaxyproject/galaxy/pull/22193>`_
|
||||
* Optimize dataset get_edit API by deferring expensive role queries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22232 <https://github.com/galaxyproject/galaxy/pull/22232>`_
|
||||
* Batch-prefetch HDCA job_state_summary in history contents listing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22256 <https://github.com/galaxyproject/galaxy/pull/22256>`_
|
||||
* Sequence datatypes: only read first character per line for setting metadata by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#22276 <https://github.com/galaxyproject/galaxy/pull/22276>`_
|
||||
* Fix slow get_private_role_user_emails_dict query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22307 <https://github.com/galaxyproject/galaxy/pull/22307>`_
|
||||
* Fix timestamp parsing in job import/export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22372 <https://github.com/galaxyproject/galaxy/pull/22372>`_
|
||||
* Ensure ``x-content-truncated`` header is string by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22386 <https://github.com/galaxyproject/galaxy/pull/22386>`_
|
||||
* Fix dataset preview rendering to preserve newlines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22397 <https://github.com/galaxyproject/galaxy/pull/22397>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Move database revision tags to separate file by `@guerler <https://github.com/guerler>`_ in `#20998 <https://github.com/galaxyproject/galaxy/pull/20998>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Remove Job.params by `@jdavcs <https://github.com/jdavcs>`_ in `#21075 <https://github.com/galaxyproject/galaxy/pull/21075>`_
|
||||
* Remove tabular chunked, binary and large file mako by `@guerler <https://github.com/guerler>`_ in `#21106 <https://github.com/galaxyproject/galaxy/pull/21106>`_
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
|
||||
* Slight improvement of mztab2 datatype by `@nguilhot <https://github.com/nguilhot>`_ in `#21258 <https://github.com/galaxyproject/galaxy/pull/21258>`_
|
||||
* Move js-client bootstrapping to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21264 <https://github.com/galaxyproject/galaxy/pull/21264>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Fix: tool execution typing improvements/fixes by `@jmchilton <https://github.com/jmchilton>`_ in `#21374 <https://github.com/galaxyproject/galaxy/pull/21374>`_
|
||||
* Add initial support for the DICOM format by `@kostrykin <https://github.com/kostrykin>`_ in `#21385 <https://github.com/galaxyproject/galaxy/pull/21385>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Discriminate decompression tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21510 <https://github.com/galaxyproject/galaxy/pull/21510>`_
|
||||
* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
|
||||
* Implement subworkflow invocation export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21512 <https://github.com/galaxyproject/galaxy/pull/21512>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Allow connecting sample sheet inputs to compatible collection inputs in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21859 <https://github.com/galaxyproject/galaxy/pull/21859>`_
|
||||
* Add new datatypes: .taf and .taf.gz by `@Maed0x <https://github.com/Maed0x>`_ in `#22242 <https://github.com/galaxyproject/galaxy/pull/22242>`_
|
||||
* Add _F/_R auto-pairing filter for forward/reverse datasets by `@jmchilton <https://github.com/jmchilton>`_ in `#22267 <https://github.com/galaxyproject/galaxy/pull/22267>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Update revision tags for release 25.1 by `@arash77 <https://github.com/arash77>`_ in `#21022 <https://github.com/galaxyproject/galaxy/pull/21022>`_
|
||||
* Merge 25.1 into dev and create alembic merge revision by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21440 <https://github.com/galaxyproject/galaxy/pull/21440>`_
|
||||
* Add Database Revision for 26.0 by `@guerler <https://github.com/guerler>`_ in `#21675 <https://github.com/galaxyproject/galaxy/pull/21675>`_
|
||||
* Fix on_complete column type mismatch by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21765 <https://github.com/galaxyproject/galaxy/pull/21765>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,44 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Various fixes around ascp file source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21372 <https://github.com/galaxyproject/galaxy/pull/21372>`_
|
||||
* Better error message for unencoded/unresolvable filesource uri by `@dannon <https://github.com/dannon>`_ in `#21562 <https://github.com/galaxyproject/galaxy/pull/21562>`_
|
||||
* Fix OMERO file source download multi channel TIFF by `@davelopez <https://github.com/davelopez>`_ in `#21856 <https://github.com/galaxyproject/galaxy/pull/21856>`_
|
||||
* Fix ascp download retries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21857 <https://github.com/galaxyproject/galaxy/pull/21857>`_
|
||||
* Fixes some more optional fields in templates by `@davelopez <https://github.com/davelopez>`_ in `#21891 <https://github.com/galaxyproject/galaxy/pull/21891>`_
|
||||
* Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21923 <https://github.com/galaxyproject/galaxy/pull/21923>`_
|
||||
* Fix OMERO temp directory handling by `@davelopez <https://github.com/davelopez>`_ in `#22262 <https://github.com/galaxyproject/galaxy/pull/22262>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add DRS compact identifier support by `@dannon <https://github.com/dannon>`_ in `#20410 <https://github.com/galaxyproject/galaxy/pull/20410>`_
|
||||
* Add service account support for Google Cloud Storage client initialization by `@dannon <https://github.com/dannon>`_ in `#21027 <https://github.com/galaxyproject/galaxy/pull/21027>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Add Custom Validation for User-Configured Templates by `@davelopez <https://github.com/davelopez>`_ in `#21155 <https://github.com/galaxyproject/galaxy/pull/21155>`_
|
||||
* Ascp plugin by `@d-callan <https://github.com/d-callan>`_ in `#21357 <https://github.com/galaxyproject/galaxy/pull/21357>`_
|
||||
* Add OMERO File Source Plugin by `@davelopez <https://github.com/davelopez>`_ in `#21367 <https://github.com/galaxyproject/galaxy/pull/21367>`_
|
||||
* Add new Azure Flat object store file source by `@guerler <https://github.com/guerler>`_ in `#21398 <https://github.com/galaxyproject/galaxy/pull/21398>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Switch Google Cloud Storage file source from fs-gcsfs to gcsfs (fsspec) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21590 <https://github.com/galaxyproject/galaxy/pull/21590>`_
|
||||
* Unify extensions of file source templates by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21594 <https://github.com/galaxyproject/galaxy/pull/21594>`_
|
||||
* Various fixes to file source template's validation system by `@davelopez <https://github.com/davelopez>`_ in `#21704 <https://github.com/galaxyproject/galaxy/pull/21704>`_
|
||||
* Adds ImageJ metadata support to TIFF export by `@davelopez <https://github.com/davelopez>`_ in `#21882 <https://github.com/galaxyproject/galaxy/pull/21882>`_
|
||||
* Use mock test server when tests don't target external galaxy server by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22103 <https://github.com/galaxyproject/galaxy/pull/22103>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,28 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix ``preferred_object_store_id`` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
|
||||
* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
|
||||
* Fix redundant empty collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22154 <https://github.com/galaxyproject/galaxy/pull/22154>`_
|
||||
* Handle ``MaxDiscoveredFilesExceededError`` for dynamic collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22402 <https://github.com/galaxyproject/galaxy/pull/22402>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add citation reminder to job completion email by `@Syrinx55 <https://github.com/Syrinx55>`_ in `#21347 <https://github.com/galaxyproject/galaxy/pull/21347>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,18 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,399 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix workflow report time handling by `@dannon <https://github.com/dannon>`_ in `#19292 <https://github.com/galaxyproject/galaxy/pull/19292>`_
|
||||
* Attempt to fix transient API test failure for jobs search. by `@jmchilton <https://github.com/jmchilton>`_ in `#20898 <https://github.com/galaxyproject/galaxy/pull/20898>`_
|
||||
* Infer type from extension for mzml by `@bgruening <https://github.com/bgruening>`_ in `#21033 <https://github.com/galaxyproject/galaxy/pull/21033>`_
|
||||
* Bump python-ldap from 3.4.0 to 3.4.5 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21042 <https://github.com/galaxyproject/galaxy/pull/21042>`_
|
||||
* Update config samples from schema by `@davelopez <https://github.com/davelopez>`_ in `#21053 <https://github.com/galaxyproject/galaxy/pull/21053>`_
|
||||
* Cross product tools: Fix typos in help section by `@RZ9082 <https://github.com/RZ9082>`_ in `#21061 <https://github.com/galaxyproject/galaxy/pull/21061>`_
|
||||
* Drop down revision for drop_job_params migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21122 <https://github.com/galaxyproject/galaxy/pull/21122>`_
|
||||
* Pin Ansible version during Docker image building by `@ksuderman <https://github.com/ksuderman>`_ in `#21131 <https://github.com/galaxyproject/galaxy/pull/21131>`_
|
||||
* Change invocation step state display selector to fix styling by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21144 <https://github.com/galaxyproject/galaxy/pull/21144>`_
|
||||
* Simplify transiently failing test (#21224) see if this stabilizes it at all by `@jmchilton <https://github.com/jmchilton>`_ in `#21239 <https://github.com/galaxyproject/galaxy/pull/21239>`_
|
||||
* Plumbing for tracking potential fixes for transient failures (and a fix demonstrating it) by `@jmchilton <https://github.com/jmchilton>`_ in `#21243 <https://github.com/galaxyproject/galaxy/pull/21243>`_
|
||||
* Fix differentiation between single handler and handler tag by `@natefoo <https://github.com/natefoo>`_ in `#21252 <https://github.com/galaxyproject/galaxy/pull/21252>`_
|
||||
* Fix quoting issue getting the Galaxy version by `@ksuderman <https://github.com/ksuderman>`_ in `#21316 <https://github.com/galaxyproject/galaxy/pull/21316>`_
|
||||
* Use uv also for the lint_openapi_schema GitHub workflow by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21319 <https://github.com/galaxyproject/galaxy/pull/21319>`_
|
||||
* Extend startup probe timeout by `@ksuderman <https://github.com/ksuderman>`_ in `#21326 <https://github.com/galaxyproject/galaxy/pull/21326>`_
|
||||
* remove a tool from sample that is no longer included in dist by `@martenson <https://github.com/martenson>`_ in `#21371 <https://github.com/galaxyproject/galaxy/pull/21371>`_
|
||||
* Various fixes around ascp file source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21372 <https://github.com/galaxyproject/galaxy/pull/21372>`_
|
||||
* Attempt to fix transiently failing tests that click this tab. by `@jmchilton <https://github.com/jmchilton>`_ in `#21376 <https://github.com/galaxyproject/galaxy/pull/21376>`_
|
||||
* Attempt to fix transient failure in list_list_copy by `@jmchilton <https://github.com/jmchilton>`_ in `#21381 <https://github.com/galaxyproject/galaxy/pull/21381>`_
|
||||
* Use icon classes instead of strings for history content item states by `@guerler <https://github.com/guerler>`_ in `#21393 <https://github.com/galaxyproject/galaxy/pull/21393>`_
|
||||
* Bump urllib3 from 2.5.0 to 2.6.0 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21399 <https://github.com/galaxyproject/galaxy/pull/21399>`_
|
||||
* Assorted tool shed fixes. by `@jmchilton <https://github.com/jmchilton>`_ in `#21424 <https://github.com/galaxyproject/galaxy/pull/21424>`_
|
||||
* Use Playwright from the Galaxy virtualenv by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21425 <https://github.com/galaxyproject/galaxy/pull/21425>`_
|
||||
* Fix tool shed repository last updated time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21427 <https://github.com/galaxyproject/galaxy/pull/21427>`_
|
||||
* Add license define for vite by `@dannon <https://github.com/dannon>`_ in `#21431 <https://github.com/galaxyproject/galaxy/pull/21431>`_
|
||||
* Create alembic merge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21447 <https://github.com/galaxyproject/galaxy/pull/21447>`_
|
||||
* Don't set OAUTHLIB_INSECURE_TRANSPORT setting in user_data by `@nuwang <https://github.com/nuwang>`_ in `#21451 <https://github.com/galaxyproject/galaxy/pull/21451>`_
|
||||
* Bump filelock from 3.20.0 to 3.20.1 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21476 <https://github.com/galaxyproject/galaxy/pull/21476>`_
|
||||
* Fixes select field clipping and filtering by `@guerler <https://github.com/guerler>`_ in `#21479 <https://github.com/galaxyproject/galaxy/pull/21479>`_
|
||||
* Add tool_shed_url config for explicit hostname setting by `@jmchilton <https://github.com/jmchilton>`_ in `#21499 <https://github.com/galaxyproject/galaxy/pull/21499>`_
|
||||
* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
|
||||
* Restrict collection of dynamic working dir output to specified directory in pulsar by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21515 <https://github.com/galaxyproject/galaxy/pull/21515>`_
|
||||
* Accept 404 as valid intermediate state when waiting for dataset purge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21521 <https://github.com/galaxyproject/galaxy/pull/21521>`_
|
||||
* Fix input tags not being copied when using copy_inputs_to_history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21529 <https://github.com/galaxyproject/galaxy/pull/21529>`_
|
||||
* Bump aiohttp from 3.13.2 to 3.13.3 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21538 <https://github.com/galaxyproject/galaxy/pull/21538>`_
|
||||
* Preserve assistant messages with tool calls by `@guerler <https://github.com/guerler>`_ in `#21545 <https://github.com/galaxyproject/galaxy/pull/21545>`_
|
||||
* Bump urllib3 from 2.6.2 to 2.6.3 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21546 <https://github.com/galaxyproject/galaxy/pull/21546>`_
|
||||
* Bump werkzeug from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21549 <https://github.com/galaxyproject/galaxy/pull/21549>`_
|
||||
* Fix width and height assignment for image metadata using Pillow by `@kostrykin <https://github.com/kostrykin>`_ in `#21554 <https://github.com/galaxyproject/galaxy/pull/21554>`_
|
||||
* Better error message for unencoded/unresolvable filesource uri by `@dannon <https://github.com/dannon>`_ in `#21562 <https://github.com/galaxyproject/galaxy/pull/21562>`_
|
||||
* Fix loading spinner positioning in admin grid by `@dannon <https://github.com/dannon>`_ in `#21564 <https://github.com/galaxyproject/galaxy/pull/21564>`_
|
||||
* Update Molstar by `@guerler <https://github.com/guerler>`_ in `#21567 <https://github.com/galaxyproject/galaxy/pull/21567>`_
|
||||
* Overhaul ChatGXY Routing approach by `@dannon <https://github.com/dannon>`_ in `#21580 <https://github.com/galaxyproject/galaxy/pull/21580>`_
|
||||
* Fix Vite 5 upgrade compatibility issues for tool shed frontend by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21581 <https://github.com/galaxyproject/galaxy/pull/21581>`_
|
||||
* Remove dummy header from JupyterLite requests by `@guerler <https://github.com/guerler>`_ in `#21585 <https://github.com/galaxyproject/galaxy/pull/21585>`_
|
||||
* Bump pyasn1 from 0.6.1 to 0.6.2 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21605 <https://github.com/galaxyproject/galaxy/pull/21605>`_
|
||||
* Fix Auto Layout crash with conditional (when) step inputs by `@jmchilton <https://github.com/jmchilton>`_ in `#21616 <https://github.com/galaxyproject/galaxy/pull/21616>`_
|
||||
* Fix toolshed tests on Python 3.14 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21617 <https://github.com/galaxyproject/galaxy/pull/21617>`_
|
||||
* Fix package test using ``--index-strategy unsafe-best-match`` to match pip behavior by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21619 <https://github.com/galaxyproject/galaxy/pull/21619>`_
|
||||
* Fix ace import in cell-based markdown editor by `@guerler <https://github.com/guerler>`_ in `#21622 <https://github.com/galaxyproject/galaxy/pull/21622>`_
|
||||
* Triage command followup fixes/tweaks by `@dannon <https://github.com/dannon>`_ in `#21629 <https://github.com/galaxyproject/galaxy/pull/21629>`_
|
||||
* Bump python-multipart from 0.0.21 to 0.0.22 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21663 <https://github.com/galaxyproject/galaxy/pull/21663>`_
|
||||
* Fix incorrect router tag in plugins API by `@dannon <https://github.com/dannon>`_ in `#21669 <https://github.com/galaxyproject/galaxy/pull/21669>`_
|
||||
* Add missing types to visualization model by `@guerler <https://github.com/guerler>`_ in `#21672 <https://github.com/galaxyproject/galaxy/pull/21672>`_
|
||||
* Fix storing origin for workflow landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21696 <https://github.com/galaxyproject/galaxy/pull/21696>`_
|
||||
* Hide interactivetools activity when disabled in config by `@dannon <https://github.com/dannon>`_ in `#21755 <https://github.com/galaxyproject/galaxy/pull/21755>`_
|
||||
* Hide ChatGXY activity when LLM API isn't configured by `@dannon <https://github.com/dannon>`_ in `#21756 <https://github.com/galaxyproject/galaxy/pull/21756>`_
|
||||
* Handle TPV floating point memory values by `@ksuderman <https://github.com/ksuderman>`_ in `#21763 <https://github.com/galaxyproject/galaxy/pull/21763>`_
|
||||
* Deserialize json string for export_metadata from old records by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21772 <https://github.com/galaxyproject/galaxy/pull/21772>`_
|
||||
* Removes unnecessary overflow restriction in upload method panel by `@davelopez <https://github.com/davelopez>`_ in `#21774 <https://github.com/galaxyproject/galaxy/pull/21774>`_
|
||||
* Fix upload local file drop zone when listing by `@davelopez <https://github.com/davelopez>`_ in `#21776 <https://github.com/galaxyproject/galaxy/pull/21776>`_
|
||||
* Fixes navigation back to added URLs in upload panel by `@davelopez <https://github.com/davelopez>`_ in `#21796 <https://github.com/galaxyproject/galaxy/pull/21796>`_
|
||||
* Fix passing invalid job_destination dict to JobState constructor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21798 <https://github.com/galaxyproject/galaxy/pull/21798>`_
|
||||
* Avoid slash duplication in display application urls by `@guerler <https://github.com/guerler>`_ in `#21809 <https://github.com/galaxyproject/galaxy/pull/21809>`_
|
||||
* Fix redirect upon impersonation by `@guerler <https://github.com/guerler>`_ in `#21810 <https://github.com/galaxyproject/galaxy/pull/21810>`_
|
||||
* Update ``get_definitions()`` to FastAPI 0.128.8 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21834 <https://github.com/galaxyproject/galaxy/pull/21834>`_
|
||||
* Fix selenium test test_rename_history by `@davelopez <https://github.com/davelopez>`_ in `#21835 <https://github.com/galaxyproject/galaxy/pull/21835>`_
|
||||
* When getting tool by uuid, get that exact tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21844 <https://github.com/galaxyproject/galaxy/pull/21844>`_
|
||||
* Fix OMERO file source download multi channel TIFF by `@davelopez <https://github.com/davelopez>`_ in `#21856 <https://github.com/galaxyproject/galaxy/pull/21856>`_
|
||||
* Fix ascp download retries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21857 <https://github.com/galaxyproject/galaxy/pull/21857>`_
|
||||
* Fix infinite request loop on dataset preview fetch failure by `@dannon <https://github.com/dannon>`_ in `#21881 <https://github.com/galaxyproject/galaxy/pull/21881>`_
|
||||
* Fixes some more optional fields in templates by `@davelopez <https://github.com/davelopez>`_ in `#21891 <https://github.com/galaxyproject/galaxy/pull/21891>`_
|
||||
* Fix missing sharable link URL in TS2.0 emails by `@jmchilton <https://github.com/jmchilton>`_ in `#21892 <https://github.com/galaxyproject/galaxy/pull/21892>`_
|
||||
* Parse input collections as well in markdown editor by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21913 <https://github.com/galaxyproject/galaxy/pull/21913>`_
|
||||
* Fix collection step Job markdown elements not rendering by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21917 <https://github.com/galaxyproject/galaxy/pull/21917>`_
|
||||
* Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21923 <https://github.com/galaxyproject/galaxy/pull/21923>`_
|
||||
* Remove unused handle_tool_shed_url_protocol by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21925 <https://github.com/galaxyproject/galaxy/pull/21925>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix HTML dataset extra files 404 in preview by `@dannon <https://github.com/dannon>`_ in `#21981 <https://github.com/galaxyproject/galaxy/pull/21981>`_
|
||||
* Fix dict leaking to process_dataset() during workflow execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21982 <https://github.com/galaxyproject/galaxy/pull/21982>`_
|
||||
* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
|
||||
* Use inference_services config for plugin chat proxy by `@dannon <https://github.com/dannon>`_ in `#21986 <https://github.com/galaxyproject/galaxy/pull/21986>`_
|
||||
* Restore file doesn't match sniffed datatype message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21988 <https://github.com/galaxyproject/galaxy/pull/21988>`_
|
||||
* Fix repo metadata persistence in fix_tool_config_paths.py by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22012 <https://github.com/galaxyproject/galaxy/pull/22012>`_
|
||||
* Fix uncaught `ImplicitConversionRequired` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22027 <https://github.com/galaxyproject/galaxy/pull/22027>`_
|
||||
* Fix toolshed "copy page link" copying relative URL instead of absolute by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22028 <https://github.com/galaxyproject/galaxy/pull/22028>`_
|
||||
* Fix AttributeError when fetching citations for missing tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22029 <https://github.com/galaxyproject/galaxy/pull/22029>`_
|
||||
* Fix invalid function schema error for tools with None parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22030 <https://github.com/galaxyproject/galaxy/pull/22030>`_
|
||||
* AttributeError when history is None during tool execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22031 <https://github.com/galaxyproject/galaxy/pull/22031>`_
|
||||
* Fix subworkflow editing navigation and enable e2e test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22032 <https://github.com/galaxyproject/galaxy/pull/22032>`_
|
||||
* Fix AttributeError when export_metadata is a string instead of dict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22033 <https://github.com/galaxyproject/galaxy/pull/22033>`_
|
||||
* Fix AttributeError serializing implicit output collections during job prep by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22034 <https://github.com/galaxyproject/galaxy/pull/22034>`_
|
||||
* Fix ToolExpressionOutput.to_model() for boolean type. by `@jmchilton <https://github.com/jmchilton>`_ in `#22038 <https://github.com/galaxyproject/galaxy/pull/22038>`_
|
||||
* Fix ``preferred_object_store_id`` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
|
||||
* Fix TypeError when column_names metadata is None by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22057 <https://github.com/galaxyproject/galaxy/pull/22057>`_
|
||||
* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
|
||||
* Fix FileNotFoundError when workflow references purged HDA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22060 <https://github.com/galaxyproject/galaxy/pull/22060>`_
|
||||
* Fix AttributeError when dataset in inheritance chain has no user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22062 <https://github.com/galaxyproject/galaxy/pull/22062>`_
|
||||
* Add check_database_connection to workflow scheduling path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22063 <https://github.com/galaxyproject/galaxy/pull/22063>`_
|
||||
* Use base64 URL instead of GitHub URL in test_stage_fetch_decompress_true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22069 <https://github.com/galaxyproject/galaxy/pull/22069>`_
|
||||
* Store tool shed search index test data in repo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22071 <https://github.com/galaxyproject/galaxy/pull/22071>`_
|
||||
* Move history panel expand button to top by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22076 <https://github.com/galaxyproject/galaxy/pull/22076>`_
|
||||
* Fix subworkflow editing navigation and enable e2e test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22082 <https://github.com/galaxyproject/galaxy/pull/22082>`_
|
||||
* Fix workflow search broken after auto layout by `@dannon <https://github.com/dannon>`_ in `#22093 <https://github.com/galaxyproject/galaxy/pull/22093>`_
|
||||
* Fix legacy_expose_api error callable returning str instead of bytes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22106 <https://github.com/galaxyproject/galaxy/pull/22106>`_
|
||||
* Fix WSGI middlewares returning strings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22108 <https://github.com/galaxyproject/galaxy/pull/22108>`_
|
||||
* Model hidden_data params as optional data in tool meta-models. by `@jmchilton <https://github.com/jmchilton>`_ in `#22116 <https://github.com/galaxyproject/galaxy/pull/22116>`_
|
||||
* Fix nested collection query performance by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22119 <https://github.com/galaxyproject/galaxy/pull/22119>`_
|
||||
* Fix CardinalityViolation in nested collection ARRAY walk scalar subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22123 <https://github.com/galaxyproject/galaxy/pull/22123>`_
|
||||
* Fix unhandled exceptions in tool form model population by `@guerler <https://github.com/guerler>`_ in `#22129 <https://github.com/galaxyproject/galaxy/pull/22129>`_
|
||||
* Use skip_locked also when updating collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22133 <https://github.com/galaxyproject/galaxy/pull/22133>`_
|
||||
* Backport transient CI fixes from #22102 to release_26.0 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22135 <https://github.com/galaxyproject/galaxy/pull/22135>`_
|
||||
* Do not render hide button on non-optional activities in activity bar by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22140 <https://github.com/galaxyproject/galaxy/pull/22140>`_
|
||||
* Fix redundant empty collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22154 <https://github.com/galaxyproject/galaxy/pull/22154>`_
|
||||
* Do not queue paused jobs by `@martenson <https://github.com/martenson>`_ in `#22156 <https://github.com/galaxyproject/galaxy/pull/22156>`_
|
||||
* Fix AmbiguousColumn error in job search for tools with long input names by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22167 <https://github.com/galaxyproject/galaxy/pull/22167>`_
|
||||
* Bump tiffviewer visualization to v0.0.4 by `@davelopez <https://github.com/davelopez>`_ in `#22168 <https://github.com/galaxyproject/galaxy/pull/22168>`_
|
||||
* Fix make all histories private controller None id bug by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22174 <https://github.com/galaxyproject/galaxy/pull/22174>`_
|
||||
* Fixes for gxformat2 by `@jmchilton <https://github.com/jmchilton>`_ in `#22179 <https://github.com/galaxyproject/galaxy/pull/22179>`_
|
||||
* Add batch celery task for history dataset purging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22180 <https://github.com/galaxyproject/galaxy/pull/22180>`_
|
||||
* Include missing tools in stock_tool_paths. by `@jmchilton <https://github.com/jmchilton>`_ in `#22181 <https://github.com/galaxyproject/galaxy/pull/22181>`_
|
||||
* Don't fail on probable delete race by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22183 <https://github.com/galaxyproject/galaxy/pull/22183>`_
|
||||
* Throw ParameterValueError instead of generic error by `@guerler <https://github.com/guerler>`_ in `#22188 <https://github.com/galaxyproject/galaxy/pull/22188>`_
|
||||
* Back port collection fixes from #22170. by `@jmchilton <https://github.com/jmchilton>`_ in `#22193 <https://github.com/galaxyproject/galaxy/pull/22193>`_
|
||||
* Cache url path lookup by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22198 <https://github.com/galaxyproject/galaxy/pull/22198>`_
|
||||
* Fix event loop blocking in async API routes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22202 <https://github.com/galaxyproject/galaxy/pull/22202>`_
|
||||
* Update fastmcp requirement to 3.0.2 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22221 <https://github.com/galaxyproject/galaxy/pull/22221>`_
|
||||
* Fix race condition in history list when rapidly changing search filters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22223 <https://github.com/galaxyproject/galaxy/pull/22223>`_
|
||||
* Fix missing focus helper by `@guerler <https://github.com/guerler>`_ in `#22225 <https://github.com/galaxyproject/galaxy/pull/22225>`_
|
||||
* Use ``/api/tool_data`` endpoints in DataTables.vue & DataManagerTable.vue by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22229 <https://github.com/galaxyproject/galaxy/pull/22229>`_
|
||||
* Optimize dataset get_edit API by deferring expensive role queries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22232 <https://github.com/galaxyproject/galaxy/pull/22232>`_
|
||||
* Fix TypeError in ExternalIdentities by always including provider_label in authnz response by `@guerler <https://github.com/guerler>`_ in `#22234 <https://github.com/galaxyproject/galaxy/pull/22234>`_
|
||||
* Add optional dataset collection mode to harmonize tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22236 <https://github.com/galaxyproject/galaxy/pull/22236>`_
|
||||
* Fix batch history purge not updating user's update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22238 <https://github.com/galaxyproject/galaxy/pull/22238>`_
|
||||
* Fix import order error from ESLint by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22240 <https://github.com/galaxyproject/galaxy/pull/22240>`_
|
||||
* Delete dummy error controller, fix type error on invalid requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22245 <https://github.com/galaxyproject/galaxy/pull/22245>`_
|
||||
* Fix file source removal by `@davelopez <https://github.com/davelopez>`_ in `#22246 <https://github.com/galaxyproject/galaxy/pull/22246>`_
|
||||
* Make sure origins for data landings are persisted by `@d-callan <https://github.com/d-callan>`_ in `#22248 <https://github.com/galaxyproject/galaxy/pull/22248>`_
|
||||
* Validate replacement_params values are strings before storing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22250 <https://github.com/galaxyproject/galaxy/pull/22250>`_
|
||||
* Fix N+1 queries in fetch_job_states for jobs_summary endpoints by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22251 <https://github.com/galaxyproject/galaxy/pull/22251>`_
|
||||
* Fix oauth2 template validation by `@davelopez <https://github.com/davelopez>`_ in `#22253 <https://github.com/galaxyproject/galaxy/pull/22253>`_
|
||||
* Drop stored workflow menu entries from user serialization by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22254 <https://github.com/galaxyproject/galaxy/pull/22254>`_
|
||||
* Replace BaseHTTPMiddleware with pure ASGI middleware for X-Frame-Options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22255 <https://github.com/galaxyproject/galaxy/pull/22255>`_
|
||||
* Batch-prefetch HDCA job_state_summary in history contents listing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22256 <https://github.com/galaxyproject/galaxy/pull/22256>`_
|
||||
* Fixes optional integer form handling in templates by `@davelopez <https://github.com/davelopez>`_ in `#22257 <https://github.com/galaxyproject/galaxy/pull/22257>`_
|
||||
* Fix HDCA lost in tool form on rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22258 <https://github.com/galaxyproject/galaxy/pull/22258>`_
|
||||
* Fix OMERO temp directory handling by `@davelopez <https://github.com/davelopez>`_ in `#22262 <https://github.com/galaxyproject/galaxy/pull/22262>`_
|
||||
* Fix DOMPurify sanitize TypeError in Library components by `@dannon <https://github.com/dannon>`_ in `#22263 <https://github.com/galaxyproject/galaxy/pull/22263>`_
|
||||
* Fix purge for anon histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22275 <https://github.com/galaxyproject/galaxy/pull/22275>`_
|
||||
* Sequence datatypes: only read first character per line for setting metadata by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#22276 <https://github.com/galaxyproject/galaxy/pull/22276>`_
|
||||
* Raise error when API client sends invalid parameter keys by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22277 <https://github.com/galaxyproject/galaxy/pull/22277>`_
|
||||
* Fix refresh time in object store caches by `@bgruening <https://github.com/bgruening>`_ in `#22279 <https://github.com/galaxyproject/galaxy/pull/22279>`_
|
||||
* Fix validation of certain classes of text validators in tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#22280 <https://github.com/galaxyproject/galaxy/pull/22280>`_
|
||||
* Fail early wehn no route match is found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22284 <https://github.com/galaxyproject/galaxy/pull/22284>`_
|
||||
* Raise MessageException instead of generic Exception in rules_dsl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22285 <https://github.com/galaxyproject/galaxy/pull/22285>`_
|
||||
* Fix toolshed static image url encoding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22286 <https://github.com/galaxyproject/galaxy/pull/22286>`_
|
||||
* Fix nested DatasetCollectionElement in dynamic options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22287 <https://github.com/galaxyproject/galaxy/pull/22287>`_
|
||||
* Fix flaky job search for HDCA inputs on PostgreSQL by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22290 <https://github.com/galaxyproject/galaxy/pull/22290>`_
|
||||
* Fix HDCA shown as unavailable on tool form rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22291 <https://github.com/galaxyproject/galaxy/pull/22291>`_
|
||||
* Fix AttributeError when anonymous user searches workflows with ``is:bookmarked`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22296 <https://github.com/galaxyproject/galaxy/pull/22296>`_
|
||||
* Improve timeout and error handling in ``/api/proxy`` endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22297 <https://github.com/galaxyproject/galaxy/pull/22297>`_
|
||||
* Downgrade authnz OAuth callback errors from ERROR/EXCEPTION to WARNING by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22300 <https://github.com/galaxyproject/galaxy/pull/22300>`_
|
||||
* Skip WorkflowHub tests when workflowhub.eu is down by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22302 <https://github.com/galaxyproject/galaxy/pull/22302>`_
|
||||
* Delay workflow scheduling when collection has unresolved 'auto' extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22303 <https://github.com/galaxyproject/galaxy/pull/22303>`_
|
||||
* Fix atomicity issues when pulling files into object store cache by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22304 <https://github.com/galaxyproject/galaxy/pull/22304>`_
|
||||
* Fix slow get_private_role_user_emails_dict query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22307 <https://github.com/galaxyproject/galaxy/pull/22307>`_
|
||||
* Pass tool_uuid as proper query parameter instead of reusing URL path id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22309 <https://github.com/galaxyproject/galaxy/pull/22309>`_
|
||||
* Strip content-length and accept-ranges headers from proxied streaming responses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22314 <https://github.com/galaxyproject/galaxy/pull/22314>`_
|
||||
* Mark dataset collections as deleted when purging a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22315 <https://github.com/galaxyproject/galaxy/pull/22315>`_
|
||||
* Wrap webhook scripts in IIFE to prevent redeclaration errors by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22320 <https://github.com/galaxyproject/galaxy/pull/22320>`_
|
||||
* Handle inaccessible history errors in route-level components by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22323 <https://github.com/galaxyproject/galaxy/pull/22323>`_
|
||||
* Ignore aborted requests in rethrowSimple by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22325 <https://github.com/galaxyproject/galaxy/pull/22325>`_
|
||||
* Fix AbortSignal being serialized as dataset view query parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22326 <https://github.com/galaxyproject/galaxy/pull/22326>`_
|
||||
* Discard rest of line in chunks in iter_start_of_line by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22332 <https://github.com/galaxyproject/galaxy/pull/22332>`_
|
||||
* Fix tool "Copy Link" generating broken /root?tool_id= URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22339 <https://github.com/galaxyproject/galaxy/pull/22339>`_
|
||||
* Backport: Fix tool discovery help data race condition and stale results by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22340 <https://github.com/galaxyproject/galaxy/pull/22340>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
* Throw RequestAbortedError instead of returning undefined by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22352 <https://github.com/galaxyproject/galaxy/pull/22352>`_
|
||||
* Remove broken serialize_urls from HDASerializer by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22358 <https://github.com/galaxyproject/galaxy/pull/22358>`_
|
||||
* Fix HideDatasetAction not applied for cached workflow jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22360 <https://github.com/galaxyproject/galaxy/pull/22360>`_
|
||||
* Fix timestamp parsing in job import/export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22372 <https://github.com/galaxyproject/galaxy/pull/22372>`_
|
||||
* Don't retry JobNotReadyException in job destination mapping by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22377 <https://github.com/galaxyproject/galaxy/pull/22377>`_
|
||||
* Fix Content-Disposition header with trailing whitespace by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22379 <https://github.com/galaxyproject/galaxy/pull/22379>`_
|
||||
* Fix workflow extract NoneType on LDDA leaf in implicit collection by `@jmchilton <https://github.com/jmchilton>`_ in `#22381 <https://github.com/galaxyproject/galaxy/pull/22381>`_
|
||||
* Show error message when display action not ready by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22383 <https://github.com/galaxyproject/galaxy/pull/22383>`_
|
||||
* Ensure ``x-content-truncated`` header is string by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22386 <https://github.com/galaxyproject/galaxy/pull/22386>`_
|
||||
* Validate workflow invocation parameters values are dicts by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22388 <https://github.com/galaxyproject/galaxy/pull/22388>`_
|
||||
* Fix invalid request error for get_metadata_file endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22389 <https://github.com/galaxyproject/galaxy/pull/22389>`_
|
||||
* Offload AsyncClient construction to worker thread by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22392 <https://github.com/galaxyproject/galaxy/pull/22392>`_
|
||||
* Fix dataset preview rendering to preserve newlines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22397 <https://github.com/galaxyproject/galaxy/pull/22397>`_
|
||||
* Serialize data provider errors as MessageException subclasses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22398 <https://github.com/galaxyproject/galaxy/pull/22398>`_
|
||||
* Handle ``MaxDiscoveredFilesExceededError`` for dynamic collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22402 <https://github.com/galaxyproject/galaxy/pull/22402>`_
|
||||
* Silence social_core's noisy handle_http_errors logging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22403 <https://github.com/galaxyproject/galaxy/pull/22403>`_
|
||||
* Unwrap HDCAs/DCEs nested in multi data input lists by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22405 <https://github.com/galaxyproject/galaxy/pull/22405>`_
|
||||
* Reject HDCA submitted to single data parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22406 <https://github.com/galaxyproject/galaxy/pull/22406>`_
|
||||
* Fix headings in selenium package readme by `@guerler <https://github.com/guerler>`_ in `#22411 <https://github.com/galaxyproject/galaxy/pull/22411>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
|
||||
* Replace Copy Dataset Mako with Vue Component by `@guerler <https://github.com/guerler>`_ in `#17507 <https://github.com/galaxyproject/galaxy/pull/17507>`_
|
||||
* Blur input path instead of requiring explicit enter in FormDirectory input by `@dannon <https://github.com/dannon>`_ in `#20047 <https://github.com/galaxyproject/galaxy/pull/20047>`_
|
||||
* Standardize FontAwesome usage by `@dannon <https://github.com/dannon>`_ in `#20334 <https://github.com/galaxyproject/galaxy/pull/20334>`_
|
||||
* Add DRS compact identifier support by `@dannon <https://github.com/dannon>`_ in `#20410 <https://github.com/galaxyproject/galaxy/pull/20410>`_
|
||||
* Fix output dataset collection visualizations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20544 <https://github.com/galaxyproject/galaxy/pull/20544>`_
|
||||
* Improve docs for `invalidjobexception_state` and `_retry` of DRMAA runners by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20612 <https://github.com/galaxyproject/galaxy/pull/20612>`_
|
||||
* Refactor/cleanup admin_cleanup_datasets.py script by `@ccoulombe <https://github.com/ccoulombe>`_ in `#20819 <https://github.com/galaxyproject/galaxy/pull/20819>`_
|
||||
* Upload user defined tools from url by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20860 <https://github.com/galaxyproject/galaxy/pull/20860>`_
|
||||
* Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by `@davelopez <https://github.com/davelopez>`_ in `#20924 <https://github.com/galaxyproject/galaxy/pull/20924>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Move database revision tags to separate file by `@guerler <https://github.com/guerler>`_ in `#20998 <https://github.com/galaxyproject/galaxy/pull/20998>`_
|
||||
* Integrate 'uv' for enhanced package management by `@arash77 <https://github.com/arash77>`_ in `#21002 <https://github.com/galaxyproject/galaxy/pull/21002>`_
|
||||
* Add service account support for Google Cloud Storage client initialization by `@dannon <https://github.com/dannon>`_ in `#21027 <https://github.com/galaxyproject/galaxy/pull/21027>`_
|
||||
* Selenium test cases for IGV. by `@jmchilton <https://github.com/jmchilton>`_ in `#21034 <https://github.com/galaxyproject/galaxy/pull/21034>`_
|
||||
* Remove History Panel proxy by `@guerler <https://github.com/guerler>`_ in `#21037 <https://github.com/galaxyproject/galaxy/pull/21037>`_
|
||||
* Convert Modal to plain JavaScript and remove from Galaxy object by `@guerler <https://github.com/guerler>`_ in `#21038 <https://github.com/galaxyproject/galaxy/pull/21038>`_
|
||||
* Selenium test for the new storage delete confirm dialog. by `@jmchilton <https://github.com/jmchilton>`_ in `#21039 <https://github.com/galaxyproject/galaxy/pull/21039>`_
|
||||
* Selenium test for #20886 (sharing private histories) by `@jmchilton <https://github.com/jmchilton>`_ in `#21040 <https://github.com/galaxyproject/galaxy/pull/21040>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Bump github/codeql-action from 3 to 4 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21048 <https://github.com/galaxyproject/galaxy/pull/21048>`_
|
||||
* Improve type annotation of job runners by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21050 <https://github.com/galaxyproject/galaxy/pull/21050>`_
|
||||
* Selenium test exercising workflow debug, failed jobs, etc... (20912) by `@jmchilton <https://github.com/jmchilton>`_ in `#21058 <https://github.com/galaxyproject/galaxy/pull/21058>`_
|
||||
* Selenium test case for basic tools list functionality. by `@jmchilton <https://github.com/jmchilton>`_ in `#21059 <https://github.com/galaxyproject/galaxy/pull/21059>`_
|
||||
* Remove jquery from legacy onload helpers and Rule Builder by `@guerler <https://github.com/guerler>`_ in `#21063 <https://github.com/galaxyproject/galaxy/pull/21063>`_
|
||||
* Remove Job.params by `@jdavcs <https://github.com/jdavcs>`_ in `#21075 <https://github.com/galaxyproject/galaxy/pull/21075>`_
|
||||
* Remove Reports Application by `@guerler <https://github.com/guerler>`_ in `#21076 <https://github.com/galaxyproject/galaxy/pull/21076>`_
|
||||
* Add Playwright Backend Support to Galaxy Browser Automation Framework by `@jmchilton <https://github.com/jmchilton>`_ in `#21102 <https://github.com/galaxyproject/galaxy/pull/21102>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21104 <https://github.com/galaxyproject/galaxy/pull/21104>`_
|
||||
* Remove tabular chunked, binary and large file mako by `@guerler <https://github.com/guerler>`_ in `#21106 <https://github.com/galaxyproject/galaxy/pull/21106>`_
|
||||
* Enhance Confirm Dialog Types and More by `@itisAliRH <https://github.com/itisAliRH>`_ in `#21108 <https://github.com/galaxyproject/galaxy/pull/21108>`_
|
||||
* Bump actions/setup-node from 5 to 6 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21116 <https://github.com/galaxyproject/galaxy/pull/21116>`_
|
||||
* Pulsar relay implementation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21118 <https://github.com/galaxyproject/galaxy/pull/21118>`_
|
||||
* Add `select all`, simple search and pagination to Zip file selector by `@davelopez <https://github.com/davelopez>`_ in `#21120 <https://github.com/galaxyproject/galaxy/pull/21120>`_
|
||||
* Remove legacy Visualization Mako and Controllers by `@guerler <https://github.com/guerler>`_ in `#21133 <https://github.com/galaxyproject/galaxy/pull/21133>`_
|
||||
* Add Custom Validation for User-Configured Templates by `@davelopez <https://github.com/davelopez>`_ in `#21155 <https://github.com/galaxyproject/galaxy/pull/21155>`_
|
||||
* Fix various bugs/hacks with tool_data_table handling. by `@jmchilton <https://github.com/jmchilton>`_ in `#21163 <https://github.com/galaxyproject/galaxy/pull/21163>`_
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Add plotly pie charts by `@guerler <https://github.com/guerler>`_ in `#21174 <https://github.com/galaxyproject/galaxy/pull/21174>`_
|
||||
* Bump actions/upload-artifact from 4 to 5 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21176 <https://github.com/galaxyproject/galaxy/pull/21176>`_
|
||||
* Refactor client imports for better ES module compatibility by `@dannon <https://github.com/dannon>`_ in `#21194 <https://github.com/galaxyproject/galaxy/pull/21194>`_
|
||||
* Replace tuswsgi with tuspyserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21201 <https://github.com/galaxyproject/galaxy/pull/21201>`_
|
||||
* Add an easy to access/obvious button to hide history panel by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21207 <https://github.com/galaxyproject/galaxy/pull/21207>`_
|
||||
* Richer tracking of transient failures. by `@jmchilton <https://github.com/jmchilton>`_ in `#21227 <https://github.com/galaxyproject/galaxy/pull/21227>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21229 <https://github.com/galaxyproject/galaxy/pull/21229>`_
|
||||
* Consolidate Dataset State Display by `@guerler <https://github.com/guerler>`_ in `#21231 <https://github.com/galaxyproject/galaxy/pull/21231>`_
|
||||
* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
|
||||
* Remove Tool Runner mako by `@guerler <https://github.com/guerler>`_ in `#21235 <https://github.com/galaxyproject/galaxy/pull/21235>`_
|
||||
* Bump actions/checkout from 4 to 5 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21236 <https://github.com/galaxyproject/galaxy/pull/21236>`_
|
||||
* Allow filtering job searches by history ID by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21257 <https://github.com/galaxyproject/galaxy/pull/21257>`_
|
||||
* Slight improvement of mztab2 datatype by `@nguilhot <https://github.com/nguilhot>`_ in `#21258 <https://github.com/galaxyproject/galaxy/pull/21258>`_
|
||||
* Add "show in multiview" to mutiple history selection by `@davelopez <https://github.com/davelopez>`_ in `#21260 <https://github.com/galaxyproject/galaxy/pull/21260>`_
|
||||
* Move js-client bootstrapping to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21264 <https://github.com/galaxyproject/galaxy/pull/21264>`_
|
||||
* Smoke test and PR by `@ksuderman <https://github.com/ksuderman>`_ in `#21277 <https://github.com/galaxyproject/galaxy/pull/21277>`_
|
||||
* Update last queue process handler by `@guerler <https://github.com/guerler>`_ in `#21288 <https://github.com/galaxyproject/galaxy/pull/21288>`_
|
||||
* Update error message handling for OIDC by `@uwwint <https://github.com/uwwint>`_ in `#21297 <https://github.com/galaxyproject/galaxy/pull/21297>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21301 <https://github.com/galaxyproject/galaxy/pull/21301>`_
|
||||
* Add workflow dispatch to artifact building workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21323 <https://github.com/galaxyproject/galaxy/pull/21323>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Add Beta Upload Activity - User Interface Redesign by `@davelopez <https://github.com/davelopez>`_ in `#21338 <https://github.com/galaxyproject/galaxy/pull/21338>`_
|
||||
* Annotates archive explorer tests as Selenium-only by `@davelopez <https://github.com/davelopez>`_ in `#21341 <https://github.com/galaxyproject/galaxy/pull/21341>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21345 <https://github.com/galaxyproject/galaxy/pull/21345>`_
|
||||
* Add citation reminder to job completion email by `@Syrinx55 <https://github.com/Syrinx55>`_ in `#21347 <https://github.com/galaxyproject/galaxy/pull/21347>`_
|
||||
* Migrate client tests from Jest to Vitest by `@dannon <https://github.com/dannon>`_ in `#21348 <https://github.com/galaxyproject/galaxy/pull/21348>`_
|
||||
* Bump peter-evans/create-pull-request from 6 to 7 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21352 <https://github.com/galaxyproject/galaxy/pull/21352>`_
|
||||
* Bump actions/checkout from 5 to 6 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21353 <https://github.com/galaxyproject/galaxy/pull/21353>`_
|
||||
* Bump actions/setup-python from 4 to 6 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21354 <https://github.com/galaxyproject/galaxy/pull/21354>`_
|
||||
* Bump jupyterhub/action-k3s-helm from 3 to 4 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21355 <https://github.com/galaxyproject/galaxy/pull/21355>`_
|
||||
* Link to an external profile when user accounts are managed by a single OIDC provider by `@marius-mather <https://github.com/marius-mather>`_ in `#21356 <https://github.com/galaxyproject/galaxy/pull/21356>`_
|
||||
* Ascp plugin by `@d-callan <https://github.com/d-callan>`_ in `#21357 <https://github.com/galaxyproject/galaxy/pull/21357>`_
|
||||
* Vitest followup: switch to happy-dom, cleanup/fixes to mocks by `@dannon <https://github.com/dannon>`_ in `#21359 <https://github.com/galaxyproject/galaxy/pull/21359>`_
|
||||
* Migrate rate limiter tests from Jest to Vitest by `@davelopez <https://github.com/davelopez>`_ in `#21361 <https://github.com/galaxyproject/galaxy/pull/21361>`_
|
||||
* Add OMERO File Source Plugin by `@davelopez <https://github.com/davelopez>`_ in `#21367 <https://github.com/galaxyproject/galaxy/pull/21367>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21368 <https://github.com/galaxyproject/galaxy/pull/21368>`_
|
||||
* Replace Webpack with Vite for client build by `@dannon <https://github.com/dannon>`_ in `#21369 <https://github.com/galaxyproject/galaxy/pull/21369>`_
|
||||
* Replace gulp with native Node.js build script by `@dannon <https://github.com/dannon>`_ in `#21370 <https://github.com/galaxyproject/galaxy/pull/21370>`_
|
||||
* Fix: tool execution typing improvements/fixes by `@jmchilton <https://github.com/jmchilton>`_ in `#21374 <https://github.com/galaxyproject/galaxy/pull/21374>`_
|
||||
* More use of base64 to improve test stability. by `@jmchilton <https://github.com/jmchilton>`_ in `#21383 <https://github.com/galaxyproject/galaxy/pull/21383>`_
|
||||
* Update fastapi to 0.123.4 and ``get_openapi()`` fork by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21384 <https://github.com/galaxyproject/galaxy/pull/21384>`_
|
||||
* Add initial support for the DICOM format by `@kostrykin <https://github.com/kostrykin>`_ in `#21385 <https://github.com/galaxyproject/galaxy/pull/21385>`_
|
||||
* Add new Azure Flat object store file source by `@guerler <https://github.com/guerler>`_ in `#21398 <https://github.com/galaxyproject/galaxy/pull/21398>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21400 <https://github.com/galaxyproject/galaxy/pull/21400>`_
|
||||
* Redesign TS landing page with prominent search box. by `@jmchilton <https://github.com/jmchilton>`_ in `#21430 <https://github.com/galaxyproject/galaxy/pull/21430>`_
|
||||
* A couple more tool shed fixes. by `@jmchilton <https://github.com/jmchilton>`_ in `#21433 <https://github.com/galaxyproject/galaxy/pull/21433>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Add Google Batch job runner by `@ksuderman <https://github.com/ksuderman>`_ in `#21443 <https://github.com/galaxyproject/galaxy/pull/21443>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21449 <https://github.com/galaxyproject/galaxy/pull/21449>`_
|
||||
* Add toolshed metadata fixing script by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21456 <https://github.com/galaxyproject/galaxy/pull/21456>`_
|
||||
* Bump actions/upload-artifact from 5 to 6 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21460 <https://github.com/galaxyproject/galaxy/pull/21460>`_
|
||||
* Bump actions/cache from 4 to 5 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21461 <https://github.com/galaxyproject/galaxy/pull/21461>`_
|
||||
* Bump peter-evans/create-pull-request from 7 to 8 by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#21462 <https://github.com/galaxyproject/galaxy/pull/21462>`_
|
||||
* Add Jupyternaut adapter for JupyterLite integration by `@guerler <https://github.com/guerler>`_ in `#21463 <https://github.com/galaxyproject/galaxy/pull/21463>`_
|
||||
* Add support for Python 3.14 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21486 <https://github.com/galaxyproject/galaxy/pull/21486>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Modernize UrlTracker into a Typescript composable by `@davelopez <https://github.com/davelopez>`_ in `#21490 <https://github.com/galaxyproject/galaxy/pull/21490>`_
|
||||
* Tool testing: add min/max attributes to test output collections by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21495 <https://github.com/galaxyproject/galaxy/pull/21495>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21500 <https://github.com/galaxyproject/galaxy/pull/21500>`_
|
||||
* Add functional test for filtering outputs by parameters in repeats by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21501 <https://github.com/galaxyproject/galaxy/pull/21501>`_
|
||||
* Various test documentation updates. by `@jmchilton <https://github.com/jmchilton>`_ in `#21507 <https://github.com/galaxyproject/galaxy/pull/21507>`_
|
||||
* Raise ConfigurationError instead etree.ParseError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21509 <https://github.com/galaxyproject/galaxy/pull/21509>`_
|
||||
* Discriminate decompression tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21510 <https://github.com/galaxyproject/galaxy/pull/21510>`_
|
||||
* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
|
||||
* Implement subworkflow invocation export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21512 <https://github.com/galaxyproject/galaxy/pull/21512>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21513 <https://github.com/galaxyproject/galaxy/pull/21513>`_
|
||||
* Fix use of function, method and argument names deprecated in pyparsing 3.0.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21517 <https://github.com/galaxyproject/galaxy/pull/21517>`_
|
||||
* Add workflow API test for use_cached_job with sample sheet collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21522 <https://github.com/galaxyproject/galaxy/pull/21522>`_
|
||||
* Add `ruff --check` to pre-commit sample config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21523 <https://github.com/galaxyproject/galaxy/pull/21523>`_
|
||||
* Add support for workflow landing requests using simple URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21525 <https://github.com/galaxyproject/galaxy/pull/21525>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21526 <https://github.com/galaxyproject/galaxy/pull/21526>`_
|
||||
* Extend `image_diff` and image content assertions to handle boolean images by `@kostrykin <https://github.com/kostrykin>`_ in `#21527 <https://github.com/galaxyproject/galaxy/pull/21527>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Migrate client package manager from Yarn to pnpm by `@dannon <https://github.com/dannon>`_ in `#21539 <https://github.com/galaxyproject/galaxy/pull/21539>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Update dependencies for IGV and Plotly by `@guerler <https://github.com/guerler>`_ in `#21543 <https://github.com/galaxyproject/galaxy/pull/21543>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21552 <https://github.com/galaxyproject/galaxy/pull/21552>`_
|
||||
* Add Claude Code slash commands for GitHub issue triage by `@jmchilton <https://github.com/jmchilton>`_ in `#21579 <https://github.com/galaxyproject/galaxy/pull/21579>`_
|
||||
* Add discarded_data option to model store import API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21582 <https://github.com/galaxyproject/galaxy/pull/21582>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Adds Vintent visualization plugin by `@guerler <https://github.com/guerler>`_ in `#21586 <https://github.com/galaxyproject/galaxy/pull/21586>`_
|
||||
* Sort data managers using case-insensitive order for display in admin UI by `@jdavcs <https://github.com/jdavcs>`_ in `#21587 <https://github.com/galaxyproject/galaxy/pull/21587>`_
|
||||
* Adds vue-eslint-parser as a dev dependency by `@davelopez <https://github.com/davelopez>`_ in `#21588 <https://github.com/galaxyproject/galaxy/pull/21588>`_
|
||||
* Switch Google Cloud Storage file source from fs-gcsfs to gcsfs (fsspec) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21590 <https://github.com/galaxyproject/galaxy/pull/21590>`_
|
||||
* Unify extensions of file source templates by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21594 <https://github.com/galaxyproject/galaxy/pull/21594>`_
|
||||
* Use ``fail-on-cache-miss`` when restoring the client cache by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21597 <https://github.com/galaxyproject/galaxy/pull/21597>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21606 <https://github.com/galaxyproject/galaxy/pull/21606>`_
|
||||
* Update to gravity 1.2.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21608 <https://github.com/galaxyproject/galaxy/pull/21608>`_
|
||||
* Move legacy Visualization Plugins API to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21612 <https://github.com/galaxyproject/galaxy/pull/21612>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Remove unused js-dependencies by `@guerler <https://github.com/guerler>`_ in `#21621 <https://github.com/galaxyproject/galaxy/pull/21621>`_
|
||||
* Migrate remaining vitest tests from `axios-mock-adapter` to `useServerMock` by `@dannon <https://github.com/dannon>`_ in `#21634 <https://github.com/galaxyproject/galaxy/pull/21634>`_
|
||||
* Fix slow startup regression by `@ksuderman <https://github.com/ksuderman>`_ in `#21637 <https://github.com/galaxyproject/galaxy/pull/21637>`_
|
||||
* Remove sanitization from built-in grep tool by `@wm75 <https://github.com/wm75>`_ in `#21648 <https://github.com/galaxyproject/galaxy/pull/21648>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21653 <https://github.com/galaxyproject/galaxy/pull/21653>`_
|
||||
* Add tests for oidc usernames by `@nuwang <https://github.com/nuwang>`_ in `#21655 <https://github.com/galaxyproject/galaxy/pull/21655>`_
|
||||
* Add agent based AI tool recommendation by `@dannon <https://github.com/dannon>`_ in `#21661 <https://github.com/galaxyproject/galaxy/pull/21661>`_
|
||||
* Improve ruff configuration to mimic our isort settings by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21666 <https://github.com/galaxyproject/galaxy/pull/21666>`_
|
||||
* Type annotations and refactorings by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21673 <https://github.com/galaxyproject/galaxy/pull/21673>`_
|
||||
* Check file source template config files for determining conditional dependencies + add constraint for zero-ice by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21688 <https://github.com/galaxyproject/galaxy/pull/21688>`_
|
||||
* Standardize agent API schemas and response metadata by `@dannon <https://github.com/dannon>`_ in `#21692 <https://github.com/galaxyproject/galaxy/pull/21692>`_
|
||||
* Various fixes to file source template's validation system by `@davelopez <https://github.com/davelopez>`_ in `#21704 <https://github.com/galaxyproject/galaxy/pull/21704>`_
|
||||
* Revert startup probe timeout by `@ksuderman <https://github.com/ksuderman>`_ in `#21748 <https://github.com/galaxyproject/galaxy/pull/21748>`_
|
||||
* Send a Slack notification if the Docker image build or smoke test fails by `@ksuderman <https://github.com/ksuderman>`_ in `#21751 <https://github.com/galaxyproject/galaxy/pull/21751>`_
|
||||
* Adds indicator to show if upload target history is current by `@davelopez <https://github.com/davelopez>`_ in `#21830 <https://github.com/galaxyproject/galaxy/pull/21830>`_
|
||||
* Replaced deprecated actions with modern equivalents by `@ksuderman <https://github.com/ksuderman>`_ in `#21849 <https://github.com/galaxyproject/galaxy/pull/21849>`_
|
||||
* Allow connecting sample sheet inputs to compatible collection inputs in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21859 <https://github.com/galaxyproject/galaxy/pull/21859>`_
|
||||
* Adds ImageJ metadata support to TIFF export by `@davelopez <https://github.com/davelopez>`_ in `#21882 <https://github.com/galaxyproject/galaxy/pull/21882>`_
|
||||
* Backports: Return redirection instead of a JSON with the redirect URI by `@davelopez <https://github.com/davelopez>`_ in `#21902 <https://github.com/galaxyproject/galaxy/pull/21902>`_
|
||||
* Update qiskit interactive tool by `@thepineapplepirate <https://github.com/thepineapplepirate>`_ in `#21948 <https://github.com/galaxyproject/galaxy/pull/21948>`_
|
||||
* Backport chat API improvements by `@dannon <https://github.com/dannon>`_ in `#21973 <https://github.com/galaxyproject/galaxy/pull/21973>`_
|
||||
* Use ParameterValueError for dataset count validation to reduce Sentry noise by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22058 <https://github.com/galaxyproject/galaxy/pull/22058>`_
|
||||
* Add linter to validate required_files include paths exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22061 <https://github.com/galaxyproject/galaxy/pull/22061>`_
|
||||
* Use mock test server when tests don't target external galaxy server by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22103 <https://github.com/galaxyproject/galaxy/pull/22103>`_
|
||||
* Add new datatypes: .taf and .taf.gz by `@Maed0x <https://github.com/Maed0x>`_ in `#22242 <https://github.com/galaxyproject/galaxy/pull/22242>`_
|
||||
* Add _F/_R auto-pairing filter for forward/reverse datasets by `@jmchilton <https://github.com/jmchilton>`_ in `#22267 <https://github.com/galaxyproject/galaxy/pull/22267>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Version 26.0.dev by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21020 <https://github.com/galaxyproject/galaxy/pull/21020>`_
|
||||
* Update revision tags for release 25.1 by `@arash77 <https://github.com/arash77>`_ in `#21022 <https://github.com/galaxyproject/galaxy/pull/21022>`_
|
||||
* Update client API schema by `@davelopez <https://github.com/davelopez>`_ in `#21147 <https://github.com/galaxyproject/galaxy/pull/21147>`_
|
||||
* Merge 25.1 into dev, fix openapi schema generation for TypedDict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21168 <https://github.com/galaxyproject/galaxy/pull/21168>`_
|
||||
* Remove unused javascript from toolshed test makos by `@guerler <https://github.com/guerler>`_ in `#21387 <https://github.com/galaxyproject/galaxy/pull/21387>`_
|
||||
* Fix tool request API for multiple select parameters with defaults. by `@jmchilton <https://github.com/jmchilton>`_ in `#21416 <https://github.com/galaxyproject/galaxy/pull/21416>`_
|
||||
* Merge 25.1 into dev and create alembic merge revision by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21440 <https://github.com/galaxyproject/galaxy/pull/21440>`_
|
||||
* Merge 25.1 into dev by `@jmchilton <https://github.com/jmchilton>`_ in `#21505 <https://github.com/galaxyproject/galaxy/pull/21505>`_
|
||||
* Add automated npm publishing for client-api package by `@dannon <https://github.com/dannon>`_ in `#21533 <https://github.com/galaxyproject/galaxy/pull/21533>`_
|
||||
* Don't return 404 when file name can't be serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21577 <https://github.com/galaxyproject/galaxy/pull/21577>`_
|
||||
* Bump default milestone to 26.1 by `@guerler <https://github.com/guerler>`_ in `#21628 <https://github.com/galaxyproject/galaxy/pull/21628>`_
|
||||
* Reduce completion monitor logging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21674 <https://github.com/galaxyproject/galaxy/pull/21674>`_
|
||||
* Add Database Revision for 26.0 by `@guerler <https://github.com/guerler>`_ in `#21675 <https://github.com/galaxyproject/galaxy/pull/21675>`_
|
||||
* Version 26.1.dev by `@guerler <https://github.com/guerler>`_ in `#21685 <https://github.com/galaxyproject/galaxy/pull/21685>`_
|
||||
* Fix `test_value_restriction_with_select_from_multiple_subworkflow_inputs` formatting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21723 <https://github.com/galaxyproject/galaxy/pull/21723>`_
|
||||
* Fix on_complete column type mismatch by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21765 <https://github.com/galaxyproject/galaxy/pull/21765>`_
|
||||
* Fix bad merge by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21790 <https://github.com/galaxyproject/galaxy/pull/21790>`_
|
||||
* Use 1-based step index in invocation metric UI by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21799 <https://github.com/galaxyproject/galaxy/pull/21799>`_
|
||||
* Backport: Fix dbkey filter returning no options when dbkey unset by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21945 <https://github.com/galaxyproject/galaxy/pull/21945>`_
|
||||
* backport MIT license change by `@mr-c <https://github.com/mr-c>`_ in `#21999 <https://github.com/galaxyproject/galaxy/pull/21999>`_
|
||||
* Show invalid tool error reasons in Tool Shed UI by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22040 <https://github.com/galaxyproject/galaxy/pull/22040>`_
|
||||
* Backport of 21939 by `@jdavcs <https://github.com/jdavcs>`_ in `#22265 <https://github.com/galaxyproject/galaxy/pull/22265>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,12 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
No recorded changes since last release
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,27 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix refresh time in object store caches by `@bgruening <https://github.com/bgruening>`_ in `#22279 <https://github.com/galaxyproject/galaxy/pull/22279>`_
|
||||
* Fix atomicity issues when pulling files into object store cache by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22304 <https://github.com/galaxyproject/galaxy/pull/22304>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add Playwright Backend Support to Galaxy Browser Automation Framework by `@jmchilton <https://github.com/jmchilton>`_ in `#21102 <https://github.com/galaxyproject/galaxy/pull/21102>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Various fixes to file source template's validation system by `@davelopez <https://github.com/davelopez>`_ in `#21704 <https://github.com/galaxyproject/galaxy/pull/21704>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,52 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
|
||||
* Add missing types to visualization model by `@guerler <https://github.com/guerler>`_ in `#21672 <https://github.com/galaxyproject/galaxy/pull/21672>`_
|
||||
* Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21923 <https://github.com/galaxyproject/galaxy/pull/21923>`_
|
||||
* Fix dict leaking to process_dataset() during workflow execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21982 <https://github.com/galaxyproject/galaxy/pull/21982>`_
|
||||
* Fix AttributeError when fetching citations for missing tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22029 <https://github.com/galaxyproject/galaxy/pull/22029>`_
|
||||
* Add batch celery task for history dataset purging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22180 <https://github.com/galaxyproject/galaxy/pull/22180>`_
|
||||
* Fix batch history purge not updating user's update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22238 <https://github.com/galaxyproject/galaxy/pull/22238>`_
|
||||
* Validate workflow invocation parameters values are dicts by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22388 <https://github.com/galaxyproject/galaxy/pull/22388>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Replace Copy Dataset Mako with Vue Component by `@guerler <https://github.com/guerler>`_ in `#17507 <https://github.com/galaxyproject/galaxy/pull/17507>`_
|
||||
* Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by `@davelopez <https://github.com/davelopez>`_ in `#20924 <https://github.com/galaxyproject/galaxy/pull/20924>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Remove legacy Visualization Mako and Controllers by `@guerler <https://github.com/guerler>`_ in `#21133 <https://github.com/galaxyproject/galaxy/pull/21133>`_
|
||||
* Allow filtering job searches by history ID by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21257 <https://github.com/galaxyproject/galaxy/pull/21257>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
|
||||
* Add support for workflow landing requests using simple URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21525 <https://github.com/galaxyproject/galaxy/pull/21525>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Add discarded_data option to model store import API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21582 <https://github.com/galaxyproject/galaxy/pull/21582>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Standardize agent API schemas and response metadata by `@dannon <https://github.com/dannon>`_ in `#21692 <https://github.com/galaxyproject/galaxy/pull/21692>`_
|
||||
* Backport chat API improvements by `@dannon <https://github.com/dannon>`_ in `#21973 <https://github.com/galaxyproject/galaxy/pull/21973>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Merge 25.1 into dev, fix openapi schema generation for TypedDict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21168 <https://github.com/galaxyproject/galaxy/pull/21168>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,31 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Attempt to fix transiently failing tests that click this tab. by `@jmchilton <https://github.com/jmchilton>`_ in `#21376 <https://github.com/galaxyproject/galaxy/pull/21376>`_
|
||||
* Fix selenium test test_rename_history by `@davelopez <https://github.com/davelopez>`_ in `#21835 <https://github.com/galaxyproject/galaxy/pull/21835>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Replace Copy Dataset Mako with Vue Component by `@guerler <https://github.com/guerler>`_ in `#17507 <https://github.com/galaxyproject/galaxy/pull/17507>`_
|
||||
* Selenium test cases for IGV. by `@jmchilton <https://github.com/jmchilton>`_ in `#21034 <https://github.com/galaxyproject/galaxy/pull/21034>`_
|
||||
* Selenium test for #20886 (sharing private histories) by `@jmchilton <https://github.com/jmchilton>`_ in `#21040 <https://github.com/galaxyproject/galaxy/pull/21040>`_
|
||||
* Remove jquery from legacy onload helpers and Rule Builder by `@guerler <https://github.com/guerler>`_ in `#21063 <https://github.com/galaxyproject/galaxy/pull/21063>`_
|
||||
* Add Playwright Backend Support to Galaxy Browser Automation Framework by `@jmchilton <https://github.com/jmchilton>`_ in `#21102 <https://github.com/galaxyproject/galaxy/pull/21102>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
|
||||
|
||||
Galaxy Browser Automation Framework
|
||||
====================================
|
||||
------------------------------------
|
||||
|
||||
.. note::
|
||||
The package is named ``galaxy-selenium`` for historical reasons, but a more accurate name
|
||||
@@ -29,8 +29,7 @@ This package provides a browser automation framework for Galaxy_ with:
|
||||
Architecture
|
||||
------------
|
||||
|
||||
Core Interfaces
|
||||
~~~~~~~~~~~~~~~
|
||||
.. rubric:: Core Interfaces
|
||||
|
||||
The framework is built around two main protocol interfaces:
|
||||
|
||||
@@ -53,8 +52,7 @@ The framework is built around two main protocol interfaces:
|
||||
- ``value_of_css_property()`` for CSS introspection
|
||||
|
||||
|
||||
Architecture Diagram
|
||||
~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Architecture Diagram
|
||||
|
||||
::
|
||||
|
||||
@@ -110,8 +108,7 @@ Architecture Diagram
|
||||
(web_element_protocol.py)
|
||||
|
||||
|
||||
Implementations
|
||||
~~~~~~~~~~~~~~~
|
||||
.. rubric:: Implementations
|
||||
|
||||
**Selenium Backend** (``has_driver.py``)
|
||||
- Uses Selenium WebDriver
|
||||
@@ -134,8 +131,7 @@ Both implementations:
|
||||
- Include full type hints
|
||||
|
||||
|
||||
Separation of Concerns
|
||||
~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Separation of Concerns
|
||||
|
||||
::
|
||||
|
||||
@@ -197,8 +193,7 @@ Building CLI Tools
|
||||
|
||||
The ``cli.py`` module provides infrastructure for building command-line automation tools.
|
||||
|
||||
Core Components
|
||||
~~~~~~~~~~~~~~~
|
||||
.. rubric:: Core Components
|
||||
|
||||
**add_selenium_arguments(parser)**
|
||||
Adds standard CLI arguments:
|
||||
@@ -217,8 +212,7 @@ Core Components
|
||||
- Provides Galaxy navigation utilities
|
||||
- Cleanup via ``finish()`` method
|
||||
|
||||
Example: dump_tour.py
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Example: dump_tour.py
|
||||
|
||||
The ``scripts/dump_tour.py`` script demonstrates CLI tool development:
|
||||
|
||||
@@ -256,8 +250,7 @@ Usage::
|
||||
python dump_tour.py my_tour.yaml --backend playwright --galaxy_url http://localhost:8080
|
||||
|
||||
|
||||
Building Your Own CLI Tool
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Building Your Own CLI Tool
|
||||
|
||||
1. **Import the CLI utilities**::
|
||||
|
||||
@@ -289,8 +282,7 @@ Building Your Own CLI Tool
|
||||
Development
|
||||
-----------
|
||||
|
||||
Package Structure
|
||||
~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Package Structure
|
||||
|
||||
::
|
||||
|
||||
@@ -318,8 +310,7 @@ Package Structure
|
||||
└── fixtures/ # HTML test pages
|
||||
|
||||
|
||||
Running Commands
|
||||
~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Running Commands
|
||||
|
||||
Always use ``uv run`` from the package directory::
|
||||
|
||||
@@ -333,8 +324,7 @@ Always use ``uv run`` from the package directory::
|
||||
uv run ruff check .
|
||||
|
||||
|
||||
Adding New Low-Level Browser Operations
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Adding New Low-Level Browser Operations
|
||||
|
||||
Low-level operations are generic browser automation primitives that work with both backends.
|
||||
|
||||
@@ -382,8 +372,7 @@ Use the ``/add-browser-operation`` slash command to automate these steps::
|
||||
This command will generate all the necessary code across all files and create tests.
|
||||
|
||||
|
||||
Adding New Smart Component Operations
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
.. rubric:: Adding New Smart Component Operations
|
||||
|
||||
Smart component operations are higher-level conveniences that may require adding low-level
|
||||
operations first. These operations make Galaxy components more ergonomic to use in tests.
|
||||
|
||||
@@ -9,6 +9,79 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Attempt to fix transient API test failure for jobs search. by `@jmchilton <https://github.com/jmchilton>`_ in `#20898 <https://github.com/galaxyproject/galaxy/pull/20898>`_
|
||||
* Drop down revision for drop_job_params migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21122 <https://github.com/galaxyproject/galaxy/pull/21122>`_
|
||||
* Plumbing for tracking potential fixes for transient failures (and a fix demonstrating it) by `@jmchilton <https://github.com/jmchilton>`_ in `#21243 <https://github.com/galaxyproject/galaxy/pull/21243>`_
|
||||
* Attempt to fix transient failure in list_list_copy by `@jmchilton <https://github.com/jmchilton>`_ in `#21381 <https://github.com/galaxyproject/galaxy/pull/21381>`_
|
||||
* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
|
||||
* Fix input tags not being copied when using copy_inputs_to_history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21529 <https://github.com/galaxyproject/galaxy/pull/21529>`_
|
||||
* Fix storing origin for workflow landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21696 <https://github.com/galaxyproject/galaxy/pull/21696>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix dict leaking to process_dataset() during workflow execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21982 <https://github.com/galaxyproject/galaxy/pull/21982>`_
|
||||
* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
|
||||
* Restore file doesn't match sniffed datatype message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21988 <https://github.com/galaxyproject/galaxy/pull/21988>`_
|
||||
* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
|
||||
* Use base64 URL instead of GitHub URL in test_stage_fetch_decompress_true by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22069 <https://github.com/galaxyproject/galaxy/pull/22069>`_
|
||||
* Fixes for gxformat2 by `@jmchilton <https://github.com/jmchilton>`_ in `#22179 <https://github.com/galaxyproject/galaxy/pull/22179>`_
|
||||
* Make sure origins for data landings are persisted by `@d-callan <https://github.com/d-callan>`_ in `#22248 <https://github.com/galaxyproject/galaxy/pull/22248>`_
|
||||
* Validate replacement_params values are strings before storing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22250 <https://github.com/galaxyproject/galaxy/pull/22250>`_
|
||||
* Fix HDCA lost in tool form on rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22258 <https://github.com/galaxyproject/galaxy/pull/22258>`_
|
||||
* Fix purge for anon histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22275 <https://github.com/galaxyproject/galaxy/pull/22275>`_
|
||||
* Fix validation of certain classes of text validators in tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#22280 <https://github.com/galaxyproject/galaxy/pull/22280>`_
|
||||
* Fix nested DatasetCollectionElement in dynamic options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22287 <https://github.com/galaxyproject/galaxy/pull/22287>`_
|
||||
* Fix AttributeError when anonymous user searches workflows with ``is:bookmarked`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22296 <https://github.com/galaxyproject/galaxy/pull/22296>`_
|
||||
* Improve timeout and error handling in ``/api/proxy`` endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22297 <https://github.com/galaxyproject/galaxy/pull/22297>`_
|
||||
* Strip content-length and accept-ranges headers from proxied streaming responses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22314 <https://github.com/galaxyproject/galaxy/pull/22314>`_
|
||||
* Fix HideDatasetAction not applied for cached workflow jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22360 <https://github.com/galaxyproject/galaxy/pull/22360>`_
|
||||
* Validate workflow invocation parameters values are dicts by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22388 <https://github.com/galaxyproject/galaxy/pull/22388>`_
|
||||
* Fix dataset preview rendering to preserve newlines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22397 <https://github.com/galaxyproject/galaxy/pull/22397>`_
|
||||
* Serialize data provider errors as MessageException subclasses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22398 <https://github.com/galaxyproject/galaxy/pull/22398>`_
|
||||
* Unwrap HDCAs/DCEs nested in multi data input lists by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22405 <https://github.com/galaxyproject/galaxy/pull/22405>`_
|
||||
* Reject HDCA submitted to single data parameter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22406 <https://github.com/galaxyproject/galaxy/pull/22406>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Selenium test exercising workflow debug, failed jobs, etc... (20912) by `@jmchilton <https://github.com/jmchilton>`_ in `#21058 <https://github.com/galaxyproject/galaxy/pull/21058>`_
|
||||
* Richer tracking of transient failures. by `@jmchilton <https://github.com/jmchilton>`_ in `#21227 <https://github.com/galaxyproject/galaxy/pull/21227>`_
|
||||
* Remove Tool Runner mako by `@guerler <https://github.com/guerler>`_ in `#21235 <https://github.com/galaxyproject/galaxy/pull/21235>`_
|
||||
* Allow filtering job searches by history ID by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21257 <https://github.com/galaxyproject/galaxy/pull/21257>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* More use of base64 to improve test stability. by `@jmchilton <https://github.com/jmchilton>`_ in `#21383 <https://github.com/galaxyproject/galaxy/pull/21383>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
|
||||
* Implement subworkflow invocation export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21512 <https://github.com/galaxyproject/galaxy/pull/21512>`_
|
||||
* Add workflow API test for use_cached_job with sample sheet collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21522 <https://github.com/galaxyproject/galaxy/pull/21522>`_
|
||||
* Add support for workflow landing requests using simple URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21525 <https://github.com/galaxyproject/galaxy/pull/21525>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Add discarded_data option to model store import API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21582 <https://github.com/galaxyproject/galaxy/pull/21582>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Type annotations and refactorings by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21673 <https://github.com/galaxyproject/galaxy/pull/21673>`_
|
||||
* Use mock test server when tests don't target external galaxy server by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22103 <https://github.com/galaxyproject/galaxy/pull/22103>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Fix tool request API for multiple select parameters with defaults. by `@jmchilton <https://github.com/jmchilton>`_ in `#21416 <https://github.com/galaxyproject/galaxy/pull/21416>`_
|
||||
* Reduce completion monitor logging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21674 <https://github.com/galaxyproject/galaxy/pull/21674>`_
|
||||
* Fix `test_value_restriction_with_select_from_multiple_subworkflow_inputs` formatting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21723 <https://github.com/galaxyproject/galaxy/pull/21723>`_
|
||||
* Backport: Fix dbkey filter returning no options when dbkey unset by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21945 <https://github.com/galaxyproject/galaxy/pull/21945>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,43 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Accept 404 as valid intermediate state when waiting for dataset purge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21521 <https://github.com/galaxyproject/galaxy/pull/21521>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix HDCA lost in tool form on rerun by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22258 <https://github.com/galaxyproject/galaxy/pull/22258>`_
|
||||
* Fix purge for anon histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22275 <https://github.com/galaxyproject/galaxy/pull/22275>`_
|
||||
* Improve timeout and error handling in ``/api/proxy`` endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22297 <https://github.com/galaxyproject/galaxy/pull/22297>`_
|
||||
* Fix HideDatasetAction not applied for cached workflow jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22360 <https://github.com/galaxyproject/galaxy/pull/22360>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Selenium test exercising workflow debug, failed jobs, etc... (20912) by `@jmchilton <https://github.com/jmchilton>`_ in `#21058 <https://github.com/galaxyproject/galaxy/pull/21058>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Add discarded_data option to model store import API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21582 <https://github.com/galaxyproject/galaxy/pull/21582>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Type annotations and refactorings by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21673 <https://github.com/galaxyproject/galaxy/pull/21673>`_
|
||||
* Use mock test server when tests don't target external galaxy server by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22103 <https://github.com/galaxyproject/galaxy/pull/22103>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Backport: Fix dbkey filter returning no options when dbkey unset by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21945 <https://github.com/galaxyproject/galaxy/pull/21945>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,21 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by `@davelopez <https://github.com/davelopez>`_ in `#20924 <https://github.com/galaxyproject/galaxy/pull/20924>`_
|
||||
* Pulsar relay implementation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21118 <https://github.com/galaxyproject/galaxy/pull/21118>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,19 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix missing sharable link URL in TS2.0 emails by `@jmchilton <https://github.com/jmchilton>`_ in `#21892 <https://github.com/galaxyproject/galaxy/pull/21892>`_
|
||||
* Store tool shed search index test data in repo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22071 <https://github.com/galaxyproject/galaxy/pull/22071>`_
|
||||
* Fix toolshed static image url encoding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22286 <https://github.com/galaxyproject/galaxy/pull/22286>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,12 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
No recorded changes since last release
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,46 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* When getting tool by uuid, get that exact tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21844 <https://github.com/galaxyproject/galaxy/pull/21844>`_
|
||||
* Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21923 <https://github.com/galaxyproject/galaxy/pull/21923>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix ToolExpressionOutput.to_model() for boolean type. by `@jmchilton <https://github.com/jmchilton>`_ in `#22038 <https://github.com/galaxyproject/galaxy/pull/22038>`_
|
||||
* Model hidden_data params as optional data in tool meta-models. by `@jmchilton <https://github.com/jmchilton>`_ in `#22116 <https://github.com/galaxyproject/galaxy/pull/22116>`_
|
||||
* Fix validation of certain classes of text validators in tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#22280 <https://github.com/galaxyproject/galaxy/pull/22280>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Add Playwright Backend Support to Galaxy Browser Automation Framework by `@jmchilton <https://github.com/jmchilton>`_ in `#21102 <https://github.com/galaxyproject/galaxy/pull/21102>`_
|
||||
* Fix various bugs/hacks with tool_data_table handling. by `@jmchilton <https://github.com/jmchilton>`_ in `#21163 <https://github.com/galaxyproject/galaxy/pull/21163>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21368 <https://github.com/galaxyproject/galaxy/pull/21368>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Tool testing: add min/max attributes to test output collections by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21495 <https://github.com/galaxyproject/galaxy/pull/21495>`_
|
||||
* Extend `image_diff` and image content assertions to handle boolean images by `@kostrykin <https://github.com/kostrykin>`_ in `#21527 <https://github.com/galaxyproject/galaxy/pull/21527>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Fix slow startup regression by `@ksuderman <https://github.com/ksuderman>`_ in `#21637 <https://github.com/galaxyproject/galaxy/pull/21637>`_
|
||||
* Remove sanitization from built-in grep tool by `@wm75 <https://github.com/wm75>`_ in `#21648 <https://github.com/galaxyproject/galaxy/pull/21648>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21653 <https://github.com/galaxyproject/galaxy/pull/21653>`_
|
||||
* Add linter to validate required_files include paths exist by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22061 <https://github.com/galaxyproject/galaxy/pull/22061>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Fix tool request API for multiple select parameters with defaults. by `@jmchilton <https://github.com/jmchilton>`_ in `#21416 <https://github.com/galaxyproject/galaxy/pull/21416>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,35 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21923 <https://github.com/galaxyproject/galaxy/pull/21923>`_
|
||||
* Backport paired or unpaired mapping fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21936 <https://github.com/galaxyproject/galaxy/pull/21936>`_
|
||||
* Fix validation of certain classes of text validators in tools. by `@jmchilton <https://github.com/jmchilton>`_ in `#22280 <https://github.com/galaxyproject/galaxy/pull/22280>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Update fastapi to 0.123.4 and ``get_openapi()`` fork by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21384 <https://github.com/galaxyproject/galaxy/pull/21384>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Merge 25.1 into dev, fix openapi schema generation for TypedDict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21168 <https://github.com/galaxyproject/galaxy/pull/21168>`_
|
||||
* Fix tool request API for multiple select parameters with defaults. by `@jmchilton <https://github.com/jmchilton>`_ in `#21416 <https://github.com/galaxyproject/galaxy/pull/21416>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,12 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
No recorded changes since last release
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,39 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Plumbing for tracking potential fixes for transient failures (and a fix demonstrating it) by `@jmchilton <https://github.com/jmchilton>`_ in `#21243 <https://github.com/galaxyproject/galaxy/pull/21243>`_
|
||||
* Remove unused handle_tool_shed_url_protocol by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21925 <https://github.com/galaxyproject/galaxy/pull/21925>`_
|
||||
* Raise MessageException instead of generic Exception in rules_dsl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22285 <https://github.com/galaxyproject/galaxy/pull/22285>`_
|
||||
* Improve timeout and error handling in ``/api/proxy`` endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22297 <https://github.com/galaxyproject/galaxy/pull/22297>`_
|
||||
* Skip WorkflowHub tests when workflowhub.eu is down by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22302 <https://github.com/galaxyproject/galaxy/pull/22302>`_
|
||||
* Discard rest of line in chunks in iter_start_of_line by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22332 <https://github.com/galaxyproject/galaxy/pull/22332>`_
|
||||
* Fix Content-Disposition header with trailing whitespace by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22379 <https://github.com/galaxyproject/galaxy/pull/22379>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Add Playwright Backend Support to Galaxy Browser Automation Framework by `@jmchilton <https://github.com/jmchilton>`_ in `#21102 <https://github.com/galaxyproject/galaxy/pull/21102>`_
|
||||
* Add Custom Validation for User-Configured Templates by `@davelopez <https://github.com/davelopez>`_ in `#21155 <https://github.com/galaxyproject/galaxy/pull/21155>`_
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Richer tracking of transient failures. by `@jmchilton <https://github.com/jmchilton>`_ in `#21227 <https://github.com/galaxyproject/galaxy/pull/21227>`_
|
||||
* Update fastapi to 0.123.4 and ``get_openapi()`` fork by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21384 <https://github.com/galaxyproject/galaxy/pull/21384>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Fix use of function, method and argument names deprecated in pyparsing 3.0.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21517 <https://github.com/galaxyproject/galaxy/pull/21517>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Add tests for oidc usernames by `@nuwang <https://github.com/nuwang>`_ in `#21655 <https://github.com/galaxyproject/galaxy/pull/21655>`_
|
||||
* Various fixes to file source template's validation system by `@davelopez <https://github.com/davelopez>`_ in `#21704 <https://github.com/galaxyproject/galaxy/pull/21704>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,93 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Preserve assistant messages with tool calls by `@guerler <https://github.com/guerler>`_ in `#21545 <https://github.com/galaxyproject/galaxy/pull/21545>`_
|
||||
* Fix incorrect router tag in plugins API by `@dannon <https://github.com/dannon>`_ in `#21669 <https://github.com/galaxyproject/galaxy/pull/21669>`_
|
||||
* Fix redirect upon impersonation by `@guerler <https://github.com/guerler>`_ in `#21810 <https://github.com/galaxyproject/galaxy/pull/21810>`_
|
||||
* Update ``get_definitions()`` to FastAPI 0.128.8 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21834 <https://github.com/galaxyproject/galaxy/pull/21834>`_
|
||||
* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
|
||||
* Use inference_services config for plugin chat proxy by `@dannon <https://github.com/dannon>`_ in `#21986 <https://github.com/galaxyproject/galaxy/pull/21986>`_
|
||||
* Fix AttributeError when fetching citations for missing tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22029 <https://github.com/galaxyproject/galaxy/pull/22029>`_
|
||||
* Fix invalid function schema error for tools with None parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22030 <https://github.com/galaxyproject/galaxy/pull/22030>`_
|
||||
* AttributeError when history is None during tool execution by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22031 <https://github.com/galaxyproject/galaxy/pull/22031>`_
|
||||
* Fix AttributeError when export_metadata is a string instead of dict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22033 <https://github.com/galaxyproject/galaxy/pull/22033>`_
|
||||
* Fix AttributeError when dataset in inheritance chain has no user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22062 <https://github.com/galaxyproject/galaxy/pull/22062>`_
|
||||
* Fix make all histories private controller None id bug by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22174 <https://github.com/galaxyproject/galaxy/pull/22174>`_
|
||||
* Add batch celery task for history dataset purging by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22180 <https://github.com/galaxyproject/galaxy/pull/22180>`_
|
||||
* Cache url path lookup by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22198 <https://github.com/galaxyproject/galaxy/pull/22198>`_
|
||||
* Fix event loop blocking in async API routes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22202 <https://github.com/galaxyproject/galaxy/pull/22202>`_
|
||||
* Update fastmcp requirement to 3.0.2 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22221 <https://github.com/galaxyproject/galaxy/pull/22221>`_
|
||||
* Use ``/api/tool_data`` endpoints in DataTables.vue & DataManagerTable.vue by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22229 <https://github.com/galaxyproject/galaxy/pull/22229>`_
|
||||
* Optimize dataset get_edit API by deferring expensive role queries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22232 <https://github.com/galaxyproject/galaxy/pull/22232>`_
|
||||
* Fix TypeError in ExternalIdentities by always including provider_label in authnz response by `@guerler <https://github.com/guerler>`_ in `#22234 <https://github.com/galaxyproject/galaxy/pull/22234>`_
|
||||
* Delete dummy error controller, fix type error on invalid requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22245 <https://github.com/galaxyproject/galaxy/pull/22245>`_
|
||||
* Make sure origins for data landings are persisted by `@d-callan <https://github.com/d-callan>`_ in `#22248 <https://github.com/galaxyproject/galaxy/pull/22248>`_
|
||||
* Replace BaseHTTPMiddleware with pure ASGI middleware for X-Frame-Options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22255 <https://github.com/galaxyproject/galaxy/pull/22255>`_
|
||||
* Fix toolshed static image url encoding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22286 <https://github.com/galaxyproject/galaxy/pull/22286>`_
|
||||
* Improve timeout and error handling in ``/api/proxy`` endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22297 <https://github.com/galaxyproject/galaxy/pull/22297>`_
|
||||
* Downgrade authnz OAuth callback errors from ERROR/EXCEPTION to WARNING by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22300 <https://github.com/galaxyproject/galaxy/pull/22300>`_
|
||||
* Fix slow get_private_role_user_emails_dict query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22307 <https://github.com/galaxyproject/galaxy/pull/22307>`_
|
||||
* Pass tool_uuid as proper query parameter instead of reusing URL path id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22309 <https://github.com/galaxyproject/galaxy/pull/22309>`_
|
||||
* Strip content-length and accept-ranges headers from proxied streaming responses by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22314 <https://github.com/galaxyproject/galaxy/pull/22314>`_
|
||||
* Fix tool "Copy Link" generating broken /root?tool_id= URLs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22339 <https://github.com/galaxyproject/galaxy/pull/22339>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
* Show error message when display action not ready by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22383 <https://github.com/galaxyproject/galaxy/pull/22383>`_
|
||||
* Fix invalid request error for get_metadata_file endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22389 <https://github.com/galaxyproject/galaxy/pull/22389>`_
|
||||
* Offload AsyncClient construction to worker thread by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22392 <https://github.com/galaxyproject/galaxy/pull/22392>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
|
||||
* Replace Copy Dataset Mako with Vue Component by `@guerler <https://github.com/guerler>`_ in `#17507 <https://github.com/galaxyproject/galaxy/pull/17507>`_
|
||||
* Tool Request API by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
|
||||
* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
|
||||
* Remove Reports Application by `@guerler <https://github.com/guerler>`_ in `#21076 <https://github.com/galaxyproject/galaxy/pull/21076>`_
|
||||
* Remove legacy Visualization Mako and Controllers by `@guerler <https://github.com/guerler>`_ in `#21133 <https://github.com/galaxyproject/galaxy/pull/21133>`_
|
||||
* Replace tuswsgi with tuspyserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21201 <https://github.com/galaxyproject/galaxy/pull/21201>`_
|
||||
* Consolidate Dataset State Display by `@guerler <https://github.com/guerler>`_ in `#21231 <https://github.com/galaxyproject/galaxy/pull/21231>`_
|
||||
* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
|
||||
* Remove Tool Runner mako by `@guerler <https://github.com/guerler>`_ in `#21235 <https://github.com/galaxyproject/galaxy/pull/21235>`_
|
||||
* Allow filtering job searches by history ID by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21257 <https://github.com/galaxyproject/galaxy/pull/21257>`_
|
||||
* Move js-client bootstrapping to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21264 <https://github.com/galaxyproject/galaxy/pull/21264>`_
|
||||
* Update error message handling for OIDC by `@uwwint <https://github.com/uwwint>`_ in `#21297 <https://github.com/galaxyproject/galaxy/pull/21297>`_
|
||||
* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
|
||||
* Add Beta Upload Activity - User Interface Redesign by `@davelopez <https://github.com/davelopez>`_ in `#21338 <https://github.com/galaxyproject/galaxy/pull/21338>`_
|
||||
* Link to an external profile when user accounts are managed by a single OIDC provider by `@marius-mather <https://github.com/marius-mather>`_ in `#21356 <https://github.com/galaxyproject/galaxy/pull/21356>`_
|
||||
* Update fastapi to 0.123.4 and ``get_openapi()`` fork by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21384 <https://github.com/galaxyproject/galaxy/pull/21384>`_
|
||||
* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
|
||||
* Add Jupyternaut adapter for JupyterLite integration by `@guerler <https://github.com/guerler>`_ in `#21463 <https://github.com/galaxyproject/galaxy/pull/21463>`_
|
||||
* Add support for Python 3.14 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21486 <https://github.com/galaxyproject/galaxy/pull/21486>`_
|
||||
* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21500 <https://github.com/galaxyproject/galaxy/pull/21500>`_
|
||||
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21526 <https://github.com/galaxyproject/galaxy/pull/21526>`_
|
||||
* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Sort data managers using case-insensitive order for display in admin UI by `@jdavcs <https://github.com/jdavcs>`_ in `#21587 <https://github.com/galaxyproject/galaxy/pull/21587>`_
|
||||
* Move legacy Visualization Plugins API to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21612 <https://github.com/galaxyproject/galaxy/pull/21612>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
* Standardize agent API schemas and response metadata by `@dannon <https://github.com/dannon>`_ in `#21692 <https://github.com/galaxyproject/galaxy/pull/21692>`_
|
||||
* Backports: Return redirection instead of a JSON with the redirect URI by `@davelopez <https://github.com/davelopez>`_ in `#21902 <https://github.com/galaxyproject/galaxy/pull/21902>`_
|
||||
* Backport chat API improvements by `@dannon <https://github.com/dannon>`_ in `#21973 <https://github.com/galaxyproject/galaxy/pull/21973>`_
|
||||
|
||||
=============
|
||||
Other changes
|
||||
=============
|
||||
|
||||
* Merge 25.1 into dev, fix openapi schema generation for TypedDict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21168 <https://github.com/galaxyproject/galaxy/pull/21168>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,12 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
No recorded changes since last release
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,29 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix WSGI middlewares returning strings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22108 <https://github.com/galaxyproject/galaxy/pull/22108>`_
|
||||
* Delete dummy error controller, fix type error on invalid requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22245 <https://github.com/galaxyproject/galaxy/pull/22245>`_
|
||||
* Fail early wehn no route match is found by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22284 <https://github.com/galaxyproject/galaxy/pull/22284>`_
|
||||
* Harden API parameter validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22351 <https://github.com/galaxyproject/galaxy/pull/22351>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Remove Reports Application by `@guerler <https://github.com/guerler>`_ in `#21076 <https://github.com/galaxyproject/galaxy/pull/21076>`_
|
||||
* Replace Webpack with Vite for client build by `@dannon <https://github.com/dannon>`_ in `#21369 <https://github.com/galaxyproject/galaxy/pull/21369>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
@@ -9,6 +9,25 @@ History
|
||||
|
||||
|
||||
|
||||
-------------------
|
||||
26.0.0 (2026-04-08)
|
||||
-------------------
|
||||
|
||||
|
||||
=========
|
||||
Bug fixes
|
||||
=========
|
||||
|
||||
* Fix differentiation between single handler and handler tag by `@natefoo <https://github.com/natefoo>`_ in `#21252 <https://github.com/galaxyproject/galaxy/pull/21252>`_
|
||||
|
||||
============
|
||||
Enhancements
|
||||
============
|
||||
|
||||
* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
|
||||
* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
|
||||
* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
|
||||
|
||||
-------------------
|
||||
25.1.2 (2026-03-09)
|
||||
-------------------
|
||||
|
||||
Reference in New Issue
Block a user