Commit Graph
76973 Commits
Author SHA1 Message Date
Matthias Bernt 9d601f8c6e Merge branch 'release_24.0' into release_24.1
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
2024-06-28 11:08:13 +02:00
Matthias Bernt ba5e53be70 Start work on 24.0.4.dev0 2024-06-28 11:08:05 +02:00
Matthias Bernt d94748193f Create version 24.0.3 v24.0.3 2024-06-28 11:08:00 +02:00
Marius van den Beek 7a7a2e125b Merge pull request #18447 from mvdbeek/exception_cleanup
[24.1] Improve workflow-related exception reporting
2024-06-28 10:13:04 +02:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
Marius van den Beek 8a52443a0a Merge pull request #18428 from mvdbeek/replace_busybox
[24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
2024-06-28 09:22:30 +02:00
mvdbeek 983048805f Raise serializable exception when loading invalid version for a workflow
Fixes https://github.com/galaxyproject/galaxy/issues/18438
2024-06-27 15:41:08 +02:00
mvdbeek 7d57020e7d Raise serializable exceptions when uploading broken workflows 2024-06-27 15:40:24 +02:00
mvdbeek 331d4954e1 Decrease log level for requesting invalid items 2024-06-27 15:40:01 +02:00
Martin Cech 9421bcd0fb Merge pull request #18434 from nsoranzo/release_24.1_mercurial_6.7.4
[24.1] Update mercurial to non-yanked 6.7.4
2024-06-24 17:33:03 +02:00
Marius van den Beek 2257c22c73 Merge pull request #18430 from dannon/fix-chargs-24.0
[24.0] Fix mounting utility usage of pinia (fixes charts form components)
2024-06-24 14:03:26 +02:00
Marius van den Beek 6f5aeebbc0 Merge pull request #18435 from nsoranzo/release_24.0_openapi_setup-node
[24.0] Install node from setup-node action
2024-06-24 14:02:21 +02:00
Marius van den BeekandNicola Soranzo 7ceef4b279 Drop extra quote
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
2024-06-24 14:02:02 +02:00
Nicola Soranzo 2fd90d1d9c Install node from setup-node action 2024-06-24 10:02:10 +01:00
Nicola Soranzo ece66de308 Update mercurial to non-yanked 6.7.4
Mercurial version 6.7rc0-6.7.3 have been yanked on PyPI with message:

```
critical bug that can destroy the changelog of repositories
```
2024-06-24 09:28:45 +01:00
John Davis 470916554d Merge pull request #18431 from jdavcs/241_admin_notes
[24.1] Add note on fastapi to admin release notes
2024-06-21 13:33:05 -04:00
John Davis c774caf7ab Add admin note on fastapi 2024-06-21 13:20:55 -04:00
Dannon Baker 98690d9604 Pinia plugin fixes when using component mounting utilities. This has
changed multiple times in descendant branches so this is a flattened,
cleaned up version for application against 24.0.
2024-06-21 13:17:14 -04:00
Marius van den Beek ebb265111b Merge pull request #18429 from dannon/more-robust-pinia-init
[24.1] Support usage of vue mounting helpers in a context without existing pinia/vue.
2024-06-21 17:31:29 +02:00
Nicola Soranzo bcca24b47b Prepare for NumPy 2.0 2024-06-21 16:58:21 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
DannonandMarius van den Beek 16b8036b79 Update client/src/utils/mountVueComponent.js
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
2024-06-21 10:00:25 -04:00
Dannon Baker 4f00347b34 Support usage of vue mounting helpers in a context without existing pinia/vue. This fixes charts initialization. 2024-06-21 09:45:57 -04:00
John Davis 4239fe1f3d Update version to 24.1.0.dev0 2024-06-20 12:29:53 -04:00
John Davis 82b482b55d Update version to 24.1. v24.1 2024-06-20 12:29:52 -04:00
John Davis 25827fbf5e Merge pull request #18424 from jdavcs/241_include_latest_prs
[24.1] Add latest PRs to release notes
2024-06-20 12:08:25 -04:00
John Davis 9a3af33c19 Add latest PRs to release notes 2024-06-20 12:06:56 -04:00
John Davis 2a2c1a87a7 Merge pull request #18218 from jdavcs/241_release_notes
[24.1] Release notes
2024-06-20 11:38:17 -04:00
John Davis bed58957d6 Add links to videos 2024-06-20 11:33:31 -04:00
Nicola Soranzo 7cfb10e9a3 Merge pull request #18423 from nsoranzo/release_24.1_pydantic_2.7.4
[24.1] Pin pydantic to >=2.7.4
2024-06-20 10:26:49 +01:00
John Davis b4605248b9 Fix item list layout of release team 2024-06-19 14:49:56 -04:00
John Davis 9838c16071 Fix release title
Keep consistent with previous releases
2024-06-19 14:44:52 -04:00
Nicola Soranzo 88d3849960 Pin pydantic to >=2.7.4
Pydantic <2.7.4 is broken on Python>=3.12.4 , see
https://github.com/pydantic/pydantic/issues/9609 .
Fixed upstream in https://github.com/pydantic/pydantic/pull/9639 .

Fix the following traceback in startup test on Python 3.12:

```
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/bin/galaxyctl", line 10, in <module>
    sys.exit(galaxyctl())
             ^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1682, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/click/core.py", line 1729, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 59, in get_command
    return name_to_command(name)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/cli.py", line 45, in name_to_command
    mod = __import__(mod_name, None, None, ["cli"])
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/commands/cmd_stop.py", line 4, in <module>
    from gravity import process_manager
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/process_manager/__init__.py", line 14, in <module>
    from gravity.config_manager import ConfigManager
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/config_manager.py", line 18, in <module>
    from gravity.state import ConfigFile, service_for_service_type
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/gravity/state.py", line 42, in <module>
    class ConfigFile(BaseModel):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 286, in __new__
    cls.__try_update_forward_refs__()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/main.py", line 807, in __try_update_forward_refs__
    update_model_forward_refs(cls, cls.__fields__.values(), cls.__config__.json_encoders, localns, (NameError,))
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 554, in update_model_forward_refs
    update_field_forward_refs(f, globalns=globalns, localns=localns)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 520, in update_field_forward_refs
    field.type_ = evaluate_forwardref(field.type_, globalns, localns or None)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.12/site-packages/pydantic/v1/typing.py", line 66, in evaluate_forwardref
    return cast(Any, type_)._evaluate(globalns, localns, set())
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: ForwardRef._evaluate() missing 1 required keyword-only argument: 'recursive_guard'
```

Example: https://github.com/galaxyproject/galaxy/actions/runs/9581802216/job/26419972297
2024-06-19 19:30:46 +01:00
John Davis 6dc2dc747c Add highlights to main announcement 2024-06-19 14:13:07 -04:00
John Davis 32417aba21 Add admin notes 2024-06-19 14:02:26 -04:00
John Davis f8fad728c7 Add latest PRs 2024-06-19 13:53:45 -04:00
John Davis fffaf7474d Drop empty section 2024-06-19 13:42:54 -04:00
John Davis 4e3af82711 Update releases index page 2024-06-19 13:29:44 -04:00
John Davis b1b0769941 Add configuration changes to release notes 2024-06-19 13:28:54 -04:00
John Davis acb21661bb Add release team 2024-06-19 13:22:44 -04:00
John Davis 1870b23605 Add media files for release notes 2024-06-19 13:22:44 -04:00
John Davis b8c21c4cf1 Add featured items 2024-06-19 13:22:44 -04:00
John Davis c2516bbbde Add release notes scaffolding (curated) 2024-06-19 13:22:44 -04:00
Nicola Soranzo 08d42ea24f Merge branch 'release_24.0' into release_24.1 2024-06-19 13:14:15 +01:00
Nicola Soranzo d2aea97a24 Merge pull request #18421 from mvdbeek/fix_linting_error
[24.0] Minor linting cleanup
2024-06-19 11:57:01 +01:00
mvdbeek 111d5632ff Run make format 2024-06-19 10:24:55 +02:00
Marius van den Beek 98bffa17e9 Merge pull request #18405 from ahmedhamidawan/fix_input_step_parameters_label_bug
[24.1] Fix `input_step_parameters` missing values that don't have a label
2024-06-19 09:37:25 +02:00
Ahmed Awan b5cabbfc08 ensure correct version routed to on workflow run
This is a bug caused in https://github.com/galaxyproject/galaxy/pull/18378 which made the `SaveChangesModal` useless because the version before the save was routed to.
Now, we instead append the version to the route after the user confirms the save (or doesn't) in the modal.
2024-06-18 15:44:10 -05:00
Ahmed Awan 72217d173b cast invocation state query route prop fromPanel to Boolean 2024-06-18 15:44:10 -05:00
Ahmed Awan f7edaabfaa [24.1] Fix input_step_parameters missing vals without label
`input_step_parameters` that did not have labels (label=None) were being excluded in the `WorkflowInvocation.to_dict()` result.

This therefore sets the label to `n: Unnamed parameter` for null labels.

Fixes https://github.com/galaxyproject/galaxy/issues/18366
2024-06-18 15:43:10 -05:00