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Commit Graph
382 Commits
Author SHA1 Message Date
mvdbeek 17adb6aa1a Pin data package requirement 2021-04-08 09:53:54 +02:00
qiagu 56f715c59d Merge branch 'dev' into ometiff2_new 2021-04-07 10:45:40 -07:00
John Chilton 071456f891 Merge pull request #11220 from gregvonkuster/mrcfile 
Add mrc datatype (and Python dependency)
 2021-04-07 09:45:32 -04:00
Marius van den Beek 4a46ea1509 Merge pull request #11779 from natefoo/installable 
Fixes for installed Galaxy
 2021-04-06 16:45:40 +02:00
Nate Coraor 698d95e52d Move all galaxy.util.* modules to the galaxy-util package. 2021-04-05 12:06:48 -04:00
Nate Coraor f6fdc66e23 Move all galaxy.datatypes.* modules to the galaxy-data package. 2021-04-05 12:02:08 -04:00
Nate Coraor a857929af5 Move all galaxy.model.* modules to the galaxy-data package. 2021-04-05 11:48:14 -04:00
Nate Coraor d8aa5a3804 Add fastapi-utils to galaxy-webapps package requirements. 2021-04-02 16:01:34 -04:00
Nate Coraor a0ecf74e1c Include galaxy.job_execution.ports in galaxy-job-execution package. 2021-04-02 16:01:01 -04:00
Nate Coraor c6cde5f5fa Relocate display application configs and include display application 
configs in galaxy-webapps package.
 2021-04-02 15:42:36 -04:00
Nate Coraor ca712beff8 Include set_metadata_tool.xml in galaxy-app package. 2021-04-02 15:04:46 -04:00
Nate Coraor 7c0cf9d1f6 Include galaxy.datatype.converters in galaxy-app package. 2021-04-02 15:04:39 -04:00
Nate Coraor ad9d7e88e6 Include galaxy.model.migrate.versions in galaxy-app package. 2021-04-02 14:16:48 -04:00
Nate Coraor 609c5d2eb9 Include sample configs in galaxy-app package. 2021-04-02 14:10:33 -04:00
Nate Coraor 38fcde0aaf Include config schemas in galaxy-app package and support loading from 
the package dir rather than a fixed path in lib/.
 2021-04-02 14:07:37 -04:00
Nate Coraor e7127f7386 Include galaxy.workflow.refactor and galaxy.workflow.reports in 
galaxy-app package.
 2021-04-02 13:51:25 -04:00
Nate Coraor 4ad0b7c10c Include galaxy.model.tool_shed_install and sub-packages in galaxy-app. 2021-04-02 13:37:46 -04:00
Nate Coraor c25e730c95 Include galaxy.util.tool_shed in galaxy-app package. 2021-04-02 13:32:39 -04:00
Nate Coraor 61a87d1a36 Include galaxy.config in galaxy-app package. 2021-04-02 13:23:13 -04:00
Nate Coraor 44e59e9665 Include galaxy.model.view in galaxy-data package. 2021-04-02 13:21:13 -04:00
Nate Coraor 72caae0ab5 Include galaxy.model.dataset_collections.types in galaxy-data package. 2021-04-02 13:19:12 -04:00
Nate Coraor 1019ff06d8 Include job runner scripts in galaxy-app package 2021-04-02 13:17:30 -04:00
Nate Coraor cc1f471490 Release process overhaul 
- Convert release Makefile targets to a script
- Update package versions from Galaxy version instead of leaving them
  uncoupled
- Use next-dev-version process on release branches when in between point
  releases
- Automatically detect and increment versions
- Test merging release branches forward before pushing releases
- Support multiple rc versions (will be more useful for package testing)
- Support building local versions of packages
- Tests for the release script
 2021-03-30 12:11:48 -04:00
mvdbeek 908708c3c0 Add celery to galaxy-app 2021-03-29 09:29:25 -04:00
mvdbeek 1afe1e1211 Break UniverseApplication into smaller parts 
so we can use a variant of app that loads managers in Celery.
 2021-03-29 09:29:25 -04:00
mvdbeek ac3fcf911e Merge branch 'release_21.01' into dev 2021-03-24 20:34:06 +01:00
John Chilton 3e0a5d7b06 Starting work on tool-util 21.1.1 2021-03-19 14:27:29 -04:00
John Chilton 883a4b9641 Version 21.1.0 of tool-util (tag galaxy-tool-util-21.1.0). 2021-03-19 14:27:10 -04:00
John Chilton 9486d96b3b Starting work on containers 21.1.1 2021-03-19 14:21:42 -04:00
John Chilton a3e2698bd6 Version 21.1.0 of containers (tag galaxy-containers-21.1.0). 2021-03-19 14:21:21 -04:00
John Chilton 1a9433b298 Starting work on util 21.1.1 2021-03-19 14:18:57 -04:00
John Chilton 4c06212424 Version 21.1.0 of util (tag galaxy-util-21.1.0). 2021-03-19 14:18:27 -04:00
John Chilton 3fe054b7e6 Prepare for 21.1.0 release of galaxy-util. 2021-03-19 14:14:08 -04:00
qiagu b8db43011f Merge branch 'dev' into ometiff2 2021-03-17 10:55:43 -07:00
Nicola Soranzo 76123657c2 Merge branch 'release_21.01' into dev 2021-03-17 12:41:24 +00:00
mvdbeek 9c2d63211f Add refgenconf package pin 2021-03-17 12:54:44 +01:00
Sergey Golitsynskiy 7fa062f30c Pin sqlalchemy in package requirements files 2021-03-17 12:12:35 +01:00
qiagu 5686c368f6 Update tifffile version 2021-03-16 22:28:58 -07:00
Sergey Golitsynskiy 2f0a024915 Pin sqlalchemy in package requirements files 2021-03-16 13:55:21 -04:00
Nicola Soranzo 6c540932c7 Merge branch 'release_21.01' into dev 2021-03-12 19:01:35 +00:00
Nicola Soranzo 283ec1772f Merge branch 'release_20.09' into release_21.01 2021-03-12 17:12:04 +00:00
Nicola Soranzo 734b08142a Use latest pip in package testing 
Fix the following error when running `tox -e test_galaxy_packages` on
Python 3.5:

```
ERROR: Could not find a version that satisfies the requirement networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4)
ERROR: No matching distribution found for networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0)
WARNING: You are using pip version 20.2.2; however, version 20.3.4 is available.
You should consider upgrading via the '/tmp/gxpkgtestenviQxuK1/bin/python -m pip install --upgrade pip' command.
ERROR: InvocationError for command /bin/bash packages/test.sh (exited with code 1)
___________________________________ summary ____________________________________
ERROR:   test_galaxy_packages: commands failed
```
 2021-03-11 22:41:10 +00:00
mvdbeek 45990803eb Merge branch 'release_21.01' into dev 2021-03-09 15:29:19 +01:00
John Chilton 6465b78836 Starting work on tool-util 21.1.0.dev7 2021-03-06 11:29:44 -05:00
mvdbeek 7025f20f68 Merge branch 'release_21.01' into dev 2021-03-02 15:10:04 +01:00
Marius van den Beek c084f5f919 Merge pull request #11512 from jmchilton/fix_pydanic_1.8 
[21.01] Fix web framework requests for pydantic 1.8 not working.
 2021-03-02 09:16:25 +01:00
Nate Coraor a2d1625780 Merge remote-tracking branch 'upstream/release_21.01' into dev 2021-03-01 16:52:02 -05:00
Nate Coraor 7ed0f5337f Merge remote-tracking branch 'upstream/release_20.09' into release_21.01 2021-03-01 16:47:23 -05:00
Nate Coraor 373489e8f4 Starting work on objectstore 20.9.2 2021-03-01 16:37:33 -05:00
Nate Coraor 0fbbf734f5 Version 20.9.1 of objectstore (tag galaxy-objectstore-20.9.1). 2021-03-01 15:29:38 -05:00