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750 Commits
Author SHA1 Message Date
Martin Cech a33ea00eaf Merge pull request #16743 from dannon/package-version-handling 
Fix package version handling for initial minor releases
 2023-10-09 16:24:32 +02:00
John Chilton 7dc0b1378b WIP: modern tool shed frontend 2023-09-27 14:30:42 -04:00
John Chilton 59cff45fb1 Decompose tool shed + schema package. 
This commit creates two new packages - below a description of these packages and why they are being created.

galaxy-schema: This package contains the pydantic models that power the API. The purpose of packaging them is to ensure they can be reused by clients with minimal external dependencies. Reusing the schema in client code would very quickly provide rapid documentation and validation and static checking for Python clients using the Galaxy API.

galaxy-tool-shed: This package contains the tool shed server code. This has been a long term project to allow the tool shed to be spun out but maintain real galaxy dependencies and maintain testing. More discussions around this project can be found as part of https://github.com/galaxyproject/galaxy/pull/8830.
 2023-09-26 13:46:55 -04:00
Dannon Baker d1c1af7b48 Fix package version handling for initial release 2023-09-26 09:15:49 -04:00
mvdbeek 09ff121dd9 Merge branch 'release_23.1' into dev 2023-09-25 10:23:14 +02:00
mvdbeek bb2daafcc9 Move config parsing to util package 2023-09-22 21:18:02 +02:00
mvdbeek cac5495b5d Fix allowlist deserialization in file sources 2023-09-22 19:37:41 +02:00
mvdbeek 0f2ef4dc0c Merge branch 'release_23.1' into dev 2023-09-14 13:43:50 +02:00
mvdbeek 63442d1d72 Fix regex validation for global inline flags 
Fixes https://github.com/galaxyproject/galaxy/issues/16676
 2023-09-13 12:00:57 +02:00
Nicola Soranzo 23185e7039 Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar 
so we will be able to drop Python 3.7 support for the rest of the code base.

Add a new `test_galaxy_packages_for_pulsar` tox environment and modify the
`test.sh` script so that when the `--for-pulsar` argument is passed:
- only the 4 packages used by Pulsar are tested
- mypy checks are skipped
- unit tests don't skip the tests marked with
  `external_dependency_management` (i.e. those conda/container-related).

Also:
- Add missing pydantic requirement to the galaxy-objectstore package
 2023-09-06 11:07:56 +01:00
mvdbeek 1ee35c46bb Add dparse to app requirements 2023-09-01 15:07:06 +02:00
mvdbeek c62da4aa33 Merge branch 'release_23.1' into dev 2023-08-09 16:06:08 +02:00
mvdbeek 35e47388e7 Exclude selenium version with broken type hints 2023-08-09 09:12:48 +02:00
mvdbeek 521405136a Merge branch 'release_23.1' into dev 2023-07-29 12:28:41 +02:00
mvdbeek c314336705 Merge branch 'release_23.0' into release_23.1 
# 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/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_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
 2023-07-29 12:28:39 +02:00
mvdbeek 2fbbfd8417 Start work on 23.0.6.dev0 2023-07-29 12:28:35 +02:00
mvdbeek af730bc6b5 Create version 23.0.5 2023-07-29 12:28:32 +02:00
Nicola Soranzo 45e020e760 Merge branch 'release_23.1' into dev 2023-07-24 17:04:54 +01:00
Nicola Soranzo 0a73e1c512 Merge branch 'release_23.0' into release_23.1 2023-07-24 15:16:11 +01:00
Nicola Soranzo 741ecf6f44 Pin pysam to >=0.21.0 
This reverts commit 353c08cbb9 .

pysam 0.20.0 doesn't build for Python 3.11 on macOS, so we need to
temporarily add the unnecessary Cython runtime dependency that
pysam 0.21 brings in.
 2023-07-21 00:58:33 +01:00
Rendani Gangazhe 753d199542 Merge dev and resolve conflicts 2023-07-03 10:54:25 +02:00
Nate Coraor 8fee25f084 Merge branch 'release_23.1' into dev 2023-06-30 17:14:03 -04:00
Nate Coraor ea07ddba98 Merge branch 'release_23.0' into release_23.1 
# 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/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_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
 2023-06-30 17:14:03 -04:00
Nate Coraor 25b52a97f7 Start work on 23.0.5.dev0 2023-06-30 17:14:00 -04:00
Nate Coraor 03d9eb63b8 Create version 23.0.4 2023-06-30 17:13:57 -04:00
Nate Coraor c18ed28896 Merge remote-tracking branch 'upstream/release_23.1' into dev 2023-06-30 15:57:32 -04:00
Nate Coraor 2ca678482f Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 2023-06-30 15:56:50 -04:00
Nate Coraor 492b2ee64b Pin fastapi to <0.99 2023-06-30 15:20:22 -04:00
Nate Coraor ab1e0485d7 Pin pydantic in packages to <2 2023-06-30 14:51:18 -04:00
Rendani Gangazhe 33dcace1f0 Add lib/galaxy/carbon_emissions module symlink to packages/app/galaxy/ directory 2023-06-30 16:11:26 +02:00
Martin Cech 469ff484b6 Merge branch 'release_23.1' into dev 2023-06-27 15:17:21 -07:00
Nicola Soranzo 4c0e27c9ab Remove pin on `packaging` in packages 
Follow-up on https://github.com/galaxyproject/galaxy/pull/16058
where the pin was removed from ``pyproject.toml`` .
 2023-06-27 12:55:24 +01:00
mvdbeek bb65b07584 Merge branch 'release_23.1' into dev 2023-06-26 09:32:44 +02:00
mvdbeek 0b1a41bd86 Merge branch 'release_23.0' into release_23.1 
# 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/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_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
 2023-06-26 09:32:42 +02:00
mvdbeek 1ef440e92c Start work on 23.0.4.dev0 2023-06-26 09:32:37 +02:00
mvdbeek b4adbb4ec5 Create version 23.0.3 2023-06-26 09:32:32 +02:00
Marius van den Beek acc7136045 Merge pull request #15300 from SergeyYakubov/oidc_tokens 
OIDC tokens
 2023-06-21 19:39:19 +02:00
mvdbeek 5413333aac Merge branch 'release_23.0' into dev 
# Conflicts:
#	lib/galaxy/version.py
 2023-06-13 17:58:26 +02:00
mvdbeek 414abff510 Start work on 23.0.3.dev0 2023-06-13 17:58:19 +02:00
mvdbeek a7f0a365be Create version 23.0.2 2023-06-13 17:58:13 +02:00
Martin Cech f52e00d1d8 Merge branch 'release_23.0' into merge230 2023-06-09 21:03:07 -07:00
mvdbeek 5d517421bd Rename galaxy-webapps back to galaxy-web-apps 
PyPI doesn't let us create projects with names that can be confused.
 2023-06-08 20:48:03 +02:00
Matthias Bernt a5f75e7ead Merge branch 'release_23.0' into dev 2023-06-08 15:54:42 +02:00
Matthias Bernt aa9cc5b9e8 Start work on 23.1.dev0 2023-06-08 15:54:32 +02:00
Matthias Bernt f722e122f7 Create version 23.0.1 2023-06-08 15:54:28 +02:00
Nicola Soranzo afc11e2ebc Merge branch 'release_23.0' into dev 2023-05-30 17:49:58 +01:00
mvdbeek d8e62f8f5a Add script for creating (point) releases 
Still working on it, but it's minimally useful already.
 2023-05-28 11:15:57 +02:00
John Chilton f9e00f597a axe testing 2023-05-24 12:54:25 -04:00
mvdbeek ff7908f6be Merge branch 'release_23.0' into dev 2023-05-17 12:15:05 +02:00
John Chilton 2111ccfed2 Merge pull request #16090 from mvdbeek/fix_package_changelogs 
[23.0] Add missing dates for versions that contain changelog entries
 2023-05-15 09:05:51 -04:00