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102 Commits
Author SHA1 Message Date
mvdbeek 917dbe718c Update version to 22.01.rc1 2022-02-01 11:07:22 +01:00
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Nicola Soranzo a37bdfd42f Merge branch 'release_21.09' into dev 2021-11-25 16:30:56 +00:00
Islam Heggy cde79eef33 Update social-auth-core library version to fix OIDC problem 2021-11-24 05:00:28 +02:00
Nicola Soranzo a65d8fade9 Add missing typing-extensions requirement 
to `pyproject.toml` and packages' `requirements.txt` .

We have been importing it explicitly since commit
fc2ce45767 (December 2020).

Also:
- Remove now unnecessary minimum version for pygithub
 2021-11-24 01:09:49 +00:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
mvdbeek 6b29202be6 Update version to 21.09. 2021-11-02 12:08:02 +01:00
John Chilton c791fea0cf Formalize dependency of galaxy-data on galaxy.files package. 
- Create a new project galaxy-files that does not depend on anything but galaxy-util.
- Add a dependency in galaxy-data on galaxy-files, use typing in galaxy.data.sniff to make this clear.
- Cleanup the galaxy-files unit tests to not depend on galaxy.datatypes.sniff code - this wasn't ideal to start with.
- Add a small integration-ish unit test test_sniff_file_sources.py to test that piece of sniff.py that depends on galaxy-files.
 2021-10-11 13:16:30 -04:00
John Chilton 336cf7b918 Package objectstore's unittest helpers and drop hacks for running test_model_copy.py in galaxy-data. 2021-09-24 12:16:54 -04:00
John Chilton 84220b6b55 Establish unittest utils for galaxy-data packages. 
Progress toward https://github.com/galaxyproject/galaxy/issues/8364. Cleans up dependency into a proper DAG so we can move for instance test_model_discovery.py into galaxy-data's unittests.
 2021-09-24 12:16:54 -04:00
Sergey Golitsynskiy e691ab866b Update SQLAlchemy to 1.4.25 2021-09-23 11:29:38 -04:00
mvdbeek 5332eb246a Update version to 22.01.dev0 2021-09-20 19:53:11 +02:00
mvdbeek 9275b34819 Update version to 21.09.rc1 2021-09-20 19:53:09 +02:00
Nicola Soranzo 520aba646a Revert "Install Tempita from a fork due to use_2to3 deprecation" 
This reverts commit 314ca33509.

Fixed on PyPI as mentioned in
https://github.com/pypa/setuptools/issues/2788#issuecomment-921962154
 2021-09-20 15:56:53 +01:00
John Chilton 62295efeb5 Merge pull request #11315 from davelopez/prepare_fastapi_route_quotas 
Prepare FastAPI route for quotas
 2021-09-08 09:14:49 -04:00
Nicola Soranzo 00c6c281cf Merge branch 'release_21.05' into dev 2021-09-07 11:54:45 +01:00
Nicola Soranzo cf5708e35d Merge branch 'release_21.01' into release_21.05 2021-09-07 11:00:33 +01:00
Nicola Soranzo 314ca33509 Install Tempita from a fork due to use_2to3 deprecation 
Fix https://github.com/galaxyproject/galaxy/issues/12412 .

We have a dependency on `Tempita` (through `sqlalchemy-migrate`), which is
abandonware and uses the `use_2to3=True` option of `setup()` in its
`setup.py` .
The new Setuptools v58.0.0 removed support for 2to3 during builds:
https://github.com/pypa/setuptools/blob/main/CHANGES.rst#v5800
As a result Tempita is installed at even older version and importing it
raises a SyntaxError.

For Galaxy as a full application this has been solved by creating a wheel on
https://wheels.galaxyproject.org . But the `galaxy-data` package (which also
depends on `sqlalchemy-migrate`) cannot automatically install the
tempita-0.5.2 wheel from our alternative package index when installed via
`pip install galaxy-data` as there is no syntax to specify that.

I've therefore resurrected Tempita from the Bitbucket Mercurial repo (thanks
to Software Heritage backups!
https://bitbucket-archive.softwareheritage.org/projects/ia/ianb/tempita.html
), converted to a GitHub repo and updated its code to Python 3.6 with 2to3
and pyupgrade.
 2021-09-07 03:51:02 +01:00
Nuwan Goonasekera df7e40c550 Added missing triggers package to galaxy data 2021-08-30 10:19:32 +05:30
Sergey Golitsynskiy 003dfc48ae Update SQLAlchmey to 1.4.20 2021-07-04 13:18:13 -04:00
Sergey Golitsynskiy 314e00e643 Update SQLAlchemy to 1.4.19 2021-06-23 11:19:58 -04:00
Sergey Golitsynskiy b3551fec8c Update SQLAlchemy to 1.4.18 2021-06-11 18:53:07 -04:00
mvdbeek 3ce0312a0a Update version to 21.05. 2021-06-10 21:23:20 +02:00
Sergey Golitsynskiy 94ce70aa8b Update SQLAlchemy to 1.4.17 2021-06-03 12:22:54 -04:00
davelopez 50d7d2e339 Fix symlink 2021-06-02 10:22:37 +02:00
David López b246bf3af4 Fix symlink 
Make it relative
 2021-06-02 10:22:37 +02:00
davelopez 1a7a09206d Add lib/galaxy/schema to packages/data/galaxy/schema 2021-06-02 10:22:37 +02:00
Sergey Golitsynskiy 9cb78f7c3d Update SA pin to 1.4.15; update requirements files 2021-05-18 19:02:40 -04:00
Sergey GolitsynskiyandNicola Soranzo 5dc250b1fb Update SQLAlchemy pin <2 in packages/data/requirements.txt 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-05-18 19:02:40 -04:00
Sergey Golitsynskiy 490655ae97 Update SA pin to 4.7; update requirements files 
Also unpin requirement in packages
 2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy 46c2e1957b Fix rebase error: add missing dep to packages 2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy fa20de7692 Remove sqlalchemy-utils from packages 2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy a9868971a8 Update SQLAlchemy pin for packages to >=1.4.5 2021-05-18 19:00:55 -04:00
Nicola Soranzo 99da99becf Merge branch 'release_21.05' into dev 2021-05-06 12:50:20 +01:00
Nicola Soranzo 65ea55bb02 Merge branch 'release_21.01' into release_21.05 2021-05-06 11:45:26 +01:00
Nicola Soranzo fa58f37f28 Merge branch 'release_20.09' into release_21.01 2021-05-06 11:39:48 +01:00
mvdbeek 07fb59937e Update version to 21.09.dev0 2021-05-05 21:48:01 +02:00
mvdbeek 40795140d9 Update version to 21.05.rc1 2021-05-05 21:30:54 +02:00
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
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 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
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
Nate Coraor d4431511d5 Version 20.9.1 of data (tag galaxy-data-20.9.1). 2021-03-02 09:03:22 -05:00
mvdbeek 61df313fb6 Add contextvars to data package requirement 2021-02-21 21:20:07 +01:00