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441 Commits
Author SHA1 Message Date
Islam Heggy cde79eef33 Update social-auth-core library version to fix OIDC problem 2021-11-24 05:00:28 +02:00
mvdbeek 512526a5f5 Version 21.9.2 of tool-util (tag galaxy-tool-util-21.9.2). 2021-11-23 13:54:07 +01:00
mvdbeek 2bda35b55e Version 21.9.1 of tool-util (tag galaxy-tool-util-21.9.1). 2021-11-03 09:52:35 +01:00
mvdbeek 6b29202be6 Update version to 21.09. 2021-11-02 12:08:02 +01:00
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
Marius van den Beek f10aecbf4c Merge pull request #11043 from bernt-matthias/topic/validator-negate 
Add `negate` attribute to validators .. and tests for all
 2021-09-16 11:54:24 +02:00
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
Marius van den Beek 68af8e46ac Merge pull request #12064 from ic4f/dev_declarative3 
Declarative mappings + tests for all models
 2021-09-08 12:11:03 +02:00
Marius van den Beek c0b65c1de2 Merge pull request #12388 from bgruening/makedirs_pyfs 
create dirs when needed for the pyfilesystem export plugins
 2021-09-08 10:41:46 +02:00
Sergey Golitsynskiy da7fdddd2b Remove references to security from util package 2021-09-07 13:13:49 -04:00
Sergey GolitsynskiyandMarius van den Beek 73d87f5d33 Update packages/util/requirements.txt 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-09-07 13:13:49 -04:00
Sergey Golitsynskiy a6ab79a95d Move object_wrapper to security package 
For context see discussion in #12064
 2021-09-07 13:13:49 -04:00
Sergey GolitsynskiyandMarius van den Beek 548e3de764 Update packages/util/requirements.txt 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-09-07 13:13:49 -04:00
Sergey Golitsynskiy ac93e08367 Add SQLAlchemy to util package requirements 
We need this is util/object_wrapper
 2021-09-07 13:13:49 -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
John Chilton e3338f8a68 Require fs for app. 2021-08-31 14:24:01 -04:00
Nuwan Goonasekera df7e40c550 Added missing triggers package to galaxy data 2021-08-30 10:19:32 +05:30
Dannon b3cf836e1c Merge pull request #12327 from jmchilton/tool_panel_views_0 
Implement tool panel views.
 2021-08-18 18:54:39 -07:00
John Chilton 2dddcac8c8 Implement tool panel views - config, toolbox, search, client. 2021-08-11 10:14:43 -04:00
John Chilton 7692e62036 Load EDAM from PyPI if not configured instead of unexpected download. 2021-08-11 10:14:43 -04:00
John Chilton 48df4b910d Systematic handling of remotely required tool files. 
- Allow tools to define "pulsar file action"-like paths for files to include and exclude during remote job setup.
- Package up a list of defaults for older tools.
 2021-08-10 14:04:32 -04:00
Matthias Bernt 44061433d1 debug package tests 2021-08-02 15:02:10 +02:00
John Chilton 93f79babef Merge pull request #12292 from jmchilton/toolbox_refactor 
Refactor base toolbox code de-coupled from app & config into tool_util.
 2021-07-28 12:35:03 -04:00
John Chilton e6de9b7496 Allow bio.tools mappings for legacy tools. 
Assigning these in the tools for new tool installs is great (https://github.com/galaxyproject/tools-iuc/pull/3411/files) but there will be thousands of old tools that are missing these and we should have a way to fill in this information as "missing info" bug fixes.
 2021-07-26 11:09:42 -04:00
John Chilton fbd2fb10ff Refactor base toolbox code de-coupled from app & config into tool_util. 
This was originally decoupled by me for this purpose and this code was in galaxy-lib years ago, but it just never made it into galaxy-tool-util. This commit clears up that oversight I think.
 2021-07-26 11:06:14 -04:00
Sergey Golitsynskiy 003dfc48ae Update SQLAlchmey to 1.4.20 2021-07-04 13:18:13 -04:00
mvdbeek 9952be7a80 Merge branch 'release_21.05' into dev 2021-07-01 10:03:48 +02:00
mvdbeek 292cd4d31d Merge branch 'release_21.01' into release_21.05 2021-07-01 09:59:09 +02:00
Sergey Golitsynskiy 314e00e643 Update SQLAlchemy to 1.4.19 2021-06-23 11:19:58 -04:00
John Chilton e2ac10eb3b Starting work on tool-util 21.1.3 2021-06-23 10:05:45 -04:00
John Chilton 7543a983da Version 21.1.2 of tool-util (tag galaxy-tool-util-21.1.2). 2021-06-23 10:05:26 -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
Nicola Soranzo 97946d0be5 Merge branch 'release_21.05' into dev 2021-05-25 22:00:09 +01:00
Nicola Soranzo 6bd30ce431 Merge branch 'release_21.01' into release_21.05 2021-05-25 21:58:57 +01:00
John Chilton 9a97d616f8 Starting work on tool-util 21.1.2 2021-05-21 14:52:02 -04:00
John Chilton abd3b7a293 Version 21.1.1 of tool-util (tag galaxy-tool-util-21.1.1). 2021-05-21 14:51:24 -04:00
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 GolitsynskiyandNicola Soranzo 3850f49506 Update SQLAlchemy pin <2 in packages/web_stack/requirements.txt 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-05-18 19:02:40 -04:00
Sergey GolitsynskiyandNicola Soranzo 0740e175db Update SQLAlchemy pin <2 in packages/web_framework/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