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1778 Commits
Author SHA1 Message Date
Dannon 2c65d8e755 Merge pull request #14035 from dannon/samples-rename 
Rename samples_tool_conf to sample_tool_conf
 2023-01-17 13:03:07 -05:00
Nicola Soranzo 39c0000c1b Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options 
Pip 20.3 added support for PEP 600, i.e. manylinux wheels using platform
tags of the form "manylinux_${GLIBCMAJOR}_${GLIBCMINOR}_${ARCH}". Fix
installation of dependencies like pysam 0.20.0 wheels, which otherwise need
to be built from source and can fail as reported by @assuntad23 in
https://gist.github.com/assuntad23/3022db63a6878f044a209961dd40e592

Also:
- Install `wheel` to fix warning like `Using legacy setup.py install for
  beaker, since package 'wheel' is not installed.`
- Drop unnecessary `defaults` channel from conda commands.
- Fix "SC2223: This default assignment may cause DoS due to globbing. Quote
  it." errors reported by `shellcheck -x` .
 2023-01-17 15:01:38 +00:00
Nicola Soranzo 921e5da2e6 Lint 2 previously excluded files with black and isort 2023-01-16 14:34:56 +00:00
Dannon Baker d04fb67396 Rename samples_tool_conf to sample_tool_conf to match datatypes/data_manager naming convention 2023-01-10 10:03:23 -05:00
Nicola Soranzo 5826b429d4 Merge pull request #14849 from mahendrapaipuri/auth_ldap3 
Add LDAP authenticator variant using `ldap3` package
 2023-01-09 15:41:54 +00:00
Mahendra Paipuri c9487b851f Improve wording based on PR comments 2023-01-09 15:16:40 +01:00
Dannon Baker 9de4e72563 Rebuild config including gravity stuff 2022-12-22 21:25:41 -05:00
Laila Los 7d7ac4111b rebuild config 2022-12-22 16:59:27 +01:00
Laila Los 34cbbc5ad6 add persistant theme swapping 2022-12-21 14:01:34 +01:00
Dannon 241b245cbc Merge pull request #14791 from anuprulez/update_tool_recommendation 
Update tool recommendation API using transformers (neural network)
 2022-12-20 20:01:46 -05:00
Martin Cech 063405a1cd replace the png favicon with svg version 
goes down from 16kb to 9kb and preserves all details

add padding to masthead logo

it now has no padding in the image itself

Add margin to svg

drop padding

since we decided to include it in logos

Slightly increase margin further
 2022-12-20 15:44:07 -08:00
Dannon Baker c0fca38cf0 Config rebuild 2022-12-19 15:32:36 -05:00
Dannon 40cf2fcb70 Update doc/source/admin/special_topics/interactivetools.rst 2022-12-19 12:52:42 -05:00
Sveinung Gundersen 9d588b8ea7 Updated nginx config for upstream proxy of path-based ITs 2022-12-17 16:56:44 +01:00
Mahendra Paipuri 51bc263ad4 Merge branch 'galaxyproject:dev' into auth_ldap3 2022-12-12 11:29:22 +01:00
mahendrapaipuri 064734b477 Merge branch 'dev' into auth_ldap3 2022-12-11 17:33:53 +01:00
mahendrapaipuri 3cf26d3b4d Address PR comments 2022-12-11 17:31:38 +01:00
John Chilton 4bd80ce6ef Flush out documentation and service-info for DRS API a bit. 2022-12-08 10:08:01 -05:00
John Chilton 8ff9fe2610 Implement initial GA4GH DRS Support. 
- Implement APIs for serving Galaxy's public datasets as DRS objects.
- Implement support in galaxy.files.uris for DRS URIs so that upload, etc... can use DRS URIs from other data repositories.

The ways this can be improved are endless:

- New object ID patterns can be implemented to allow access to composite data, metadata files from a bundle view of datasets.
- New object ID patterns can be implemented to allow access to collections as bundles of datasets.
- More auth types and AccessMethods could be implemented for loading datasets from clients.
- Some sort of scheme for providing authenticated URLs to non-public data could be implemented to provide access to more of Galaxy's data if user's can implement.

Despite all these limitations - I think having the guts in like this provide useful points for interested parties to go and add functionality to enable their desired usecases.
 2022-12-08 10:07:11 -05:00
guerler 72fd52f087 Deprecate brand title text option, logo now contains text 2022-11-30 17:19:07 -05:00
Linelle 9c5f5bc3a2 changed references from sample XML to sample YML 
added a sentence about where to find the XMLs as well in case people are still using those (it's me, i'm people)
 2022-11-30 14:50:19 -05:00
Linelle ec504562e3 change resubmission example link from xml to yml 
Test case for resubmission location used to be https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.xml which leads to 404, have changed it to https://github.com/galaxyproject/galaxy/blob/dev/test/integration/resubmission_job_conf.yml and made it linked text instead of plain URL
 2022-11-30 14:29:52 -05:00
Nate Coraor 1cdb7b5bcd Replace XML job conf sample with YAML. 
Prefer loading job_conf.yml, fall back to job_conf.xml with a warning if
it exists.
 2022-11-17 19:58:24 -05:00
Nate Coraor bb41d1f6e3 Merge pull request #14867 from dannon/release-next-update-23.1 
Update release-next to 23.0
 2022-11-16 12:21:04 -05:00
John Chilton 1a2a534695 Merge pull request #14965 from jmchilton/remove_no_longer_useful_wsgi_middleware 
Remove old WSGI middleware that is no longer useful.
 2022-11-10 23:13:45 +01:00
John Davis b11c18eb21 Merge pull request #14825 from neoformit/dev-html-email 
Looks great! Thanks, @neoformit 

For future ref/todo: we do need a more systematic/unified approach to handling path construction that handles tests that are arun both as standalone unit tests and as part of package tests (as per observation by @neoformit)
 2022-11-10 11:30:42 -05:00
John Chilton 92a885e280 Remove old WSGI middleware that is no longer useful. 2022-11-10 05:28:24 -05:00
Simon Bray 91674ac9de small change to job runner docs 
to state more explicitly what `check_watched_item()` should return
 2022-11-08 11:47:09 +01:00
Nicola Soranzo 581d001828 Remove unused `require_new and GALAXY_TEST_HISTORY_ID` 2022-11-07 15:44:02 +00:00
Nicola Soranzo afa7b713bc Replace `GALAXY_TEST_INCLUDE_SLOW env variable with external_dependency_management` pytest marker 
Fix mulled tests missing tests in `test/unit/tool_util/test_conda_resolution.py` .

Also:
- Add `coverage` tox factor to generate coverage report.
 2022-11-03 21:43:37 +00:00
DannonandNicola Soranzo 9f5ac39923 Apply suggestion swapping to 23.0. 
This seems the group leaning at this point, and it sounds good to me.

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-11-01 19:58:21 -04:00
mvdbeek eec177839f Drop scripts/function_tests.py 2022-11-01 18:45:08 +00:00
Nicola Soranzo 5ca0aea54a Drop nose 
It's deprecated and unmaintained, and is broken under Python 3.10 .
 2022-11-01 18:45:07 +00:00
Dannon Baker 4b681f1258 Update release-next to 23.1 2022-10-27 08:34:35 -04:00
mahendrapaipuri 04b52c7686 Add documentation about ldap3 auth provider 2022-10-24 21:45:11 +02:00
Cameron Hyde e2119e4750 Update config description 2022-10-20 14:25:49 +10:00
Cameron Hyde dc27533344 Account activation email rendered from text/html templates 2022-10-20 14:06:17 +10:00
Dannon c7216e4b85 Merge pull request #14776 from mahendrapaipuri/add_request_obj_authmanager 
Make HTTP request object available to `AuthManager`
 2022-10-18 09:23:10 -04:00
Marius van den Beek 672ed4984f Merge pull request #14694 from sveinugu/dev 
Allow path-based interactive tools using nginx proxy
 2022-10-17 11:24:38 +02:00
Marius van den Beek 241da69672 Merge pull request #12288 from dannon/sorted-tools-in-sections 
Automatically sort tools in sections by name
 2022-10-17 10:49:17 +02:00
Marius van den Beek ce26561b33 Merge pull request #14708 from jdavcs/dev_celery_config 
Enable fine-grained celery configuration
 2022-10-17 10:37:24 +02:00
Marius van den BeekandNicola Soranzo a5dc788bf3 Tweak wording and example for verifying remote_ip in custom LDAP authenticator 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-10-17 10:33:29 +02:00
Marius van den Beek 934369aa3a Merge pull request #14792 from jdavcs/dev_sqlalchemy_engine_options 
Make connect_args for SQLAlchemy's engine configurable
 2022-10-17 10:30:44 +02:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
John Davis d310635895 Celery config option result_backend is required 2022-10-14 19:28:17 -04:00
John Davis d26ad37e97 Remove celery_backend from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis b6b49897dc Remove celery_broker from config_schema, use celery_conf instead 2022-10-14 19:28:17 -04:00
John Davis 2de79dd7d1 Add default task routes to config schema 2022-10-14 19:28:17 -04:00
John Davis 71829ae6af Add more details to setting db engine options to config schema 2022-10-14 13:18:35 -04:00
mahendrapaipuri c0002c1ffb Update authentication documentation with an example on how to use request object in auth flows 2022-10-14 09:46:59 +02:00