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2dd0eed46b8beefdc650493948dbbcfe0eae01a4
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1607 Commits
Author SHA1 Message Date
Dannon Baker 2dd0eed46b Fix several 'to to' redundant word typos. 2021-10-21 12:28:45 -04:00
John Chilton cd2e6527fc Merge pull request #12255 from bernt-matthias/topic/deprecate_datamanager_version 
Deprecate data manager version
 2021-09-08 14:36:01 -04:00
mvdbeek ecc54ba00c Merge branch 'release_21.05' into dev 2021-08-09 18:45:05 +02:00
Nate Coraor 038045a600 Add a GDPR-friendly user purge to pgcleanup. 2021-07-23 14:55:54 -04:00
Matthias Bernt c2a113bc85 add script for fixing shed_data_manager_conf.xml 2021-07-14 17:13:26 +02:00
mvdbeek fdb36c7ed7 Run client-y tests with --frozen-lockfile 
Seems to be best-practice and may be a little faster
 2021-06-30 13:06:24 +02:00
mvdbeek 24d825856a Merge branch 'release_21.05' into 'release_21.09' 2021-06-10 21:23:23 +02:00
Marius van den Beek f115fee4a7 Merge pull request #11938 from mvdbeek/21.05_release_notes 
Release notes for 21.05
 2021-06-10 20:34:50 +02:00
mvdbeek 91795d198d Lint fix 2021-06-10 19:41:24 +02:00
Helena Rasche 364286df04 munge filenames 2021-06-10 18:59:56 +02:00
Helena Rasche 3093c2dcef handle subsections of configurations a bit better 2021-06-10 18:56:17 +02:00
Helena Rasche 1c66b755a6 include config schemas in diffing 2021-06-10 18:52:59 +02:00
Sergey Golitsynskiy 680db562f7 Do not use legacy string interpolation on URL obj 
This fixes the pgcleanup script and an integration test.

The test fails because of an error in the script.
The error is caused by incorrect string formatting.
The new SQLAlchemy URL object extends collections.namedtuple, and a
tuple is incompatible with printf-style formating.

Ref:
https://github.com/sqlalchemy/sqlalchemy/blob/18dbd6aa12a7eca0acb1e2c4f752088e24d6adae/lib/sqlalchemy/engine/url.py#L36
https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting
 2021-05-18 19:00:55 -04:00
Sergey Golitsynskiy 3cd1c7f1c7 Handle DedupedColumnCollection in db_indexes 
This should fix the `scripts/check_model.py` script and the database
indexes github workflow.

Accessing index columns has changed: index.columns gives access to a
DedupedColumnCollection instead of a ColumnCollection.
Columns can be accessed by key; keys are accessed via keys() attr.

Ref:
https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#select-objects-and-derived-from-clauses-allow-for-duplicate-columns-and-column-labels
https://docs.sqlalchemy.org/en/14/core/sqlelement.html?highlight=dedupecolumncollection#sqlalchemy.sql.expression.ColumnCollection
 2021-05-18 19:00:55 -04:00
mvdbeek 37a15c5319 Merge branch 'release_21.05' into dev 2021-05-18 09:52:08 +02:00
Dannon Baker 22e7601653 First pass fstring conversion 2021-05-11 13:47:00 -04:00
mvdbeek 9e9343ccd2 Fix cleanup_datasets.py script 2021-05-11 18:34:30 +02:00
mvdbeek bb3e9bffab Don't set default pool 2021-05-07 11:17:02 +02:00
Nate Coraor 9ee437d57f Fix usage of sed -i on macOS in release script 2021-05-06 11:27:48 -04:00
mvdbeek de8ef76092 Make sure web handlers don't become job handlers if handlers section exists 
And add a default pool, so that exisiting job setups that don't specify
a pool (for instance those that previously used db-preassign) will just
continue working.
 2021-04-13 10:13:42 +02:00
John Chilton c313635676 Merge pull request #11772 from mvdbeek/run_sh_gunicorn 
Add circus + gunicorn option when using run.sh
 2021-04-12 10:31:30 -04:00
mvdbeek 8157300d1d Restore pastescript, make new stack depend on APP_WEBSERVER=dev 2021-04-07 14:39:06 +02:00
mvdbeek d97c6e1e21 Set up default logging if running run.sh with --daemon 2021-04-07 14:39:06 +02:00
Marius van den Beek 32cb259274 Merge pull request #11641 from natefoo/release-process-overhaul 
Overhaul make-based release process
 2021-04-06 16:45:12 +02:00
mvdbeek 47d4e18c3b Replace paster with circusd, add basic functionality to run.sh 2021-04-02 18:47:41 +02:00
mvdbeek 201b1e5e9f Drop scripts/paster.py and pastescript 2021-04-02 18:47:41 +02:00
mvdbeek c8c08ca84c Merge branch 'release_21.01' into dev 2021-03-31 12:09:44 +02:00
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 ca6f2fa68e Create install database with create_db.sh 2021-03-30 13:44:36 +02:00
mvdbeek 8d5c7003ce Fix linting error in bootstrap script 2021-03-16 18:41:40 +01:00
Dannon Baker 3ae00d18e6 Merge remote-tracking branch 'upstream/release_21.01' into dev 2021-03-16 11:25:32 -04:00
Sergey Golitsynskiy 72c3cee00e Update wording 2021-03-15 12:10:54 -04:00
mvdbeek 6ce5b63275 Add release testing credits to template 2021-03-15 15:22:42 +01:00
mvdbeek 75b641b89c Tweak release issue template 2021-03-10 18:36:48 +01:00
mvdbeek 09de447b6d Skip PRs that are already in the release notes 
When updating the (already edited) release notes during the PR process
it is a major pain which PRs are really new. This makes that much
easier. Just be sure to keep the anchors (`.. bug`, `.. enhancement`) in until we are ready to
publish the release
 2021-03-10 16:55:42 +01:00
Dannon Baker 00270ace03 Drop CLIENT_DEV_SERVER from webserver internals completely (we just proxy instead) 2021-03-05 09:52:02 -05:00
John Chilton 53e1bc466e Some more progress on 21.01 release notes. 2021-02-16 16:42:26 -05:00
John Chilton e3dedd86bc Performance metrics for tests. 2021-02-12 20:44:05 -05:00
Sergey Golitsynskiy 66d2d4b40e Fix printing non-dict output 2021-02-02 16:04:44 -05:00
mvdbeek 7276e4af0c Drop scripts/fapi.py 2021-01-29 17:17:46 +01:00
Marius van den Beek f02040272e Merge pull request #11194 from ic4f/dev_api_script_fix_bug 
Fix bug: code expects dictionary, but value can be string
 2021-01-22 11:16:16 +01:00
Sergey Golitsynskiy 211b5d599e Fix bug: i can be str, not dict 
Example cause: api/datatypes endpoint returns a list of strings
 2021-01-21 22:09:30 -05:00
Nicola Soranzo 70def633f1 Replace pipenv with poetry. Update all dependencies 2021-01-21 20:30:00 +00:00
Nicola Soranzo d26b3d9848 Fix all E203, E741 and W504 flake8 errors 2021-01-18 10:35:41 +00:00
John Chilton 3a9596a66f Cleanup galaxy_test.base.api_util. 
- Rename get_master_api_key to get_admin_api_key - less offesnive and more accurate since it doesn't need to be the bootstrap key.
- Add types and cleanup docstrings.
 2021-01-16 20:11:39 -05:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +00:00
John Chilton fa685e4fd0 uvicorn-compatible factory function for fastapi. 2021-01-13 11:34:19 -05:00
Nicola Soranzo e225de9b00 Merge pull request #11103 from jmchilton/more_docs_stuff_3 2021-01-12 17:58:24 +00:00
John Chilton ee3280ad52 Mark pre-annoucnement page as orphan. 
I guess I always imagined we would link these but then I was told we shouldn't - so I don't even know why we're generating them to be honest then.
 2021-01-12 09:29:55 -05:00
mvdbeek e93627a435 Lint fixes, prompt for sqlalchemy_schemadisplay install 2021-01-12 08:23:10 -05:00