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Author SHA1 Message Date
Marius van den Beek e5ffb06772 Merge pull request #10988 from jmchilton/workflow_lint 
UI & API for Supporting Best Practice Workflows
 2020-12-30 10:13:21 +01:00
John Chilton f2f12e0966 Refactor action extract_legacy_parameter should work on parameters defined only in rename PJA also. 2020-12-29 22:00:32 -05:00
John Chilton fc2ce45767 API for structured workflow refactoring. 2020-12-29 22:00:32 -05:00
John Chilton 8afe895f5e Use text step parameters as replacement_params in PJA (replacement_dict). 2020-12-29 22:00:32 -05:00
John Chilton 39b9e19ca9 UI for linting workflows for best practices. 2020-12-29 22:00:32 -05:00
John Chilton 1d93a1aa1c More structured workflow parameter parsing in editor client. 2020-12-29 21:45:08 -05:00
John Chilton 64ca9210dc If a workflow defines explicit workflow_outputs, respect those. 
Currently the editor just makes everything an output that isn't hidden.

Without this change, I don't see a way to have non-hidden outputs to tool steps that are not workflow outputs.
 2020-12-29 21:45:08 -05:00
Björn Grüning 989b3a0a32 Merge pull request #11009 from jmchilton/mypy_more_packages 
mypy type checking for more Galaxy packages
 2020-12-30 00:35:45 +01:00
Björn Grüning 2f580de203 Merge pull request #11001 from jmchilton/editor_unify 
Simplify workflow editor metadata handling.
 2020-12-29 21:16:17 +01:00
Björn Grüning cf5ee5aed0 Merge pull request #11007 from jmchilton/mypy_galaxy_data 
Type checking fixes for galaxy-data (datatypes and models).
 2020-12-29 21:11:29 +01:00
John Chilton ef3c3d2dbf Revert some typing stuff in galaxy.web_stack.message. 
Prevented json decoding of these dict objects.
 2020-12-29 09:22:02 -05:00
John Chilton 055759a19f mypy fixes for galaxy-webapps 2020-12-29 00:52:29 -05:00
John Chilton 04b1e0a785 Mypy type checking for galaxy-web-apps. 2020-12-29 00:29:51 -05:00
John Chilton 51f8a6f16b mypy typing checking for galaxy-web-framework 2020-12-28 23:55:00 -05:00
John Chilton d3b2f71bbd mypy typing for galaxy-web-stack. 2020-12-28 23:41:44 -05:00
John Chilton be3f17a3ac mypy type checking for auth 2020-12-28 23:41:27 -05:00
John Chilton 0397ccdd12 Typing checking for galaxy-job-execution. 2020-12-28 23:24:06 -05:00
John Chilton a7b6f08446 Type checking fixes for galaxy-data (datatypes and models). 2020-12-28 16:43:14 -05:00
Björn Grüning 4ba40970d2 Merge pull request #11003 from bgruening/more_mutable_fixes 
More mutable fixes
 2020-12-28 18:32:51 +01:00
Björn GrüningandNicola Soranzo 19c7279ad1 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2020-12-28 17:08:24 +01:00
Bjoern Gruening aabde1baa3 remove unused enumerate and replace getattr() by accessing the property directly 2020-12-28 14:33:34 +01:00
Bjoern Gruening f0a28e0daf mutable argument fixes, remove some unused enumerate usage 2020-12-28 14:31:16 +01:00
Bjoern Gruening 2a1aad9f93 more mutable argument fixes 2020-12-28 14:28:30 +01:00
Marius van den Beek e04035a825 Merge pull request #11000 from jmchilton/more_types_0 
Check Python typing for galaxy-containers and galaxy-tool-util during CI.
 2020-12-28 07:49:59 +01:00
Marius van den Beek c3c6fb3511 Merge pull request #10999 from jmchilton/editor_save 
Only enable the workflow save button if it has changes.
 2020-12-28 07:42:55 +01:00
John Chilton c9c786362b Eliminate extra workflow version creation. 2020-12-28 00:50:44 -05:00
John Chilton b2ee7ea995 Simplify updating license/creator. 2020-12-28 00:50:44 -05:00
John Chilton 68f005e3ba Rework renaming in the workflow editor to unify things into Index.vue 2020-12-28 00:50:44 -05:00
John Chilton 001dfb4218 Rework annotation handling in the workflow editor. 2020-12-28 00:46:40 -05:00
John Chilton 6a6f2b181e Only enable the workflow save button if it has changes. 
It makes this check internally anyway before firing the request. I think it is helpful to understand if there are outstanding changes as well.

Also add a unit test for Workflow/Editor/Options.vue and add selectors to allow writing cleaner integration tests/tours.
 2020-12-28 00:46:40 -05:00
Björn Grüning 64e7b0ffc4 Merge pull request #10995 from jmchilton/dataset_storage_cleanup 
Test case and cleanup for DatasetStorage.vue.
 2020-12-27 23:00:42 +01:00
John Chilton 976197115b mypy containers and tool-util packages 2020-12-27 15:50:51 -05:00
John Chilton f96543b58c Type annotations and fixes to get galaxy-tool-util to lint. 2020-12-27 15:50:51 -05:00
John Chilton 9690bf9c1b Type annotations to get galaxy-containers to lint. 2020-12-27 14:04:06 -05:00
John Chilton a8664a0ecb Only enable the workflow save button if it has changes. 
It makes this check internally anyway before firing the request. I think it is helpful to understand if there are outstanding changes as well.

Also add a unit test for Workflow/Editor/Options.vue and add selectors to allow writing cleaner integration tests/tours.
 2020-12-27 13:36:05 -05:00
Björn Grüning e3d1295bf6 Merge pull request #10992 from jmchilton/mypy 
Start mypy type checking during CI
 2020-12-27 17:47:48 +01:00
John Chilton aa33f7c058 Merge pull request #10998 from bgruening/mutable_data_arguments 
remove mutatable arguments from function calls
 2020-12-27 10:58:41 -05:00
Bjoern Gruening 911366dcba remove a few mutatable arguments 2020-12-27 13:41:17 +01:00
Björn Grüning 768862be13 Merge pull request #10987 from jmchilton/fix_wf_metadata 
Fixes for license and creator saving and updating.
 2020-12-27 12:26:11 +01:00
Björn Grüning 40343c5d3d Merge pull request #10993 from jmchilton/galaxy_files_imp_exp 
API support for history import/export from/to galaxy.files plugins
 2020-12-27 12:18:31 +01:00
Nicola Soranzo 085fa88fb9 Merge pull request #10996 from bgruening/warn_warning 2020-12-27 03:01:10 +00:00
Björn Grüning 6e4962282e its still called warn in the warning module 2020-12-27 02:42:14 +01:00
Bjoern Gruening 255eb8f0cb convert log.warn to log.warning 2020-12-27 01:50:30 +01:00
Bjoern Gruening 3ec8fa71ce convert log.warn to log.warning 2020-12-27 01:34:08 +01:00
John ChiltonandBjörn Grüning a4938885d9 Apply suggestions from code review 
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
 2020-12-26 19:29:25 -05:00
John Chilton 3e1c0b63c0 Test case and cleanup for DatasetStorage.vue. 2020-12-26 19:27:55 -05:00
John Chilton 492de4a91a Merge pull request #10991 from bgruening/clean_htcondor 
drop migration hack from htcondor
 2020-12-26 13:00:04 -05:00
John Chilton ca5c84e254 Allow history export to galaxy.files plugins. 2020-12-26 08:36:48 -05:00
John Chilton d1d85b0291 Allow history imports from galaxy.files plugins. 2020-12-25 20:04:55 -05:00
John Chilton 80746cd5d9 mypy testing for galaxy-job-metrics 2020-12-25 19:29:43 -05:00