John Chilton
0f2d862fb9
Typing for model discovery module.
2022-01-05 16:34:12 -05:00
mvdbeek
6794d6be93
Resolve circular dependency for ToolEvaluator
...
by placing ComputeEnvironment and ActionBox under job_execution.
2021-11-29 11:22:42 +01:00
Michael R. Crusoe
7819fdc7a6
tighten type ignores
2021-11-23 13:12:07 +01:00
Michael R. Crusoe
cc3ece8ddc
No more changes needed to check_untyped_defs of galaxy.managers.workflows
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
e0fb5d3fac
improve typing of lib/galaxy/managers/tools.py.
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
3e755917fd
improve typing of lib/galaxy/managers/collections.py.
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
2eb4afb59c
improve typing of lib/galaxy/managers/collections_util.py.
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
ee6b5aa1d8
improve typing of lib/galaxy/tools/__init__.py
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
6921c9cc05
improve typing of lib/galaxy/tools/actions/__init__.py
2021-11-15 11:37:15 +01:00
Michael R. Crusoe
ee6eeb6fe6
improve typing of lib/galaxy/tools/evaluation.py
2021-11-15 11:37:14 +01:00
Michael R. Crusoe
069c604aa8
improve typing of lib/galaxy/tools/execute.py
2021-11-15 11:37:14 +01:00
Michael R. Crusoe
960a5a6f54
improve typing of lib/galaxy/tools/parameters/basic.py
2021-11-15 11:37:14 +01:00
Michael R. Crusoe
a4926ee16c
improve typing of lib/galaxy/tools/parameters/grouping.py
2021-11-15 11:37:14 +01:00
Michael R. Crusoe
6220748f6a
improve type hints for lib/galaxy/config/__init__.py.
2021-11-12 19:00:35 +01:00
Michael R. Crusoe
c13eb3a771
improve type hints for lib/galaxy/datatypes/data.py.
2021-11-12 19:00:34 +01:00
Michael R. Crusoe
36c2e33ed9
improve type hints for test/integration/test_upload_configuration_options.py.
2021-11-12 19:00:33 +01:00
Michael R. Crusoe
ac28ab90f2
improve type hints for lib/galaxy/tool_util/cwl/parser.py.
2021-11-12 19:00:32 +01:00
Michael R. Crusoe
76029697d3
improve type hints for lib/galaxy/tool_util/cwl/util.py.
2021-11-12 19:00:31 +01:00
Michael R. Crusoe
bfa60a039d
improve typing of lib/galaxy/tools/wrappers.py
2021-11-11 12:09:00 +01:00
Michael R. Crusoe
1c171e4463
improve typing of lib/galaxy/util/compression_utils.py
2021-11-11 11:55:06 +01:00
Michael R. Crusoe
0f185683b7
improve typing of lib/galaxy/workflow/modules.py
2021-11-11 11:55:05 +01:00
Michael R. Crusoe
03e796a94c
improve typing of lib/galaxy/workflow/run.py
...
lib/galaxy/workflow/run.py:333: error: Item "DatasetCollection" of "Union[HistoryDatasetCollectionAssociation, DatasetCollection]" has no attribute "collection"
2021-11-11 11:55:05 +01:00
Michael R. Crusoe
c30437d576
improve typing of lib/galaxy/workflow/run_request.py
2021-11-11 11:55:04 +01:00
Nicola Soranzo
7b1eb02aa3
Show error codes when running mypy
...
E.g. this error:
```
lib/galaxy/tool_util/cwl/schema.py:38: error: "LoadingContext" has no attribute "relax_path_checks"
```
becomes
```
lib/galaxy/tool_util/cwl/schema.py:38: error: "LoadingContext" has no attribute "relax_path_checks" [attr-defined]
```
making it easier to Google for solutions or to add a
`# type: ignore[error-code]` comment.
2021-11-10 10:53:31 +01:00
John Chilton
8643daf1dd
Attempt to type more upload related things.
2021-11-05 11:58:53 -04:00
John Chilton
ee6242ccad
Type fixes for markdown_parse.
2021-11-05 11:58:53 -04:00
Marius van den Beek
7856c4d784
Merge pull request #12813 from jmchilton/pdf_cleanup_2
...
Fixes and test for PDF generation.
2021-10-30 09:03:35 +02:00
John Chilton
f5670ec1cd
Cleanup/refactor markdown_util ahead of async task based version.
2021-10-29 15:10:26 -04:00
John Chilton
2a9b0dcbe5
Improved typing of histories.
2021-10-29 12:05:27 -04:00
John Chilton
5310960e8a
Types fixes for jobs manager.
2021-10-29 12:05:27 -04:00
Björn Grüning
a666631e81
Merge pull request #12801 from jmchilton/type_fixes_managers_4
...
More type fixes for various pieces of managers code.
2021-10-28 21:40:52 +02:00
John Chilton
e9db538fc1
Remove unused manager containers code.
2021-10-27 13:41:58 -04:00
John Chilton
c3ea408eeb
Define protocol for serializers - mypy check all the serialiers in manager layer.
2021-10-27 13:41:42 -04:00
John Chilton
74a6d15913
Enable stricter type checking of galaxy.model.tags.
2021-10-27 13:34:31 -04:00
John Chilton
ba9d51ccff
Progress toward a stronger typed manager layer.
...
ModelManager still needs to use generics to really start providing a lot of benefit.
2021-10-27 13:34:17 -04:00
John Chilton
ad7933d926
Type fixes for genome data providers.
2021-10-26 10:27:58 -04:00
John Chilton
3332f4f328
type fixes for phyloviz data provider code
2021-10-26 10:27:58 -04:00
John Chilton
6b334d92fa
Type checking in visualization plugins resource parser.
...
Remove some unused code based on what would definitely cause bugs.
2021-10-26 10:27:58 -04:00
John Chilton
51d9e9ea42
Type fixes for data provider registry.
2021-10-26 10:27:58 -04:00
John Chilton
74d1eb45d6
Typing fixes for vis plugin parser.
2021-10-26 10:27:58 -04:00
John Chilton
203421dc7f
Typing for phyloviz baseparser.
2021-10-26 10:27:58 -04:00
John Chilton
1d8a2bd22f
Type clarifications visualization.genome.
2021-10-26 10:27:58 -04:00
John Chilton
5ed68074ff
Add types for galaxy.visualizations.plugins.plugin.
2021-10-26 10:27:58 -04:00
John Chilton
d8fc9b3ab4
Fixes for LDDA manager - clearly that didn't work at all.
2021-10-25 20:24:01 -04:00
John Chilton
00c30ca493
Strong typing around HDAs manager.
2021-10-25 20:24:01 -04:00
John Chilton
a6c46f9bfc
Typing clarification for datasets manager.
2021-10-25 11:51:40 -04:00
John Chilton
edd15d1d5e
Typing fixes for galaxy.exceptions.
2021-10-25 11:51:40 -04:00
John Chilton
78da479dea
typing fixes for integration testing framework stuff...
...
I wonder if there is a better way to model mixins - seems heavy to annotate everything we need from the derived class.
2021-10-14 00:51:59 -04:00
John Chilton
8412cb53b0
Type and bug fixes for api/extended_metadata.py.
2021-10-14 00:51:59 -04:00
John Chilton
14fb067c4e
Fix bug and typing in library_datasets.py
2021-10-14 00:51:10 -04:00
John Chilton