opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
72,292 Commits 69 Branches 243 Tags
4fa0403fedcfc71ebeded76e0a29c2abe6fe0ed0
Commit Graph
47 Commits
Author SHA1 Message Date
John Chilton bbe0ee217b Merge pull request #16959 from jmchilton/typing_fixes_90 
Remove sentry.py from mypy exclusions.
 2023-11-02 11:05:42 -04:00
John Chilton da213af8cf Remove sentry.py from mypy exclusions. 
Seems like typing has been fixed in it?
 2023-11-01 16:18:14 -04:00
Nicola Soranzo 0cd32e59f7 Fix `exclude` regexp in mypy configuration 
to not exclude the `lib/tool_shed/test/functional/` directory.
 2023-10-24 10:27:22 +01:00
John Chilton 8852f0733b Progress toward exercising less of the tool shed upload API. 
So we can kill it.
 2023-09-26 13:46:56 -04:00
John Chilton d0622fce7b Remove metadata_generator from mypy exclusions... 2023-09-26 13:46:53 -04:00
John Davis 7ff212c3fc Update mypy.ini 2023-08-09 14:04:40 -04:00
John Chilton b6fcce9ae3 Selenium type fixes and annotations. 2023-06-13 17:00:09 -04:00
Nicola Soranzo c07ce72c51 Fix new errors reported by mypy 1.1.1 2023-03-29 08:55:52 +01:00
Nicola Soranzo 08e60ebdee Move mypy option from command invocation to mypy.ini 2023-03-29 08:55:51 +01:00
Nicola Soranzo 443ee27b58 Enable `strict_equality` mypy option 
Also fix the following mypy error:

```
lib/galaxy/util/path/__init__.py:247: error: Non-overlapping equality check (left operand type: "struct_passwd", right operand type: "str")  [comparison-overlap]
            or (file_owner == username and owner_permissions >= 4)
```
 2023-03-15 17:01:02 +00:00
Nicola Soranzo 85a92be30a Merge pull request #15177 from jmchilton/fixup_refactoring_types 
Fixup types surrounding workflow refactoring testing.
 2022-12-13 10:48:41 +00:00
John Chilton 350899bdca Fix up security for galaxy.tool_util.verify.asserts 2022-12-12 14:18:36 -05:00
John Chilton 2f46f05d48 Typing galaxy.security. 2022-12-12 14:18:28 -05:00
John Chilton 0180bf67a1 Fixup types surrounding workflow refactoring testing. 2022-12-12 10:18:20 -05:00
Alireza Heidari 3591576149 replace published history test name in mypy.ini 
`test_published_histories_grid` to `test_histories_published`
 2022-12-01 10:58:55 +01:00
John Davis 99cc5adee5 Do not type-check workflow unit test test_refactor_ models 2022-11-29 14:59:17 -05:00
John Davis 4c96135b6c Fix reexport error (selenium) by direct import 2022-11-29 14:59:17 -05:00
John Davis ec0cdc718a Fix implicit reexport error for selenium 
lib/galaxy/selenium/smart_components.py:1: error: Module "selenium.webdriver.support.ui" does not explicitly export attribute "Select"; implicit reexport disabled  [attr-defined]
    from selenium.webdriver.support.ui import Select
    ^
lib/galaxy/selenium/sizzle.py:6: error: Module "selenium.webdriver.support.ui" does not explicitly export attribute "WebDriverWait"; implicit reexport disabled  [attr-defined]
    from selenium.webdriver.support.ui import WebDriverWait
 2022-11-29 14:59:17 -05:00
Michael R. Crusoe 2e69f64496 mypy 0.991 + bonus extra typing 2022-11-28 04:50:00 +00:00
Nicola Soranzo d165c380fa Add type annotations to `config_manage.py` 
And some code cleanups.
 2022-10-24 15:32:35 +01:00
Marius van den Beek 52c13b458a Merge pull request #14824 from jmchilton/tool_repo_cache 
Move ToolShedRepositoryCache into galaxy.tool_shed.
 2022-10-24 15:44:41 +02:00
John Chilton c638757db9 Refactor ToolShedRepositoryCache into galaxy.tool_shed.cache 
Things required to perform tool shed installs should be galaxy.tool_shed - this module doesn't require anything in galaxy-app - galaxy-data is sufficient.
 2022-10-20 11:15:50 -04:00
John Chilton 2bf10821c0 Move base tool data infrastructure into tool_util package. 
Keep the refgenie stuff in Galaxy's app package because it brings in additional dependencies.

This is a small part of a larger ongoing project to cleanup tool shed dependencies and allow tool shed repository installations with minimal dependencies.
 2022-10-19 13:49:00 -04:00
John Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. 
Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.
 2022-10-16 09:56:58 +02:00
John Chilton 156977f65a Merge pull request #14691 from jmchilton/tool_util_testing_3 
More typing and unit testing for tool test verification functions
 2022-09-24 08:41:04 -04:00
John Chilton 42134f4c82 Typing improvements for galaxy.tool_util.verify and related code. 2022-09-23 09:06:15 -04:00
John Chilton 5751a0535c A lot more typing for tool shed install and relevant utility code. 2022-09-22 17:50:44 -04:00
John Chilton 797db736fe Remove typing exceptions for tool shed tests. 
The testing seems fixed.
 2022-09-20 18:25:47 -04:00
John Chilton 678d702fbd Remove unused mypy entry. 2022-09-20 18:25:47 -04:00
John Chilton 49c990a53b Typing for tool shed registry. 2022-09-16 13:03:39 -04:00
John Chilton e1daab1768 Merge pull request #14629 from jmchilton/toolbox_typing 
Type annotations for base toolbox functionality.
 2022-09-16 09:22:33 -04:00
John Chilton cf298957e3 Toolbox typing. 2022-09-15 21:14:04 -04:00
John Chilton b0a230b8f0 Script for finding unused mypy.ini entries. 2022-09-15 13:20:04 -04:00
John Chilton c32e736f85 Restructure mypy.ini to distinguish between "good" exclusions and "bad" ones. 2022-09-15 12:29:14 -04:00
John Chilton 506921c2d8 Remove mypy exceptions for deleted files. 2022-09-13 17:41:22 -04:00
Matej Troják 7d1807fc1e Merge branch 'dev' into sybila-tools-datatypes 2022-08-31 12:07:18 +01:00
John Chilton bd9c8314ed Stronger type checking for provided_metadata. 2022-08-25 12:26:18 -04:00
John Chilton df7fcb0283 Fix typing issue in galaxy.tool_util.client.staging. 2022-08-25 12:26:18 -04:00
John Chilton 960c9cde48 Improved type checking for galaxy.selenium.context. 2022-08-25 12:26:18 -04:00
John Chilton adeb9e7b84 Drop deleted file from mypy.ini... 2022-08-25 12:26:18 -04:00
John Chilton 02e3f0be2b Improved typing for galaxy.util.permutations. 2022-08-25 12:26:18 -04:00
John Chilton ff80452421 Strong typing for galaxy.util.properties. 2022-08-24 17:37:08 -04:00
Matej Trojak e5fcef62b7 Added Storm and BCSL tests to mypy typing exception list 2022-07-28 21:18:23 -05:00
Michael R. Crusoe 8e05b6da24 improve typing 
make: add remove-unused-imports target to clean up code
 2022-07-26 23:28:41 +01:00
Evan Bolyen 66422e3d34 mypy: skip datatype tests for qiime2 2022-07-05 09:43:30 -07:00
Nicola Soranzo 3bca59b8e9 Remove uses of six library 
Remove unused file `tools/data_source/hbvar_filter.py` .
 2022-06-10 10:32:00 +01:00
Nicola Soranzo e9b2262dd3 Move mypy configuration to `mypy.ini` 
So packages can use `setup.cfg` to replace `setup.py` .
 2022-06-08 10:35:18 +01:00