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Author SHA1 Message Date
John Chilton 0f9dbb4045 Remove more datatype legacy handling code. 2022-09-14 11:51:39 -04:00
John Chilton 3b1331de51 Remove code and config option related to loading shed datatypes. 2022-09-14 11:51:38 -04:00
Marius van den Beek 2ee253cbbd Merge pull request #14612 from jmchilton/ts_unused_1 
Remove unused tool shed functions.
 2022-09-14 10:32:28 +02:00
Nicola Soranzo f3912e9135 Merge pull request #14613 from jmchilton/unused_mypy_exceptions 
Remove mypy exceptions for deleted files.
 2022-09-14 01:12:36 +01:00
Aysam Guerler 4f6fa6a18f Merge pull request #14608 from dannon/multipanel-cleanup 
Multipanel cleanup, remove dead code
 2022-09-13 19:50:57 -04:00
John Chilton d99c6f8a73 Run linting in Github actions when mypy config is updated. 2022-09-13 18:55:44 -04:00
John Chilton 506921c2d8 Remove mypy exceptions for deleted files. 2022-09-13 17:41:22 -04:00
John Chilton 3fe2674aa1 Remove unused function in shed common_util - get_tool_dependencies. 2022-09-13 17:31:33 -04:00
John Chilton 6d1e86ea48 Remove unused function in shed common_util - get_non_shed_tool_panel_configs. 2022-09-13 17:31:33 -04:00
John Chilton 7caef14a23 Remove unused function from tool shed common_util. 2022-09-13 17:31:23 -04:00
Dannon c1008f5228 Merge pull request #14587 from ElectronicBlueberry/tag-colors 
Use hsluv to generate colors instead of hsl
 2022-09-13 14:34:34 -04:00
Dannon Baker d18504fb83 Unused import 2022-09-13 13:33:33 -04:00
Dannon Baker b3f8fd84c6 TODO: Track down side effect in HistoryViewEdit... 2022-09-13 12:55:47 -04:00
Dannon Baker 1b446979c2 Attr order linting 2022-09-13 11:38:20 -04:00
Dannon Baker 1fe0adb278 Eslint disable for unused jquery in bundleEntries, since it's now not directly used. 2022-09-13 11:37:20 -04:00
Dannon Baker 3849850739 Drop old history multi-panel 2022-09-13 11:19:40 -04:00
Nicola Soranzo fcfaede15b Merge branch 'release_22.05' into dev 2022-09-13 13:46:02 +01:00
Nicola Soranzo 463779b1b5 Merge branch 'release_22.01' into release_22.05 2022-09-13 12:28:05 +01:00
Laila Los b905aae838 add bright yellow tones 
remove contrasting color
 2022-09-13 13:15:40 +02:00
Nicola Soranzo 7b870dce88 Merge pull request #14607 from nsoranzo/release_22.01_pin_CacheControl 
[22.01] Pin CacheControl to prevent missing dependency
 2022-09-13 12:07:02 +01:00
Laila Los e4c5e56143 use hsluv to generate colors instead of hsl 2022-09-13 12:17:03 +02:00
Nicola Soranzo 77553d1711 Pin CacheControl to prevent missing dependency 
schema-salad currently requires:
- "CacheControl >= 0.11.7, < 0.13"
- "lockfile >= 0.9", which is needed for CacheControl's FileCache until 0.12.11

but CacheControl 0.12.12 replaced lockfile with filelock.

Prevent the following traceback:

```
self = <cachecontrol.caches.file_cache.FileCache object at 0x7fe36ac5d190>
directory = PosixPath('/tmp/.cache/salad'), forever = False, filemode = 384
dirmode = 448, lock_class = None

    def __init__(
        self,
        directory,
        forever=False,
        filemode=0o0600,
        dirmode=0o0700,
        lock_class=None,
    ):

        try:
            if lock_class is None:
>               from filelock import FileLock
E               ModuleNotFoundError: No module named 'filelock'

/tmp/gxpkgtestenvcy0lxY/lib/python3.7/site-packages/cachecontrol/caches/file_cache.py:74: ModuleNotFoundError
```
 2022-09-12 21:57:43 +01:00
Dannon 29f1de220d Merge pull request #14543 from assuntad23/13190/bug/editing-preexisting-rule-in-RBU 
Allow changing type of regex rule in RBU
 2022-09-12 15:28:53 -04:00
John Chilton 42364892ac Merge pull request #14604 from bernt-matthias/topic/lint-duplicate-inputs 
linter: check for inputs with duplicated names
 2022-09-12 15:24:01 -04:00
Nicola Soranzo 36ce5bbfe7 Merge branch 'release_22.05' into dev 2022-09-12 20:17:02 +01:00
Dannon d7fdf0ddc2 Merge pull request #14576 from jmchilton/compute_dataset_hash 
Implement API endpoint for calculating dataset hashes asynchronously
 2022-09-12 11:55:46 -04:00
John Chilton e60280230e Merge pull request #14582 from jmchilton/tool_data_table_tests 
Unit tests and type fixes for tool data tables code.
 2022-09-12 10:37:42 -04:00
John Chilton 3a643433c5 Merge pull request #14598 from jmchilton/path_typing 
Some additional typing for galaxy.util.path.
 2022-09-12 10:35:35 -04:00
Matthias Bernt 3ff56e1276 fix typing issue 2022-09-12 16:25:58 +02:00
David López 4d14bb4ae7 Merge pull request #14603 from nsoranzo/release_22.05_backport_14283 
[22.05] Backport #14283
 2022-09-12 15:52:21 +02:00
Matthias Bernt ec04666cc1 linter: check for inputs with duplicated names 
and outputs
 2022-09-12 15:23:50 +02:00
Helena 53a88b900a Update robots.txt 2022-09-12 12:55:34 +01:00
Bjoern Gruening 32fdbfa8d7 fix linting 2022-09-11 13:05:50 +02:00
Bjoern Gruening 84a21b29f2 fix bad merge 2022-09-11 12:22:00 +02:00
Björn Grüning 764ac42e5f fix spelling of testcase 2022-09-11 02:16:35 +02:00
Björn Grüning 2db5af6890 Merge pull request #14535 from dannon/panel-cleanup 
Panel init template cleanup
 2022-09-10 20:53:18 +02:00
Björn Grüning 2168933d7c fix PathLike annotation 2022-09-10 20:12:54 +02:00
Björn Grüning 78960c6fc6 Merge pull request #14553 from jmchilton/more_ts_api_tests 
More API tests for the tool shed.
 2022-09-10 20:01:15 +02:00
Björn Grüning 6fb1e24898 Merge pull request #13985 from itisAliRH/new-history-multiple-view 
New history multiple view
 2022-09-10 19:20:19 +02:00
Nicola Soranzo cb7c0d46d3 Merge pull request #14599 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2022-09-10 11:17:37 +01:00
galaxybot 1c4dfd85d4 Update Python dependencies 2022-09-10 03:57:44 +00:00
John Chilton d31c9ac5dd Some typing for galaxy.util.path... 2022-09-09 18:52:14 -04:00
Nicola Soranzo e08deef224 Merge pull request #14592 from nsoranzo/misc_fixes_202209 
Misc fixes 202209
 2022-09-09 21:34:38 +01:00
Dannon Baker f39f71bde9 Lint fixes 2022-09-09 13:48:03 -04:00
David López 2141078ae8 Merge pull request #14593 from nsoranzo/wheelforge_for_python_deps 
Update docs on adding Python dependencies
 2022-09-09 19:45:17 +02:00
Dannon Baker d7b096803d Avoid creating panelConfig, just use galaxyConfig 2022-09-09 13:44:47 -04:00
Dannon Baker f7c767acd0 No need to create this if we're not calling panel setup... 2022-09-09 13:44:47 -04:00
Dannon Baker 1438658d2c Drop broken panel_init from toolshed/base_panels 2022-09-09 13:44:47 -04:00
Dannon Baker 1fa25b7d6b Drop empty inits from templates. 2022-09-09 13:44:47 -04:00
guerler 51a0b0b3fe Augment promise queue test case 2022-09-09 13:20:34 -04:00