Nicola Soranzo 5fe5b53bf3 Fix new ruff 0.11.0 errors ...

Also:
- Add and fix type annotations
- Fix call of `object_store_allows_id_selection()` method

2025-03-15 17:12:02 +00:00

..

api

Fix new ruff 0.11.0 errors

2025-03-15 17:12:02 +00:00

auth

…

cleanup_datasets

Fix new ruff 0.11.0 errors

2025-03-15 17:12:02 +00:00

grt

Type annotation improvements

2025-02-21 15:46:14 +00:00

loc_files

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

metagenomics

Fix UP031 errors

2024-11-24 21:35:23 +00:00

microbes

Fix new ruff 0.11.0 errors

2025-03-15 17:12:02 +00:00

objectstore

…

slideshow

…

taxonomy

…

tool_shed

Type annotation improvements

2025-02-21 15:46:14 +00:00

tools

Fix UP031 errors

2024-11-24 21:35:23 +00:00

__init__.py

…

apply_tags.py

Format code with black 25.1.0

2025-02-16 18:07:51 +00:00

bootstrap_test_shed.py

Allow bootstrap_test_shed to bypass errors in tool shed 1.0 API.

2025-03-03 20:39:27 -05:00

build_toolbox.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

celery_shell.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

check_and_update_purged_on_duplicated_uuid.py

Add migration that makes dataset uuid unique

2024-09-20 10:40:12 +02:00

check_eggs.py

…

check_model.py

Remove future, autocommit args from session and engine creation

2024-04-05 13:54:39 -04:00

check_python.py

Drop support for Python 3.8

2025-02-25 19:20:46 +00:00

common_startup_functions.sh

activate the conda env before the python venv

2023-07-21 00:58:35 +01:00

common_startup.sh

Drop support for Python 3.8

2025-02-25 19:20:46 +00:00

config_parse.py

…

config_sample_to_kwalify.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

cwl_conformance_to_test_cases.py

cwl conformance tests: use id field, not label

2023-09-07 13:14:03 +02:00

db_dev.py

…

db_dev.sh

…

db_shell.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

db.py

…

drmaa_external_killer.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

drmaa_external_runner.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

dump_library_paths.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

dump_openapi_schema.py

Drop unused code from dump_openapi_schema.py

2024-01-10 17:43:30 +01:00

edam_mapping.py

Create wrapper for requests with default user agent

2024-04-16 17:54:29 +02:00

external_chown_script.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

extract_dataset_part.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

extract_toolbox_sections.py

…

fetch_eggs.py

…

fix_dm_versions.py

Enable flake8-comprehensions ruff rules

2024-03-09 19:11:20 +00:00

galaxy_main.py

Format code with black 25.1.0

2025-02-16 18:07:51 +00:00

galaxy_schemadisp.py

…

galaxy-main

…

helper.py

Replace file_name property with get_file_name function

2023-11-08 17:17:14 -05:00

maintenance.sh

…

manage_db.py

Remove legacy ref to sqlalchemy migrate

2024-05-22 14:57:53 -04:00

manage_tool_dependencies.py

…

mypy_config_utils.py

…

pages_identifier_conversion.py

Remove transaction helper from scripts

2025-01-23 11:39:25 -05:00

patch.sh

…

plugin_staging.py

…

release-diff.py

…

release.sh

Maybe change the initial 1.dev0 version to 0.dev0 ?

2024-02-13 17:06:21 +01:00

resumable_upload.py

Revert some requests import changes

2024-05-23 15:55:56 +01:00

rst2html.py

Enable flake8-implicit-str-concat ruff rules

2024-04-29 13:37:54 +01:00

run_alembic.py

…

run_alembic.sh

…

runtime_stats.py

Fix UP031 errors

2024-11-24 21:35:23 +00:00

secret_decoder_ring.py

Accept any number of arguments to the secret decoder ring

2023-12-14 13:07:37 -05:00

set_dataset_sizes.py

Type annotation improvements

2025-02-21 15:46:14 +00:00

set_user_disk_usage.py

Type annotation improvements

2025-02-21 15:46:14 +00:00

summarize_timings.py

…

tests_markdown_compare.tpl

…

tests_markdown.py

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

tests_markdown.tpl

…

toolshed_db.py

…

update_cwl_conformance_tests.sh

Adjust update_cwl_conformance_tests.sh for removed branch

2024-04-05 13:49:31 +02:00

update_shed_config_path.py

Remove transaction helper from scripts

2025-01-23 11:39:25 -05:00

validate_tools.sh

…

validate_tours.sh

…