mvdbeek 130d2b078e Update and apply ruff refactorings ...

ruff 0.280.0 has a bug that would turn the imports guarded by `if
TYPE_CHECKING` into their non-string variant, which would break the
runtime. So we can't merge 23.1 into dev without this.

2023-08-09 17:14:07 +02:00

..

api

Update and apply ruff refactorings

2023-08-09 17:14:07 +02:00

auth

Apply black formatting.

2022-02-03 07:42:20 -05:00

cleanup_datasets

Fix select stmts in scripts

2023-07-19 11:05:55 -04:00

grt

Format Python code with black 23.1.0

2023-02-01 23:51:03 +00:00

loc_files

Apply black formatting.

2022-02-03 07:42:20 -05:00

metagenomics

Apply black formatting.

2022-02-03 07:42:20 -05:00

microbes

Fix new B018 errors raised by ruff 0.0.260

2023-04-13 16:53:01 +01:00

objectstore

Apply black formatting.

2022-02-03 07:42:20 -05:00

slideshow

Apply black formatting.

2022-02-03 07:42:20 -05:00

taxonomy

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tool_shed

Fix select stmts in scripts

2023-07-19 11:05:55 -04:00

tools

Apply black formatting.

2022-02-03 07:42:20 -05:00

__init__.py

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apply_tags.py

Fix B023 warnings from flake8-bugbear 22.7.1

2022-07-05 12:28:37 +01:00

build_toolbox.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

celery_shell.py

Fix a typo in celery_shell.py

2022-05-25 19:46:47 +02:00

check_eggs.py

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check_model.py

Update db index testing: test both models, gxy and tsi

2022-03-09 18:41:03 -05:00

check_python.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

common_startup_functions.sh

activate the conda env before the python venv

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

common_startup.sh

Merge branch 'release_23.0' into release_23.1

2023-07-24 15:16:11 +01:00

config_parse.py

Use `load_app_properties()` to load Galaxy config file

2022-04-26 09:48:18 +01:00

config_sample_to_kwalify.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

cwl_conformance_to_test_cases.py

Update lists of non-passing CWL conformance tests

2023-01-17 17:40:11 +00:00

db_dev.py

Add --repair argument to upgrade/downgrade commands on db_dev script

2023-04-26 08:53:35 -04:00

db_dev.sh

Split script into admin and dev

2022-09-28 15:45:00 -04:00

db_shell.py

Disable verbose parso logging in db_shell.py

2023-07-16 09:21:22 +10:00

db.py

Edit db wrapper scripts for consistency, add TS script

2023-02-08 00:33:48 -05:00

drmaa_external_killer.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

drmaa_external_runner.py

remove more leftover references to cluster_files_directory

2022-08-12 16:07:35 +02:00

dump_library_paths.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

dump_openapi_schema.py

Small fixes to YAML export of OpenAPI schema.

2022-12-12 19:44:19 -05:00

edam_mapping.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

external_chown_script.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

extract_dataset_part.py

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2022-02-03 07:42:20 -05:00

extract_toolbox_sections.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

fetch_eggs.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

fix_dm_versions.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

galaxy_main.py

First pass in dropping uwsgi specific things

2022-03-15 21:31:59 +01:00

galaxy_schemadisp.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

galaxy-main

Adjust galaxy-main script so we can import from it for easy app setup

2020-12-22 11:18:00 +01:00

helper.py

Fix SA2.0 syntax, fix bug

2023-07-21 00:12:34 -04:00

maintenance.sh

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manage_db.py

Update inline documentation in scripts

2022-05-31 10:30:30 -04:00

manage_tool_dependencies.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

mypy_config_utils.py

Script for finding unused mypy.ini entries.

2022-09-15 13:20:04 -04:00

pages_identifier_conversion.py

Wrap session.flush in pages_identifier_conversion scripts

2023-06-09 13:05:26 -04:00

patch.sh

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plugin_staging.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

release-diff.py

Write admin announce, add deferred datasets to user announcement

2022-08-19 16:11:41 +02:00

release.sh

Fix release script to be compatible with YY.X dates

2023-04-10 16:51:05 -04:00

resumable_upload.py

Merge branch 'release_22.01' into release_22.05

2022-07-02 18:07:38 +02:00

rst2html.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

run_alembic.py

Add shell wrapper for alembic CLI, improve inline docs

2022-09-30 10:34:58 -04:00

run_alembic.sh

Add shell wrapper for alembic CLI, improve inline docs

2022-09-30 10:34:58 -04:00

runtime_stats.py

Fix UP031 errors reported by ruff

2023-03-29 08:55:54 +01:00

secret_decoder_ring.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

set_dataset_sizes.py

Wrap session.flush in set_dataset_sizes script

2023-06-09 13:05:26 -04:00

set_user_disk_usage.py

Implement quota tracking options per ObjectStore.

2023-02-19 10:33:21 -05:00

summarize_timings.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

tests_markdown_compare.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

tests_markdown.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

tests_markdown.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

toolshed_db.py

Edit db wrapper scripts for consistency, add TS script

2023-02-08 00:33:48 -05:00

update_cwl_conformance_tests.sh

Add CWL conformance API tests

2021-11-23 14:10:21 +00:00

update_shed_config_path.py

Wrap session.flush in update_shed_config_path script

2023-06-09 13:05:26 -04:00

validate_tools.sh

Switch to lxml for xml parsing

2020-05-12 15:00:27 +02:00

validate_tours.sh

Tour validation.

2022-06-02 14:53:55 -04:00