galaxy

api

Fix new E721 errors from ruff 0.0.290

2023-09-20 01:43:40 +01:00

auth

Apply black formatting.

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

cleanup_datasets

Fix SA2.0 error: joinedload does not take str args

2024-04-02 10:08:53 -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 B018 errors reported by flake8-bugbear 23.12.2

2023-12-11 21:00:54 +00:00

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

…

apply_tags.py

Enable flake8-comprehensions ruff rules

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

bootstrap_test_shed.py

Fixes...

2023-09-27 14:30:42 -04:00

build_toolbox.py

Apply black formatting.

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

celery_shell.py

Update to black 2024 stable style

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

check_eggs.py

Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run

2015-11-06 11:06:11 -05:00

check_model.py

Update to black 2024 stable style

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

check_python.py

Python 3.8 as new minimum version

2023-11-26 18:34:09 +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

Python 3.8 as new minimum version

2023-11-26 18:34:09 +00:00

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

cwl conformance tests: use id field, not label

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

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

Update to black 2024 stable style

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

dump_openapi_schema.py

Drop unused code from dump_openapi_schema.py

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

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

Update to black 2024 stable style

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

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

Enable flake8-comprehensions ruff rules

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

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

Replace file_name property with get_file_name function

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

maintenance.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00

manage_db.py

Update to black 2024 stable style

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

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

Add the script I used to create security patches

2016-02-24 16:54:30 -05:00

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

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

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

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

Accept any number of arguments to the secret decoder ring

2023-12-14 13:07:37 -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

Enable flake8-comprehensions ruff rules

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

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

Adjust update_cwl_conformance_tests.sh for removed branch

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

update_shed_config_path.py

Add future=True flag to SA engine

2023-12-12 09:54:08 -05:00

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