mvdbeek 63eb3d9994 Stage only tracked package files in release commits ...

An untracked packages/uv.lock left over from before the root uv workspace was committed into the 26.2.rc1 version bump.

2026-10-14 10:52:25 +02:00

..

api

Apply 2026 black style

2026-01-20 10:25:45 +00:00

auth

…

cleanup_datasets

remove the OIDC link to users as well, when users are purged

2026-09-01 21:07:42 +02:00

grt

Apply 2026 black style

2026-01-20 10:25:45 +00:00

loc_files

Apply 2026 black style

2026-01-20 10:25:45 +00:00

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

Migrate 3 scripts from psycopg2 to SQLAlchemy

2026-03-25 20:18:39 +00:00

taxonomy

…

tool_shed

Fix repo metadata persistence in fix_tool_config_paths.py

2026-03-09 15:09:45 +01:00

tool_source

source store: ship the populator as a galaxy-app console script

2026-07-14 19:05:51 +02:00

tools

Apply 2026 black style

2026-01-20 10:25:45 +00:00

__init__.py

…

apply_tags.py

Code cleanups from pyupgrade

2025-07-31 11:17:22 +01:00

bootstrap_test_shed.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

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

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

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

2026-06-25 15:12:05 +01:00

common_startup_functions.sh

Resolve conditional dependencies from tool_shed.yml for the Tool Shed

2026-07-30 12:45:42 +02:00

common_startup.sh

Merge branch 'release_26.1' into dev

2026-08-11 16:17:23 -04:00

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

Apply 2026 black style

2026-01-20 10:25:45 +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

…

db_shell.py

Fix new UP031 errors from ruff 0.4.2

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

db.py

Edit db wrapper scripts for consistency, add TS script

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

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

Apply 2026 black style

2026-01-20 10:25:45 +00:00

extract_dataset_part.py

Update to black 2024 stable style

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

extract_tool_sections_from_api.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

extract_toolbox_sections.py

…

fetch_eggs.py

…

fix_dm_versions.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

galaxy_main.py

Apply 2026 black style

2026-01-20 10:25:45 +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

…

markdown_directives_doc.py

Type markdown_directives_doc.py

2026-09-30 10:58:00 -04:00

mypy_config_utils.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

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

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

release.sh

Stage only tracked package files in release commits

2026-10-14 10:52:25 +02:00

reorganize_tool_data.py

Run make format

2025-05-09 10:53:43 +02:00

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

Migrate 3 scripts from psycopg2 to SQLAlchemy

2026-03-25 20:18:39 +00:00

secret_decoder_ring.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

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

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_ieee_2791_schemas.py

Add script to refresh vendored IEEE-2791 schemas

2026-09-02 14:40:03 +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

…