Nicola Soranzo fc7d1dee35 Switch galaxyproject package index to `--extra-index-url` ...

so that `uv pip install` treats it with higher priority:

https://docs.astral.sh/uv/concepts/indexes/#-index-url-and-extra-index-url

Note that `pip` treats all indexes with the same priority:

https://pip.pypa.io/en/stable/cli/pip_install/#finding-packages

Allows uv to install the Python 3.14 wheel of pysam==0.23.3 from
wheels.galaxyproject.org instead of trying to build it from the source
package from PyPI.

2025-12-24 15:15:11 +00:00

..

api

Fix new ruff 0.11.0 errors

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

auth

Apply black formatting.

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

cleanup_datasets

Fix assertion on python version

2025-07-24 21:15:28 -04:00

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

Apply black formatting.

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

slideshow

Apply black formatting.

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

taxonomy

…

tool_shed

Add toolshed metadata fixing script

2025-12-15 12:09:23 +01:00

tools

Fix UP031 errors

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

__init__.py

…

apply_tags.py

Code cleanups from pyupgrade

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

bootstrap_test_shed.py

Code cleanups from pyupgrade

2025-07-31 11:17:22 +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

Add migration that makes dataset uuid unique

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

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

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

Switch galaxyproject package index to `--extra-index-url`

2025-12-24 15:15:11 +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

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

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

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

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

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

Merge release_25.0 into dev

2025-06-16 14:12:30 +02:00

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

Remove legacy ref to sqlalchemy migrate

2024-05-22 14:57:53 -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

Remove transaction helper from scripts

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

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

Shellcheck fixes

2025-10-29 18:45:26 +00:00

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

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

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

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

Fix new UP031 errors from ruff 0.4.2

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

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

Remove transaction helper from scripts

2025-01-23 11:39:25 -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