Nicola Soranzo 62497462e0 Don't always install node in the virtualenv ...

if it's already installed system-wide at the correct version.

Prevent node installation issues during CI builds where we install
node with the setup-node action but it was ignored because it was
not inside the virtualenv, e.g.:

https://github.com/galaxyproject/galaxy/actions/runs/5530959878/jobs/10091018774

2023-07-12 19:26:02 +01:00

..

api

Format Python code with black 23.1.0

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

auth

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cleanup_datasets

Merge branch 'release_22.05' into release_23.0

2023-04-03 16:31:48 +01:00

grt

Format Python code with black 23.1.0

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loc_files

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metagenomics

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microbes

Format Python code with black 23.1.0

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objectstore

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slideshow

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taxonomy

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tool_shed

Combine "as" imports with other "from" imports

2022-06-20 20:06:30 +01:00

tools

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

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

apply_tags.py

Fix B023 warnings from flake8-bugbear 22.7.1

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

bootstrap_history.py

Converge release process auth discovery.

2023-05-30 13:11:27 -04:00

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

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 db index testing: test both models, gxy and tsi

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

check_python.py

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

common_startup_functions.sh

Bump minimum pip version to 20.3 . Ignore `--replace-pip and --no-replace-pip` startup options

2023-01-17 15:01:38 +00:00

common_startup.sh

Don't always install node in the virtualenv

2023-07-12 19:26:02 +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

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

create_toolshed_db.py

Apply black, isort (squashed)

2022-03-09 18:41:49 -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

Remove duplication

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

db_dev.sh

Split script into admin and dev

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

db_shell.py

Drop create_db.sh, create_db.py (see note)

2022-09-28 15:25:43 -04:00

db.py

Remove duplication

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

drmaa_external_killer.py

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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

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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

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

external_chown_script.py

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extract_dataset_part.py

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

extract_toolbox_sections.py

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

fetch_eggs.py

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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

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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

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

maintenance.sh

Fix issues reported by ShellCheck

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

manage_db.py

Update inline documentation in scripts

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

manage_tool_dependencies.py

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migrate_toolshed_db.py

Apply black, isort (squashed)

2022-03-09 18:41:49 -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

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

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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

Format Python code with black 23.1.0

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

secret_decoder_ring.py

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

set_dataset_sizes.py

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

set_user_disk_usage.py

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summarize_timings.py

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tests_markdown_compare.tpl

Performance metrics for tests.

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tests_markdown.py

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tests_markdown.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -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

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2022-02-03 07:42:20 -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