John Davis ad7f7f9268 Remove run_alembic.sh from root; user scripts/run_alembic.py instead. ...

Rationale: move developer-focused scripts out of galaxy root.

2022-09-16 00:39:44 -04:00

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api

Combine "as" imports with other "from" imports

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

auth

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

cleanup_datasets

s/eagerload/joinedload (SQLAlchemy 2.0)

2022-03-16 16:48:33 -04:00

grt

Merge branch 'release_22.01' into dev

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

loc_files

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metagenomics

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microbes

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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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__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

bootstrap_history.py

Update a couple PR titles, strip trailing . from PR titles

2022-08-19 12:29:25 +02:00

build_toolbox.py

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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

Fix first startup when only python3 is on PATH

2022-08-08 16:28:26 +02:00

common_startup.sh

Updates for Poetry 1.2.0

2022-09-05 17:23:18 +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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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

2022-07-04 14:15:01 +01:00

db_shell.py

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

2022-09-16 00:39:03 -04:00

db.py

Rename db.sh > manage_db.sh, following code review feedback

2022-09-16 00:39:44 -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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edam_mapping.py

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external_chown_script.py

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extract_dataset_part.py

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extract_toolbox_sections.py

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fetch_eggs.py

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fix_dm_versions.py

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functional_tests.py

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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

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

Update release.sh script for new packaging layout

2022-08-23 16:04:24 +02:00

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

Remove run_alembic.sh from root; user scripts/run_alembic.py instead.

2022-09-16 00:39:44 -04:00

runtime_stats.py

Upgrade syntax to Python 3.7

2022-03-14 14:57:43 +00:00

secret_decoder_ring.py

Apply black formatting.

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

Merge branch 'release_22.01' into dev

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

summarize_timings.py

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tests_markdown_compare.tpl

Performance metrics for tests.

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

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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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