Nate Coraor 0297eb1bc8 Ensure $GRAVITY_STATE_DIR is present in venv activate script any time ...

run.sh/common_startup.sh is called normally (without --skip-venv or
--no-create-venv).

2022-02-16 10:09:50 -05:00

..

api

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

auth

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

cleanup_datasets

Drop old sqlalchemy patterns

2021-12-16 12:30:49 +01:00

grt

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

interactivetools

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

loc_files

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

metagenomics

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

microbes

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

objectstore

Remove unnecessary list creations

2021-11-29 16:33:05 +00:00

slideshow

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

taxonomy

…

tool_shed

Drop old sqlalchemy patterns

2021-12-16 12:30:49 +01:00

tools

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

__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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

bootstrap_history.py

Adjust check_blocking_issues to PyGithub usage

2021-11-01 13:01:02 +01:00

build_toolbox.py

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

celery_shell.py

Add interactive shell for celery tasks

2021-11-29 10:34:01 +01:00

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

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

check_python.py

Drop support for Python 3.6, add Python 3.10

2021-12-08 08:14:10 +00:00

common_startup_functions.sh

Only set $GALAXY_DAEMON_LOG when using gravity since other servers have

2022-01-26 14:50:39 -05:00

common_startup.sh

Ensure $GRAVITY_STATE_DIR is present in venv activate script any time

2022-02-16 10:09:50 -05:00

config_sample_to_kwalify.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

create_db.py

Create install database with create_db.sh

2021-03-30 13:44:36 +02:00

cwl_conformance_to_test_cases.py

Remove unnecessary list creations

2021-11-29 16:33:05 +00:00

db_shell.py

Add interactive shell for celery tasks

2021-11-29 10:34:01 +01:00

docker_swarm_manager.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

drmaa_external_runner.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

2018-02-01 13:05:16 -05:00

edam_mapping.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

external_chown_script.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_dataset_part.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

extract_toolbox_sections.py

Fix all E203, E741 and W504 flake8 errors

2021-01-18 10:35:41 +00:00

fetch_eggs.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

fix_dm_versions.py

add script for fixing shed_data_manager_conf.xml

2021-07-14 17:13:26 +02:00

functional_tests.py

Cleanup galaxy_test.base.api_util.

2021-01-16 20:11:39 -05:00

galaxy

Make Galaxy installable the Pythonic way via setup.py. Incomplete, but

2016-07-07 13:49:27 -04:00

galaxy_main.py

First pass fstring conversion

2021-05-11 13:47:00 -04:00

galaxy_schemadisp.py

Lint fixes, prompt for sqlalchemy_schemadisplay install

2021-01-12 08:23:10 -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

get_platforms.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

get_uwsgi_args.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

helper.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

maintenance.sh

Fix issues reported by ShellCheck

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

manage_db.py

Enable on-screen logging for create_db.py and manage_db.py

2019-08-18 11:17:34 +01:00

manage_tool_dependencies.py

Rework config locating logic (it was reading the sample again).

2019-07-08 11:28:31 +02:00

nosetests.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

pages_identifier_conversion.py

clean-fix-page-api - move page revision creation to manager.

2019-05-29 13:43:49 -04:00

paster.py

Restore pastescript, make new stack depend on APP_WEBSERVER=dev

2021-04-07 14:39:06 +02:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

release-diff.py

Adjust release-diff.py

2022-01-19 18:20:19 +00:00

release.sh

Test Galaxy release script

2021-12-08 10:43:09 +00:00

resumable_upload.py

Adapt scripts/resumable_upload.py to fetch API

2021-10-13 18:05:42 +02:00

rst2html.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

runtime_stats.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

secret_decoder_ring.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

set_dataset_sizes.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

set_user_disk_usage.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

summarize_timings.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

tests_markdown_compare.tpl

Performance metrics for tests.

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

tests_markdown.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

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

Don't use triple-quoted strings as comments

2021-11-29 23:02:34 +00:00

validate_tools.sh

Switch to lxml for xml parsing

2020-05-12 15:00:27 +02:00