John Chilton d194520fdf Merge pull request #8152 from jmchilton/tool_deps_serialize ...

Re-try dependency manager serialization and embedded config.

2019-07-07 12:44:35 +02:00

..

api

Use `yaml.safe_load() instead of load()`

2019-04-23 16:50:55 +01:00

auth

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

cleanup_datasets

Fix issues reported by ShellCheck

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

communication

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

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

grt

swap to exception

2019-04-26 13:29:12 +02:00

loc_files

Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()

2018-09-18 10:06:13 +01:00

metagenomics

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

microbes

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

migrate_tools

Fix issues reported by ShellCheck

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

slideshow

Fix many links

2018-09-03 14:34:13 +01:00

taxonomy

Tweaks to taxonomy tools

2010-11-15 15:04:59 -05:00

tool_shed

Update import paths for loader_directory

2019-07-06 00:52:45 +02:00

tools

Python3: fix remaining print statements

2017-10-12 18:34:29 +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

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

bootstrap_history.py

Fixes and enhancements for release note generation.

2019-05-24 16:59:32 -04:00

build_toolbox.py

Fix all E722 errors and ignore E741

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

build_universe_config.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

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_galaxy.py

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

check_python.py

Drop support for Python 3.4. Officially support Python >=3.5

2019-01-31 23:31:44 +00:00

common_startup_functions.sh

Fix activation of `_galaxy_` conda env

2018-12-14 00:22:12 +00:00

common_startup.sh

Fix comments

2019-04-14 18:02:42 +01:00

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

2017-08-10 13:14:55 -04:00

create_db.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

db_shell.py

Fix traceback in `printquery()`

2019-06-11 11:31:40 +01:00

docker_swarm_manager.py

Make the swarm manager recover on uncaught exceptions. It should do a

2018-04-13 12:34:55 -04:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

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

drmaa_external_runner.py

external_runner: load json template first

2018-11-09 17:48:36 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

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

dump_tour.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

edam_mapping.py

Backport of hardening fixes to 17.09

2017-10-18 13:03:49 -04:00

external_chown_script.py

Fix all E201 and E202 style errors

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

extract_dataset_part.py

Fix all E201 and E202 style errors

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

extract_toolbox_sections.py

Fix deprecated `getchildren()`

2019-04-23 12:51:13 +01:00

fetch_eggs.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

functional_tests.py

Rework and simplify data manager testing

2018-08-13 17:19:25 +02:00

galaxy-main

Refactor to cleanup dependencies around galaxy.web.stack.

2019-06-26 18:54:52 -04:00

get_platforms.py

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

get_uwsgi_args.py

Drop static-safe navigation to plugin dirs. These are no longer symlinks, they are staged files.

2019-03-14 13:23:45 -04:00

helper.py

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

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

maintenance.sh

Fix issues reported by ShellCheck

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

manage_db.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

manage_tool_dependencies.py

Re-try dependency manager serialization and embedded config.

2019-06-20 14:36:40 -04:00

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

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

Update plugin_staging to actually stage instead of symlink, since it no longer needs to be quite as fast (on startup). This will allow us to drop unnecessary trust rules from uwsgi static.

2019-03-14 13:18:43 -04:00

rst2html.py

Fix all E722 errors and ignore E741

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

runtime_stats.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +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

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

set_user_disk_usage.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

summarize_timings.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

sync_reports_config.py

Mark scripts/* that don't work with YAML configuraiton options as deprecated.

2018-03-23 16:14:49 -04:00

transfer.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

update_shed_config_path.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

validate_tools.sh

Fix issues reported by ShellCheck

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