Nate Coraor acb9bc1ea1 Merge pull request #9306 from dannon/blue-elimination ...

Clean up old 'blue' style path, update documentation and samples

2020-02-05 09:31:34 -05:00

..

api

Make str.join()s more efficient

2020-01-23 11:06:32 +00:00

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

Remove broken script

2020-02-03 18:48:57 +00:00

communication

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

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

grt

Write unicode strings to files opened with io.open(path, w, encoding=utf-8)

2020-01-09 17:51:24 +00:00

interactivetools

Fix interactivetool python 3 support and tests

2020-01-09 14:40:48 +01:00

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

add .gitattributes file and normalize line endings to use LF instead of CLRF

2019-09-18 22:03:37 -04:00

slideshow

Fix many links

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

taxonomy

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tool_shed

Make str.join()s more efficient

2020-01-23 11:06:32 +00:00

tools

Python3: fix remaining print statements

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

__init__.py

…

apply_tags.py

Change all remaining old-style classes to new style

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

bootstrap_history.py

Make str.join()s more efficient

2020-01-23 11:06:32 +00:00

build_toolbox.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +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_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 startup checks when using a Conda env

2019-08-19 01:28:35 +01:00

common_startup.sh

If we're running webpack dev server, skip the client build on startup.

2019-11-21 17:19:54 -05:00

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

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

create_db.py

Refactor tool_shed webapp out of Galaxy.

2019-11-11 12:32:19 -05:00

db_shell.py

Fix traceback in `printquery()`

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

docker_swarm_manager.py

Make str.join()s more efficient

2020-01-23 11:06:32 +00:00

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

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

Migrate selenium tests into lib/galaxy_test for packaging.

2019-11-12 09:05:08 -05:00

galaxy

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

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

galaxy-main

Fix missed control_worker->queue_worker rename

2019-08-22 10:58:01 +02:00

get_platforms.py

Python3: fix remaining print statements

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

get_uwsgi_args.py

Clean up old 'blue' style path, update documentation and samples to refer to plain old 'static' now.

2020-02-03 22:41:29 -05:00

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

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

Remove log_tempfile.

2019-07-08 14:52:13 +02:00

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

Refactor into model

2019-08-14 16:15:49 +02:00

summarize_timings.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