galaxy

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

Print help if no action is selected

2020-03-05 13:26:28 +01:00

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

…

tool_shed

Small refactor to `validate_password()`. Add back deleted line

2020-06-04 18:52:59 +01:00

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

Merge remote-tracking branch 'upstream/release_20.05' into dev

2020-06-17 12:05:55 -04:00

build_toolbox.py

Fix all E722 errors and ignore E741

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

check_eggs.py

…

check_python.py

Python 2.7 is officially unsupported on 20.05

2020-06-20 19:04:57 +01:00

common_startup_functions.sh

Hide "python: not found" error when Python 2 is not installed

2020-04-27 02:32:06 +01:00

common_startup.sh

Create Python3 virtualenv by default

2020-02-26 10:53:43 +01:00

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

Decouple API and Selenium tests from galaxy-test-driver (and the whole app!)

2020-07-06 13:57:48 -04:00

galaxy

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

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

galaxy-main

Missed one new style class here.

2020-06-26 08:20:49 -04:00

get_platforms.py

Python3: fix remaining print statements

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

get_uwsgi_args.py

Update static-safe mappings to match new layout, rebuild client.

2020-08-11 10:26:06 -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

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

release-diff.py

Add script to diff two release config files.

2020-09-22 11:11:30 +02:00

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

Switch to lxml for xml parsing

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