mvdbeek 159a94b95d Move index logic to lib.tool_shed.util.shed_index ...

Since we need the index for browsing repos in the new client
we should incrementally build the index with every repo update.
Having this in tool_shed will make re-use easier.

2020-03-21 13:27:53 +01:00

..

api

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

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

auth

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cleanup_datasets

Merge pull request #8908 from bernt-matthias/topic/pgcleanup-also-delete

2019-11-04 10:21:04 +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

Move index logic to lib.tool_shed.util.shed_index

2020-03-21 13:27:53 +01:00

tools

Python3: fix remaining print statements

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

__init__.py

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apply_tags.py

Change all remaining old-style classes to new style

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

bootstrap_history.py

Add missing pygithub dev-requirement

2020-02-29 01:55:05 +00:00

build_toolbox.py

Fix all E722 errors and ignore E741

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

check_eggs.py

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check_python.py

Create Python3 virtualenv by default

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

common_startup_functions.sh

Source the full path of conda activate script

2020-02-23 23:06:01 +00:00

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 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

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

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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

Drop static-safe from DEFAULT_ARGS, relying on an explicit add now.

2020-02-06 13:27:33 -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

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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