Sergey GolitsynskiyandNicola Soranzo b9093e33da Update scripts/check_model.py ...

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>

2020-10-03 02:26:40 -04:00

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api

Make str.join()s more efficient

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

auth

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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

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microbes

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

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

objectstore

Another import re-ordering :(

2020-09-11 16:49:24 -04:00

slideshow

Fix many links

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

taxonomy

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tool_shed

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

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

tools

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__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

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

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

build_toolbox.py

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check_eggs.py

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check_model.py

Update scripts/check_model.py

2020-10-03 02:26:40 -04:00

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

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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

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drmaa_external_runner.py

external_runner: load json template first

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

dump_library_paths.py

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edam_mapping.py

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external_chown_script.py

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extract_dataset_part.py

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extract_toolbox_sections.py

Fix deprecated `getchildren()`

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

fetch_eggs.py

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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

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galaxy-main

Missed one new style class here.

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

get_platforms.py

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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

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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

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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

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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

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validate_tools.sh

Switch to lxml for xml parsing

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