John Chilton
079b5189dc
Remove unused code from basic_util.
2022-09-22 11:29:19 -04:00
John Chilton
4dae7c6f21
Disable implicit re-imports across the projects.
...
Exclude galaxy.util for now, but the exclusion is tracked in setup.cfg. Elimiantes a bunch of flake exception markers.
2022-03-15 19:58:42 -04:00
John Chilton
da116be7d1
Refactor tool_shed basic_util into Galaxy.
2019-11-10 22:05:29 -05:00
Nicola Soranzo
9b4de72ca6
Fix all E722 errors and ignore E741
...
Introduced in flake8 3.5.0
Fix import order.
2017-10-24 11:29:09 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Dannon Baker
0fd152c0cc
Merge branch 'release_16.04' into dev
2016-06-15 10:15:36 -04:00
Dannon Baker
37242c8a7c
Merge branch 'release_16.01' into release_16.04
2016-06-15 10:15:07 -04:00
Nicola Soranzo
d95e9b840d
Refactor move_file() method
2016-06-09 17:59:39 +01:00
Dannon Baker
aba34eecda
Update to 'new' except style.
2016-05-16 13:37:53 -04:00
Marius van den Beek
a22af161ad
For python2/3 compatibility, replace basestring with six's string_types, unicode with six's text_type.
2016-02-20 13:01:05 +01:00
Nate Coraor
97ad53f570
Merge remote-tracking branch 'upstream/dev' into smash_eggs
...
Conflicts:
eggs.ini
lib/galaxy/__init__.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/eggs/__init__.py
lib/galaxy/eggs/dist.py
lib/galaxy/eggs/scramble.py
lib/galaxy/exceptions/__init__.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/check.py
lib/galaxy/model/orm/__init__.py
lib/galaxy/model/tool_shed_install/migrate/check.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/web/framework/helpers/__init__.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/framework/openid_manager.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/reports/controllers/workflows.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/search/repo_search.py
lib/galaxy/webapps/tool_shed/search/tool_search.py
lib/galaxy_ext/metadata/set_metadata.py
lib/pulsar/client/config_util.py
lib/tool_shed/galaxy_install/install_manager.py
lib/tool_shed/galaxy_install/migrate/check.py
lib/tool_shed/grids/admin_grids.py
lib/tool_shed/grids/repository_grids.py
lib/tool_shed/repository_types/repository_suite_definition.py
lib/tool_shed/repository_types/tool_dependency_definition.py
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
lib/tool_shed/scripts/check_repositories_for_functional_tests.py
lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
lib/tool_shed/util/basic_util.py
lib/tool_shed/util/encoding_util.py
lib/tool_shed/util/hg_util.py
scripts/check_eggs.py
scripts/dist-scramble.py
scripts/fetch_eggs.py
scripts/make_egg_packager.py
scripts/scramble.py
scripts/scramble/lib/scramble_lib.py
scripts/scramble/scripts/DRMAA_python-macosx.py
scripts/scramble/scripts/DRMAA_python-solaris.py
scripts/scramble/scripts/DRMAA_python.py
scripts/scramble/scripts/MySQL_python-solaris.py
scripts/scramble/scripts/MySQL_python.py
scripts/scramble/scripts/PyRods.py
scripts/scramble/scripts/bx_python-solaris.py
scripts/scramble/scripts/generic.py
scripts/scramble/scripts/pbs_python.py
scripts/scramble/scripts/psycopg2-linux.py
scripts/scramble/scripts/psycopg2-macosx.py
scripts/scramble/scripts/psycopg2-solaris.py
scripts/scramble/scripts/psycopg2.py
scripts/scramble/scripts/pysam-solaris.py
scripts/scramble/scripts/pysqlite.py
scripts/test_dist_egg.py
2015-09-21 15:02:47 -04:00
Nicola Soranzo
df808d0c1e
flake8 lib/tool_shed/ .
...
Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
2015-09-09 19:57:41 +01:00
Greg Von Kuster
d6a854006f
Reworked fix for the change_directory action, and enhancements for
...
directory actions to now make use of $TMP_WORK_DIR in recipes.
2015-08-05 14:38:55 -04:00
Nate Coraor
033b1e88da
Remove all imports of galaxy.eggs and all calls to
...
`{eggs,pkg_resources}.require`. Probably broke some stuff where we were
trying to be smart about whether a particular egg was available, but
Galaxy does at least start.
2015-07-13 15:37:59 -04:00
Nate Coraor
9803afdca9
Merge next-stable to default.
2014-12-03 13:41:00 -05:00
Dannon Baker
dfc4e52fd3
Fix size_string; this would have thrown an exception on being called due to an unimported 'util'.
2014-12-03 09:24:44 -05:00
Dannon Baker
d1cde6b943
Pep8 tool_shed/util/basic_util
2014-12-03 09:23:14 -05:00
Dannon Baker
b9027d69ef
Bump NO_OUTPUT_TIMEOUT to 60m; Bjoern said it's causing issues w/ some tools for being too short.
2014-12-03 09:21:54 -05:00
Björn Grüning
53e7653429
Update the Dockerfile template to the latest version our Galaxy Docker Container. The new container will be release together with Galaxy next week.
2014-11-28 19:18:58 +00:00
Greg Von Kuster
595d737fa8
Add a very basic framework to the Tool Shed for creating a Galaxy flavor Docker Image that uses Bjoern Gruning's Galaxy Docker project. This is a proof-of-concept that should be enhanced if kept.
2014-07-01 21:44:49 -04:00
Greg Von Kuster
bba63a24b0
Handle exporting and importing repository capsules with new ExportRepositoryManager and ImportRepositoryMnager classes respectively.
2014-06-24 13:11:24 -04:00
Dave Bouvier
e547936b70
Use the same capitalization for eggs.require as is present in the egg's name. This resolves the install and test buildbot's failure on step 4, delete empty directories.
2014-06-09 14:37:36 -04:00
Greg Von Kuster
390d05bbd1
Eliminate the Tool Shed's td_common_util.py module by moving the functions to appropriate classes.
2014-05-28 15:49:02 -04:00
Greg Von Kuster
b2f3d6a551
Continued down-sizing of the Tool Shed's shed_util_common module by moving certain functions to more appropriate locations. Some fixes for adding and removing entries to the Tool Shed's repository registry.
2014-05-28 11:17:50 -04:00
John Chilton