Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6c82266546c77361f9d2265ab749db1446142150
https://github.com/galaxyproject/galaxy/commit/6c82266546c77361f9d2265ab749…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge nearly-identical methods in shed_util_common.
Commit: d74dfbefd4f24fa93a437b782d340d4fd152c079
https://github.com/galaxyproject/galaxy/commit/d74dfbefd4f24fa93a437b782d34…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Add missing docstring.
Commit: bb7cbc7ee556f6a0146e669792f5cc953893cf98
https://github.com/galaxyproject/galaxy/commit/bb7cbc7ee556f6a0146e669792f5…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Correct parameters.
Commit: 5d4d32a43221d4a0725a2d16d6bac02c9b867d4d
https://github.com/galaxyproject/galaxy/commit/5d4d32a43221d4a0725a2d16d6ba…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/galaxy_install/repair_repository_manager.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #651 from davebx/suc_cleanup
Merge nearly-identical methods in shed_util_common.
Compare: https://github.com/galaxyproject/galaxy/compare/0409ad6c4a54...5d4d32a43221
Branch: refs/heads/release_15.07
Home: https://github.com/galaxyproject/galaxy
Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240
https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Fix for server error when installing some repos.
Examples: IUC's gatk2 repository, devteam's samtools_rmdup.
When attempting to install either of those, or another repository
that has tool tests with an input parameter that does not have a
value attribute, the repository would be stuck in state 'Cloning'
and show a debug link in the log. This commit resolves that error.
Commit: 19c85e070534f4318cca3e728c52c91a27163f4a
https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52…
Author: Jeremy Goecks <jgoecks(a)gwu.edu>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/viz/sweepster.js
M static/maps/mvc/tools.js.map
M static/maps/viz/sweepster.js.map
M static/scripts/mvc/tools.js
M static/scripts/viz/sweepster.js
Log Message:
-----------
Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes.
Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77
https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec296…
Author: nitesh1989 <nitesh.turaga(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Fix: rdata extension type
Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009
https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc…
Author: nitesh1989 <nitesh.turaga(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Fix: Typo the other way. Supposed to be "RData"
Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html
Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de
https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d08…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/tool_shed/util/web_util.py
Log Message:
-----------
Fix for toolshed escape method, where an error/log message contains non-ASCII characters.
Commit: d2e61e8af4c933b733c640f46f831bf424bc0197
https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f83…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M static/maps/mvc/ui/ui-select-library.js.map
M static/scripts/mvc/ui/ui-select-library.js
Log Message:
-----------
Filter deleted library datasets
Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934
https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b256…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Correct examples in workflow invocations.
Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db
https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
R templates/webapps/tool_shed/message.mako
Log Message:
-----------
Stop creating database/message.mako.py
Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a
https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a65…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M templates/webapps/reports/base_panels.mako
Log Message:
-----------
fix the class for reports brand so it is actually shown
and not black text on dark background
Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617
https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/tools.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/viz/sweepster.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/web_util.py
M static/maps/mvc/tools.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/viz/sweepster.js.map
M static/scripts/mvc/tools.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/viz/sweepster.js
M templates/webapps/reports/base_panels.mako
R templates/webapps/tool_shed/message.mako
Log Message:
-----------
Merge pull request #657 from jmchilton/dev_1507_backports
[15.07] Backport various dev fixes.
Compare: https://github.com/galaxyproject/galaxy/compare/71125326f842...4fcdf9fda1d2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1041cad9ec4f50837158f8bbfe5d27f9e3db7d0e
https://github.com/galaxyproject/galaxy/commit/1041cad9ec4f50837158f8bbfe5d…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/jobs_specified_month_in_error.mako
Log Message:
-----------
Centered headers in firefox
Made page selection divs not wrap when window size is too small
Changed name for action in Jobs in error per day this month which
fixes crash
Commit: 865d0153954e3be07d139f6100d21bdf5543a2f9
https://github.com/galaxyproject/galaxy/commit/865d0153954e3be07d139f6100d2…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M client/galaxy/scripts/mvc/ui/ui-button-menu.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
A client/galaxy/scripts/mvc/upload/composite/composite-row.js
A client/galaxy/scripts/mvc/upload/composite/composite-view.js
A client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
R client/galaxy/scripts/mvc/upload/upload-row.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M config/tool_data_table_conf.xml.sample
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/util/bunch.py
M lib/galaxy/util/jstree.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/util/common_util.py
M scripts/cleanup_datasets/cleanup_datasets.py
M static/maps/mvc/ui/ui-button-menu.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-popover.js.map
A static/maps/mvc/upload/composite/composite-row.js.map
A static/maps/mvc/upload/composite/composite-view.js.map
A static/maps/mvc/upload/default/default-row.js.map
A static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
R static/maps/mvc/upload/upload-row.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
M static/scripts/mvc/ui/ui-button-menu.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-popover.js
A static/scripts/mvc/upload/composite/composite-row.js
A static/scripts/mvc/upload/composite/composite-view.js
A static/scripts/mvc/upload/default/default-row.js
A static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-row.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
A test/qunit/test-app.js
M test/qunit/test-common.js
A test/qunit/test-data/bootstrapped.js
A test/qunit/test-data/fakeserver.js
A test/qunit/tests/upload_dialog_tests.html
A test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/workflow_editor_tests.js
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0000_basic_repository_features.py
M test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_0020_basic_repository_dependencies.py
M test/tool_shed/functional/test_0030_repository_dependency_revisions.py
M test/tool_shed/functional/test_0040_repository_circular_dependencies.py
M test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_0060_workflows.py
M test/tool_shed/functional/test_0070_invalid_tool.py
M test/tool_shed/functional/test_0080_advanced_circular_dependencies.py
M test/tool_shed/functional/test_0090_tool_search.py
M test/tool_shed/functional/test_0100_complex_repository_dependencies.py
M test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py
M test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_0130_datatype_converters.py
M test/tool_shed/functional/test_0140_tool_help_images.py
M test/tool_shed/functional/test_0150_prior_installation_required.py
M test/tool_shed/functional/test_0160_circular_prior_installation_required.py
M test/tool_shed/functional/test_0170_complex_prior_installation_required.py
M test/tool_shed/functional/test_0300_reset_all_metadata.py
M test/tool_shed/functional/test_0310_hg_push_from_api.py
M test/tool_shed/functional/test_0400_repository_component_reviews.py
M test/tool_shed/functional/test_0410_repository_component_review_access_control.py
M test/tool_shed/functional/test_0420_citable_urls_for_repositories.py
M test/tool_shed/functional/test_0430_browse_utilities.py
M test/tool_shed/functional/test_0440_deleting_dependency_definitions.py
M test/tool_shed/functional/test_0450_skip_tool_tests.py
M test/tool_shed/functional/test_0460_upload_to_repository.py
M test/tool_shed/functional/test_0470_tool_dependency_repository_type.py
M test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py
M test/tool_shed/functional/test_0490_export_import_repositories.py
M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py
M test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py
M test/tool_shed/functional/test_0520_import_export_circular_dependencies.py
M test/tool_shed/functional/test_0530_repository_admin_feature.py
M test/tool_shed/functional/test_1000_install_basic_repository.py
M test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py
M test/tool_shed/functional/test_1060_install_repository_with_workflow.py
M test/tool_shed/functional/test_1070_invalid_tool.py
M test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py
M test/tool_shed/functional/test_1085_repository_dependency_handling.py
M test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py
M test/tool_shed/functional/test_1090_install_tool_from_tool_search.py
M test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py
M test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py
M test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py
M test/tool_shed/functional/test_1130_datatype_converters.py
M test/tool_shed/functional/test_1140_tool_help_images.py
M test/tool_shed/functional/test_1150_prior_installation_required.py
M test/tool_shed/functional/test_1160_circular_prior_installation_required.py
M test/tool_shed/functional/test_1170_complex_prior_installation_required.py
M test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/tool_shed/functional/test_1300_reset_all_metadata.py
M test/tool_shed/functional/test_1400_review_migration_stages.py
M test/tool_shed/functional/test_1410_update_manager.py
M test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py
M test/tool_shed/functional/test_1430_repair_installed_repository.py
M test/tool_shed/functional/test_1440_missing_env_sh_files.py
M test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py
M test/tool_shed/functional/test_1460_data_managers.py
M test/tool_shed/functional/test_1470_updating_installed_repositories.py
M test/tool_shed/functional_tests.py
M test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_toolbox_filters.py
R tool-data/fastx_clipper_sequences.txt
M tools/extract/liftOver_wrapper.xml
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
Conflicts:
static/style/blue/base.css
Commit: 4a4ed87f11c8a47dcc838bdc6a42389def73afe9
https://github.com/galaxyproject/galaxy/commit/4a4ed87f11c8a47dcc838bdc6a42…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M client/galaxy/style/less/reports.less
M static/style/blue/base.css
M static/style/blue/reports.css
M templates/webapps/reports/jobs_specified_month_in_error.mako
Log Message:
-----------
Merge pull request #656 from Airistotal/dev
Reports - Small bug fixes
Compare: https://github.com/galaxyproject/galaxy/compare/f5ca24ee2bae...4a4ed87f11c8
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b8362b71509013566694280cb89e967dca704a31
https://github.com/galaxyproject/galaxy/commit/b8362b71509013566694280cb89e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Include link expiration time in password reset email.
Commit: 299d628531bba44d403bc191b53ae09437f050be
https://github.com/galaxyproject/galaxy/commit/299d628531bba44d403bc191b53a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Validate user email input prior to attempting to reset.
Commit: 29d510f7dee48bf54776773f8a2f971781b08052
https://github.com/galaxyproject/galaxy/commit/29d510f7dee48bf54776773f8a2f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Force lowercase comparison for password reset. TODO: Look for more places this is potentially an issue.
Commit: a98e3ff6de51d0fe43db97ade602ccd6b8eea468
https://github.com/galaxyproject/galaxy/commit/a98e3ff6de51d0fe43db97ade602…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Swap to config.pretty_datetime_format
Commit: 9356ae5f3fa6155b68eba98b8eac9862bd53ba57
https://github.com/galaxyproject/galaxy/commit/9356ae5f3fa6155b68eba98b8eac…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Switch password reset tokens to use UTC. This is kind of a mess, we're using both UTC and localized time in various places.
Commit: c337fccbeb967c782339b5f6c812daa70014dc99
https://github.com/galaxyproject/galaxy/commit/c337fccbeb967c782339b5f6c812…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Use case-insensitive email selection only when case-sensitive comes up empty.
Commit: f5ca24ee2baea35ad7a3bc62db7f5a996ccaa2a7
https://github.com/galaxyproject/galaxy/commit/f5ca24ee2baea35ad7a3bc62db7f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Merge pull request #655 from dannon/password_reset_tweaks
Password reset tweaks
Compare: https://github.com/galaxyproject/galaxy/compare/949b3de56860...f5ca24ee2bae
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2fccd0c11f91fedabd979fc62064e4ea31a33ae2
https://github.com/galaxyproject/galaxy/commit/2fccd0c11f91fedabd979fc62064…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M test/base/asserts/__init__.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
Log Message:
-----------
Finish flake8 of test/ .
Commit: 6f1e1cea82aae5695b669a57d870ec173f6b8d6a
https://github.com/galaxyproject/galaxy/commit/6f1e1cea82aae5695b669a57d870…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M test/qunit/package.json
Log Message:
-----------
Add mandatory "version" field to package.json .
Commit: 93716ec08a1c5aedd476b137ed2b670b2e73d114
https://github.com/galaxyproject/galaxy/commit/93716ec08a1c5aedd476b137ed2b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M test/qunit/README.txt
Log Message:
-----------
Suggest to install grunt-cli globally to have grunt in PATH.
Commit: 949b3de56860242c6c20c04e0b18ffc694384b76
https://github.com/galaxyproject/galaxy/commit/949b3de56860242c6c20c04e0b18…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-08-27 (Thu, 27 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M test/base/asserts/__init__.py
M test/base/interactor.py
M test/base/twilltestcase.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
M test/install_and_test_tool_shed_repositories/base/twilltestcase.py
M test/install_and_test_tool_shed_repositories/base/util.py
M test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
M test/qunit/README.txt
M test/qunit/package.json
Log Message:
-----------
Merge pull request #653 from nsoranzo/dev
Finish flake8 of test/ .
Compare: https://github.com/galaxyproject/galaxy/compare/c2fca17c9830...949b3de56860
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7b3fbcbd7f4e4464e7471b9d634165a20e24e834
https://github.com/galaxyproject/galaxy/commit/7b3fbcbd7f4e4464e7471b9d6341…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Expose tool config file path to admins via the API. This is useful (not to mention already kinda exposed when using wrappers) for interfacing with planemo for the smc work and I would expect other automation tasks.
Commit: 5e9d1becfca27882ab9a106df2ea80e3d7d96404
https://github.com/galaxyproject/galaxy/commit/5e9d1becfca27882ab9a106df2ea…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Actually use the method instead of just checking it's existence
Commit: dc7f7f2e3babf35dab06297245464fe16b97c8de
https://github.com/galaxyproject/galaxy/commit/dc7f7f2e3babf35dab0629724546…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M test/unit/tools/test_toolbox_filters.py
Log Message:
-----------
Fix mock_trans to provide a user_is_admin member
Commit: aea250334f319788aa6281bdb2d4ddfdfcb12b84
https://github.com/galaxyproject/galaxy/commit/aea250334f319788aa6281bdb2d4…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2015-08-26 (Wed, 26 Aug 2015)
Changed paths:
M lib/galaxy/tools/__init__.py
M test/unit/tools/test_toolbox_filters.py
Log Message:
-----------
Merge pull request #652 from dannon/tool_path_expose
Expose tool config file path to admins via the API. This is useful (…
Compare: https://github.com/galaxyproject/galaxy/compare/b0f2eaec0312...aea250334f31