Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0bf9417fbaf56ff52edfa62458d9f66bada6a449
https://github.com/galaxyproject/galaxy/commit/0bf9417fbaf56ff52edfa62458d9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Minimally functional metadata file fetching via the API
Commit: e219dfef95a565bee081ff89cb8110a860722bdd
https://github.com/galaxyproject/galaxy/commit/e219dfef95a565bee081ff89cb81…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
Log Message:
-----------
Add download url for metadata file.
Commit: f87b08efa0d0d2c127eab88cf31233df3e867ec1
https://github.com/galaxyproject/galaxy/commit/f87b08efa0d0d2c127eab88cf312…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Consolidate usage of 'valid_chars' in the application.
Commit: ce04973b20e3c21a274f8f3560b1d2086d0d410c
https://github.com/galaxyproject/galaxy/commit/ce04973b20e3c21a274f8f3560b1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-05 (Fri, 05 Aug 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Rename get_metadata_file route to just metadata_file. Thanks @carlfeberhard.
Commit: c9ac723174ae7200230575b7101c91353744e319
https://github.com/galaxyproject/galaxy/commit/c9ac723174ae7200230575b7101c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Revert genomespace tool changes related to FILENAME_VALID_CHARS
Commit: b40e9938d68b3d5d2d818e178ae24e9317ee3728
https://github.com/galaxyproject/galaxy/commit/b40e9938d68b3d5d2d818e178ae2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge pull request #2741 from dannon/expose_metadata_api
Metadata file fetching via the API
Compare: https://github.com/galaxyproject/galaxy/compare/49f58dd01771...b40e9938d68b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c
https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
enable conda_auto_init in sample, adjust wording
Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec
https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix string substitution
Commit: 730233f48a4ba64c338969036845b0d2aeea5035
https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #15 from mvdbeek/fix_string_substitution
Fix string substitution
Commit: e35c6295694c4065fc880e00fabe43f0c1905748
https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/first_startup.sh
Log Message:
-----------
Extend startup time
Commit: 702891e3efc79fa75ed8e7475e712760355d825c
https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/first_startup.sh
Log Message:
-----------
Merge pull request #16 from mvdbeek/fix_string_substitution
Extend startup time
Commit: a7be24e111de2c37c52af580c8a776ee0478ec92
https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2759 from martenson/conda_config
[16.07] install Conda at startup; enable conda_auto_init in sample conf
Commit: 4ffbedd844b077b48c09092ed0d406ab73060148
https://github.com/galaxyproject/galaxy/commit/4ffbedd844b077b48c09092ed0d4…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/13b8067d91f8...4ffbedd844b0
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c
https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
enable conda_auto_init in sample, adjust wording
Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec
https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix string substitution
Commit: 730233f48a4ba64c338969036845b0d2aeea5035
https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-09 (Tue, 09 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #15 from mvdbeek/fix_string_substitution
Fix string substitution
Commit: e35c6295694c4065fc880e00fabe43f0c1905748
https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/first_startup.sh
Log Message:
-----------
Extend startup time
Commit: 702891e3efc79fa75ed8e7475e712760355d825c
https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/first_startup.sh
Log Message:
-----------
Merge pull request #16 from mvdbeek/fix_string_substitution
Extend startup time
Commit: a7be24e111de2c37c52af580c8a776ee0478ec92
https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-08-11 (Thu, 11 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2759 from martenson/conda_config
[16.07] install Conda at startup; enable conda_auto_init in sample conf
Compare: https://github.com/galaxyproject/galaxy/compare/9c03d4c16fad...a7be24e111de
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4a72f49901c9739413769a42eeb809cf7f7ed5f0
https://github.com/galaxyproject/galaxy/commit/4a72f49901c9739413769a42eeb8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
Log Message:
-----------
Avoid user role checks for individual datasets during workflow model build
Commit: 5e397af1663f2b2e4ad387420e918d5b8b875702
https://github.com/galaxyproject/galaxy/commit/5e397af1663f2b2e4ad387420e91…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Disable detailed user role checks for regular and workflow forms
Commit: 0052a1c3bba1cfc27667fca5b1238a2709ac1a82
https://github.com/galaxyproject/galaxy/commit/0052a1c3bba1cfc27667fca5b123…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
Log Message:
-----------
Merge pull request #2766 from guerler/workflow_build_performance
Avoid user role checks for individual dataset when building the tool form models
Compare: https://github.com/galaxyproject/galaxy/compare/34d7210ddd5c...0052a1c3bba1
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 33c4025fabc057a412c2da662b3606afc0726902
https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Fix misplaced parenthesis
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e
https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M tox.ini
Log Message:
-----------
Pin flake8 version
Do not pin when forward-merging to dev branch.
Also ignore .tox/ and eggs/ as in #2650 .
Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc
https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package
[16.01] Fix misplaced parenthesis
Commit: f2f62f340ecd92ebdde51e6d13d5145a6f40cc9e
https://github.com/galaxyproject/galaxy/commit/f2f62f340ecd92ebdde51e6d13d5…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Conflicts:
.ci/flake8_blacklist.txt
tox.ini
Commit: 9c03d4c16fad7d86b56baf65fb11be7fcc5809b6
https://github.com/galaxyproject/galaxy/commit/9c03d4c16fad7d86b56baf65fb11…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
flake8 pinned also for py27-lint-imports-include-list testenv
Commit: 34d7210ddd5cb59356382d529d235431313bdbfd
https://github.com/galaxyproject/galaxy/commit/34d7210ddd5cb59356382d529d23…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
flake8 unpinned, because this is dev
Compare: https://github.com/galaxyproject/galaxy/compare/5d57b4474181...34d7210ddd5c
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: 33c4025fabc057a412c2da662b3606afc0726902
https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Fix misplaced parenthesis
Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304
Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e
https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M tox.ini
Log Message:
-----------
Pin flake8 version
Do not pin when forward-merging to dev branch.
Also ignore .tox/ and eggs/ as in #2650 .
Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc
https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package
[16.01] Fix misplaced parenthesis
Commit: f2f62f340ecd92ebdde51e6d13d5145a6f40cc9e
https://github.com/galaxyproject/galaxy/commit/f2f62f340ecd92ebdde51e6d13d5…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Conflicts:
.ci/flake8_blacklist.txt
tox.ini
Commit: 9c03d4c16fad7d86b56baf65fb11be7fcc5809b6
https://github.com/galaxyproject/galaxy/commit/9c03d4c16fad7d86b56baf65fb11…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M tox.ini
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
flake8 pinned also for py27-lint-imports-include-list testenv
Compare: https://github.com/galaxyproject/galaxy/compare/a297a0467116...9c03d4c16fad