October 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 15713c: Remove historical config_xml.
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15713c265fe0ebe4c976857922d9391d3fce7b71 https://github.com/galaxyproject/galaxy/commit/15713c265fe0ebe4c976857922d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Remove historical config_xml. Commit: 0f0d14ae513096963d0bf3b5d30bd1c062c6b0f9 https://github.com/galaxyproject/galaxy/commit/0f0d14ae513096963d0bf3b5d30b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #960 from dannon/quick_fix S3ObjectStore followup fix Compare: https://github.com/galaxyproject/galaxy/compare/849458f37b11...0f0d14ae5130

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[galaxyproject/galaxy] 6f5aaf: For require_login=True, redirect directly to login...
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 6f5aafe6279337b318149058e90b749e94838eaa https://github.com/galaxyproject/galaxy/commit/6f5aafe6279337b318149058e90b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- For require_login=True, redirect directly to login without showing empty (and broken) looking panels, and potentially hitting an endless reload cycle. Commit: 92666cdf66914e98535567cd46946b745d02673e https://github.com/galaxyproject/galaxy/commit/92666cdf66914e98535567cd4694… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #965 from dannon/login_req [15.10] Fix endless redirect cycle when login is required Compare: https://github.com/galaxyproject/galaxy/compare/d53e13a4a997...92666cdf6691

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[galaxyproject/galaxy] 24dba3: Fix small bug in galaxy.tools.parser.interface.
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 24dba3b479ab270c302902d78997058bd85975ce https://github.com/galaxyproject/galaxy/commit/24dba3b479ab270c302902d78997… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/parser/interface.py Log Message: ----------- Fix small bug in galaxy.tools.parser.interface. Commit: 652bd0fc30f1e69d7683f48fcc44543db65af97c https://github.com/galaxyproject/galaxy/commit/652bd0fc30f1e69d7683f48fcc44… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py M test/functional/tools/simple_constructs.yml Log Message: ----------- Support selections in interface dict rep of tools. Expose and test through experimental YAML representation of tools. This doesn't represent official support of (vastly superior) YAML tools, this representation continues to serve as an easy way to exercise the abstract tool parsing interface. Brings simple_constructs.yml and simple_constructs.xml further in line also. Test: ./run_tests.sh -framework -id simple_constructs_y Commit: 849458f37b1184c9be0fd35b0f3e3bb60e9a4e7f https://github.com/galaxyproject/galaxy/commit/849458f37b1184c9be0fd35b0f3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/simple_constructs.yml Log Message: ----------- Merge pull request #955 from common-workflow-language/yaml_select Improvements and fixes for abstract tool interface Compare: https://github.com/galaxyproject/galaxy/compare/320724a183fb...849458f37b11

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[galaxyproject/usegalaxy-playbook] 5ed93e: Mutable configs on Main (installed new tool)
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ed93e4726f83d683c0f0a447f88b100422f6a7d https://github.com/galaxyproject/usegalaxy-playbook/commit/5ed93e4726f83d68… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Main (installed new tool)

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[galaxyproject/usegalaxy-playbook] 0f89db: update Main
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0f89db40aeac538d6fea336fe9002912b4ca25ba https://github.com/galaxyproject/usegalaxy-playbook/commit/0f89db40aeac538d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- update Main

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[galaxyproject/galaxy] 0c0197: StorableObject: parent to MetadataFile and Dataset
by GitHub 21 Oct '15

21 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c0197d855882b625e51091b467f48b916b2a2e9 https://github.com/galaxyproject/galaxy/commit/0c0197d855882b625e51091b467f… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- StorableObject: parent to MetadataFile and Dataset Makes the documentation clearer Commit: 86c0e273aad64efb4f827fbbee06c58a69f3317d https://github.com/galaxyproject/galaxy/commit/86c0e273aad64efb4f827fbbee06… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py M test/unit/test_objectstore.py Log Message: ----------- pep257 compliant doc upgrade Line wrapped to 79 charecters, except for some doc summary lines. Dropped the no-op, unused CachingObjectStore Renamed `create_object_in_session()` to `_create_object_in_session()` to mark it as private. Commit: bf2e59d69ad703e3559ccc14d6dd04b1048f89fa https://github.com/galaxyproject/galaxy/commit/bf2e59d69ad703e3559ccc14d6dd… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- fix doc build errors Commit: 5b4880df8019394047c9a4cea66c039ab51f5fc4 https://github.com/galaxyproject/galaxy/commit/5b4880df8019394047c9a4cea66c… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/jobs/command_factory.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py Log Message: ----------- flake8 / sphinx cleanup Commit: b3bad81fb2da8fb8d158019612a6837526b64746 https://github.com/galaxyproject/galaxy/commit/b3bad81fb2da8fb8d158019612a6… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M CONTRIBUTING.md Log Message: ----------- doc tox Commit: 13a8e4b2ee2149814786fc079bb2505281e67419 https://github.com/galaxyproject/galaxy/commit/13a8e4b2ee2149814786fc079bb2… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- explaining Commit: 1a5bff0e891242e057ac4119e9237fd540a794f6 https://github.com/galaxyproject/galaxy/commit/1a5bff0e891242e057ac4119e923… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-10-15 (Thu, 15 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- remove whitespace Commit: 304670455540fffe9cf417da310e4bf6da403844 https://github.com/galaxyproject/galaxy/commit/304670455540fffe9cf417da310e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Revert most of the 79-char linewrapping in objectstore -- we may want to revisit some of the longer function definitions, but this reverts them to how they were prior to the documentation overhaul. Commit: 4f0ec1eaf262f170877863687215e3657df087bc https://github.com/galaxyproject/galaxy/commit/4f0ec1eaf262f170877863687215… Author: Michael R. Crusoe <michael.crusoe(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M lib/galaxy/objectstore/__init__.py Log Message: ----------- Merge pull request #1 from dannon/storableobject Revert most of the 79-char linewrapping in objectstore Commit: 320724a183fb6391fa54d3e385f01af11c45aecf https://github.com/galaxyproject/galaxy/commit/320724a183fb6391fa54d3e385f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-21 (Wed, 21 Oct 2015) Changed paths: M CONTRIBUTING.md M lib/galaxy/jobs/command_factory.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M test/unit/test_objectstore.py Log Message: ----------- Merge pull request #853 from mr-c/storableobject doc updates for ObjectStore Compare: https://github.com/galaxyproject/galaxy/compare/e5cde4f8143f...320724a183fb

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[galaxyproject/galaxy] 27ab6f: Use the database temp directory store the Mako tem...
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27ab6fe8f935686c066d59b84ea1f55c3d982472 https://github.com/galaxyproject/galaxy/commit/27ab6fe8f935686c066d59b84ea1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Use the database temp directory store the Mako template cache when running framework tests. Commit: e5cde4f8143fb667afb907cc996daf93dea69bd1 https://github.com/galaxyproject/galaxy/commit/e5cde4f8143fb667afb907cc996d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M scripts/functional_tests.py Log Message: ----------- Merge pull request #956 from natefoo/fix-tests Use the database temp directory to store the Mako template cache when running framework tests. Compare: https://github.com/galaxyproject/galaxy/compare/4b3bc68ae05c...e5cde4f8143f

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[galaxyproject/galaxy] 732b4f: fix missing analytics on the analysis page
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 732b4f5b1f45a6e676ff70590944f3b6dcf8a77f https://github.com/galaxyproject/galaxy/commit/732b4f5b1f45a6e676ff70590944… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- fix missing analytics on the analysis page we abandoned base_panels for this page so the script was missing Commit: d53e13a4a997beec3cef5532ce39558296f54977 https://github.com/galaxyproject/galaxy/commit/d53e13a4a997beec3cef5532ce39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M templates/webapps/galaxy/root/index.mako Log Message: ----------- Merge pull request #958 from martenson/fix-google-analytics [15.10] Fix google analytics on the analysis page Compare: https://github.com/galaxyproject/galaxy/compare/0f9067d24445...d53e13a4a997

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[galaxyproject/galaxy] bc9972: Testing: update casperjs functional tests; change ...
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc9972bae27d9b24904744c280c9d52f873d43d2 https://github.com/galaxyproject/galaxy/commit/bc9972bae27d9b24904744c280c9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-19 (Mon, 19 Oct 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Testing: update casperjs functional tests; change expected size string; remove nice_size from expected history api keys; remove test for rerun button on uploaded dataset; attempt to fix linux+python unicode error in hda api tests Commit: 4b3bc68ae05c47156c3f8f3607bb5ceff901e982 https://github.com/galaxyproject/galaxy/commit/4b3bc68ae05c47156c3f8f3607bb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js Log Message: ----------- Merge pull request #944 from carlfeberhard/1510.casper Testing: update casperjs functional tests; change expected size strin… Compare: https://github.com/galaxyproject/galaxy/compare/6ee7f77cb341...4b3bc68ae05c

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[galaxyproject/galaxy] dd2d69: Fixed missing trackster navigation pane (issue #94...
by GitHub 20 Oct '15

20 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: dd2d6960db3cd14238a9b10595cc0f5840e8f92b https://github.com/galaxyproject/galaxy/commit/dd2d6960db3cd14238a9b10595cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fixed missing trackster navigation pane (issue #946) Please enter the commit message for your changes. Lines starting Commit: 0f9067d2444575760f138e7fe9c4b6302b172ace https://github.com/galaxyproject/galaxy/commit/0f9067d2444575760f138e7fe9c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-20 (Tue, 20 Oct 2015) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #957 from guerler/fix_trackster_001 [15.10] Fixed missing trackster navigation pane (issue #946) Compare: https://github.com/galaxyproject/galaxy/compare/b7dfeb417418...0f9067d24445

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