July 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 74c7ef: Update readme with sudo -> become
by GitHub 06 Jul '16

06 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 74c7ef3fda564044b5227b2d78238c9338eb212d https://github.com/galaxyproject/ansible-galaxy/commit/74c7ef3fda564044b522… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M README.md Log Message: ----------- Update readme with sudo -> become Commit: bf923e5b6c51ae8d1dd63c2b6a233ba444c5587e https://github.com/galaxyproject/ansible-galaxy/commit/bf923e5b6c51ae8d1dd6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M README.md Log Message: ----------- Merge pull request #15 from mvdbeek/readme_update Update readme with sudo -> become Compare: https://github.com/galaxyproject/ansible-galaxy/compare/7ccdf33d5fe1...bf92…

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[galaxyproject/usegalaxy-playbook] 829825: Update Main builds.txt from Test
by GitHub 06 Jul '16

06 Jul '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8298250e29b45b9632cd3152add52c61d9bbc65f https://github.com/galaxyproject/usegalaxy-playbook/commit/8298250e29b45b96… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M files/galaxy/usegalaxy.org/config/builds.txt Log Message: ----------- Update Main builds.txt from Test Commit: 8a200a9e655c5814b0a0bee8b919aca16315e5fc https://github.com/galaxyproject/usegalaxy-playbook/commit/8a200a9e655c5814… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-07-06 (Wed, 06 Jul 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/bd322e8de6c1...…

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[galaxyproject/galaxy] 1507bd: More defensive proxying
by GitHub 05 Jul '16

05 Jul '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 1507bd37fe8cb872975e46a6e7be468e984db0d8 https://github.com/galaxyproject/galaxy/commit/1507bd37fe8cb872975e46a6e7be… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- More defensive proxying Commit: f8e40bb5951cc38dce118cebcc09a5cc3ca96930 https://github.com/galaxyproject/galaxy/commit/f8e40bb5951cc38dce118cebcc09… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/web/proxy/js/lib/proxy.js Log Message: ----------- Merge pull request #2585 from erasche/backport-proxy-fix [16.04] Backport proxy fixes Compare: https://github.com/galaxyproject/galaxy/compare/1069a69ae08a...f8e40bb5951c

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[galaxyproject/galaxy] 56b500: Tabular dataset chunking fix which should prevent ...
by GitHub 05 Jul '16

05 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56b5002aababf39a11d8e6fd794a19382f5f767f https://github.com/galaxyproject/galaxy/commit/56b5002aababf39a11d8e6fd794a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Tabular dataset chunking fix which should prevent duplicated lines. Skipping to the newline previously shifted the chunk past where it should read. Commit: 0ab502baa1ae0e16c9345c3ac816a1dde5cb54d9 https://github.com/galaxyproject/galaxy/commit/0ab502baa1ae0e16c9345c3ac816… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-22 (Wed, 22 Jun 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Rename vars to be sensible, add comment to clarify what this is doing. Commit: a630c92df447ce67d145bb6c22a24cd9ab647259 https://github.com/galaxyproject/galaxy/commit/a630c92df447ce67d145bb6c22a2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #2527 from dannon/fix_tabular_display_chunking Fix tabular display chunking Compare: https://github.com/galaxyproject/galaxy/compare/3eeedc61e84c...a630c92df447

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[galaxyproject/galaxy] 861740: Fix dataset matcher when no tool available.
by GitHub 05 Jul '16

05 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 861740bd6080bf0ab280594d24460143cbee1033 https://github.com/galaxyproject/galaxy/commit/861740bd6080bf0ab280594d2446… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Fix dataset matcher when no tool available. Broken with 80ac816af94d43d7214671582db127483baea2d3. Commit: 3eeedc61e84c6007223777b09b6629f8f83ad385 https://github.com/galaxyproject/galaxy/commit/3eeedc61e84c6007223777b09b66… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #2540 from zipho/dev Fix dataset matcher when no tool available. Compare: https://github.com/galaxyproject/galaxy/compare/dd1298077718...3eeedc61e84c

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[galaxyproject/galaxy] adb5be: Add a password expiration config option
by GitHub 05 Jul '16

05 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: adb5be5b71a87de85d0397da2c72673a5730a675 https://github.com/galaxyproject/galaxy/commit/adb5be5b71a87de85d0397da2c72… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/webapps/galaxy/controllers/user.py M templates/user/change_password.mako Log Message: ----------- Add a password expiration config option Add a "last_password_change" field to user table and user object. Add a config option "password expiration_period" to allow admins to require users to change passwords every so many days. On login, check for the presence of the config option and if the user pw has expired, redirect to the "change password" page. Commit: 188df8c84265ddcf55712d4cf0e8a485cad7665b https://github.com/galaxyproject/galaxy/commit/188df8c84265ddcf55712d4cf0e8… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix missing whitespace around arithmetic operator warning Commit: d31ce0d95949d3ed2f956398d5883d28fa7f65fd https://github.com/galaxyproject/galaxy/commit/d31ce0d95949d3ed2f956398d588… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-06-10 (Fri, 10 Jun 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Improve wording of password expired message. Stylistic changes Commit: 201a514cfde26dd0f3c2089f9544f2d2693cf2fb https://github.com/galaxyproject/galaxy/commit/201a514cfde26dd0f3c2089f9544… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix file permissions. Commit: 7a480e8c9ee180f6699535a4c321d959ba684699 https://github.com/galaxyproject/galaxy/commit/7a480e8c9ee180f6699535a4c321… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-06-15 (Wed, 15 Jun 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Don't actually log the person in in the event that their password has expired. Change 'about to expire' warning to a warning and not an error. Commit: 0e6a09e94fbaaaae7ce5fe0e028fd37cdf758d3c https://github.com/galaxyproject/galaxy/commit/0e6a09e94fbaaaae7ce5fe0e028f… Author: Ben Fulton <benmarkfulton(a)gmail.com> Date: 2016-06-17 (Fri, 17 Jun 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1 from dannon/ForcePasswordChange Fix file permissions. Commit: d9e3d69b78b863823302d59af9bf0eeeb5cba1e8 https://github.com/galaxyproject/galaxy/commit/d9e3d69b78b863823302d59af9bf… Author: Ben Fulton <befulton(a)iu.edu> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M lib/galaxy/webapps/tool_shed/config.py Log Message: ----------- Add password_expiration_period to toolshed config This is necessary as it shares the user class with the galaxy app. Commit: dd12980777181092984b16c786ed1eaf3aafa08b https://github.com/galaxyproject/galaxy/commit/dd12980777181092984b16c786ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/tool_shed/config.py M templates/user/change_password.mako Log Message: ----------- Merge pull request #2486 from benfulton/ForcePasswordChange Add a password expiration config option (resolves #2485) Compare: https://github.com/galaxyproject/galaxy/compare/a946b0431680...dd1298077718

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[galaxyproject/galaxy] a77e3f: Add tox.ini config params for python3.5
by GitHub 05 Jul '16

05 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a77e3ff6607a86a85a30bfa552402e57602ab0e2 https://github.com/galaxyproject/galaxy/commit/a77e3ff6607a86a85a30bfa55240… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M tox.ini Log Message: ----------- Add tox.ini config params for python3.5 Commit: c9cbcf6f79b8d6ae3fa6fa6178c0d59440b8545b https://github.com/galaxyproject/galaxy/commit/c9cbcf6f79b8d6ae3fa6fa6178c0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Python3: fix passwords.py Commit: bd92dc17fc8314806db39354c1c6d07286a97550 https://github.com/galaxyproject/galaxy/commit/bd92dc17fc8314806db39354c1c6… Author: Xiaoqian Jiang <jxq198409(a)hotmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/unit/managers/base.py M tox.ini Log Message: ----------- Python3: test/unit/managers/base.py Commit: dd931f9691f2599b4c6642015c95bc10a7f6590a https://github.com/galaxyproject/galaxy/commit/dd931f9691f2599b4c6642015c95… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/unit/test_galaxy_mapping.py Log Message: ----------- Python3: test/unit/test_galaxy_mapping.py Commit: dba8d0bb0a717427a9f3647f9f32935f60c5f063 https://github.com/galaxyproject/galaxy/commit/dba8d0bb0a717427a9f3647f9f32… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M tools/stats/aggregate_scores_in_intervals.py Log Message: ----------- Python3: tools/stats/aggregate_scores_in_intervals.py Commit: 17fc7ac5bc8b3a2f973fd2ed8337682223d514c6 https://github.com/galaxyproject/galaxy/commit/17fc7ac5bc8b3a2f973fd2ed8337… Author: Xiaoqian Jiang <jxq198409(a)hotmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_DatasetManager.py Log Message: ----------- Python3: test/unit/managers/test_DatasetManager.py Commit: 2fd84dd4995c03f966dbdd1df26dc984e3bbd975 https://github.com/galaxyproject/galaxy/commit/2fd84dd4995c03f966dbdd1df26d… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/interval_to_coverage.py Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_coverage.py Commit: ac07c6238136bf2e2a90fd259dcd6d7312786e90 https://github.com/galaxyproject/galaxy/commit/ac07c6238136bf2e2a90fd259dcd… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'python3' of github.com:bxlab/galaxy_hackathon into python3 Commit: 7d7396f18f65e393ff330cdb9f509fd7036eb804 https://github.com/galaxyproject/galaxy/commit/7d7396f18f65e393ff330cdb9f50… Author: Junzhou Wang <junzhouwang(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py Log Message: ----------- Python3: test/api/ Commit: 5939c5fc2666ecd649ab033c23d432f6572eb7b1 https://github.com/galaxyproject/galaxy/commit/5939c5fc2666ecd649ab033c23d4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/dataset_collections/structure.py M lib/galaxy/security/__init__.py Log Message: ----------- Python3: lib/galaxy/dataset_collections/ and lib/galaxy/security/ Commit: 1fadc336a0bb228c9b96f3826e44fec327261740 https://github.com/galaxyproject/galaxy/commit/1fadc336a0bb228c9b96f3826e44… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/binary.py Log Message: ----------- Python3: lib/galaxy/datatypes/binary.py Commit: c9ad6e31ba5a29d1c7d23842ea23fb6d222738c1 https://github.com/galaxyproject/galaxy/commit/c9ad6e31ba5a29d1c7d23842ea23… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py Commit: 578ed609b7f836733c7225e5ee44a09536a39160 https://github.com/galaxyproject/galaxy/commit/578ed609b7f836733c7225e5ee44… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M lib/galaxy/datatypes/converters/interval_to_bed_converter.py Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_bed_converter.py Commit: 4b9f433f2d9b63b04477063e7321a8ac19fc370c https://github.com/galaxyproject/galaxy/commit/4b9f433f2d9b63b04477063e7321… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Forgot py3_sources.txt for prev commit Commit: a04f6589eae995352e5bbcc9c0a73481a3abe8a8 https://github.com/galaxyproject/galaxy/commit/a04f6589eae995352e5bbcc9c0a7… Author: Junzhou Wang <junzhouwang(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M scripts/api/data_manager_example_execute.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py Log Message: ----------- Python3: test/shed_functional/ and test/unit/ Commit: 44d895ae500b1d20ec615aa839cfd2f56efc6d30 https://github.com/galaxyproject/galaxy/commit/44d895ae500b1d20ec615aa839cf… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/sequence.py Log Message: ----------- Python3: lib/galaxy/datatypes/sequence.py Commit: f01c98bdccb8f4215f3beb525a7dc5e43bc061b4 https://github.com/galaxyproject/galaxy/commit/f01c98bdccb8f4215f3beb525a7d… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py Log Message: ----------- Python3: more lib/galaxy/datatypes/converters/ lib/galaxy/datatypes/converters/fastq_to_fqtoc.py lib/galaxy/datatypes/converters/gff_to_bed_converter.py Commit: dc37a5f19c456376a8f9d996a5a73fbd1c42e212 https://github.com/galaxyproject/galaxy/commit/dc37a5f19c456376a8f9d996a5a7… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M tox.ini Log Message: ----------- flake8 2.6.2 released Commit: 9c3e8e5f95b64fcbb764578fa45b3aaf26832dbc https://github.com/galaxyproject/galaxy/commit/9c3e8e5f95b64fcbb764578fa45b… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M tox.ini Log Message: ----------- Merge branch 'python3' of github.com:bxlab/galaxy_hackathon into python3 Commit: 6ea74e2c1f272dc7c71e480a98b6c125a6fafde6 https://github.com/galaxyproject/galaxy/commit/6ea74e2c1f272dc7c71e480a98b6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/sniff.py Log Message: ----------- Python3: lib/galaxy/datatypes/sniff.py Commit: 9fd77057339260e3c0c2cba802510e93db761c6f https://github.com/galaxyproject/galaxy/commit/9fd77057339260e3c0c2cba80251… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/bed_to_gff_converter.py Log Message: ----------- Python3: lib/galaxy/datatypes/converters/bed_to_gff_converter.py Commit: 3f4f7af2f147ef534372e903b68e1877e86fc8cb https://github.com/galaxyproject/galaxy/commit/3f4f7af2f147ef534372e903b68e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/tabular.py Log Message: ----------- Python3: lib/galaxy/datatypes/tabular.py Commit: e45f8abb54a3008e11eb22a478c0521d39626629 https://github.com/galaxyproject/galaxy/commit/e45f8abb54a3008e11eb22a478c0… Author: Junzhou Wang <junzhouwang(a)gmail.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py Log Message: ----------- Python3:script/api/ Commit: 3b31f02d07834882a46ebcd2ff82423c2f4b5df2 https://github.com/galaxyproject/galaxy/commit/3b31f02d07834882a46ebcd2ff82… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py Log Message: ----------- Python 3: more lib/galaxy/datatypes/converters/ lib/galaxy/datatypes/converters/lped_to_fped_converter.py lib/galaxy/datatypes/converters/lped_to_pbed_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py Commit: ef335721679618b9c53b6024610d6bc024129774 https://github.com/galaxyproject/galaxy/commit/ef335721679618b9c53b6024610d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-25 (Sat, 25 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/util/gff_util.py Log Message: 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lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/pbed_to_lped_converter.py lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py Commit: 1b06c52e8d62c864e9a4f45a038cd3482db9f9d6 https://github.com/galaxyproject/galaxy/commit/1b06c52e8d62c864e9a4f45a038c… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Python3: sort, remove dup in .ci/py3_sources.txt Commit: 2c67f1e7e59939d17fd91ca13c8d898ae887a8b7 https://github.com/galaxyproject/galaxy/commit/2c67f1e7e59939d17fd91ca13c8d… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M 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lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py Commit: de99c7efe2d6c540d6388206ae7673a54204d85d https://github.com/galaxyproject/galaxy/commit/de99c7efe2d6c540d6388206ae76… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py Log Message: ----------- Python3: lib/galaxy/visualization/ Commit: 005429acbb2c9e09b4b653dc93b4eff2ee883a77 https://github.com/galaxyproject/galaxy/commit/005429acbb2c9e09b4b653dc93b4… Author: Timur Shtatland <shtatland(a)neb.com> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M 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lib/galaxy/model/migrate/versions/0022_visualization_tables.py lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py Commit: 9ad9c0c80a1521abec0404e319ef41d89d5a9c50 https://github.com/galaxyproject/galaxy/commit/9ad9c0c80a1521abec0404e319ef… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M 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lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M 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lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M 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lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py Log Message: ----------- Python 3: remaining model migrations Commit: 6a870a7345353d2ad24b0d9280d87dcd3770325e https://github.com/galaxyproject/galaxy/commit/6a870a7345353d2ad24b0d9280d8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Simplify .ci/py3_sources.txt Commit: 5feefc73b367c09be6775c1372f0872830ce448d https://github.com/galaxyproject/galaxy/commit/5feefc73b367c09be6775c1372f0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-27 (Mon, 27 Jun 2016) Changed paths: M .ci/py3_sources.txt Log Message: ----------- Simplify .ci/py3_sources.txt Commit: 40f85f291327c217d7603f59c5454f38016d1e71 https://github.com/galaxyproject/galaxy/commit/40f85f291327c217d7603f59c545… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-27 (Mon, 27 Jun 2016) Changed paths: M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M test/api/test_workflows.py Log Message: ----------- Python3: add missing print_function imports Commit: 9a97a2952f3c33a496157e86719fc41e10d32382 https://github.com/galaxyproject/galaxy/commit/9a97a2952f3c33a496157e86719f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-06-29 (Wed, 29 Jun 2016) Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py Log Message: ----------- Python3: test/unit/ Commit: a946b04316802f56f493b867d0755692a4f9753f https://github.com/galaxyproject/galaxy/commit/a946b04316802f56f493b867d075… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-07-05 (Tue, 05 Jul 2016) Changed paths: M .ci/py3_sources.txt M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py M scripts/api/data_manager_example_execute.py M scripts/api/example_watch_folder.py M scripts/api/form_create_from_xml.py M scripts/api/history_create_history.py M scripts/api/history_delete_history.py M scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge pull request #2574 from bxlab/python3 Python3: port 215 files Compare: https://github.com/galaxyproject/galaxy/compare/6c995f73fb5b...a946b0431680

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[galaxyproject/galaxy] aeb05e: Add Makefile target for fetching updated bower dep...
by GitHub 03 Jul '16

03 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aeb05e7645a37ffd5cd60b382a429959fca4a20b https://github.com/galaxyproject/galaxy/commit/aeb05e7645a37ffd5cd60b382a42… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-06-23 (Thu, 23 Jun 2016) Changed paths: M Makefile Log Message: ----------- Add Makefile target for fetching updated bower dependencies. This mirrors the existing `client` target and serves as top-level documentation for how to perform this action. Commit: 6c995f73fb5bd815c03d1ed2ac9284dac607f483 https://github.com/galaxyproject/galaxy/commit/6c995f73fb5bd815c03d1ed2ac92… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-03 (Sun, 03 Jul 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #2534 from jmchilton/client-install-deps Add Makefile target for fetching updated bower dependencies. Compare: https://github.com/galaxyproject/galaxy/compare/00556bd91275...6c995f73fb5b

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[galaxyproject/galaxy] 3d688e: Allow users to purge datasets by default
by GitHub 01 Jul '16

01 Jul '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3d688e6bcf49e15fc12f45590250d34cccd0d8cb https://github.com/galaxyproject/galaxy/commit/3d688e6bcf49e15fc12f45590250… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-06-26 (Sun, 26 Jun 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Allow users to purge datasets by default Commit: 00556bd9127579e7b46811f186a0ed3b40dd4b66 https://github.com/galaxyproject/galaxy/commit/00556bd9127579e7b46811f186a0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-07-01 (Fri, 01 Jul 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Merge pull request #2553 from natefoo/user-purge-default Allow users to purge datasets by default Compare: https://github.com/galaxyproject/galaxy/compare/537b917b4f56...00556bd91275

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