- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 562489: Fix #3990, don't chown non-galaxy files
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 562489ad013a3322c584b7665a0381ba39590fbd https://github.com/galaxyproject/galaxy/commit/562489ad013a3322c584b7665a03… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix #3990, don't chown non-galaxy files Commit: 3529897b88889b98e61efcec8e50fa56395281b4 https://github.com/galaxyproject/galaxy/commit/3529897b88889b98e61efcec8e50… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #4186 from dpryan79/fix3990 Fix #3990, don't chown non-galaxy files Compare: https://github.com/galaxyproject/galaxy/compare/dab07a67151e...3529897b8888

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[galaxyproject/galaxy] 55956f: Expose 4 more rows from the galaxy_user table to h...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55956fe2ca49fe9a1d1a8fc52b221e6fc05e07a6 https://github.com/galaxyproject/galaxy/commit/55956fe2ca49fe9a1d1a8fc52b22… Author: Tim Thompson <tim.thompson(a)xdbio.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Expose 4 more rows from the galaxy_user table to help out sys admins doing user management via the API Commit: e320fd4a2009aa4c155d0cbbdd549a9f07295108 https://github.com/galaxyproject/galaxy/commit/e320fd4a2009aa4c155d0cbbdd54… Author: XDtim <tim.thompson(a)xdbio.com> Date: 2017-07-03 (Mon, 03 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Impliment review comments from @nsoranzo Commit: 57d5b485b505f64fa9035a1c739c4030ae8951d9 https://github.com/galaxyproject/galaxy/commit/57d5b485b505f64fa9035a1c739c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-04 (Tue, 04 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge remote-tracking branch 'XDtim/dev' into users_api Commit: d9607684ef7d880e213d4e08d07ed2582875e286 https://github.com/galaxyproject/galaxy/commit/d9607684ef7d880e213d4e08d07e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py A test/integration/test_config_options_users.py Log Message: ----------- Tweak exposing user attributes to use an include list instead of exclude list. This allows for the addition of new dictifiable attributes on user like in 55956fe2ca49fe9a1d1a8fc52b221e6fc05e07a6 without exposing these attributes to non-admin users. Commit: dab07a67151e59ae989c6dd07ea272a03acdb36b https://github.com/galaxyproject/galaxy/commit/dab07a67151e59ae989c6dd07ea2… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/users.py A test/integration/test_config_options_users.py Log Message: ----------- Merge pull request #4274 from jmchilton/users_api Expose more user properties to admins via the API. Compare: https://github.com/galaxyproject/galaxy/compare/9eb3c0f40a42...dab07a67151e

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af5399… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 9eb3c0f40a425b74adc03ee0e72442a292225c98 https://github.com/galaxyproject/galaxy/commit/9eb3c0f40a425b74adc03ee0e724… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/style/blue/base.css test/functional/tools/sample_datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/7baf86f7c137...9eb3c0f40a42

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Commit: d0893b91ae281a17b3ae1bc210f197c6f259103c https://github.com/galaxyproject/galaxy/commit/d0893b91ae281a17b3ae1bc210f1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/bd2d52800e77...d0893b91ae28

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Commit: bfb3ce6e79074c42803444701e814c65631ac0cd https://github.com/galaxyproject/galaxy/commit/bfb3ce6e79074c42803444701e81… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.10' into release_17.01 Conflicts: test/functional/tools/sample_datatypes_conf.xml Compare: https://github.com/galaxyproject/galaxy/compare/96e1cf58f480...bfb3ce6e7907

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Commit: fada8d2a60e625cf16fce7e20715422f86d6f40c https://github.com/galaxyproject/galaxy/commit/fada8d2a60e625cf16fce7e20715… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/490e565611b5...fada8d2a60e6

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[galaxyproject/galaxy] f88ee3: avoids broken mercurial conda version
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f88ee34792d86766fb68109fc518d9defcc469bd https://github.com/galaxyproject/galaxy/commit/f88ee34792d86766fb68109fc518… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- avoids broken mercurial conda version Commit: 7baf86f7c1373572db5d5b18a4686a7b90056b89 https://github.com/galaxyproject/galaxy/commit/7baf86f7c1373572db5d5b18a468… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #4227 from bwlang/galaxy_with_conda_python avoids broken version of mercurial in conda Compare: https://github.com/galaxyproject/galaxy/compare/20ef3eebcf2c...7baf86f7c137

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[galaxyproject/galaxy] 0ff61d: Fix Registry.get_datatype_by_extension() to return...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 0ff61d9ffc93063f8c2e6261a1ea6c36c1176d77 https://github.com/galaxyproject/galaxy/commit/0ff61d9ffc93063f8c2e6261a1ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix Registry.get_datatype_by_extension() to return None if ext is unknown Without this fix, the Cheetah expression: $dataset.is_of_type('unknown_ext') in a tool command would be equivalent to: $dataset.is_of_type('txt') meaning that if the dataset datatype is a subclass of Text, the expression would evaluate to True without any warning. xref. https://github.com/galaxyproject/tools-iuc/issues/1373 Also add missing `xml` datatype to `test/functional/tools/sample_datatypes_conf.xml` which is needed by 3 test tools. Commit: 5a39d47b0adde675fc195c5d8b9c82c13917a233 https://github.com/galaxyproject/galaxy/commit/5a39d47b0adde675fc195c5d8b9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4230 from nsoranzo/release_16.07_backport_4224 [16.07] Backport #4224 Compare: https://github.com/galaxyproject/galaxy/compare/80ecc79a4cb8...5a39d47b0add

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[galaxyproject/galaxy] c8eff8: Remove float style from color picker label
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c8eff858d68cdbea85524c4e366cc479ba556dcd https://github.com/galaxyproject/galaxy/commit/c8eff858d68cdbea85524c4e366c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove float style from color picker label Commit: bd2d52800e7776ead1c8c7af53995d13cd288397 https://github.com/galaxyproject/galaxy/commit/bd2d52800e7776ead1c8c7af5399… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Merge pull request #4233 from guerler/fix_color_picker_release [17.05] Remove float style from color picker label Compare: https://github.com/galaxyproject/galaxy/compare/9dca211e2fe5...bd2d52800e77

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[galaxyproject/galaxy] 6f9863: Fix import order and Python3 compatibility for 51 ...
by GitHub 05 Jul '17

05 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6f98634dd51ac40848a2e16662782378f8022bfd https://github.com/galaxyproject/galaxy/commit/6f98634dd51ac40848a2e1666278… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py Log Message: ----------- Fix import order and Python3 compatibility for 51 files xref. https://github.com/galaxyproject/galaxy/issues/1715 Also remove unused `get_track_window()` method of some datatypes. Commit: 20ef3eebcf2cf02fa79ca752f79e430b14802800 https://github.com/galaxyproject/galaxy/commit/20ef3eebcf2cf02fa79ca752f79e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/dataset_collections/matching.py M lib/galaxy/dataset_collections/registry.py M lib/galaxy/dataset_collections/structure.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/model/tool_shed_install/mapping.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/webhooks/__init__.py M lib/galaxy/work/context.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/render.py M lib/galaxy/workflow/run_request.py M lib/galaxy/workflow/scheduling_manager.py M lib/log_tempfile.py Log Message: ----------- Merge pull request #4236 from nsoranzo/python3 Fix import order and Python3 compatibility for 51 files Compare: https://github.com/galaxyproject/galaxy/compare/79f3dc00a61d...20ef3eebcf2c

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