- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 989b6b: Change to only inheriting 'name' tags -- we may wa...
by GitHub 24 May '17

24 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 989b6be3390e35d896122ef044ffe114f8959949 https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively. Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7 https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst Log Message: ----------- initial version of RN Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5 https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add 17.05 to the release list Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/_thanks.rst M doc/source/releases/older_releases.rst Log Message: ----------- fix links to wiki/hub Commit: 56874e163086b89d97dae17d59afa004777936bd https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- rn improvements Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966 https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new options from galaxy.ini diff Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89 https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- link to proper release-bound sample config Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new datatypes section to the announce Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Do not modify self.app.config.tool_data_path and self.app.config.tool_data_table_config_path during metadata setting. xref https://github.com/galaxyproject/tools-iuc/issues/1315. I suspect multiple threads installing tool simultaneously may have led to self.app.config.tool_data_path and/or self.app.config.tool_data_table_config_path being set to a temporary directory. Initial testing looks like this is not necessary. Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0 https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-05-21 (Sun, 21 May 2017) Changed paths: M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml Log Message: ----------- update openbabel to version 2.4.1 Commit: d5f298baa59c05015fa19967443915e1c4faf595 https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa199674439… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add Thoba's email Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00 https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4095 from martenson/contrib-email [17.05] add Thoba's email to contributors Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950 https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- polish release notes, add links to tutorials Commit: 15556c0a71eb7bbdf33f35158239b4a243441510 https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst Log Message: ----------- Merge pull request #4075 from martenson/17.05_release_notes [17.05] release notes Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d71313… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- listify new contributors Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415 https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml Log Message: ----------- Merge pull request #4094 from bgruening/openbabel_update [17.05] Open Babel update for datatype converters Commit: 9ebc464ba3f4d78822603638df00331864a1acf9 https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df00… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- Merge pull request #4100 from martenson/17.05_release_notes [17.05] release notes- listify new contributors Commit: 6f8472e525345b74fb6818bd2d89cd486435c822 https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fixes repeat handling in workflow editor, store values as passed from ui Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25 https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #4104 from dannon/tags_continued [17.05] Change to only inheriting 'name' tags Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #4089 from mvdbeek/no_global_changes [17.05] Do not modify self.app.config.tool_data_path Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7 https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #4107 from guerler/fix_repeats_in_workflows [17.05] Fixes repeat handling in workflow editor, store values as passed from ui Commit: e0c01115249a68abbd96fbc2f4e991578f5a5433 https://github.com/galaxyproject/galaxy/commit/e0c01115249a68abbd96fbc2f4e9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M CONTRIBUTORS.md A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/2aec5dda9ad7...e0c01115249a

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[galaxyproject/galaxy] 6f8472: Fixes repeat handling in workflow editor, store va...
by GitHub 23 May '17

23 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 6f8472e525345b74fb6818bd2d89cd486435c822 https://github.com/galaxyproject/galaxy/commit/6f8472e525345b74fb6818bd2d89… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fixes repeat handling in workflow editor, store values as passed from ui Commit: 0268f5078c28d5cfb05845fd09aaab783ad015c7 https://github.com/galaxyproject/galaxy/commit/0268f5078c28d5cfb05845fd09aa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Merge pull request #4107 from guerler/fix_repeats_in_workflows [17.05] Fixes repeat handling in workflow editor, store values as passed from ui Compare: https://github.com/galaxyproject/galaxy/compare/3d1da8e11d5a...0268f5078c28

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[galaxyproject/galaxy] a1c14e: Do not modify self.app.config.tool_data_path
by GitHub 23 May '17

23 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: a1c14ee8faca1e47ac8fca3691d734f47b587f6b https://github.com/galaxyproject/galaxy/commit/a1c14ee8faca1e47ac8fca3691d7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-19 (Fri, 19 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Do not modify self.app.config.tool_data_path and self.app.config.tool_data_table_config_path during metadata setting. xref https://github.com/galaxyproject/tools-iuc/issues/1315. I suspect multiple threads installing tool simultaneously may have led to self.app.config.tool_data_path and/or self.app.config.tool_data_table_config_path being set to a temporary directory. Initial testing looks like this is not necessary. Commit: 3d1da8e11d5acfebddda760ea2de74b22b3856eb https://github.com/galaxyproject/galaxy/commit/3d1da8e11d5acfebddda760ea2de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #4089 from mvdbeek/no_global_changes [17.05] Do not modify self.app.config.tool_data_path Compare: https://github.com/galaxyproject/galaxy/compare/aa8aafb10958...3d1da8e11d5a

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[galaxyproject/galaxy] 989b6b: Change to only inheriting 'name' tags -- we may wa...
by GitHub 23 May '17

23 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 989b6be3390e35d896122ef044ffe114f8959949 https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Change to only inheriting 'name' tags -- we may want to branch this out further in the future, but we'll start conservatively. Commit: aa8aafb10958d555874d4288c6a3bedffcac1f25 https://github.com/galaxyproject/galaxy/commit/aa8aafb10958d555874d4288c6a3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #4104 from dannon/tags_continued [17.05] Change to only inheriting 'name' tags Compare: https://github.com/galaxyproject/galaxy/compare/9ebc464ba3f4...aa8aafb10958

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[galaxyproject/galaxy] 47339b: Catch specific exception type
by GitHub 23 May '17

23 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47339bf1f33b52fade0db00a1af23eba34648da5 https://github.com/galaxyproject/galaxy/commit/47339bf1f33b52fade0db00a1af2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Catch specific exception type Also remove unused variable Commit: a033a5821ad11fbe0465b01984c97e591785623c https://github.com/galaxyproject/galaxy/commit/a033a5821ad11fbe0465b01984c9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Allow empty <environment_variable> Presently trying to install a ToolShed tool dependency defined as <tool_dependency> <set_environment version="1.0"> <environment_variable name="MYVAR" action="set_to"></environment_variable> </set_environment> </tool_dependency> results in EnvManager.create_env_var_dict() returning None, which in turn causes the dependency silently not being installed with this error in the logs: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler DEBUG 2017-05-23 10:08:23,798 Error setting environment for tool dependency: local variable 'tool_dependency' referenced before assignment Commit: e4de203c7da50aee3a95edacaf7f00d79b1ac416 https://github.com/galaxyproject/galaxy/commit/e4de203c7da50aee3a95edacaf7f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Raise an exception if name or action are not defined instead of silently skipping the <environment_variable> tool dependency Commit: 2aec5dda9ad7b66b0da6de08873b919d472b0309 https://github.com/galaxyproject/galaxy/commit/2aec5dda9ad7b66b0da6de08873b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #4105 from nsoranzo/ts_tool_dep_install_fixes ToolShed tool dependency install fixes Compare: https://github.com/galaxyproject/galaxy/compare/1bc8ea69c950...2aec5dda9ad7

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[galaxyproject/galaxy] 1bdd16: listify new contributors
by GitHub 22 May '17

22 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 1bdd1620fe16a7036fae04d7131356e7c80a1ccf https://github.com/galaxyproject/galaxy/commit/1bdd1620fe16a7036fae04d71313… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- listify new contributors Commit: 9ebc464ba3f4d78822603638df00331864a1acf9 https://github.com/galaxyproject/galaxy/commit/9ebc464ba3f4d78822603638df00… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- Merge pull request #4100 from martenson/17.05_release_notes [17.05] release notes- listify new contributors Compare: https://github.com/galaxyproject/galaxy/compare/0b3e29199f33...9ebc464ba3f4

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[galaxyproject/galaxy] 9ec6c1: update openbabel to version 2.4.1
by GitHub 22 May '17

22 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0 https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2017-05-21 (Sun, 21 May 2017) Changed paths: M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml Log Message: ----------- update openbabel to version 2.4.1 Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415 https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml Log Message: ----------- Merge pull request #4094 from bgruening/openbabel_update [17.05] Open Babel update for datatype converters Compare: https://github.com/galaxyproject/galaxy/compare/15556c0a71eb...0b3e29199f33

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[galaxyproject/galaxy] d1ce1a: initial version of RN
by GitHub 22 May '17

22 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7 https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst Log Message: ----------- initial version of RN Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5 https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/index.rst Log Message: ----------- add 17.05 to the release list Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/_thanks.rst M doc/source/releases/older_releases.rst Log Message: ----------- fix links to wiki/hub Commit: 56874e163086b89d97dae17d59afa004777936bd https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- rn improvements Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966 https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new options from galaxy.ini diff Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89 https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- link to proper release-bound sample config Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-17 (Wed, 17 May 2017) Changed paths: M doc/source/releases/17.05_announce.rst Log Message: ----------- add new datatypes section to the announce Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950 https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst Log Message: ----------- polish release notes, add links to tutorials Commit: 15556c0a71eb7bbdf33f35158239b4a243441510 https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: A doc/source/releases/17.05.rst M doc/source/releases/17.05_announce.rst A doc/source/releases/17.09_announce.rst M doc/source/releases/_thanks.rst M doc/source/releases/index.rst M doc/source/releases/older_releases.rst Log Message: ----------- Merge pull request #4075 from martenson/17.05_release_notes [17.05] release notes Compare: https://github.com/galaxyproject/galaxy/compare/f94fa8edbe12...15556c0a71eb

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[galaxyproject/galaxy] d5f298: add Thoba's email
by GitHub 22 May '17

22 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: d5f298baa59c05015fa19967443915e1c4faf595 https://github.com/galaxyproject/galaxy/commit/d5f298baa59c05015fa199674439… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- add Thoba's email Commit: f94fa8edbe12c8af3e2deb62c5c65cf9b437ca00 https://github.com/galaxyproject/galaxy/commit/f94fa8edbe12c8af3e2deb62c5c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Merge pull request #4095 from martenson/contrib-email [17.05] add Thoba's email to contributors Compare: https://github.com/galaxyproject/galaxy/compare/73bf5b4f7502...f94fa8edbe12

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[galaxyproject/galaxy] a2ed7f: More workflow test case fixes for #4047.
by GitHub 20 May '17

20 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2ed7f2fc83dfbbe3bd32b7da7a0957a4c552864 https://github.com/galaxyproject/galaxy/commit/a2ed7f2fc83dfbbe3bd32b7da7a0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-20 (Sat, 20 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- More workflow test case fixes for #4047. I think previously this button would be there on page load and now it is loaded after the page in JS. Commit: 1bc8ea69c950eeb9525b393c86bf92b93e2efcfc https://github.com/galaxyproject/galaxy/commit/1bc8ea69c950eeb9525b393c86bf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-20 (Sat, 20 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #4093 from jmchilton/selenium_fixes_14 More workflow test case fixes for #4047. Compare: https://github.com/galaxyproject/galaxy/compare/3f4d820b466d...1bc8ea69c950

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