Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 989b6be3390e35d896122ef044ffe114f8959949 https://github.com/galaxyproject/galaxy/commit/989b6be3390e35d896122ef044ffe... Author: Dannon Baker <dannon.baker@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/d1ce1a623772d19f5fe9039c81e47... Author: Martin Cech <marten@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/4cb13b2404e4562c3d79e87076406... Author: Martin Cech <marten@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/5aaf95e0459bc2331492df9423d2c... Author: Martin Cech <marten@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/56874e163086b89d97dae17d59afa... Author: Martin Cech <marten@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/c8250ae68aea09fb7a1f15109aa5f... Author: Martin Cech <marten@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/f0570a20a8aab422aa6e3674a5aed... Author: Martin Cech <marten@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/c459cd66ba7ebb5fbd0bb49557eab... Author: Martin Cech <marten@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/a1c14ee8faca1e47ac8fca3691d73... Author: mvdbeek <m.vandenbeek@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/9ec6c13fa9196b87e30ed5a977695... Author: Bjoern Gruening <bjoern.gruening@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/d5f298baa59c05015fa1996744391... Author: Martin Cech <marten@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/f94fa8edbe12c8af3e2deb62c5c65... Author: Dannon Baker <dannon.baker@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/f9f206ca45e21a72c96ddaa7f0b2f... Author: Martin Cech <marten@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/15556c0a71eb7bbdf33f35158239b... Author: John Chilton <jmchilton@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/1bdd1620fe16a7036fae04d713135... Author: Martin Cech <marten@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/0b3e29199f33ad2f8ec0db3c9a750... Author: Nicola Soranzo <nsoranzo@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/9ebc464ba3f4d78822603638df003... Author: Nicola Soranzo <nsoranzo@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/6f8472e525345b74fb6818bd2d89c... Author: guerler <aysam.guerler@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/aa8aafb10958d555874d4288c6a3b... Author: Martin Cech <marten@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/3d1da8e11d5acfebddda760ea2de7... Author: Martin Cech <marten@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/0268f5078c28d5cfb05845fd09aaa... Author: Martin Cech <marten@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/e0c01115249a68abbd96fbc2f4e99... Author: Nicola Soranzo <nicola.soranzo@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