Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71c79fda324877fb133f5f4194ac546be3041ee2 https://github.com/galaxyproject/galaxy/commit/71c79fda324877fb133f5f4194ac5... Author: E Rasche <hxr@hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- File sizes were not being added Commit: 6a20984c57501b49a74dccb7992799a19abf7e6e https://github.com/galaxyproject/galaxy/commit/6a20984c57501b49a74dccb799279... Author: E Rasche <hxr@hx42.org> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- try harder to handle unexpected values Commit: 624e9028cc3b359dc3b546f735ab62ec00439f97 https://github.com/galaxyproject/galaxy/commit/624e9028cc3b359dc3b546f735ab6... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-02 (Wed, 02 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- [18.01] More tool state performance fixes. Fix performance problems that can be encountered when matching collection inputs. It would use the old style matching to find an initial value to plug into the tool state - if there were no collections that matched or there were some big collections toward the top of the history that did not match this could completely undo performance fixes in 5997. More Pythonic input type conditional logic. Commit: f371d3f7094086ae183b3abc9cb3dc38ff361886 https://github.com/galaxyproject/galaxy/commit/f371d3f7094086ae183b3abc9cb3d... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix paired identifier casting issue. Commit: 3b5d8ae99c5d6d8f040d6554320bb50e41fa58a4 https://github.com/galaxyproject/galaxy/commit/3b5d8ae99c5d6d8f040d6554320bb... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Fix x in column definition screen to eliminate correct def. Commit: 5bd2cbd80b35cc5ddddce808f17c13ce1381bc36 https://github.com/galaxyproject/galaxy/commit/5bd2cbd80b35cc5ddddce808f17c1... Author: vjalili <jalili.vahid@gmail.com> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Alter `extra_data` column on an oidc-related table from TXT to JSON. Commit: 545b7a4fe2bee6c967f0b4dcf850df842491e6bc https://github.com/galaxyproject/galaxy/commit/545b7a4fe2bee6c967f0b4dcf850d... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py Log Message: ----------- Merge pull request #6046 from jmchilton/tool_state_part_2 [18.01] More tool state performance fixes. Commit: 1b41cbba59bb09bdac305ff9de8d64dc4f873ee9 https://github.com/galaxyproject/galaxy/commit/1b41cbba59bb09bdac305ff9de8d6... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py Log Message: ----------- Merge pull request #6057 from VJalili/alter_extra_data [18.05] Alter the type of extra_data column of OIDC table. Commit: 96dcf54c438809c988eb063cf079bc7dbf4a5fe0 https://github.com/galaxyproject/galaxy/commit/96dcf54c438809c988eb063cf079b... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix quota styling for new anchor/link. Commit: 6bb5fa02fc20fdfbb69085a5a0bfe57dfc7ef93a https://github.com/galaxyproject/galaxy/commit/6bb5fa02fc20fdfbb69085a5a0bfe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Use standard styling for quotameter; this fixes danger/warning/success indicators and visibility. Commit: 8bee7b80cbe7c898da0c9968d1aae291da807b6d https://github.com/galaxyproject/galaxy/commit/8bee7b80cbe7c898da0c9968d1aae... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Improve error message for mismatched data inputs Commit: 89c12d6da2c797dbe2803768ad27657ac9a8e999 https://github.com/galaxyproject/galaxy/commit/89c12d6da2c797dbe2803768ad276... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- More standard quota-meter-text color Commit: f7354c0eb3e2198ba3536d22b4a6fad27822650e https://github.com/galaxyproject/galaxy/commit/f7354c0eb3e2198ba3536d22b4a6f... Author: Dannon <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/permutations.py Log Message: ----------- Merge pull request #6060 from mvdbeek/improve_error_message_unmatched_collections [18.01] Improve error message for mismatched data inputs Commit: 011e76a72647a48a3415a36bd19c17e2688175df https://github.com/galaxyproject/galaxy/commit/011e76a72647a48a3415a36bd19c1... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge pull request #6056 from jmchilton/rule_Builder_fixes_2 [18.05] Yet more rule builder fixes. Commit: b7c8fbe7c20c8c02cef182d7843a21d15346c1f1 https://github.com/galaxyproject/galaxy/commit/b7c8fbe7c20c8c02cef182d7843a2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Tinker with brand-succcess, address the brightness concern (which makes many locations look better, at least to me) Commit: 19d06cb971c23444065df718260ac307293c8926 https://github.com/galaxyproject/galaxy/commit/19d06cb971c23444065df718260ac... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: d729c31ffd6e7198e5970eaeda2bcf3a65c20ba6 https://github.com/galaxyproject/galaxy/commit/d729c31ffd6e7198e5970eaeda2bc... Author: John Chilton <jmchilton@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: 23b0169a17f3a4b1b705ee0dc0afe613e1cc29cd https://github.com/galaxyproject/galaxy/commit/23b0169a17f3a4b1b705ee0dc0afe... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix non-capped usage display as well. Commit: 2a9e44e7a217f0ec3d48dd10811b23bd8da86c44 https://github.com/galaxyproject/galaxy/commit/2a9e44e7a217f0ec3d48dd10811b2... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #6065 from jmchilton/rule_fixes_4 [18.05] Rules - bug fix for apply_rules tool on nested collections. Commit: 7c44139dc82e6cf1486b23593c811e0f653af932 https://github.com/galaxyproject/galaxy/commit/7c44139dc82e6cf1486b23593c811... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6062 from dannon/fix_quotameter_styling Fix quotameter styling Commit: ca48d49ea87b0716d27e8968c677b252c83b5ae9 https://github.com/galaxyproject/galaxy/commit/ca48d49ea87b0716d27e8968c677b... Author: guerler <aysam.guerler@gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Style fix for published grid pages Commit: 8aaee18cae21f645170e14a32db0fc0f172cfd01 https://github.com/galaxyproject/galaxy/commit/8aaee18cae21f645170e14a32db0f... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js Log Message: ----------- Merge pull request #6067 from guerler/bootstrap_shared_grid Style fix for published grid pages Commit: 400bcf1b04adf6afb8e83efc6379e527c93fa810 https://github.com/galaxyproject/galaxy/commit/400bcf1b04adf6afb8e83efc6379e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-06 (Sun, 06 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #6064 from jmchilton/rule_fixes_3 [18.05] Rules - test case & bug fixes for adding cols from regex groups. Commit: 8255d1ccc819c88c7d5ee197bbb5ed9d49759fc4 https://github.com/galaxyproject/galaxy/commit/8255d1ccc819c88c7d5ee197bbb5e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #5613 from erasche/fix-fraking-grt [18.01] File sizes not being annotated in GRT Commit: 0cfac515b546334e810caecf5cd02de8298de30a https://github.com/galaxyproject/galaxy/commit/0cfac515b546334e810caecf5cd02... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: c67c4b4b82dd4280e9fcef4003a9956c6c0ca062 https://github.com/galaxyproject/galaxy/commit/c67c4b4b82dd4280e9fcef4003a99... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/util/permutations.py M lib/galaxy/util/rules_dsl.py M scripts/grt/export.py M static/style/blue/base.css M test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3e49e31707fc...c67c4b4b82dd **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.