- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 63f674: Add routes for workflow import view, apply consist...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63f674c26d371569a3aaf8887a53f97e8707f951 https://github.com/galaxyproject/galaxy/commit/63f674c26d371569a3aaf8887a53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add routes for workflow import view, apply consistent routes Commit: 962811b586e7e2cbf4213fbeff914aac0c66a755 https://github.com/galaxyproject/galaxy/commit/962811b586e7e2cbf4213fbeff91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: A client/galaxy/scripts/components/WorkflowImport.vue Log Message: ----------- Add vue component for workflow import form Commit: 20ce0e42d9ef5a26539de08e1749eb1617e2960a https://github.com/galaxyproject/galaxy/commit/20ce0e42d9ef5a26539de08e1749… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Remove legacy view Commit: e55f8c5f56fceae6d3ec2e53a019c43407b4dba3 https://github.com/galaxyproject/galaxy/commit/e55f8c5f56fceae6d3ec2e53a019… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add import workflow from file option to api endpoint Commit: f086080c65e98ed60794fae6e4f7e552d5c9c42c https://github.com/galaxyproject/galaxy/commit/f086080c65e98ed60794fae6e4f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused controller endpoint, and disabled legacy option Commit: 68af8c9e780417a4e34de1ca349b1e5ace7c8e58 https://github.com/galaxyproject/galaxy/commit/68af8c9e780417a4e34de1ca349b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary check Commit: 5173d6f222c684d132c05684aae3b6e0c47b6e0c https://github.com/galaxyproject/galaxy/commit/5173d6f222c684d132c05684aae3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore broken installed_repository_file option Commit: b6ee0a53ec5c116e2aacb4f9e8f47868ba76bb51 https://github.com/galaxyproject/galaxy/commit/b6ee0a53ec5c116e2aacb4f9e8f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unnecessary spacing and unused variable Commit: 8a51d02ce641184bdb9da51eb6017004cfdfd777 https://github.com/galaxyproject/galaxy/commit/8a51d02ce641184bdb9da51eb601… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix library usage, and parameter naming Fix file reading caller Avoid using bare except Fix file parameter name Add missing library Commit: e5a564ef17990ba4b7c6db6381ef8fb98cd5bab9 https://github.com/galaxyproject/galaxy/commit/e5a564ef17990ba4b7c6db6381ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add additional checks for installed repository handler, open files using with-block Commit: 6a57ba8d28fb2f7c95850411118adb9e17c23c72 https://github.com/galaxyproject/galaxy/commit/6a57ba8d28fb2f7c95850411118a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Use archive_source and not url Commit: 51e32b6beaabe35fbd8a1cbaf38200d46ce33e3f https://github.com/galaxyproject/galaxy/commit/51e32b6beaabe35fbd8a1cbaf382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix error message Commit: 4c483a884a0948f86ca47e4b32494fc40e6764b8 https://github.com/galaxyproject/galaxy/commit/4c483a884a0948f86ca47e4b3249… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/WorkflowImport.vue M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Show warning if import was successful but has errors Commit: 12096d2a9fa4a7d177b419e0a7c7bbff9d1af982 https://github.com/galaxyproject/galaxy/commit/12096d2a9fa4a7d177b419e0a7c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix spacing in import block Commit: 3f34055e8ae3dccdaf8d235662b3e82591959bbd https://github.com/galaxyproject/galaxy/commit/3f34055e8ae3dccdaf8d235662b3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Attempt to fix selenium tests Fix lint Commit: 368691624bc408bdad2383f04e6fb5c266e2ff4a https://github.com/galaxyproject/galaxy/commit/368691624bc408bdad2383f04e6f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M scripts/common_startup.sh M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'exact_version_handling' into workflow_import Commit: 3a3c796fcf154e94d910f24e6e40b59afa999265 https://github.com/galaxyproject/galaxy/commit/3a3c796fcf154e94d910f24e6e40… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix failing tests Commit: 8ba207de7199c66090f9526e451b8095751790d8 https://github.com/galaxyproject/galaxy/commit/8ba207de7199c66090f9526e451b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore error handling variation Commit: 2fa340842cca7b46da121743153f5d31afe16eea https://github.com/galaxyproject/galaxy/commit/2fa340842cca7b46da121743153f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Remove api flag check from workflow manager Commit: 8d5c1d08d8e3eb8a459343b2b4f4e4376407ea5d https://github.com/galaxyproject/galaxy/commit/8d5c1d08d8e3eb8a459343b2b4f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Add source to workflow name Commit: 75c2c4f2494be66a459aece8e1707a6024e36e61 https://github.com/galaxyproject/galaxy/commit/75c2c4f2494be66a459aece8e170… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix import from myexperiment service Commit: 2cb4d52d4dbb1b3a74a5bcf01205cfa6cb3181f1 https://github.com/galaxyproject/galaxy/commit/2cb4d52d4dbb1b3a74a5bcf01205… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fix default parameters for 3rd party workflow import controller Commit: fbd9d81409df888cd99c4d3f05875721b4505baf https://github.com/galaxyproject/galaxy/commit/fbd9d81409df888cd99c4d3f0587… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Remove unused variable Commit: ffe9c3bd294c55b4c4576dcc5187a3593d1bf9a1 https://github.com/galaxyproject/galaxy/commit/ffe9c3bd294c55b4c4576dcc5187… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Remove unused source identifier Commit: fe4bff1fb9d84c057b40f04a9285ca5ca4dfb5fc https://github.com/galaxyproject/galaxy/commit/fe4bff1fb9d84c057b40f04a9285… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/config.py M lib/galaxy/managers/configuration.py M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Merge pull request #5804 from guerler/workflow_import Use vue and api to handle workflow imports Compare: https://github.com/galaxyproject/galaxy/compare/679083c935c1...fe4bff1fb9d8

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[galaxyproject/galaxy] fc546c: allow admins to set any role for library datasets ...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fc546cb1abd2060eea159cc1198e09b55fbaaf41 https://github.com/galaxyproject/galaxy/commit/fc546cb1abd2060eea159cc1198e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- allow admins to set any role for library datasets permissions this bug led to a funny problem where admins couldn't add themselves Commit: 51c05d7a28926a1257fb0b9b82d16f0a5b9d7ab2 https://github.com/galaxyproject/galaxy/commit/51c05d7a28926a1257fb0b9b82d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- modify checks that will never be true Commit: 7f9fcf99e403194558f5eb7a3f5545ee25a91c65 https://github.com/galaxyproject/galaxy/commit/7f9fcf99e403194558f5eb7a3f55… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- refactor the lib dataset update permissions process to mirror the library's Commit: 679083c935c10013dc4a24f9f2a8ead77651c567 https://github.com/galaxyproject/galaxy/commit/679083c935c10013dc4a24f9f2a8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/api/library_datasets.py Log Message: ----------- Merge pull request #5899 from martenson/fix-admin-datalib-perms Fix admin datalib dataset perms Compare: https://github.com/galaxyproject/galaxy/compare/921fde4b8cdc...679083c935c1

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[galaxyproject/galaxy] bf4f43: Rough implentation of the DockerAPIInterface.
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf4f43d96a4cf3bdf090d82822a688677600e3f2 https://github.com/galaxyproject/galaxy/commit/bf4f43d96a4cf3bdf090d82822a6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Rough implentation of the DockerAPIInterface. Commit: 2e9c25da28535c268467e9dc5dc982b067ed14bc https://github.com/galaxyproject/galaxy/commit/2e9c25da28535c268467e9dc5dc9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Create a general method for handling galaxy.containers param -> docker-py param mapping. Plus some cleanup. Commit: b7531593697175ad9c8f110e9943c9086c779ae4 https://github.com/galaxyproject/galaxy/commit/b7531593697175ad9c8f110e9943… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Corrections to Docker spec handling Commit: ac9fce9a3c5e6995bafa5fbac602c2b2a4ccb003 https://github.com/galaxyproject/galaxy/commit/ac9fce9a3c5e6995bafa5fbac602… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- WIP Docker Swarm API interface Commit: 0bba56d106dbeedfac2c67226a749bf6354df4e2 https://github.com/galaxyproject/galaxy/commit/0bba56d106dbeedfac2c67226a74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker API TLS support Commit: 26d265e0107143a62e7799ecf51ea85ac698696c https://github.com/galaxyproject/galaxy/commit/26d265e0107143a62e7799ecf51e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker service fixes Commit: c8ab4fae4db13b106dcd1dbc4f109cc66c305d8a https://github.com/galaxyproject/galaxy/commit/c8ab4fae4db13b106dcd1dbc4f10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Enable setting defaults for docker API data structures. Commit: 360e43095a5036c8cedd452a5809160780f361a8 https://github.com/galaxyproject/galaxy/commit/360e43095a5036c8cedd452a5809… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Docker swarm interface for the API Commit: 0e357ca73729f67f27a31b83a7df6c5c74c43c99 https://github.com/galaxyproject/galaxy/commit/0e357ca73729f67f27a31b83a7df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Lint fixes Commit: 2794a650f5cd885f684d79e5124e349ccdf09879 https://github.com/galaxyproject/galaxy/commit/2794a650f5cd885f684d79e5124e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Fixes for swarm manager. Commit: 806703a5e2ac679bcac496bb9acd36a9b248ce48 https://github.com/galaxyproject/galaxy/commit/806703a5e2ac679bcac496bb9acd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Move DockerVolume to containers lib model and fix bugs. Commit: 9cd589508d260a8e04191701aa86e98548e97def https://github.com/galaxyproject/galaxy/commit/9cd589508d260a8e04191701aa86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/util/__init__.py Log Message: ----------- More detailed swarm manager state logging Commit: 605a156d618b352c0755af0b3e6e9e0922c126f8 https://github.com/galaxyproject/galaxy/commit/605a156d618b352c0755af0b3e6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Attempt to handle "phantom" docker tasks Commit: 0d90235b1c5e6742bc65f270c5ac0e19b48ee1d0 https://github.com/galaxyproject/galaxy/commit/0d90235b1c5e6742bc65f270c5ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix lint/unit test errors Commit: 9de17e248feb2fa39e3a026727df75a5f42b7c59 https://github.com/galaxyproject/galaxy/commit/9de17e248feb2fa39e3a026727df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add some error handling to the Docker API interface Commit: 507fed9e3c2e2ea6a7fc9938400c7642701bc3ad https://github.com/galaxyproject/galaxy/commit/507fed9e3c2e2ea6a7fc9938400c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix lint error Commit: 10e0314e8fe8d378fdeb97bfa0b3466e95e35f07 https://github.com/galaxyproject/galaxy/commit/10e0314e8fe8d378fdeb97bfa0b3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/util/json.py Log Message: ----------- Move json format function to galaxy.util.json Commit: 8369d88295554639926ad5ddac445a20e449a0e4 https://github.com/galaxyproject/galaxy/commit/8369d88295554639926ad5ddac44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add conditional docker dependency for containers interface Commit: 5537ce1fa748422a27aea062165095cfba07c754 https://github.com/galaxyproject/galaxy/commit/5537ce1fa748422a27aea0621650… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py Log Message: ----------- Handle the case where a node claims a task exists but the tasks/services API disagrees Commit: 559fb9df9ba0379b975aaa2b5df7ac963c18f037 https://github.com/galaxyproject/galaxy/commit/559fb9df9ba0379b975aaa2b5df7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Allow docker client callers to pass in a test function that the client wrapper will call on certain types of expected failures. If the function returns a truthy value, it is returned instead. This is useful for state-altering changes where the request may have succeeded but the response failed. Commit: 9db3d23eaca5ce7270a9480038acd52f52951298 https://github.com/galaxyproject/galaxy/commit/9db3d23eaca5ce7270a9480038ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py Log Message: ----------- Use consistent whitespace in containers lib classes Commit: c42d642233d962fc513c1039771acb00718d7348 https://github.com/galaxyproject/galaxy/commit/c42d642233d962fc513c1039771a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Containers: - Improve documentation of docker API param mapping - Improve sample containers config file - Fix constraints - A couple other minor bug/logging fixes Commit: b205956b3882a4b1dbc0529742ba8f5aafddafe5 https://github.com/galaxyproject/galaxy/commit/b205956b3882a4b1dbc0529742ba… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Docker: Don't retry 4xx errors indefinitely. Possibly need to do this for more APIErrors. Commit: 9e2ada9a008addbfbcf1d764d80d216dca6978a0 https://github.com/galaxyproject/galaxy/commit/9e2ada9a008addbfbcf1d764d80d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Infinite loop retry is probably bad. This should help with surviving transient errors. Commit: ca7b3fd59355df39304d37972f46940e88f1a975 https://github.com/galaxyproject/galaxy/commit/ca7b3fd59355df39304d37972f46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Fix tests due to missing name in mock module Commit: 91a25d0a08b969c9d6b7161fae6f34eff1c66f59 https://github.com/galaxyproject/galaxy/commit/91a25d0a08b969c9d6b7161fae6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker.py Log Message: ----------- Support manager failover for Docker Swarm mode Commit: 5127fd29570171f55d41e7458a5e2d7cec9a9837 https://github.com/galaxyproject/galaxy/commit/5127fd29570171f55d41e7458a5e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm_manager.py Log Message: ----------- Swarm manager: log services that do not have tasks on any node. Commit: e651b34156a3af022bac250464d92ca6394c3d85 https://github.com/galaxyproject/galaxy/commit/e651b34156a3af022bac250464d9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py A scripts/docker_swarm_manager.py Log Message: ----------- Remove swarm manager from lib Commit: d3038f859a03ad4b29eb6143ea9d88f915cfaac2 https://github.com/galaxyproject/galaxy/commit/d3038f859a03ad4b29eb6143ea9d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/app.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Load containers interface on app load if enable_beta_containers_interface is set. Commit: 860aaf8241759f915501dba221a49b80a18a4e3e https://github.com/galaxyproject/galaxy/commit/860aaf8241759f915501dba221a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/containers/docker.py Log Message: ----------- Fix docker interface failover by making the docker.APIClient wrapper use class vars, since we only ever want callers to use one APIClient. Commit: 564f7ecafe61d0c890cb9cde58640ce221935067 https://github.com/galaxyproject/galaxy/commit/564f7ecafe61d0c890cb9cde5864… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M scripts/docker_swarm_manager.py Log Message: ----------- Make the swarm manager recover on uncaught exceptions. It should do a better job of catching them in the application, but this is good enough for the moment. Commit: feb3e9ddf039e56f972149e7338138fb662745b4 https://github.com/galaxyproject/galaxy/commit/feb3e9ddf039e56f972149e73381… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Fix lint error Commit: 921fde4b8cdce2ab32846ba473846f1388b0592a https://github.com/galaxyproject/galaxy/commit/921fde4b8cdce2ab32846ba47384… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/app.py M lib/galaxy/containers/__init__.py M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py R lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/util/__init__.py M lib/galaxy/util/json.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py A scripts/docker_swarm_manager.py Log Message: ----------- Merge pull request #5861 from natefoo/containers-docker-lib Implement the API version of the Docker containers interface Compare: https://github.com/galaxyproject/galaxy/compare/881dc3601823...921fde4b8cdc

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[galaxyproject/infrastructure-playbook] dd951a: Block a specific pervasive spam message
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dd951a455bd8adada7a7d7246a33614239853ed5 https://github.com/galaxyproject/infrastructure-playbook/commit/dd951a455bd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/galaxy/inventory M roles/postfix/templates/local.cf.j2 Log Message: ----------- Block a specific pervasive spam message

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[galaxyproject/usegalaxy-playbook] 2e8637: Replaced sbtas_se with btman
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e8637f67c843a5c23eb0f98aaadaf7461c26396 https://github.com/galaxyproject/usegalaxy-playbook/commit/2e8637f67c843a5c… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Replaced sbtas_se with btman

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[galaxyproject/infrastructure-playbook] 968bc9: Correct slurm_user format (why didn't this cause f...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 968bc99aa90fdd56959e7af6ea73e6e86e083893 https://github.com/galaxyproject/infrastructure-playbook/commit/968bc99aa90… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/slurmclients/vars.yml Log Message: ----------- Correct slurm_user format (why didn't this cause failures?) Commit: be0fb386736f8999433559cc0d2403ca59f98529 https://github.com/galaxyproject/infrastructure-playbook/commit/be0fb386736… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/all.yml Log Message: ----------- Add mount definition for switching NFS servers as needed Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/654ae08ccf…

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[galaxyproject/galaxy] 5522c7: Add `index` to OIDC controller to list authnzs ass...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5522c78d9d1ebcb490285528a8587ff7157a6d6d https://github.com/galaxyproject/galaxy/commit/5522c78d9d1ebcb490285528a858… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Add `index` to OIDC controller to list authnzs associated with a user. Commit: 68dad22d1e15a30d8ee49f2f8002cdd7d7dfc723 https://github.com/galaxyproject/galaxy/commit/68dad22d1e15a30d8ee49f2f8002… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add router to authnz index. Commit: 881dc3601823da61c3a883f17907132f07afd0bd https://github.com/galaxyproject/galaxy/commit/881dc3601823da61c3a883f17907… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #5908 from VJalili/oidc_index OIDC controller index Compare: https://github.com/galaxyproject/galaxy/compare/b71a163a8ce8...881dc3601823

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[galaxyproject/galaxy] 100904: Add OIDC and OAuth2.0 config to authentication doc...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10090476267c1a2cec8103c4d3844057e682c730 https://github.com/galaxyproject/galaxy/commit/10090476267c1a2cec8103c4d384… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Add OIDC and OAuth2.0 config to authentication docs Commit: b71a163a8ce84403cec829e12265573e44d4f668 https://github.com/galaxyproject/galaxy/commit/b71a163a8ce84403cec829e12265… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Merge pull request #5906 from VJalili/patch-6 Add OIDC and OAuth2.0 config to authentication docs Compare: https://github.com/galaxyproject/galaxy/compare/60b5a9a52ab8...b71a163a8ce8

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[galaxyproject/galaxy] b24a1b: Small fix for workflow editor Selenium testing.
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b24a1b723dd0d378b5f5c181f74f3340409839d8 https://github.com/galaxyproject/galaxy/commit/b24a1b723dd0d378b5f5c181f74f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small fix for workflow editor Selenium testing. Commit: 54721122e7439eeea2d2c6840ed668f827eed577 https://github.com/galaxyproject/galaxy/commit/54721122e7439eeea2d2c6840ed6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Small fixes, enhancements for workflow run Selenium tests. Commit: 8f529d177ada3ef179a982d05dd4f04ba82e8abe https://github.com/galaxyproject/galaxy/commit/8f529d177ada3ef179a982d05dd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Improve a few workflow run API test cases. Use the more abstract test_data specification that will translate to GUI testing. Commit: aafd9de76ba61e2e3b2467188bb53e93c8b6fb2b https://github.com/galaxyproject/galaxy/commit/aafd9de76ba61e2e3b2467188bb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Add more complicated workflow run test case. Re-use test_data specification used by many of the API workflow tests and a workflow used by another test. Add abstractions and DOM element for mapping labeled test data to tool form inputs. Commit: 60b5a9a52ab853bf9ff3adf09bbcc6ae0c4d7992 https://github.com/galaxyproject/galaxy/commit/60b5a9a52ab853bf9ff3adf09bbc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #5886 from jmchilton/selenium_workflow_run More, better workflow run Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/3922065d8a29...60b5a9a52ab8

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[galaxyproject/infrastructure-playbook] 654ae0: Create slurm log directory and rotate logs
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 654ae08ccf30844b0f5b7332e32f20703d66c0ed https://github.com/galaxyproject/infrastructure-playbook/commit/654ae08ccf3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A roles/slurm/files/logrotate-slurm M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmd.yml Log Message: ----------- Create slurm log directory and rotate logs

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[galaxyproject/galaxy] 767a45: Fix proxy, add logo and example file to repo for h...
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 767a456544335b302a9c9b42fba30df34c61c296 https://github.com/galaxyproject/galaxy/commit/767a456544335b302a9c9b42fba3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Fix proxy, add logo and example file to repo for hivtrace Delete example file Commit: 3922065d8a294b609a2b2f9c2a89cbb0f192b9b4 https://github.com/galaxyproject/galaxy/commit/3922065d8a294b609a2b2f9c2a89… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Merge pull request #5902 from guerler/add_logo_hivtrace Add proxy, logo and example file for hivtrace Compare: https://github.com/galaxyproject/galaxy/compare/19ed0e224235...3922065d8a29

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[galaxyproject/galaxy] cfa48d: Remove unused client route
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfa48d4aa6c1602a7bdef578ccbc31653a75ee26 https://github.com/galaxyproject/galaxy/commit/cfa48d4aa6c1602a7bdef578ccbc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused client route Commit: 19ed0e224235a5b10ce34d012d06075f07ea4a0c https://github.com/galaxyproject/galaxy/commit/19ed0e224235a5b10ce34d012d06… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Merge pull request #5907 from guerler/remove_unused_route Remove unused client route Compare: https://github.com/galaxyproject/galaxy/compare/5d82c1a09f9a...19ed0e224235

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[galaxyproject/infrastructure-playbook] aba8bf: Fix vars files for slurm on Jetstream
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: aba8bf0cd1b845e0ad3f7fb4d9f0818d238a4f3a https://github.com/galaxyproject/infrastructure-playbook/commit/aba8bf0cd1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/jscommon/group_vars/slurmclients/vars.yml R env/jsiu/group_vars/slurmclients.yml A env/jsiu/group_vars/slurmclients/common_vars.yml A env/jsiu/group_vars/slurmclients/common_vault.yml A env/jsiu/group_vars/slurmclients/vars.yml R env/jstacc/group_vars/slurmclients.yml A env/jstacc/group_vars/slurmclients/common_vars.yml A env/jstacc/group_vars/slurmclients/common_vault.yml A env/jstacc/group_vars/slurmclients/vars.yml Log Message: ----------- Fix vars files for slurm on Jetstream

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[galaxyproject/usegalaxy-playbook] bfbeca: update test
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfbecad6a84fec79403ed876b16b3b99b1295944 https://github.com/galaxyproject/usegalaxy-playbook/commit/bfbecad6a84fec79… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M common_roles M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update test Commit: 16bf5fb4e35961a1831d4ba3357ba9151605a955 https://github.com/galaxyproject/usegalaxy-playbook/commit/16bf5fb4e35961a1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- swap back to dev, remove message Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a6bd075e83b6...…

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[galaxyproject/infrastructure-playbook] b0158b: Fix errors with missing dict members
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b0158b830f1fb9980ce1f35db32f503a46bcd338 https://github.com/galaxyproject/infrastructure-playbook/commit/b0158b830f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Fix errors with missing dict members Commit: 502d8e6ef29fdc0dc17c4e08088553c5e9357139 https://github.com/galaxyproject/infrastructure-playbook/commit/502d8e6ef29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/jscommon/templates/slurm/slurm.conf.j2 M env/tacc/templates/slurm/slurm.conf.j2 A roles/slurm/defaults/main.yml M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmctld.yml M roles/slurm/tasks/slurmd.yml M roles/slurm/tasks/slurmdbd.yml Log Message: ----------- Slurm upgrades Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/430f65ff7e…

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[galaxyproject/galaxy] 3c060a: Gulpfile cleanup.
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c060ac37f3f9d309b6e105729352e2feea0d645 https://github.com/galaxyproject/galaxy/commit/3c060ac37f3f9d309b6e10572935… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Gulpfile cleanup. Commit: 2086960bdf9061b2c132a92929c2623ef24fca70 https://github.com/galaxyproject/galaxy/commit/2086960bdf9061b2c132a92929c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add bootstrap4 and peer dependency popper. Commit: b10fc343d749e1ea26ddbb8aef127d4d18ae7a73 https://github.com/galaxyproject/galaxy/commit/b10fc343d749e1ea26ddbb8aef12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: R client/galaxy/style/less/autocomplete_tagging.less R client/galaxy/style/less/base.less R client/galaxy/style/less/bootstrap.less R client/galaxy/style/less/bootstrap/alerts.less R client/galaxy/style/less/bootstrap/badges.less R client/galaxy/style/less/bootstrap/bootstrap.less R client/galaxy/style/less/bootstrap/breadcrumbs.less R client/galaxy/style/less/bootstrap/button-groups.less R client/galaxy/style/less/bootstrap/buttons.less R client/galaxy/style/less/bootstrap/carousel.less R client/galaxy/style/less/bootstrap/close.less R client/galaxy/style/less/bootstrap/code.less R client/galaxy/style/less/bootstrap/component-animations.less R client/galaxy/style/less/bootstrap/dropdowns.less R client/galaxy/style/less/bootstrap/forms.less R client/galaxy/style/less/bootstrap/glyphicons.less R client/galaxy/style/less/bootstrap/grid.less R client/galaxy/style/less/bootstrap/input-groups.less R client/galaxy/style/less/bootstrap/jumbotron.less R client/galaxy/style/less/bootstrap/labels.less R client/galaxy/style/less/bootstrap/list-group.less R client/galaxy/style/less/bootstrap/media.less R client/galaxy/style/less/bootstrap/mixins.less R client/galaxy/style/less/bootstrap/modals.less R client/galaxy/style/less/bootstrap/navbar.less R client/galaxy/style/less/bootstrap/navs.less R client/galaxy/style/less/bootstrap/normalize.less R client/galaxy/style/less/bootstrap/pager.less R client/galaxy/style/less/bootstrap/pagination.less R client/galaxy/style/less/bootstrap/panels.less R client/galaxy/style/less/bootstrap/popovers.less R client/galaxy/style/less/bootstrap/print.less R client/galaxy/style/less/bootstrap/progress-bars.less R client/galaxy/style/less/bootstrap/responsive-utilities.less R client/galaxy/style/less/bootstrap/scaffolding.less R client/galaxy/style/less/bootstrap/tables.less R client/galaxy/style/less/bootstrap/theme.less R client/galaxy/style/less/bootstrap/thumbnails.less R client/galaxy/style/less/bootstrap/tooltip.less R client/galaxy/style/less/bootstrap/type.less R client/galaxy/style/less/bootstrap/utilities.less R client/galaxy/style/less/bootstrap/variables.less R client/galaxy/style/less/bootstrap/wells.less R client/galaxy/style/less/charts.less R client/galaxy/style/less/circster.less R client/galaxy/style/less/collection.less R client/galaxy/style/less/dataset.less R client/galaxy/style/less/embed_item.less R client/galaxy/style/less/flex.less R client/galaxy/style/less/fontawesome/bordered-pulled.less R client/galaxy/style/less/fontawesome/core.less R client/galaxy/style/less/fontawesome/fixed-width.less R client/galaxy/style/less/fontawesome/font-awesome.less R client/galaxy/style/less/fontawesome/icons.less R client/galaxy/style/less/fontawesome/larger.less R client/galaxy/style/less/fontawesome/list.less R client/galaxy/style/less/fontawesome/mixins.less R client/galaxy/style/less/fontawesome/path.less R client/galaxy/style/less/fontawesome/rotated-flipped.less R client/galaxy/style/less/fontawesome/spinning.less R client/galaxy/style/less/fontawesome/stacked.less R client/galaxy/style/less/fontawesome/variables.less R client/galaxy/style/less/frame.less R client/galaxy/style/less/galaxy_bootstrap.less R client/galaxy/style/less/galaxy_bootstrap/overrides.less R client/galaxy/style/less/galaxy_bootstrap/variables.less R client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/history.less R client/galaxy/style/less/iconic_stroke.less R client/galaxy/style/less/job.less R client/galaxy/style/less/jstree.less R client/galaxy/style/less/library.less R client/galaxy/style/less/list-item.less R client/galaxy/style/less/reports.less R client/galaxy/style/less/select2.less R client/galaxy/style/less/theme/blue.less R client/galaxy/style/less/theme/plain.less R client/galaxy/style/less/toastr.less R client/galaxy/style/less/tour.less R client/galaxy/style/less/trackster.less R client/galaxy/style/less/ui.less R client/galaxy/style/less/ui/dataset-choice.less R client/galaxy/style/less/ui/error-modal.less R client/galaxy/style/less/ui/icon-btn.less R client/galaxy/style/less/ui/pagination.less R client/galaxy/style/less/ui/paired-collection-creator.less R client/galaxy/style/less/ui/peek-column-selector.less R client/galaxy/style/less/ui/search-input.less R client/galaxy/style/less/upload.less A client/galaxy/style/scss/autocomplete_tagging.scss A client/galaxy/style/scss/base.scss A client/galaxy/style/scss/bootstrap.scss A client/galaxy/style/scss/bootstrap/alerts.scss A client/galaxy/style/scss/bootstrap/badges.scss A client/galaxy/style/scss/bootstrap/bootstrap.scss A client/galaxy/style/scss/bootstrap/breadcrumbs.scss A client/galaxy/style/scss/bootstrap/button-groups.scss A client/galaxy/style/scss/bootstrap/buttons.scss A client/galaxy/style/scss/bootstrap/carousel.scss A client/galaxy/style/scss/bootstrap/close.scss A client/galaxy/style/scss/bootstrap/code.scss A client/galaxy/style/scss/bootstrap/component-animations.scss A client/galaxy/style/scss/bootstrap/dropdowns.scss A client/galaxy/style/scss/bootstrap/forms.scss A client/galaxy/style/scss/bootstrap/glyphicons.scss A client/galaxy/style/scss/bootstrap/grid.scss A client/galaxy/style/scss/bootstrap/input-groups.scss A client/galaxy/style/scss/bootstrap/jumbotron.scss A client/galaxy/style/scss/bootstrap/labels.scss A client/galaxy/style/scss/bootstrap/list-group.scss A client/galaxy/style/scss/bootstrap/media.scss A client/galaxy/style/scss/bootstrap/mixins.scss A client/galaxy/style/scss/bootstrap/modals.scss A client/galaxy/style/scss/bootstrap/navbar.scss A client/galaxy/style/scss/bootstrap/navs.scss A client/galaxy/style/scss/bootstrap/normalize.scss A client/galaxy/style/scss/bootstrap/pager.scss A client/galaxy/style/scss/bootstrap/pagination.scss A client/galaxy/style/scss/bootstrap/panels.scss A client/galaxy/style/scss/bootstrap/popovers.scss A client/galaxy/style/scss/bootstrap/print.scss A client/galaxy/style/scss/bootstrap/progress-bars.scss A client/galaxy/style/scss/bootstrap/responsive-utilities.scss A client/galaxy/style/scss/bootstrap/scaffolding.scss A client/galaxy/style/scss/bootstrap/tables.scss A client/galaxy/style/scss/bootstrap/theme.scss A client/galaxy/style/scss/bootstrap/thumbnails.scss A client/galaxy/style/scss/bootstrap/tooltip.scss A client/galaxy/style/scss/bootstrap/type.scss A client/galaxy/style/scss/bootstrap/utilities.scss A client/galaxy/style/scss/bootstrap/variables.scss A client/galaxy/style/scss/bootstrap/wells.scss A client/galaxy/style/scss/charts.scss A client/galaxy/style/scss/circster.scss A client/galaxy/style/scss/collection.scss A client/galaxy/style/scss/dataset.scss A client/galaxy/style/scss/embed_item.scss A client/galaxy/style/scss/flex.scss A client/galaxy/style/scss/fontawesome/bordered-pulled.scss A client/galaxy/style/scss/fontawesome/core.scss A client/galaxy/style/scss/fontawesome/fixed-width.scss A client/galaxy/style/scss/fontawesome/font-awesome.scss A client/galaxy/style/scss/fontawesome/icons.scss A client/galaxy/style/scss/fontawesome/larger.scss A client/galaxy/style/scss/fontawesome/list.scss A client/galaxy/style/scss/fontawesome/mixins.scss A client/galaxy/style/scss/fontawesome/path.scss A client/galaxy/style/scss/fontawesome/rotated-flipped.scss A client/galaxy/style/scss/fontawesome/spinning.scss A client/galaxy/style/scss/fontawesome/stacked.scss A client/galaxy/style/scss/fontawesome/variables.scss A client/galaxy/style/scss/frame.scss A client/galaxy/style/scss/galaxy_bootstrap.scss A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss A client/galaxy/style/scss/galaxy_bootstrap/variables.scss A client/galaxy/style/scss/galaxy_variables.scss A client/galaxy/style/scss/history.scss A client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/job.scss A client/galaxy/style/scss/jstree.scss A client/galaxy/style/scss/library.scss A client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/reports.scss A client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/sprite-fugue.scss A client/galaxy/style/scss/sprite-history-buttons.scss A client/galaxy/style/scss/sprite-history-states.scss A client/galaxy/style/scss/theme/blue.scss A client/galaxy/style/scss/theme/plain.scss A client/galaxy/style/scss/toastr.scss A client/galaxy/style/scss/tour.scss A client/galaxy/style/scss/trackster.scss A client/galaxy/style/scss/ui.scss A client/galaxy/style/scss/ui/dataset-choice.scss A client/galaxy/style/scss/ui/error-modal.scss A client/galaxy/style/scss/ui/icon-btn.scss A client/galaxy/style/scss/ui/pagination.scss A client/galaxy/style/scss/ui/paired-collection-creator.scss A client/galaxy/style/scss/ui/peek-column-selector.scss A client/galaxy/style/scss/ui/search-input.scss A client/galaxy/style/scss/upload.scss Log Message: ----------- Convert existing .less to scss (still needs builders) Commit: 37d819d39b2c2abedf8f1182d4542b06f773cda1 https://github.com/galaxyproject/galaxy/commit/37d819d39b2c2abedf8f1182d454… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M .gitignore R client/galaxy/style/scss/sprite-fugue.scss R client/galaxy/style/scss/sprite-history-buttons.scss R client/galaxy/style/scss/sprite-history-states.scss Log Message: ----------- Strip sprite build artifacts Commit: 17e7066539cc830e6d8202feb47344685bda501b https://github.com/galaxyproject/galaxy/commit/17e7066539cc830e6d8202feb473… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add gulp-sass Commit: 2b888ec993a9048f9bf7fd2a198330910f547385 https://github.com/galaxyproject/galaxy/commit/2b888ec993a9048f9bf7fd2a1983… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Incremental cleanup/gulping of final remaining grunt tasks Commit: 1ccf17489b6eb81d88b0050c9f9fa1eaf01ea01f https://github.com/galaxyproject/galaxy/commit/1ccf17489b6eb81d88b0050c9f9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/grunt-tasks/style.js Log Message: ----------- Drop rudimentary and unused 'style' configuration support. Commit: 4b8a9ee325a17c677dcc4310dcd9e8775012b8a5 https://github.com/galaxyproject/galaxy/commit/4b8a9ee325a17c677dcc4310dcd9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/bootstrap.scss M client/galaxy/style/scss/bootstrap/bootstrap.scss M client/galaxy/style/scss/bootstrap/theme.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/fontawesome/font-awesome.scss M client/galaxy/style/scss/galaxy_bootstrap.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/library.scss M client/gulpfile.js Log Message: ----------- Fix scss imports. Commit: 5ca65eaf11e066a6cd4dc0ea959085367e58f761 https://github.com/galaxyproject/galaxy/commit/5ca65eaf11e066a6cd4dc0ea9590… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss R client/galaxy/style/scss/bootstrap.scss R client/galaxy/style/scss/bootstrap/alerts.scss R client/galaxy/style/scss/bootstrap/badges.scss R client/galaxy/style/scss/bootstrap/bootstrap.scss R client/galaxy/style/scss/bootstrap/breadcrumbs.scss R client/galaxy/style/scss/bootstrap/button-groups.scss R client/galaxy/style/scss/bootstrap/buttons.scss R client/galaxy/style/scss/bootstrap/carousel.scss R client/galaxy/style/scss/bootstrap/close.scss R client/galaxy/style/scss/bootstrap/code.scss R client/galaxy/style/scss/bootstrap/component-animations.scss R client/galaxy/style/scss/bootstrap/dropdowns.scss R client/galaxy/style/scss/bootstrap/forms.scss R client/galaxy/style/scss/bootstrap/glyphicons.scss R client/galaxy/style/scss/bootstrap/grid.scss R client/galaxy/style/scss/bootstrap/input-groups.scss R client/galaxy/style/scss/bootstrap/jumbotron.scss R client/galaxy/style/scss/bootstrap/labels.scss R client/galaxy/style/scss/bootstrap/list-group.scss R client/galaxy/style/scss/bootstrap/media.scss R client/galaxy/style/scss/bootstrap/mixins.scss R client/galaxy/style/scss/bootstrap/modals.scss R client/galaxy/style/scss/bootstrap/navbar.scss R client/galaxy/style/scss/bootstrap/navs.scss R client/galaxy/style/scss/bootstrap/normalize.scss R client/galaxy/style/scss/bootstrap/pager.scss R client/galaxy/style/scss/bootstrap/pagination.scss R client/galaxy/style/scss/bootstrap/panels.scss R client/galaxy/style/scss/bootstrap/popovers.scss R client/galaxy/style/scss/bootstrap/print.scss R client/galaxy/style/scss/bootstrap/progress-bars.scss R client/galaxy/style/scss/bootstrap/responsive-utilities.scss R client/galaxy/style/scss/bootstrap/scaffolding.scss R client/galaxy/style/scss/bootstrap/tables.scss R client/galaxy/style/scss/bootstrap/theme.scss R client/galaxy/style/scss/bootstrap/thumbnails.scss R client/galaxy/style/scss/bootstrap/tooltip.scss R client/galaxy/style/scss/bootstrap/type.scss R client/galaxy/style/scss/bootstrap/utilities.scss R client/galaxy/style/scss/bootstrap/variables.scss R client/galaxy/style/scss/bootstrap/wells.scss Log Message: ----------- Use bootstrap scss from node_modules instead of a copy in the repo Commit: 2769c2837e83a43c54824798059c93a43014ea0b https://github.com/galaxyproject/galaxy/commit/2769c2837e83a43c54824798059c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/galaxy_variables.scss Log Message: ----------- More cleanup from unused tmp-site-config vars Commit: fcaf1cc6917821971af0a8a2ac742b916114a993 https://github.com/galaxyproject/galaxy/commit/fcaf1cc6917821971af0a8a2ac74… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Add fontawesome dep Commit: 680d4a1262fe99ea419e4cd08c907ce792855c9e https://github.com/galaxyproject/galaxy/commit/680d4a1262fe99ea419e4cd08c90… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/flex.scss M client/galaxy/style/scss/fontawesome/path.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Incremental progress overhauling styles w/ bootstrap4. Lots of conversions to do... Commit: 8e84b9176dabb0578dc8e5f68ed06efeb222f07e https://github.com/galaxyproject/galaxy/commit/8e84b9176dabb0578dc8e5f68ed0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/trackster.scss Log Message: ----------- Interpolate mixin param correctly for trackster styles. Commit: f9c594fc5f8d629b89131be02c8a138a52871782 https://github.com/galaxyproject/galaxy/commit/f9c594fc5f8d629b89131be02c8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/collection.scss Log Message: ----------- Collection class extension fixes (todo: rename things that aren't mixins to not call themselves mixins) Commit: 9367fac17df4de54d94f798565241dfab5c2c0b9 https://github.com/galaxyproject/galaxy/commit/9367fac17df4de54d94f79856524… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/ui/error-modal.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss Log Message: ----------- Fix class extensions in ui Commit: 8f23b878d2bfd31fa5c9efe0e038c880dca4d6a0 https://github.com/galaxyproject/galaxy/commit/8f23b878d2bfd31fa5c9efe0e038… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- Fix a few things in history.scss Commit: 4ed845286c4010f615735a6129edd291eb08298a https://github.com/galaxyproject/galaxy/commit/4ed845286c4010f615735a6129ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss Log Message: ----------- List as optional (temporarily?) some compond extend rules in dataset styles. Need to figure out if these were actually unused, or if they are now broken. Commit: 9e06517ab99910bf0870928f0599eb7cf47642e7 https://github.com/galaxyproject/galaxy/commit/9e06517ab99910bf0870928f0599… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Tweaks to base; need to follow up more on label->badge across the app. Commit: 64e8ef2b94c2f0702d0e271142757dd8cccaf2b4 https://github.com/galaxyproject/galaxy/commit/64e8ef2b94c2f0702d0e27114275… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Var definitions (galaxy use of bootstrap vars) needs to be before the import. They are all defined with `!default`, so these will take precedence. Overrides after. Commit: 316c81132539f7c6bbd29856cac62a8bea4b4d4a https://github.com/galaxyproject/galaxy/commit/316c81132539f7c6bbd29856cac6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/GruntFile.js R client/grunt-tasks/style.js Log Message: ----------- Keep on slimming down Grunt tasks; now it only runs spritesmith. Commit: f9e4e0bc18342fc9e27a32afceb620b4545432c3 https://github.com/galaxyproject/galaxy/commit/f9e4e0bc18342fc9e27a32afceb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- DevDependency overhaul to trim to what we actually need of Grunt currently. Commit: 6cf50ecec150918db37fd1ea8a75a30779e2ea64 https://github.com/galaxyproject/galaxy/commit/6cf50ecec150918db37fd1ea8a75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/gulpfile.js M client/package.json Log Message: ----------- Fix style building package scripts; add style watching gulp task. Commit: 1d1fead178f4b738207d2141c5906fd582abd191 https://github.com/galaxyproject/galaxy/commit/1d1fead178f4b738207d2141c590… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/gulpfile.js Log Message: ----------- Update style watcher to watch all sources, not just primary bundles Commit: 247f8c0ad936dd632dc3d0c5b3f69737b621b902 https://github.com/galaxyproject/galaxy/commit/247f8c0ad936dd632dc3d0c5b3f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: R client/galaxy/style/scss/galaxy_bootstrap.scss Log Message: ----------- Strip old, unused galaxy_bootstrap.scss Commit: 718ab56c054d794d9c6a9456962c09e5418ddf8e https://github.com/galaxyproject/galaxy/commit/718ab56c054d794d9c6a9456962c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/gulpfile.js M client/package.json M client/yarn.lock Log Message: ----------- Add fontawesome composite package; we can use resources straight from here. Commit: 9da827ab5ec210c52436a6800aa9f9fc27b5a12b https://github.com/galaxyproject/galaxy/commit/9da827ab5ec210c52436a6800aa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/dataset.scss R client/galaxy/style/scss/fontawesome/bordered-pulled.scss R client/galaxy/style/scss/fontawesome/core.scss R client/galaxy/style/scss/fontawesome/fixed-width.scss R client/galaxy/style/scss/fontawesome/font-awesome.scss R client/galaxy/style/scss/fontawesome/icons.scss R client/galaxy/style/scss/fontawesome/larger.scss R client/galaxy/style/scss/fontawesome/list.scss R client/galaxy/style/scss/fontawesome/mixins.scss R client/galaxy/style/scss/fontawesome/path.scss R client/galaxy/style/scss/fontawesome/rotated-flipped.scss R client/galaxy/style/scss/fontawesome/spinning.scss R client/galaxy/style/scss/fontawesome/stacked.scss R client/galaxy/style/scss/fontawesome/variables.scss Log Message: ----------- Upgrade fontawesome, swap to npm-installed FA Commit: 6e8efa9e9684d4c6bece4f0b1479b08deb7f71fb https://github.com/galaxyproject/galaxy/commit/6e8efa9e9684d4c6bece4f0b1479… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Ensure scss functions exist prior to any var defs Commit: a6e81369593c2857c8918ba2a48aa6be4bf71ebd https://github.com/galaxyproject/galaxy/commit/a6e81369593c2857c8918ba2a48a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- is a bootstrap var we don't want to override; rename to avoid collision with new bs4 vars Commit: 31ff246bdaec1565c390ffbf47cfcb999547706e https://github.com/galaxyproject/galaxy/commit/31ff246bdaec1565c390ffbf47cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Add simple pxToRem converter Commit: bea9a16c4e4f8c887cecd34c0fd469be035bfadc https://github.com/galaxyproject/galaxy/commit/bea9a16c4e4f8c887cecd34c0fd4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Convert remaining vars used in calculation to rems. Ugly, but it lives. Commit: 2f862c1ea10bd32b84bacfeef15f5e528252ef55 https://github.com/galaxyproject/galaxy/commit/2f862c1ea10bd32b84bacfeef15f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Converting navbar to bs4 styling Commit: 5d7216ccaaaab9840b41b2dfa1586d6453cc08f1 https://github.com/galaxyproject/galaxy/commit/5d7216ccaaaab9840b41b2dfa158… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Fontawesome path fixes; still need to stage new font versions Commit: 7b9c190f55540c0e447d02e89eae47be2fcd7ce3 https://github.com/galaxyproject/galaxy/commit/7b9c190f55540c0e447d02e89eae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/gulpfile.js A static/images/fonts/FontAwesome.otf M static/images/fonts/fontawesome-webfont.eot A static/images/fonts/fontawesome-webfont.svg M static/images/fonts/fontawesome-webfont.ttf M static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 Log Message: ----------- Fontawesome font staging, update. Commit: 67842142eaad24a4567cd496e4cf1157d8f33448 https://github.com/galaxyproject/galaxy/commit/67842142eaad24a4567cd496e4cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/gulpfile.js M client/package.json Log Message: ----------- Refactor file staging a bit, combine libs/font staging into a single task that always runs. TODO: Drop these artifacts from repo Commit: 51829e85698c7bbfe4111715a5a31afec787d63b https://github.com/galaxyproject/galaxy/commit/51829e85698c7bbfe4111715a5a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Fix double slash in fa-font-path (no need for trailing slash here) Commit: a11b1ab5407d6636081ddcf286dc6ef7bf488203 https://github.com/galaxyproject/galaxy/commit/a11b1ab5407d6636081ddcf286dc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css Log Message: ----------- Add styles. Not concatenating to keep subsequent diffs much smaller (and easier to read). Commit: 4dd290e46aa8b9f793c2ca8ddf5d9fb512096952 https://github.com/galaxyproject/galaxy/commit/4dd290e46aa8b9f793c2ca8ddf5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Drop pager vars (deprecated and unused) Commit: 77c602ba12f146ae45d30006b752e0ce4765b550 https://github.com/galaxyproject/galaxy/commit/77c602ba12f146ae45d30006b752… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Fix color calculations -- it's starting to look a lot like Galaxy Commit: df28efcfd209831ad6127abf51b71adc57a148dd https://github.com/galaxyproject/galaxy/commit/df28efcfd209831ad6127abf51b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Masthead work, org Commit: ae0a76980557972ddb881d919c56a7f5ee5c7466 https://github.com/galaxyproject/galaxy/commit/ae0a76980557972ddb881d919c56… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Menu cleanup done when digging through restructuring options. Commit: 4686df416b3ed462cf58f42d0005302de5dfaa0d https://github.com/galaxyproject/galaxy/commit/4686df416b3ed462cf58f42d0005… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Drop subnavbar Commit: baa7c6f2e043c5e0facb107a43ce7fc5c65b6769 https://github.com/galaxyproject/galaxy/commit/baa7c6f2e043c5e0facb107a43ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M .gitignore Log Message: ----------- Add old less source to gitignore to avoid accidentally adding them back when swapping branches Commit: afbffb08f3d5871db69055d4597188c34af69160 https://github.com/galaxyproject/galaxy/commit/afbffb08f3d5871db69055d45971… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M static/style/blue/base.css Log Message: ----------- Incremental work on navbar Commit: 4c4149b18a98f5b98eadf463893bbc657336d6a5 https://github.com/galaxyproject/galaxy/commit/4c4149b18a98f5b98eadf463893b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix some busted workflow list markup prior to refactoring for bs4 dropdown buttons Commit: 1ad656ced07a1b5d784f8609b3d773520693c66c https://github.com/galaxyproject/galaxy/commit/1ad656ced07a1b5d784f8609b3d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix busted 'each' invocation causing js errors in some contexts, restructure some bootstrap 4 dropdowns. Still needs 'popper'. Commit: d4c318bfa0ecd24c87aa0195ba2e6cdcfaac1400 https://github.com/galaxyproject/galaxy/commit/d4c318bfa0ecd24c87aa0195ba2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Explicitly add popper (necessary due to peer dependency) Commit: 46419ca168d0a6a4f623abbb12b43cdcb7f0adfd https://github.com/galaxyproject/galaxy/commit/46419ca168d0a6a4f623abbb12b4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-20 (Tue, 20 Mar 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Import tweaks, force bootstrap js -- this breaks the Galaxy, temporarily Commit: efb830241df74e743a7fa7b90c819bd713c8589b https://github.com/galaxyproject/galaxy/commit/efb830241df74e743a7fa7b90c81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Fix popper.js/popper discrepancy. Commit: c310f9738ecfb8b98c905557919e7402fc81d2d8 https://github.com/galaxyproject/galaxy/commit/c310f9738ecfb8b98c905557919e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Fix manual tooltip destroy blowing up with bootstrap4 -- destroy is now dispose, at least for tips. Commit: 732a1848535a7b9fba0b32e277a2405ecbdac0b6 https://github.com/galaxyproject/galaxy/commit/732a1848535a7b9fba0b32e277a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: R client/galaxy/scripts/libs/bootstrap.js M client/webpack.config.js Log Message: ----------- Remove old (conflicting) bootstrap Commit: 6f72ed2527a67347313f7fef2d6e1b94d12fe30e https://github.com/galaxyproject/galaxy/commit/6f72ed2527a67347313f7fef2d6e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-28 (Wed, 28 Mar 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/ui/filter-control.js M client/galaxy/style/scss/ui/icon-btn.scss M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- Convert rest of btn-default to btn-secondary Commit: 887f0e3a3aa4eefe9a02951a970a2b4080906655 https://github.com/galaxyproject/galaxy/commit/887f0e3a3aa4eefe9a02951a970a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M templates/user/login.mako Log Message: ----------- Fix login form using flex-column (we should revisit general flex handling in forms, though) Commit: 31000b5c9f3cdc71f17f69ec210c22a6e1589255 https://github.com/galaxyproject/galaxy/commit/31000b5c9f3cdc71f17f69ec210c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Working towards more standard styling of masthead/navbar Commit: 9d5b0973c0bcdbe286062c25699c599ff545ac0a https://github.com/galaxyproject/galaxy/commit/9d5b0973c0bcdbe286062c25699c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Leave brand/quota as absolutely positioned for now (yech...), center-justify tabs Commit: cd670a48605489437d28859302afa76cca58c261 https://github.com/galaxyproject/galaxy/commit/cd670a48605489437d28859302af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/menu.js Log Message: ----------- rename generic-nav-view to communication-server-view so it's at least remotely descriptive Commit: 0047bffd05d55c75daae3158c1dde3bada794aaa https://github.com/galaxyproject/galaxy/commit/0047bffd05d55c75daae3158c1dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-29 (Thu, 29 Mar 2018) Changed paths: M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/theme/blue.scss Log Message: ----------- Minor formatting for clarity in scss rules. Commit: f3580ee70e154f2e8a97ba1e88cb6603b83220f2 https://github.com/galaxyproject/galaxy/commit/f3580ee70e154f2e8a97ba1e88cb… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Masthead: small fix to make masthead a bit more useable Commit: afb744234449f85b4f60bb94fb20f9c959001883 https://github.com/galaxyproject/galaxy/commit/afb744234449f85b4f60bb94fb20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-30 (Fri, 30 Mar 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Merge pull request #27 from jxtx/dannon-bs4 Masthead: small fix to make masthead a bit more useable Commit: 241c273e012ec69ddba09e3d8b1b55405942ec67 https://github.com/galaxyproject/galaxy/commit/241c273e012ec69ddba09e3d8b1b… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: A client/galaxy/docs/bootstrap.md M client/package.json A client/styleguide.config.js M client/yarn.lock Log Message: ----------- Style: Adding vue-stylguidest. In `client`, run `yarn styleguide` to serve the styleguide on localhost. Currently this only include bootstrap buttons and no actual vue components, but it is useful for editing the styles. I will flesh this out with more of the bootstrap components we actually use and some Galaxy styles. Commit: eb0f924ce90a7fe4ad7c1006c7d9e749832ebf48 https://github.com/galaxyproject/galaxy/commit/eb0f924ce90a7fe4ad7c1006c7d9… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/theme/blue.scss M static/style/blue/base.css Log Message: ----------- Style: restoring Galaxy colors as primary theme colors. Commit: 5a4d26e1c995f2750d29059aab29515a97398b45 https://github.com/galaxyproject/galaxy/commit/5a4d26e1c995f2750d29059aab29… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-03-31 (Sat, 31 Mar 2018) Changed paths: M client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/styleguide.config.js Log Message: ----------- Style: adding more bootstrap and some key Galaxy styles to styleguide Commit: cd99baa7ef2c8ef7266089d1467b0ea77056c08f https://github.com/galaxyproject/galaxy/commit/cd99baa7ef2c8ef7266089d1467b… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-01 (Sun, 01 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css Log Message: ----------- Styles: Improving colors and clearning up config. Hardcoded the old derived colors to use as a base, and then deriving from those. We may want to update even the base colors (blue, green, etc) using thise. Alert backgrounds are now very close. Since these are the history background colors they are the most important to match to maintain the look. Removed lots of configuration variables that are not used anymore for bootstrap 4. Commit: a303d0d520c36080a6ad448ca4baaeb3e2eb194c https://github.com/galaxyproject/galaxy/commit/a303d0d520c36080a6ad448ca4ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss M client/package.json A client/styleguide.config.js M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'jxtx/dannon-bs4' into bs4 Commit: d51d25fca2f7d6d03872090bd157471682fffea8 https://github.com/galaxyproject/galaxy/commit/d51d25fca2f7d6d03872090bd157… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Update and re-lock vue-loader/vue-template-compiler to fix incompatible versions in build. Commit: 45559e29facd187fed1a550f82b52d90e069dda2 https://github.com/galaxyproject/galaxy/commit/45559e29facd187fed1a550f82b5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/circster.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/embed_item.scss M client/galaxy/style/scss/flex.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/job.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/reports.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/toastr.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/dataset-choice.scss M client/galaxy/style/scss/ui/icon-btn.scss M client/galaxy/style/scss/ui/pagination.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M client/galaxy/style/scss/ui/peek-column-selector.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/yarn.lock M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css Log Message: ----------- Upgrade prettier (now handles .scss well), apply to style sources. Commit: 035a063e99835f26b165ddfa6b3ac32d601ae944 https://github.com/galaxyproject/galaxy/commit/035a063e99835f26b165ddfa6b3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M static/style/blue/base.css A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: bbabf30ba82e3b58675206ac1ae81488f932daf2 https://github.com/galaxyproject/galaxy/commit/bbabf30ba82e3b58675206ac1ae8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Upgrade vue to 2.5.16, lock alongside vue-template-compiler Commit: 8d7e3be889be59177647008a51da1172227951e0 https://github.com/galaxyproject/galaxy/commit/8d7e3be889be59177647008a51da… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Style: Fix buttons. Made primary button background light for consistency with old Galaxy. Galaxy buttons should be upgraded to use the contrast functions to select text based on background (someday). Fixed caret mixin (needed to be one level higher). All permutations of action/menu button look correct now. Tweaked spacing on alerts. Commit: ff64b6f06c03810bcfe727d4fdac2993cc501148 https://github.com/galaxyproject/galaxy/commit/ff64b6f06c03810bcfe727d4fdac… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M Makefile M README.rst M client/.babelrc M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/scss/autocomplete_tagging.scss M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/circster.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/embed_item.scss M client/galaxy/style/scss/flex.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/iconic_stroke.scss M client/galaxy/style/scss/job.scss M client/galaxy/style/scss/jstree.scss M client/galaxy/style/scss/library.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/reports.scss M client/galaxy/style/scss/select2.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/theme/plain.scss M client/galaxy/style/scss/toastr.scss M client/galaxy/style/scss/tour.scss M client/galaxy/style/scss/trackster.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/ui/dataset-choice.scss M client/galaxy/style/scss/ui/icon-btn.scss M client/galaxy/style/scss/ui/pagination.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M client/galaxy/style/scss/ui/peek-column-selector.scss M client/galaxy/style/scss/ui/search-input.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/galaxy.yml.sample M config/job_conf.xml.sample_advanced M config/plugins/visualizations/csg/config/csg.xml A config/plugins/visualizations/csg/static/logo.png M config/plugins/visualizations/graphviz/config/graphviz.xml M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M 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lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/common_startup.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge branch 'bs4' of git://github.com/dannon/galaxy into dannon-bs4 Commit: bfb2650d6915f2c9a1ec560c862e69c1ba146ebb https://github.com/galaxyproject/galaxy/commit/bfb2650d6915f2c9a1ec560c862e… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Style: restore lighter button color lost in merge Commit: c80682e96cb98b50fb007f3e988b21d176861514 https://github.com/galaxyproject/galaxy/commit/c80682e96cb98b50fb007f3e988b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md 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 #29 from jxtx/dannon-bs4 Dannon bs4 Commit: 8f70087927c8e7c5cd3f0242a968de7efc348704 https://github.com/galaxyproject/galaxy/commit/8f70087927c8e7c5cd3f0242a968… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Style build, including button styling fixes. Commit: 4e64c32c0629be6a3cca1f8ea640ccfcfa7f1a3c https://github.com/galaxyproject/galaxy/commit/4e64c32c0629be6a3cca1f8ea640… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/styleguide.config.js Log Message: ----------- Prettierify styleguide driver. Commit: 8c6109dd4475bee81a805e389b74dafdb1f19b96 https://github.com/galaxyproject/galaxy/commit/8c6109dd4475bee81a805e389b74… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Styles: fixes for popmenus. Commit: beb47d46c4318f43bb68d5879c16e6dc20976ed8 https://github.com/galaxyproject/galaxy/commit/beb47d46c4318f43bb68d5879c16… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-04-02 (Mon, 02 Apr 2018) Log Message: ----------- Merge branch 'bs4' of git://github.com/dannon/galaxy into dannon-bs4 Commit: 05081b11a55ac9eb0453573220b39606f46afc7d https://github.com/galaxyproject/galaxy/commit/05081b11a55ac9eb0453573220b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'jxtx/dannon-bs4' into bs4 Commit: f507d95df8f14288890a9557b1ede92a1f820894 https://github.com/galaxyproject/galaxy/commit/f507d95df8f14288890a9557b1ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Fix empty tool tips. Fixes upload button in bs4 branch. Commit: bd2fcd604dda66f812d84e5ad4d97336d660d7ce https://github.com/galaxyproject/galaxy/commit/bd2fcd604dda66f812d84e5ad4d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Cleanup in ui-buttons I did while fixing tooltip bug, rebased over @jmchilton's commit doing the same fix. Commit: 22b10a9ea47c7ed2b7d8127e798a4418fd4983d9 https://github.com/galaxyproject/galaxy/commit/22b10a9ea47c7ed2b7d8127e798a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Re-sync client formatting. Commit: fef37a1f3f7dd5a8aa4336fe5b1a6f0dfecb961e https://github.com/galaxyproject/galaxy/commit/fef37a1f3f7dd5a8aa4336fe5b1a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- Upload modal width fix. Commit: 891212949a4e5d570c8b57efb2bc88286dbbab61 https://github.com/galaxyproject/galaxy/commit/891212949a4e5d570c8b57efb2bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Fixes to tab styling. They stay in a line again now, some problems with active indicator I think still though. Commit: 7ba7b0f94237545b07de8747cea87cbb196bc1eb https://github.com/galaxyproject/galaxy/commit/7ba7b0f94237545b07de8747cea8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Tabs - fix active indicator. Commit: f1ab83aac61b0841902fb50559578d45e070c4fa https://github.com/galaxyproject/galaxy/commit/f1ab83aac61b0841902fb5055957… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-02 (Mon, 02 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Selenium fixes for BS4 style changes. Commit: 933abad8a76e6cdd659816e6ffe8acb5c8283595 https://github.com/galaxyproject/galaxy/commit/933abad8a76e6cdd659816e6ffe8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml Log Message: ----------- Small button fixes - fixes workflow list & history options. As well as a few more Selenium tests. Commit: d091850e894a4f702ca19fe5788fd96a57fbbaee https://github.com/galaxyproject/galaxy/commit/d091850e894a4f702ca19fe5788f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add tabs to styleguide. Commit: 310866d2c9da0cfcbd631ef8788eb069938e4f64 https://github.com/galaxyproject/galaxy/commit/310866d2c9da0cfcbd631ef8788e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Fix more tooltips in ui-frames, ui-options. Commit: 31cfef98f88ceb0d4aa68a18d76d55b89d07795e https://github.com/galaxyproject/galaxy/commit/31cfef98f88ceb0d4aa68a18d76d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-options.js Log Message: ----------- Cleanup in ui-frames, ui-tabs while looking at tooltip handling. Commit: 18fbb0d99761c4449a93ebdec09268d1ff92bdc9 https://github.com/galaxyproject/galaxy/commit/18fbb0d99761c4449a93ebdec092… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add radio button to styleguide (exactly as generated in a test of ui-options -- looks like we need to close those inputs?) Commit: 9094a86f6314229aedec74a3925f7778b38b9f09 https://github.com/galaxyproject/galaxy/commit/9094a86f6314229aedec74a3925f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/bower.json R client/galaxy/scripts/libs/bootstrap-tour.js M client/galaxy/scripts/mvc/tours.js M client/package.json M client/webpack.config.js M client/yarn.lock Log Message: ----------- Upgrade bootstrap-tour and use from npm Commit: 679edd1661718256d46f260bc4ad170d0602120f https://github.com/galaxyproject/galaxy/commit/679edd1661718256d46f260bc4ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Go off-yarn to github's master branch for bs4-compatible bootstrap-tour. Commit: 40637a64050d4779025f60234d3af59dfa08f211 https://github.com/galaxyproject/galaxy/commit/40637a64050d4779025f60234d3a… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Take auto height for labels of radio buttons Commit: fafcd6e39a2d6e584373b6863e216bfb3def7370 https://github.com/galaxyproject/galaxy/commit/fafcd6e39a2d6e584373b6863e21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui/paired-collection-creator.scss M static/style/blue/base.css Log Message: ----------- Fix paired collection creator for BS4 branch. This is ugly to say the least, but the upstream flex styles (like .flex-row) are marking their directions as important so we need to mark these as important for the embedded flex stuff to work I think. Commit: 2eccc293f548bafed6ca1f019f331ed27fc5e413 https://github.com/galaxyproject/galaxy/commit/2eccc293f548bafed6ca1f019f33… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Merge pull request #30 from anuprulez/dev Take auto height for labels of radio buttons Commit: 7e627c1ccc652a0b048f0ad09542cc3639fe2f46 https://github.com/galaxyproject/galaxy/commit/7e627c1ccc652a0b048f0ad09542… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M test/selenium_tests/test_registration.py Log Message: ----------- Fix registration.test_landing selenium test for BS4 branch. Commit: aeeaefed00d8cc3c86d1f1be3d9e3e04fb341621 https://github.com/galaxyproject/galaxy/commit/aeeaefed00d8cc3c86d1f1be3d9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Fix import order in tours.js Commit: d8c4315d79032aff1e689fd0a7ed3fed86fb944d https://github.com/galaxyproject/galaxy/commit/d8c4315d79032aff1e689fd0a7ed… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Build radio fixes Commit: ada2989aced9e35e2ee9f50066ef2e2a815c8002 https://github.com/galaxyproject/galaxy/commit/ada2989aced9e35e2ee9f50066ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Add nametags display to galaxy style examples Commit: c3d4e849ca91535a57a55b8ae1e4ea544b40d283 https://github.com/galaxyproject/galaxy/commit/c3d4e849ca91535a57a55b8ae1e4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix nametag display (instead of keeping over the old label classes, just upgrade everything to badge) Commit: b936102f9f6aba685beb46a68c326438de1d7c19 https://github.com/galaxyproject/galaxy/commit/b936102f9f6aba685beb46a68c32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js Log Message: ----------- Convert toolpanel 'labels' into 'badges' Commit: ed1764969596ad7defd49c7532680946fd58b46f https://github.com/galaxyproject/galaxy/commit/ed1764969596ad7defd49c753268… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Fix modal in workflow editor for BS4 branch changes. Commit: 3dc4cf11c07599651973ce21a1b95b1befc33543 https://github.com/galaxyproject/galaxy/commit/3dc4cf11c07599651973ce21a1b9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Swap hashtags to badge-primary (they were info before, but primary more closely fits the color). Also drop example from galaxy styleguide, since they're just normal old badges, covered in the bootstrap examples of the styleguide Commit: eeea5b6b296a2c0084267cdfdc6549d3ad79fd55 https://github.com/galaxyproject/galaxy/commit/eeea5b6b296a2c0084267cdfdc65… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Fix alignment of terminals in workflow editor. Commit: 7ce621f0355cf7214efe7e256f0e9261ac73cb7c https://github.com/galaxyproject/galaxy/commit/7ce621f0355cf7214efe7e256f0e… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix radio input horizontal alignment issue Commit: b553d72c09e621b930f03ec157568e1afc9d3669 https://github.com/galaxyproject/galaxy/commit/b553d72c09e621b930f03ec15756… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/ui.scss Log Message: ----------- Merge pull request #31 from anuprulez/dev Fix radio input horizontal alignment issue Commit: d7b4d5e9fd7e6c4c5196b46f9050d1af8a2e6947 https://github.com/galaxyproject/galaxy/commit/d7b4d5e9fd7e6c4c5196b46f9050… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- BS4 - place rule builder buttons on one row again. Buttons got a bit bigger causing a row break in my two browsers at least, adding this extra 10 pixes seems to be enough. Commit: 7f7fc3ac08b1714a49aeede2a9c9bb0f391f95b0 https://github.com/galaxyproject/galaxy/commit/7f7fc3ac08b1714a49aeede2a9c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset info section usage. Figured out why the nested selectors won't work -- addressing the other inheritance issues worked around with in subsequent commits Commit: baf3f9e65769fa0cdb823de381ae4196cde33bf9 https://github.com/galaxyproject/galaxy/commit/baf3f9e65769fa0cdb823de381ae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix a button hover @extend as well as the vertical-spacing and info-section inheritance Commit: b92e1a63ca05d8c31e15d68f9446b181f83a2ad3 https://github.com/galaxyproject/galaxy/commit/b92e1a63ca05d8c31e15d68f9446… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/collection.scss Log Message: ----------- Drop !optional from collection fa-lg; this exists now that fontawesome is integrated Commit: 9c71fb98da859d9ef7f048efb776085d2e024a69 https://github.com/galaxyproject/galaxy/commit/9c71fb98da859d9ef7f048efb776… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix tag editor spacing. Commit: d41c5a7731e89ea50e4a964914b33923563c45a3 https://github.com/galaxyproject/galaxy/commit/d41c5a7731e89ea50e4a964914b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix final !optional tagged styles, this resolves the hda display issues. Commit: 6a0eeea368fc824c3d0b9d773f387dedbbea3193 https://github.com/galaxyproject/galaxy/commit/6a0eeea368fc824c3d0b9d773f38… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Resync client-format Commit: 360e33bf6ba0eb0ab6d4c4cbdb25cbfc88d48688 https://github.com/galaxyproject/galaxy/commit/360e33bf6ba0eb0ab6d4c4cbdb25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Bootstrap adjustments for masthead Commit: fab65eabbbab59bd3871ec1c954740e063cae3c8 https://github.com/galaxyproject/galaxy/commit/fab65eabbbab59bd3871ec1c9547… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-03 (Tue, 03 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md Log Message: ----------- Simple tool forms in style guides. One to demonstrate simple mako forms are broken, another to demonstrate the more complex stuff generated by mvc.form seems to work fine. Is there any way to actually use the JS to generate these automatically? The tool form generates too complex of HTML for this approach to seem maintainable. Commit: d1568ca50d708b2a2ef912d5ecf3bf5ba2327265 https://github.com/galaxyproject/galaxy/commit/d1568ca50d708b2a2ef912d5ecf3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- Merge branch 'bs4_masthead' into bs4 Commit: 4e1580c2ce679e77c8520f7e6c4965d5dcc41e58 https://github.com/galaxyproject/galaxy/commit/4e1580c2ce679e77c8520f7e6c49… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- Minor formatting in merged menu Commit: 6a345d1ef07a288e67704db51e59947888bf3051 https://github.com/galaxyproject/galaxy/commit/6a345d1ef07a288e67704db51e59… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Selenium test fixes for 360e33bf6ba0eb0ab6d4c4cbdb25cbfc88d48688. Commit: 6a317958f7982dbc056d4613c4c38a6d68c85278 https://github.com/galaxyproject/galaxy/commit/6a317958f7982dbc056d4613c4c3… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss Log Message: ----------- Update the hashtags styling Commit: c2e7a9f8122f97257f14b2301d88c3d105e366af https://github.com/galaxyproject/galaxy/commit/c2e7a9f8122f97257f14b2301d88… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix td, th alignment in the dataset upload modal Commit: c40443136e558966bdf3b3dc2d8f0752af23aefc https://github.com/galaxyproject/galaxy/commit/c40443136e558966bdf3b3dc2d8f… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Fix upload button background color and fontsize and add its backdrop Commit: a6024d617fc35832a01eb0595d0ac4f3111790b9 https://github.com/galaxyproject/galaxy/commit/a6024d617fc35832a01eb0595d0a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- The old floor/ceil handling of hN vars doesn't work w/ rem, rounds basically everything to 1em -- this fixes many header sizes back to old functionality. Commit: 5d9c5e86e77492934f96220a65b6c37b8df0220b https://github.com/galaxyproject/galaxy/commit/5d9c5e86e77492934f96220a65b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js Log Message: ----------- Fix tourpage formatting Commit: 2b975b2d6a5cc4bce11001d6b4900a64479fe580 https://github.com/galaxyproject/galaxy/commit/2b975b2d6a5cc4bce11001d6b490… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- add classes necessary for pagination in bs4 Commit: 77a4ed7625138bce9a53ea4cfe09e22c47748903 https://github.com/galaxyproject/galaxy/commit/77a4ed7625138bce9a53ea4cfe09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix link targeting for 'back to shareable' list Commit: 9a37920acf261668bd6bad9ba27889df22e99ce3 https://github.com/galaxyproject/galaxy/commit/9a37920acf261668bd6bad9ba278… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Fix navbar-brand-link being clickable to home Commit: 76d059297b23044c6f3c42121c6ced4c89d5dad0 https://github.com/galaxyproject/galaxy/commit/76d059297b23044c6f3c42121c6c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix brand link text decoration Commit: 8e876963612ba9a043b0ce7d168b767d390bd0ca https://github.com/galaxyproject/galaxy/commit/8e876963612ba9a043b0ce7d168b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix more pagination styles in libraries, add example to guide Commit: 103025a471dd98a13d7e0b4c2847947257e557f2 https://github.com/galaxyproject/galaxy/commit/103025a471dd98a13d7e0b4c2847… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M static/style/blue/base.css Log Message: ----------- Lots of var cleanup, incremental commit to avoid merge conflicts Commit: 2a7ea1cb370a25590a66b6870561c1358093da85 https://github.com/galaxyproject/galaxy/commit/2a7ea1cb370a25590a66b6870561… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix scratchpad icon Commit: 712fb6b084fe66c84db7251adb2f8b1ad2ff57bc https://github.com/galaxyproject/galaxy/commit/712fb6b084fe66c84db7251adb2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #34 from guerler/scratchicon Fix scratchpad icon Commit: 1aa5f673d22d24b90fbd8e14ada269f387b99870 https://github.com/galaxyproject/galaxy/commit/1aa5f673d22d24b90fbd8e14ada2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/user/login.mako Log Message: ----------- Force block display for form-rows for now, instead of using flex Commit: d59508c9029876a79eb27f6bf327c3b38d37a8fd https://github.com/galaxyproject/galaxy/commit/d59508c9029876a79eb27f6bf327… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- replace toolbar control with flexbox Commit: 9239883fb46b7dd40b788c7bd954f131294a83a2 https://github.com/galaxyproject/galaxy/commit/9239883fb46b7dd40b788c7bd954… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Remove custom icon from dropdown menu Commit: 3924569d19367c1d7e856a701dfe68fe27f603ad https://github.com/galaxyproject/galaxy/commit/3924569d19367c1d7e856a701dfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #35 from guerler/fixdropdowns Remove custom icon from dropdown menu Commit: 3181fbb442b6a048255439c6dce1222f2a4dc919 https://github.com/galaxyproject/galaxy/commit/3181fbb442b6a048255439c6dce1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- convert folder toolbar into flexfox, clean up styles Commit: 6b90e8f6c73637bb1c64177d68180111e5dae9f2 https://github.com/galaxyproject/galaxy/commit/6b90e8f6c73637bb1c64177d6818… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M static/style/blue/base.css M templates/user/login.mako Log Message: ----------- Merge branch 'bs4' of github.com:dannon/galaxy into bs4 Commit: f05a1393a19e15f942376db22dd51334d6232676 https://github.com/galaxyproject/galaxy/commit/f05a1393a19e15f942376db22dd5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- replace the now-removed btn-xs with btn-sm project-wide Commit: c93bc84628f0c6f71fadc68d9024cd7d7012e893 https://github.com/galaxyproject/galaxy/commit/c93bc84628f0c6f71fadc68d9024… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M static/welcome.html.sample M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako Log Message: ----------- replace the rest of btn-xs project-wide Commit: bdc902a9dfa3805ef368becee9b80a860944602c https://github.com/galaxyproject/galaxy/commit/bdc902a9dfa3805ef368becee9b8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M static/welcome.html.sample Log Message: ----------- rename the btn-default in accordance to bs4 Commit: 643a1aa2ea8d265002471dd9555b85684b56f9a2 https://github.com/galaxyproject/galaxy/commit/643a1aa2ea8d265002471dd9555b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js Log Message: ----------- fix all uses of breadcrumbs, bs4 requires item annotation Commit: 3a85f8189271326c9c30f60cbc0405e157ab16d2 https://github.com/galaxyproject/galaxy/commit/3a85f8189271326c9c30f60cbc04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Cleanup while looking into grid zooming in chrome Commit: 8045724984c161b055ed8aec65bc1acd58d80699 https://github.com/galaxyproject/galaxy/commit/8045724984c161b055ed8aec65bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Improve error messages for tour Selenium test failures. Looks like the failing scratchbook tour is being caused by the upload settings buttons being broken, a known issue. Commit: 52ccc66a2e684eca639af9969db6297a2b9e4973 https://github.com/galaxyproject/galaxy/commit/52ccc66a2e684eca639af9969db6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix nametag tests for switch to badges in BS4 branch. Commit: 9674735c4aa6d772121a2a69da2161648d42a22c https://github.com/galaxyproject/galaxy/commit/9674735c4aa6d772121a2a69da21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Fix failing paired colleciton builder test by increasing test window size. This isn't an ideal fix - someone probably should go in and compress that widget to fit in the original 900 px. Commit: 6aa5b70b0a16d2e486c22f31570ac659af9b4774 https://github.com/galaxyproject/galaxy/commit/6aa5b70b0a16d2e486c22f31570a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow tagging test case for BS4 branch. Commit: c27434bcf380fb2267dcf12c4c35b80742838ec8 https://github.com/galaxyproject/galaxy/commit/c27434bcf380fb2267dcf12c4c35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow rename test case for BS4 branch. Commit: 8df00ffedb718a2fd44b1e913a120df3aecf1485 https://github.com/galaxyproject/galaxy/commit/8df00ffedb718a2fd44b1e913a12… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix radiobuttons, fix tabs in styleguide Commit: 4cfddc12b91abfbf3fcbb63e83303397d9b51403 https://github.com/galaxyproject/galaxy/commit/4cfddc12b91abfbf3fcbb63e8330… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Hide default dropdown icon, restore custom icon Commit: b4a5b2a45ced7bb2515eeee8406fe390e9ce9c6c https://github.com/galaxyproject/galaxy/commit/b4a5b2a45ced7bb2515eeee8406f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css M static/welcome.html.sample M templates/user/login.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py Log Message: ----------- Merge branch 'bs4' into fixradio Commit: beb8e521ad0649485d9e498263419f107362401c https://github.com/galaxyproject/galaxy/commit/beb8e521ad0649485d9e49826341… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-04 (Wed, 04 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Restore custom dropdown icon, required for workflow editor Commit: 438158dd9193bf3b44194701a08173d9da330b21 https://github.com/galaxyproject/galaxy/commit/438158dd9193bf3b44194701a081… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #36 from guerler/fixradio Fix radiobuttons, fix tabs in styleguide Commit: 3904139c3940f7eb91ec41f5750ec8a9d9f73b40 https://github.com/galaxyproject/galaxy/commit/3904139c3940f7eb91ec41f5750e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Cleanup in grid-view Commit: a46df8ce6bbc0a7f62d798b1699ea3584b1326ce https://github.com/galaxyproject/galaxy/commit/a46df8ce6bbc0a7f62d798b1699e… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix js and css issues with popover Commit: 10780c1d694e08191a7fc5ed2c8d38a501789e24 https://github.com/galaxyproject/galaxy/commit/10780c1d694e08191a7fc5ed2c8d… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Add arrows for the popovers Commit: 8e5f6b25cf0c51a8f09fd2e211922effdb1d9e00 https://github.com/galaxyproject/galaxy/commit/8e5f6b25cf0c51a8f09fd2e21192… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Client build and lint Commit: 54db0df20ba977b239cf4ec5db12e31ab74b5d06 https://github.com/galaxyproject/galaxy/commit/54db0df20ba977b239cf4ec5db12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix chrome zoom bug with grid headers per 'https://github.com/galaxyproject/galaxy/issues/5848#issuecomment-378708567' Commit: 75d03ddf19f697ae048e9bbd6775388888351031 https://github.com/galaxyproject/galaxy/commit/75d03ddf19f697ae048e9bbd6775… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Fix for popup top Commit: 6fcd63beaa059628bf131becbeb444ef916d6b35 https://github.com/galaxyproject/galaxy/commit/6fcd63beaa059628bf131becbeb4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M static/style/blue/base.css Log Message: ----------- Add popover static Commit: 7f302be2ac7500879287cc4f0d8a1b2fddabde65 https://github.com/galaxyproject/galaxy/commit/7f302be2ac7500879287cc4f0d8a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss Log Message: ----------- Removal/org of some unused bootstrap/fontawesome vars. Commit: a1e15083ccaa6090d2ad11ad2b3dee7b65ada559 https://github.com/galaxyproject/galaxy/commit/a1e15083ccaa6090d2ad11ad2b3d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Glyphicons are gone, fontawesome is the way now. Commit: 9c911ce68911be9ca25486ea960d59a017946529 https://github.com/galaxyproject/galaxy/commit/9c911ce68911be9ca25486ea960d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/charts.scss M client/galaxy/style/scss/dataset.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss Log Message: ----------- Continued bootstrap variables work. Commit: e8e62aa21e33cce202fc064e5cfa2d4d32dc2011 https://github.com/galaxyproject/galaxy/commit/e8e62aa21e33cce202fc064e5cfa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/frame.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss Log Message: ----------- Finish removing unused bootstrap vars. The ones that are no longer bootstrap vars, but we are using, I have relocated to galaxy variables (since they aren't bootstrap customizations) Commit: 717695a68cb2d64191c4afeed01b7a3e9935d55d https://github.com/galaxyproject/galaxy/commit/717695a68cb2d64191c4afeed01b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix incorrect tooltip init; improve bs4 styling Commit: e06393a0827c14c4df692bed0b42814f3dba1323 https://github.com/galaxyproject/galaxy/commit/e06393a0827c14c4df692bed0b42… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- rename from table-condensed to table-sm as bs4 did Commit: f0cc88024fdd9e028eda0a06a74747a30840fb1b https://github.com/galaxyproject/galaxy/commit/f0cc88024fdd9e028eda0a06a747… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/trackster.scss M static/style/blue/trackster.css Log Message: ----------- Track down tag/label translation goof, fixing top trackster label track. Commit: 164701b943ce543627d96242458940031ba50577 https://github.com/galaxyproject/galaxy/commit/164701b943ce543627d962424589… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M client/galaxy/style/scss/trackster.scss M static/style/blue/trackster.css Log Message: ----------- Fix icon-hover-mixin for trackster. This fixes the little track configuration icons. Commit: 52af42989b6937be3e80e8a8818906ae5d244ed9 https://github.com/galaxyproject/galaxy/commit/52af42989b6937be3e80e8a88189… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Fix scratchbook tour handles. This should fix one remaining selenium test for BS4. Commit: f1cd7813371516937f4e42e2ab790b49f5e92669 https://github.com/galaxyproject/galaxy/commit/f1cd7813371516937f4e42e2ab79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-05 (Thu, 05 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Fix workflow management selenium test (I hope) Commit: 3d7c8a233c1838200431dd057990ff373235c696 https://github.com/galaxyproject/galaxy/commit/3d7c8a233c1838200431dd057990… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M test/selenium_tests/test_library_landing.py Log Message: ----------- Fix one failing library selenium test. Commit: f990661ba8f5754ddf9e7eae0f09e095eb9c0256 https://github.com/galaxyproject/galaxy/commit/f990661ba8f5754ddf9e7eae0f09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-06 (Fri, 06 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Cleanup and build Commit: f85c575975e4ff5d10014f682d4c27d456f31049 https://github.com/galaxyproject/galaxy/commit/f85c575975e4ff5d10014f682d4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix radiobutton toggling Commit: 33f5f4db5d2b241fb16710439c71e11e5e4de502 https://github.com/galaxyproject/galaxy/commit/33f5f4db5d2b241fb16710439c71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #37 from guerler/toggle_radio Fix radio button toggling Commit: ae8b8d9fdfd3bcaaa91d40acefa2bfba4b970715 https://github.com/galaxyproject/galaxy/commit/ae8b8d9fdfd3bcaaa91d40acefa2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M client/README.md M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/gulpfile.js M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/visualizations/common/templates/chart_entry_point.mako M config/plugins/visualizations/csg/templates/csg.mako M config/plugins/visualizations/cytoscape/config/cytoscape.xml M config/plugins/visualizations/drawrna/config/drawrna.xml M config/plugins/visualizations/example/config/example.xml M config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/pv/config/pv.xml M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/test_scripts.py A test/selenium_tests/test_admin_app.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: c99d121674dc2ab51509d0dc548b841aeb590900 https://github.com/galaxyproject/galaxy/commit/c99d121674dc2ab51509d0dc548b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Post-merge cleanup and build. Commit: eec4533d6957f29b055352d5e5d2b0a5b500c420 https://github.com/galaxyproject/galaxy/commit/eec4533d6957f29b055352d5e5d2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/utils.js Log Message: ----------- Remove view specific utility function from shared utils Commit: 5baccd5e305d3c7d3c31dbcea39e0029afe8e855 https://github.com/galaxyproject/galaxy/commit/5baccd5e305d3c7d3c31dbcea39e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Fix masthead highlighting Commit: bda1567fd7921bb343ac29324fd0b948ddf25243 https://github.com/galaxyproject/galaxy/commit/bda1567fd7921bb343ac29324fd0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js Log Message: ----------- Remove unused model index Commit: cd1585a38e34d3246f8f6688ab480bde41c77f42 https://github.com/galaxyproject/galaxy/commit/cd1585a38e34d3246f8f6688ab48… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix background color of active tab Commit: 72b3f5635140596a86dbf2897181c6e9b14f4d9b https://github.com/galaxyproject/galaxy/commit/72b3f5635140596a86dbf2897181… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix dropdown operations buttons in grids Commit: 3ccb57152efdc734ea34a88d554fa4c2d7aa30d5 https://github.com/galaxyproject/galaxy/commit/3ccb57152efdc734ea34a88d554f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Fix pagination style for grids Commit: 21b700ba27fbcada8c0529a032af0eea45a8f7f3 https://github.com/galaxyproject/galaxy/commit/21b700ba27fbcada8c0529a032af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js Log Message: ----------- Merge pull request #39 from guerler/fix_dropdown_grids Fix dropdown operations buttons and pagination links in grids Commit: 05740cfb48e2b74101e961a89c8530f8352b8778 https://github.com/galaxyproject/galaxy/commit/05740cfb48e2b74101e961a89c85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M Makefile M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 187fde6be5ce10a18cd494bc043b93a37b8eeaec https://github.com/galaxyproject/galaxy/commit/187fde6be5ce10a18cd494bc043b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- datalibs: change the default tooltip trigger to back to only hover Commit: deb398f62ef36990ab919d5e1c3473c717276785 https://github.com/galaxyproject/galaxy/commit/deb398f62ef36990ab919d5e1c34… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-libraryrow-view.js Log Message: ----------- move tooltip that renders on top of button to the left which would trigger showing/hiding endlessly Commit: a3a472cdbaff61f65ce1e2fd0909ce1d6b59d4c5 https://github.com/galaxyproject/galaxy/commit/a3a472cdbaff61f65ce1e2fd0909… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/package.json M client/yarn.lock M static/style/blue/base.css Log Message: ----------- Bump to bootstrap 4.1 (second try -- sorry for the rebase) Commit: d5a345f8e9498e0d0ae346d25cf029cf572586bc https://github.com/galaxyproject/galaxy/commit/d5a345f8e9498e0d0ae346d25cf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Attempt to fix jenkins selenium building git/cache bug. Commit: 405ed92b3dac12f9ad004194cb8b6a34c13e7b54 https://github.com/galaxyproject/galaxy/commit/405ed92b3dac12f9ad004194cb8b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- fix empty history message being rendered on the bottom bs4 messes with out flex settings in some way Commit: 938bb010897e593a81beab28ae85d449640edddd https://github.com/galaxyproject/galaxy/commit/938bb010897e593a81beab28ae85… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M .ci/jenkins/selenium/run_tests.sh Log Message: ----------- Strip failed attempt to fix yarn cache/git issue for jenkins Commit: 4eb40607dee22381861933747c07e44ca824c691 https://github.com/galaxyproject/galaxy/commit/4eb40607dee22381861933747c07… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- re-add our default border to all buttons we want to bootstrapize more, but this will ensure that the transition period will be less broken Commit: 05c99b9ff7e172a36f0ff265179144ee04f2defe https://github.com/galaxyproject/galaxy/commit/05c99b9ff7e172a36f0ff2651791… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- fix popover for multihistory filtering Commit: fd3f8c9b635ed6e51b21068bd14c929487980573 https://github.com/galaxyproject/galaxy/commit/fd3f8c9b635ed6e51b21068bd14c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- fix multihistory button margins also make 'Done' stand out more Commit: 674a48cee3f1508843c2ac0580df3d5092e869b5 https://github.com/galaxyproject/galaxy/commit/674a48cee3f1508843c2ac0580df… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/utils/utils.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #38 from guerler/fix_masthead_highlighting Fix masthead highlighting Commit: 9a36dc3a98751c6d4b498790cef7b29486c28e24 https://github.com/galaxyproject/galaxy/commit/9a36dc3a98751c6d4b498790cef7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/toolshed/groups/group-detail-view.js M client/galaxy/scripts/toolshed/groups/group-list-view.js Log Message: ----------- More (minor) post-merge cleanup Commit: 9148865ee3bfb68ee3702f4ff12b869ef5ecd367 https://github.com/galaxyproject/galaxy/commit/9148865ee3bfb68ee3702f4ff12b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/style/scss/galaxy_bootstrap/overrides.scss M static/style/blue/base.css Log Message: ----------- Constrain gray border to btn-secondary (the gray one); it looked strange around other classes, though we can certainly add color-appropriate borders to those if we need. Commit: e4ab6d2464aa8142bdc99291111c295211868d89 https://github.com/galaxyproject/galaxy/commit/e4ab6d2464aa8142bdc99291111c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix masthead color Commit: 7d00ee25d151cb4aebc19eb82f72e4fa224c8a58 https://github.com/galaxyproject/galaxy/commit/7d00ee25d151cb4aebc19eb82f72… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js Log Message: ----------- Explicitly state button style in grid templates. Commit: b2c8eb9e575480aa90256c9192ef92f0bb28c60a https://github.com/galaxyproject/galaxy/commit/b2c8eb9e575480aa90256c9192ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Fix popovers in masthead Commit: 20c061c6c57c3cc6a6113d9a8cdcd7d330c2af67 https://github.com/galaxyproject/galaxy/commit/20c061c6c57c3cc6a6113d9a8cdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Allow modal scrolling Commit: 70788984d40b72090590dec979a475e95328d085 https://github.com/galaxyproject/galaxy/commit/70788984d40b72090590dec979a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-view.js Log Message: ----------- Upload default-view refactoring while looking for popover issues Commit: 37cd8cf8cad56bcc085dc2cb545e0afd4fcddcdb https://github.com/galaxyproject/galaxy/commit/37cd8cf8cad56bcc085dc2cb545e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js Log Message: ----------- Fix visibility of custom popover handler Commit: 4618bb25cfc869bd632817a8e753399c508bc1fa https://github.com/galaxyproject/galaxy/commit/4618bb25cfc869bd632817a8e753… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Move style fixes into custom popover Remove debug test Commit: e4665061ef9b9bb9413e7c69396b97c9ff61ebba https://github.com/galaxyproject/galaxy/commit/e4665061ef9b9bb9413e7c69396b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #40 from guerler/popup Popover fixes Commit: 4d117c83d3a71cf60f174d54b40201dcbe1cf065 https://github.com/galaxyproject/galaxy/commit/4d117c83d3a71cf60f174d54b402… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-popover.js Log Message: ----------- Popover refactoring. Commit: ab385d42a33c4d8396b6c791e313521d859a3c48 https://github.com/galaxyproject/galaxy/commit/ab385d42a33c4d8396b6c791e313… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css Log Message: ----------- Merge, cleanup, rebuild after popup fixes. Commit: 01d33124e54586d08313d1009ebc383604802951 https://github.com/galaxyproject/galaxy/commit/01d33124e54586d08313d1009ebc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Use button group in workflows list Commit: c8806c9a3dd6bf0458556b1eb36ab40574a37252 https://github.com/galaxyproject/galaxy/commit/c8806c9a3dd6bf0458556b1eb36a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-11 (Wed, 11 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix split button usage in workflows list; now looks like other grids. This is getting rewritten, but I wanted to change it since this looks like a bug to the end-user. Commit: 82d71a2aee1077e6394c056fe0de4517a944ed06 https://github.com/galaxyproject/galaxy/commit/82d71a2aee1077e6394c056fe0de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- datalibs remove toolbar paginator, big buttons need more space Commit: 40e923ceb88c28bac7a951e66af28302369b56eb https://github.com/galaxyproject/galaxy/commit/40e923ceb88c28bac7a951e66af2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix alignment of folder rows Commit: bc7da96bb63c14bef2a1b7081171c4d791223f8c https://github.com/galaxyproject/galaxy/commit/bc7da96bb63c14bef2a1b7081171… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-node.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/galaxy.yml.sample A config/oidc_backends_config.xml.sample A config/oidc_config.xml.sample M doc/source/admin/galaxy_options.rst M lib/galaxy/app.py A lib/galaxy/authnz/__init__.py A lib/galaxy/authnz/managers.py A lib/galaxy/authnz/psa_authnz.py M lib/galaxy/config.py M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh A lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/configuration.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/controllers/authnz.py M templates/user/login.mako M templates/webapps/galaxy/workflow/editor.mako M test/base/workflows_format_2/main.py M test/galaxy_selenium/components.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: f56d8b6bd2ec48ff17cace8d94274fa8bec00679 https://github.com/galaxyproject/galaxy/commit/f56d8b6bd2ec48ff17cace8d9427… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow dropdown navigation Commit: 4babdd1d6d3a8614fd5299acf84801162a613ead https://github.com/galaxyproject/galaxy/commit/4babdd1d6d3a8614fd5299acf848… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Fix workflow index name navigation Commit: faba3e88c1efcfe13c998b31ca799217d6c8dbf9 https://github.com/galaxyproject/galaxy/commit/faba3e88c1efcfe13c998b31ca79… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js Log Message: ----------- remove unused id attr Commit: 08e80cf42bb4f21070ccb627980c0b140e55c75c https://github.com/galaxyproject/galaxy/commit/08e80cf42bb4f21070ccb627980c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js Log Message: ----------- datalibs: fix styling of menu in dataset detail Commit: 7daa7143511d688f7538aa822a7a1e54b1c87214 https://github.com/galaxyproject/galaxy/commit/7daa7143511d688f7538aa822a7a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_management.py Log Message: ----------- Fix final workflow management test for new list structure. Commit: 267e2cc182085d3c73ecb1632635969d33aead28 https://github.com/galaxyproject/galaxy/commit/267e2cc182085d3c73ecb1632635… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- reduce size of the span so the tooltip is more reliable Commit: 57ad6d76d7354a3d2558ddfe65475d788a5a3152 https://github.com/galaxyproject/galaxy/commit/57ad6d76d7354a3d2558ddfe6547… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py Log Message: ----------- Avoid mutable default arguments in navigates_galaxy Commit: d0a4024a84c8fa28ab3ad1839ba9dc4596b83932 https://github.com/galaxyproject/galaxy/commit/d0a4024a84c8fa28ab3ad1839ba9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M test/selenium_tests/test_saved_histories.py Log Message: ----------- Fix saved history testing menu options to work with new dropdowns. Commit: 2624e63c26ce01dcab2ea48ea2f3ce1c09011b1b https://github.com/galaxyproject/galaxy/commit/2624e63c26ce01dcab2ea48ea2f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/style/scss/library.scss M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Drop [Done] button from multiview, rebuild and format client. Commit: 22f095edfb14c3f7f0da997501576dd31418021e https://github.com/galaxyproject/galaxy/commit/22f095edfb14c3f7f0da99750157… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Multi-panel refactoring while looking into fixes. Commit: 3a0d459c76fe741efe5299c85492cefc854e8a43 https://github.com/galaxyproject/galaxy/commit/3a0d459c76fe741efe5299c85492… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix flex direction for multihistory w/ column expansion off the page to the right. Commit: f7f8bfcc0c16230aa658486c30f247b830f7fdbd https://github.com/galaxyproject/galaxy/commit/f7f8bfcc0c16230aa658486c30f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M doc/source/admin/cluster.md M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M test/api/test_workflows.py A test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml R test/selenium_tests/_workflow_fixtures.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 1861d11e42f66bcd5970a15e3be821dcc434e7c0 https://github.com/galaxyproject/galaxy/commit/1861d11e42f66bcd5970a15e3be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/gulpfile.js Log Message: ----------- Re-stage bootstrap-tours/etc which are depended on by external plugins -- we can fix this when that isn't the case. Fix default task duplication in gulpfile (minor). Commit: 54a2bea27c4bd734518eb8fd7b2d15959c927b7a https://github.com/galaxyproject/galaxy/commit/54a2bea27c4bd734518eb8fd7b2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix tool describing tour test selectors. Commit: 5599b41c07586b8638864ceaf1a467ef8ba798b1 https://github.com/galaxyproject/galaxy/commit/5599b41c07586b8638864ceaf1a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/ui/paired-collection-creator.scss M static/style/blue/base.css Log Message: ----------- Swap pull-* for float-* across the board. Commit: 5f9a64c233736f81233b285d391d130dddc3ef8a https://github.com/galaxyproject/galaxy/commit/5f9a64c233736f81233b285d391d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Refactor multipanel controls to not use float-*, use normal in-panel positioning. Commit: 4f41e9d2742da555959b7494d2efe802630305aa https://github.com/galaxyproject/galaxy/commit/4f41e9d2742da555959b7494d2ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Improve foreground clipping of inactive histories Commit: 4ea51e9fc491bf64b24bade16dc45495f77f28b8 https://github.com/galaxyproject/galaxy/commit/4ea51e9fc491bf64b24bade16dc4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M Makefile M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js A client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/karma.config.js M client/package.json M client/yarn.lock M lib/galaxy/datatypes/annotation.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/phylip.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.afg A lib/galaxy/datatypes/test/1.arff A lib/galaxy/datatypes/test/1.hdt A lib/galaxy/datatypes/test/1.obo A lib/galaxy/datatypes/test/1.owl A lib/galaxy/datatypes/test/1.phyloxml A lib/galaxy/datatypes/test/1.stockholm A lib/galaxy/datatypes/test/1.ttl A lib/galaxy/datatypes/test/1.xmfa A lib/galaxy/datatypes/test/2.tabular A lib/galaxy/datatypes/test/2.txt A lib/galaxy/datatypes/test/3.txt A lib/galaxy/datatypes/test/Acanium.hmm M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/util/compression_utils.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test-data/rules/uniprot.json A test/base/data/rules_dsl_spec.yml M test/selenium_tests/test_uploads.py M test/unit/workflows/test_modules.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into bs4 Commit: 793b47025119ba708ec6d0a841c4c1ae3179b784 https://github.com/galaxyproject/galaxy/commit/793b47025119ba708ec6d0a841c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Fix botched merge (I think). Commit: df7a3ddb02189237d4085d409b51b216c11c932d https://github.com/galaxyproject/galaxy/commit/df7a3ddb02189237d4085d409b51… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix qunit test app imports for bootstrap4 Commit: e97018ae238f23f07cb3ff36d0bbdf2df30f9d7a https://github.com/galaxyproject/galaxy/commit/e97018ae238f23f07cb3ff36d0bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Fix more tooltip/title usage. Resolves one broken qunit test. Commit: 99f0db584553ba51d34e87593aac5e28a1bb7653 https://github.com/galaxyproject/galaxy/commit/99f0db584553ba51d34e87593aac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js M client/galaxy/style/scss/dataset.scss Log Message: ----------- Cleanup while tracking down qunit test fails. Commit: f9f571476bf3cb69fd6db4e48aebccddab3fa077 https://github.com/galaxyproject/galaxy/commit/f9f571476bf3cb69fd6db4e48aeb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/form_tests.js Log Message: ----------- update default color for qunit test Commit: a9598060c5dd84a5721acee648cbaf57143b4147 https://github.com/galaxyproject/galaxy/commit/a9598060c5dd84a5721acee648cb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M static/style/blue/base.css Log Message: ----------- radically increase the contrast of bs dropdown items the default hover was barely visible, also the 'active' state is now bright so you can clearle notice what you clicked Commit: 48df5f4d0eb13ee2a865959ff755208f05f57e31 https://github.com/galaxyproject/galaxy/commit/48df5f4d0eb13ee2a865959ff755… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix more datalib dropdown items to be properly bs4 Commit: 8901f075b10841dc4bfa18721e87dcc8eb52716f https://github.com/galaxyproject/galaxy/commit/8901f075b10841dc4bfa18721e87… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Incremental work fixing a bunch of masthead tests, adding new ones. Commit: 244efc6593486e495882825191068b9d560fa793 https://github.com/galaxyproject/galaxy/commit/244efc6593486e49588282519106… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/layout/scratchbook.js Log Message: ----------- Fix some scratchbook js while working on qunit tests. Commit: 127167d1f320dd880eee500a249afccfa5561834 https://github.com/galaxyproject/galaxy/commit/127167d1f320dd880eee500a249a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/masthead_tests.js Log Message: ----------- Finish masthead QUnit tests Commit: 6dcb3120cad949020aed8dea8a5aad3fb133e91e https://github.com/galaxyproject/galaxy/commit/6dcb3120cad949020aed8dea8a5a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/tests/ui_tests.js Log Message: ----------- Fix final qunit tests Commit: c8baad98859b84fc2cd53d62d6b9dbfbe0cbb270 https://github.com/galaxyproject/galaxy/commit/c8baad98859b84fc2cd53d62d6b9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix formatting of test-app.js Commit: 5d82c1a09f9afb727df3f7ea29a72f54138a6a77 https://github.com/galaxyproject/galaxy/commit/5d82c1a09f9afb727df3f7ea29a7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M .gitignore M client/GruntFile.js M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/components/PluginList.vue M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/bootstrap-tour.js R client/galaxy/scripts/libs/bootstrap.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/error-modal.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M 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client/galaxy/style/less/galaxy_bootstrap/variables.less R client/galaxy/style/less/galaxy_variables.less R client/galaxy/style/less/history.less R client/galaxy/style/less/iconic_stroke.less R client/galaxy/style/less/job.less R client/galaxy/style/less/jstree.less R client/galaxy/style/less/library.less R client/galaxy/style/less/list-item.less R client/galaxy/style/less/reports.less R client/galaxy/style/less/select2.less R client/galaxy/style/less/theme/blue.less R client/galaxy/style/less/theme/plain.less R client/galaxy/style/less/toastr.less R client/galaxy/style/less/tour.less R client/galaxy/style/less/trackster.less R client/galaxy/style/less/ui.less R client/galaxy/style/less/ui/dataset-choice.less R client/galaxy/style/less/ui/error-modal.less R client/galaxy/style/less/ui/icon-btn.less R client/galaxy/style/less/ui/pagination.less R client/galaxy/style/less/ui/paired-collection-creator.less R client/galaxy/style/less/ui/peek-column-selector.less R client/galaxy/style/less/ui/search-input.less R client/galaxy/style/less/upload.less A client/galaxy/style/scss/autocomplete_tagging.scss A client/galaxy/style/scss/base.scss A client/galaxy/style/scss/charts.scss A client/galaxy/style/scss/circster.scss A client/galaxy/style/scss/collection.scss A client/galaxy/style/scss/dataset.scss A client/galaxy/style/scss/embed_item.scss A client/galaxy/style/scss/flex.scss A client/galaxy/style/scss/frame.scss A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss A client/galaxy/style/scss/galaxy_bootstrap/variables.scss A client/galaxy/style/scss/galaxy_variables.scss A client/galaxy/style/scss/history.scss A client/galaxy/style/scss/iconic_stroke.scss A client/galaxy/style/scss/job.scss A client/galaxy/style/scss/jstree.scss A client/galaxy/style/scss/library.scss A client/galaxy/style/scss/list-item.scss A client/galaxy/style/scss/reports.scss A client/galaxy/style/scss/select2.scss A client/galaxy/style/scss/theme/blue.scss A 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static/images/fonts/fontawesome-webfont.woff A static/images/fonts/fontawesome-webfont.woff2 M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/circster.css M static/style/blue/embed_item.css M static/style/blue/library.css M static/style/blue/reports.css M static/style/blue/trackster.css M static/welcome.html.sample M templates/base/base_panels.mako M templates/sharing_base.mako M templates/webapps/galaxy/dataset/copy_view.mako M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/reports/index.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/view_repository.mako M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_library_landing.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_saved_histories.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #5807 from dannon/bs4 Bootstrap 4 !!!! Compare: https://github.com/galaxyproject/galaxy/compare/8ed3854f07e9...5d82c1a09f9a

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[galaxyproject/galaxy] ac409c: adding initial hivtrace-viz visualization
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ac409cf558914ec128b507a812d67b79bf1be615 https://github.com/galaxyproject/galaxy/commit/ac409cf558914ec128b507a812d6… Author: Steven Weaver <sweaver(a)temple.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- adding initial hivtrace-viz visualization Commit: f1b5849f33463670bf37ba9dab1d296a8efa8851 https://github.com/galaxyproject/galaxy/commit/f1b5849f33463670bf37ba9dab1d… Author: Steven Weaver <sweaver(a)temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M .ci/flake8_blacklist.txt M .gitignore M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/README.md M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/form/form-wrapper.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js A client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-ftp.js A client/galaxy/scripts/mvc/upload/upload-utils.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/visualization/chart/components/model.js M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js M client/galaxy/scripts/mvc/visualization/chart/views/groups.js M client/galaxy/scripts/mvc/visualization/chart/views/menu.js M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js M client/galaxy/scripts/mvc/visualization/visualization-model.js R client/galaxy/scripts/mvc/visualization/visualization-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/pagination.js M client/galaxy/scripts/ui/peek-column-selector.js M 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config/plugins/visualizations/graphviz/templates/graphviz.mako M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml M config/plugins/visualizations/msa/config/msa.xml M config/plugins/visualizations/msa/static/script.js M config/plugins/visualizations/ngl/config/ngl.xml M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M 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config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml M config/plugins/visualizations/phyloviz/config/phyloviz.xml A config/plugins/visualizations/phyloviz/static/logo.png M config/plugins/visualizations/pv/config/pv.xml A config/plugins/visualizations/scatterplot/.babelrc M config/plugins/visualizations/scatterplot/package.json A config/plugins/visualizations/scatterplot/src/jqglobals.js M config/plugins/visualizations/scatterplot/src/scatterplot.js A config/plugins/visualizations/scatterplot/static/logo.png M config/plugins/visualizations/scatterplot/static/scatterplot.js M config/plugins/visualizations/scatterplot/templates/scatterplot.mako M config/plugins/visualizations/trackster/config/trackster.xml A config/plugins/visualizations/trackster/static/logo.png M config/plugins/visualizations/unipept/config/unipept.xml M config/plugins/visualizations/unipept/templates/unipept.mako M config/plugins/visualizations/venn/config/venn.xml M config/plugins/visualizations/venn/src/script.js M config/plugins/visualizations/venn/static/script.js M config/reports.yml.sample M config/tool_conf.xml.main M config/tool_conf.xml.sample M config/tool_shed.yml.sample A config/workflow_resource_mapper_conf.yml.sample A config/workflow_resource_params_conf.xml.sample M doc/source/admin/cluster.md M doc/source/admin/galaxy_options.rst M doc/source/admin/nginx.md M doc/source/admin/scaling.md M doc/source/releases/18.01_announce.rst M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml M lib/galaxy/datatypes/converters/interval_to_fli.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/1.genbank A lib/galaxy/datatypes/test/1.genbank.gz M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/pinned-hashed-requirements.txt A lib/galaxy/dependencies/pinned-requirements.txt R lib/galaxy/dependencies/pinned-requirements.txt A lib/galaxy/dependencies/pipfiles/default/Pipfile A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh R lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/error_reports/plugins/sentry.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/repositories.py M lib/galaxy/tools/verify/interactor.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/jobs.py A lib/galaxy/webapps/galaxy/api/plugins.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/config_schema.yml M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/workflow/modules.py A lib/galaxy/workflow/resources/__init__.py A lib/galaxy/workflow/resources/example.py.sample M lib/galaxy/workflow/run_request.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_util.py A scripts/apply_tags.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/common_startup.sh M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py M static/style/blue/base.css R templates/admin/view_data_tables_registry.mako M templates/admin/view_datatypes_registry.mako M templates/webapps/galaxy/admin/view_display_applications.mako M templates/webapps/galaxy/data_manager/index.mako A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/populators.py M test/docker/base/Dockerfile M test/functional/tools/sample_datatypes_conf.xml M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/test_scripts.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/framework.py A test/selenium_tests/test_admin_app.py M test/selenium_tests/test_collection_builders.py M test/selenium_tests/test_jupyter.py M test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M tools/data_source/upload.py M tools/data_source/upload.xml M tox.ini Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: ff15eeddbc8083ecd56a0dbaa03ca8cda7226111 https://github.com/galaxyproject/galaxy/commit/ff15eeddbc8083ecd56a0dbaa03c… Author: Steven Weaver <sweaver(a)temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- updating hivtrace plugin to use new static paths Commit: cea328effab5b56e9fca19b1a20f3289165a595a https://github.com/galaxyproject/galaxy/commit/cea328effab5b56e9fca19b1a20f… Author: Steven Weaver <sweaver(a)temple.edu> Date: 2018-04-09 (Mon, 09 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M config/plugins/visualizations/hivtrace/config/hivtrace.xml Log Message: ----------- adding hivtrace datatype and updating visualization to use it Commit: 8ed3854f07e93f28774f76ed83f505471153ddb7 https://github.com/galaxyproject/galaxy/commit/8ed3854f07e93f28774f76ed83f5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample A config/plugins/visualizations/hivtrace/config/hivtrace.xml A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2 A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2 A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff A config/plugins/visualizations/hivtrace/static/hivtrace.css A config/plugins/visualizations/hivtrace/static/hivtrace.css.map A config/plugins/visualizations/hivtrace/static/hivtrace.js A config/plugins/visualizations/hivtrace/static/hivtrace.js.map A config/plugins/visualizations/hivtrace/static/vendor.js A config/plugins/visualizations/hivtrace/static/vendor.js.map A config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Merge pull request #5869 from veg/dev HIV-TRACE visualization plug-in Compare: https://github.com/galaxyproject/galaxy/compare/2ad87ac71b52...8ed3854f07e9

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[galaxyproject/galaxy] 43cd93: Fix for Selenium workflow editor test not fully up...
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43cd9335f1bd1111dd339b7d09085cb86de2d9d7 https://github.com/galaxyproject/galaxy/commit/43cd9335f1bd1111dd339b7d0908… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Fix for Selenium workflow editor test not fully updating annotation. Sometimes the last character of the annotation is missing - gotta wait for the last update of form listener I suppose. Commit: 2ad87ac71b521704a810689c2776a987ad9779b1 https://github.com/galaxyproject/galaxy/commit/2ad87ac71b521704a810689c2776… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Merge pull request #5896 from jmchilton/selenium_fixes_42 Fix for Selenium workflow editor test not fully updating annotation. Compare: https://github.com/galaxyproject/galaxy/compare/ebf288f63e72...2ad87ac71b52

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[galaxyproject/galaxy] 19e056: Skip new script tests in dev branch, they are brea...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19e05677fa5e9a3a5a8947a551369204a00d535c https://github.com/galaxyproject/galaxy/commit/19e05677fa5e9a3a5a8947a55136… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 1ff16ddfc401ffcf6edf3b9d14585293ced728a4 https://github.com/galaxyproject/galaxy/commit/1ff16ddfc401ffcf6edf3b9d1458… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: c4e1242312702aea4734a5a96a2bcd15b017c2ec https://github.com/galaxyproject/galaxy/commit/c4e1242312702aea4734a5a96a2b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5893 from martenson/backport-skip [18.01] Skip new script tests in dev branch, breaking integration suite Commit: ebf288f63e7221ca70360fe2c96b389f8fdb3dc5 https://github.com/galaxyproject/galaxy/commit/ebf288f63e7221ca70360fe2c96b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f6b52bafe386...ebf288f63e72

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[galaxyproject/galaxy] 19e056: Skip new script tests in dev branch, they are brea...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 19e05677fa5e9a3a5a8947a551369204a00d535c https://github.com/galaxyproject/galaxy/commit/19e05677fa5e9a3a5a8947a55136… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Skip new script tests in dev branch, they are breaking integration suite. Commit: 1ff16ddfc401ffcf6edf3b9d14585293ced728a4 https://github.com/galaxyproject/galaxy/commit/1ff16ddfc401ffcf6edf3b9d1458… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: c4e1242312702aea4734a5a96a2bcd15b017c2ec https://github.com/galaxyproject/galaxy/commit/c4e1242312702aea4734a5a96a2b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5893 from martenson/backport-skip [18.01] Skip new script tests in dev branch, breaking integration suite Compare: https://github.com/galaxyproject/galaxy/compare/3e56c24d0a13...c4e124231270

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[galaxyproject/galaxy] 6ea22b: Exclude only test_grt_export integration test
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ea22bfe18b60374f9ed6ed49c34f5a6ff4b707f https://github.com/galaxyproject/galaxy/commit/6ea22bfe18b60374f9ed6ed49c34… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Exclude only test_grt_export integration test which takes 35' by itself. Commit: f6b52bafe3866f469da8090ce06bbad659e0a731 https://github.com/galaxyproject/galaxy/commit/f6b52bafe3866f469da8090ce06b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M test/integration/test_scripts.py Log Message: ----------- Merge pull request #5892 from nsoranzo/test_most_scripts Exclude only test_grt_export integration test Compare: https://github.com/galaxyproject/galaxy/compare/2bb388db201f...f6b52bafe386

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[galaxyproject/galaxy] 59002f: Fix update_repository when hg repo has local modif...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e30950… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Commit: 2bb388db201fc261afcfe9bb9337ad383f9e2734 https://github.com/galaxyproject/galaxy/commit/2bb388db201fc261afcfe9bb9337… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a1d76681f6c8...2bb388db201f

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[galaxyproject/galaxy] 59002f: Fix update_repository when hg repo has local modif...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 59002f69e6657c1e7f88f8e3095000136f0ffcf0 https://github.com/galaxyproject/galaxy/commit/59002f69e6657c1e7f88f8e30950… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix update_repository when hg repo has local modifications Fix the following traceback: ``` 149.155.222.206 - - [13/Apr/2018:11:04:46 +0100] "GET /admin_toolshed/update_to_changeset_revision?name=deseq2&latest_ctx_rev=14&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&o wner=iuc&changeset_revision=3660c9088494&latest_changeset_revision=d0c39b5e78cf HTTP/1.1" 500 - "https://galaxy.tgac.ac.uk/admin/repositories?__identifer=lhviib0n1kh" "Mozilla/5.0 (X11 ; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36" Traceback (most recent call last): File "lib/galaxy/web/framework/middleware/batch.py", line 75, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__ return self.app(environ, start_response) File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__ return self.application(environ, replacement_start_response) File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__ response = self.exception_handler(exc_info, environ) File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler get_vars = wsgilib.parse_querystring(environ) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring strict_parsing=False) File "/usr/lib64/python2.7/urlparse.py", line 408, in parse_qsl pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')] File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__ app_iter = self.application(environ, sr_checker) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "/opt/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "lib/galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "lib/galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "lib/galaxy/web/framework/decorators.py", line 98, in decorator return func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1650, in update_to_changeset_revision hg_util.update_repository(repo, latest_ctx_rev) File "lib/tool_shed/util/hg_util.py", line 460, in update_repository commands.update(get_configured_ui(), repo, rev=ctx_rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/commands.py", line 6973, in update ret = hg.update(repo, rev) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 680, in update stats = updaterepo(repo, node, False) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/hg.py", line 676, in updaterepo labels=['working copy', 'destination']) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1532, in update stats = applyupdates(repo, actions, wc, p2, overwrite, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 1196, in applyupdates complete, r = ms.preresolve(f, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 502, in preresolve return self._resolve(True, dfile, wctx, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/merge.py", line 457, in _resolve labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 680, in premerge return _filemerge(True, repo, mynode, orig, fcd, fco, fca, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 627, in _filemerge r = _premerge(repo, fcd, fco, fca, toolconf, files, labels=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/filemerge.py", line 324, in _premerge r = simplemerge.simplemerge(ui, a, b, c, quiet=True, label=labels) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/simplemerge.py", line 397, in simplemerge out = opener(os.path.basename(local), "w", atomictemp=True) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/scmutil.py", line 530, in __call__ self.audit(path) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 61, in __call__ or _lowerclean(parts[0]) in ('.hg', '.hg.', '') File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/pathutil.py", line 16, in _lowerclean return encoding.hfsignoreclean(s.lower()) File "/opt/galaxy/.venv/lib/python2.7/site-packages/mercurial/encoding.py", line 35, in hfsignoreclean if "\xe2" in s or "\xef" in s: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 0: ordinal not in range(128) ``` Also, use the Mercurial command line interface instead of the internal API, as recommended in https://www.mercurial-scm.org/wiki/MercurialApi . Commit: 3e56c24d0a13f4c0c7bac4deb795de163e214e8c https://github.com/galaxyproject/galaxy/commit/3e56c24d0a13f4c0c7bac4deb795… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #5890 from nsoranzo/fix_update_repository [18.01] Fix update_repository when hg repo has local modifications Compare: https://github.com/galaxyproject/galaxy/compare/68b87a07635f...3e56c24d0a13

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[galaxyproject/galaxy] 0ab89c: Implement specification for rules DSL, useful for ...
by GitHub 16 Apr '18

16 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ab89c9c7c46115c542da7f25559695e6e0dec98 https://github.com/galaxyproject/galaxy/commit/0ab89c9c7c46115c542da7f25559… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: A test/base/data/rules_dsl_spec.yml Log Message: ----------- Implement specification for rules DSL, useful for testing both Python and JS. Commit: 1b90d89814ea7a140d830cf0b499eb35e2a9fea9 https://github.com/galaxyproject/galaxy/commit/1b90d89814ea7a140d830cf0b499… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json Log Message: ----------- Mocha based client unit testing of rule tests. Commit: a1d76681f6c816ac55ea7fac859822f6d4e908ea https://github.com/galaxyproject/galaxy/commit/a1d76681f6c816ac55ea7fac8598… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-16 (Mon, 16 Apr 2018) Changed paths: M Makefile A client/galaxy/scripts/mocha/test.js A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/karma.config.js M client/package.json A test/base/data/rules_dsl_spec.yml Log Message: ----------- Merge pull request #5888 from jmchilton/mocha_tests Mocha/Chai test framework + Rules DSL specification w/tests. Compare: https://github.com/galaxyproject/galaxy/compare/30e3658b8b0e...a1d76681f6c8

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[galaxyproject/infrastructure-playbook] 430f65: Remove some cruft
by GitHub 13 Apr '18

13 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 430f65ff7e8432de897962705d883ee80f824005 https://github.com/galaxyproject/infrastructure-playbook/commit/430f65ff7e8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M README.md R play-galaxy Log Message: ----------- Remove some cruft

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