March 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 0914c0: fix metadata failure for large count tables
by GitHub 06 Mar '17

06 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0914c05f8823759af21b37ff0ea8a7e757c4ba3a https://github.com/galaxyproject/galaxy/commit/0914c05f8823759af21b37ff0ea8… Author: shiltemann <zazkia(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix metadata failure for large count tables Commit: fe41ec185f85cdca4e0eb4a5705b511d20f699aa https://github.com/galaxyproject/galaxy/commit/fe41ec185f85cdca4e0eb4a5705b… Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- fix typos Commit: b769da1b3d67195d3a2cd908321f0f200dc2a8b0 https://github.com/galaxyproject/galaxy/commit/b769da1b3d67195d3a2cd908321f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-06 (Mon, 06 Mar 2017) Changed paths: M lib/galaxy/datatypes/mothur.py Log Message: ----------- Merge pull request #3706 from shiltemann/mothur-dataype-fix Mothur datatypes: fix metadata failure for large count tables Compare: https://github.com/galaxyproject/galaxy/compare/4aec70cae28f...b769da1b3d67

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[galaxyproject/galaxy] 293726: Support Docker Engine swarm mode
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 293726c57933cb2465a650d005332241eac0f912 https://github.com/galaxyproject/galaxy/commit/293726c57933cb2465a650d00533… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Support Docker Engine swarm mode Commit: 4aec70cae28f336212a6bc8f5d24a325cb851bab https://github.com/galaxyproject/galaxy/commit/4aec70cae28f336212a6bc8f5d24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M config/plugins/interactive_environments/neo/config/neo.ini.sample M config/plugins/interactive_environments/phinch/config/phinch.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A cron/clean_docker_swarm_mode_services.sh M doc/source/admin/interactive_environments.rst M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3666 from natefoo/docker-swarm-mode Support Docker Engine swarm mode for Interactive Environments Compare: https://github.com/galaxyproject/galaxy/compare/bb604e65ee0f...4aec70cae28f

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[galaxyproject/usegalaxy-playbook] 217776: Update Test (it was already updated once before ma...
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 21777674694404bcb7ff18f8036487a90133e46d https://github.com/galaxyproject/usegalaxy-playbook/commit/21777674694404bc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M stage/galaxy_version.yml Log Message: ----------- Update Test (it was already updated once before manually to d3840c5.

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[galaxyproject/galaxy] 4fa76c: Set $HOME to a temp directory rather than conda_pr...
by GitHub 03 Mar '17

03 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4fa76caf67e33ce38f2e45325d504e2f1ff824a7 https://github.com/galaxyproject/galaxy/commit/4fa76caf67e33ce38f2e45325d50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Commit: bb604e65ee0f34ccce664f5798c55adbcedc9e5e https://github.com/galaxyproject/galaxy/commit/bb604e65ee0f34ccce664f5798c5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-03-03 (Fri, 03 Mar 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3701 from natefoo/conda_home_temp Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. Compare: https://github.com/galaxyproject/galaxy/compare/d3840c5c4140...bb604e65ee0f

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[galaxyproject/usegalaxy-playbook] dbaff9: Set conda_prefix so conda uses /cvmfs for shebangs...
by GitHub 02 Mar '17

02 Mar '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dbaff915e1bd2c4ddf4d66c84959a2f45d3e3ee7 https://github.com/galaxyproject/usegalaxy-playbook/commit/dbaff915e1bd2c4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- Set conda_prefix so conda uses /cvmfs for shebangs and whatnot, instead of /galaxy/test/deps, which is a symlink to /cvmfs/test.galaxyproject.org/deps

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[galaxyproject/galaxy] ce7f9e: Annotate converters that appear to need galaxy on ...
by GitHub 02 Mar '17

02 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: ce7f9e91ca8893ce290aeeac4836e18db07af3a5 https://github.com/galaxyproject/galaxy/commit/ce7f9e91ca8893ce290aeeac4836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Annotate converters that appear to need galaxy on PYTHONPATH. Should fix #3499 (thanks for the explicit heads up @mvdbeek). Commit: 93a802bd450658f0c66d4226c626112e8163d5a6 https://github.com/galaxyproject/galaxy/commit/93a802bd450658f0c66d4226c626… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-02 (Thu, 02 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3690 from jmchilton/converter_galaxy_lib_fixes [17.01] Annotate converters that appear to need galaxy on PYTHONPATH. Compare: https://github.com/galaxyproject/galaxy/compare/ca5bb99ee043...93a802bd4506

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[galaxyproject/galaxy] dda11d: [17.01] Fix container resolver log statements expo...
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: dda11d21c2e88f6b935f9f90f270a7aeccd929da https://github.com/galaxyproject/galaxy/commit/dda11d21c2e88f6b935f9f90f270… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- [17.01] Fix container resolver log statements exposing pointers. These log statements: ``` 2017-02-27 12:11:50,959 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.explicit.ExplicitContainerResolver object at 0x10b211590>] found description [None] 2017-02-27 12:11:51,062 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.CachedMulledContainerResolver object at 0x10b2115d0>] found description [None] 2017-02-27 12:11:51,490 INFO [galaxy.tools.deps.containers] Checking with container resolver [<galaxy.tools.deps.container_resolvers.mulled.MulledContainerResolver object at 0x10b211610>] found description [<galaxy.tools.deps.requirements.ContainerDescription object at 0x10d6f1550>] ``` Become: ``` 2017-02-27 13:19:06,201 INFO [galaxy.tools.deps.containers] Checking with container resolver [ExplicitContainerResolver[]] found description [None] 2017-02-27 13:19:06,251 INFO [galaxy.tools.deps.containers] Checking with container resolver [CachedMulledContainerResolver[namespace=None]] found description [None] 2017-02-27 13:19:06,679 INFO [galaxy.tools.deps.containers] Checking with container resolver [MulledContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/seqtk:1.2--0,type=docker]] ``` Rebased with suggestion from @nsoranzo :eagle::eyes: Commit: ca5bb99ee043587fe37cc9354885d3de6fbd5ce3 https://github.com/galaxyproject/galaxy/commit/ca5bb99ee043587fe37cc9354885… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/requirements.py Log Message: ----------- Merge pull request #3679 from jmchilton/fix_logs [17.01] Fix container resolver log statements exposing pointers. Compare: https://github.com/galaxyproject/galaxy/compare/7824cd31fd7b...ca5bb99ee043

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[galaxyproject/galaxy] fd0826: Parse name to label on module initialization
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fd082663866c06afb35a179327b1df6efd9c77c7 https://github.com/galaxyproject/galaxy/commit/fd082663866c06afb35a179327b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Parse name to label on module initialization Commit: 8a4c0eb7e3ea096ed56471a010003e6717f31957 https://github.com/galaxyproject/galaxy/commit/8a4c0eb7e3ea096ed56471a01000… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use shared initialization procedure for subworkflows Commit: fc1e0702542af846c28e2910d77cbd07f0913769 https://github.com/galaxyproject/galaxy/commit/fc1e0702542af846c28e2910d77c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Hide name input fields for data input modules Commit: b91680a5b2dfc83b8ee974fdc9ed6f2ab405829c https://github.com/galaxyproject/galaxy/commit/b91680a5b2dfc83b8ee974fdc9ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Use shared label/annotation input parameter building process Commit: e13958ffcd14f2eb62b29f446a535487dd344904 https://github.com/galaxyproject/galaxy/commit/e13958ffcd14f2eb62b29f446a53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M static/maps/mvc/tool/tool-form-workflow.js.map M static/scripts/mvc/tool/tool-form-workflow.js Log Message: ----------- Remove tool module related annotation input parameter Commit: 92bd559c11e62ef1ab704b967621966a31f71e39 https://github.com/galaxyproject/galaxy/commit/92bd559c11e62ef1ab704b967621… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move label/annotation input parameters at top for all modules Commit: 0f742a6d8380af15ac87a9e654e1119a177bd426 https://github.com/galaxyproject/galaxy/commit/0f742a6d8380af15ac87a9e654e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Move workflow related tool form to workflow directory Commit: 3a7e6b0b744b9331ec175d8104a17519687fa464 https://github.com/galaxyproject/galaxy/commit/3a7e6b0b744b9331ec175d8104a1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: A client/galaxy/scripts/mvc/workflow/workflow-forms.js R client/galaxy/scripts/mvc/workflow/workflow-view-form.js M client/galaxy/scripts/mvc/workflow/workflow-view.js R static/maps/mvc/workflow/workflow-view-form.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/scripts/mvc/workflow/workflow-view-form.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Enable labels for all modules, used shared building process Commit: ff7ab0853d6ea901253ba6175aa343fd9ef3a108 https://github.com/galaxyproject/galaxy/commit/ff7ab0853d6ea901253ba6175aa3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix comments, show default wrapper first in code file Commit: b03904b52c6064e77a378347d9213ec0b270ebb9 https://github.com/galaxyproject/galaxy/commit/b03904b52c6064e77a378347d921… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Allow input specific error handling, fix input parameter configuration Commit: c9b765794bb14adbaee13a44290e9df242778ffe https://github.com/galaxyproject/galaxy/commit/c9b765794bb14adbaee13a44290e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix form handler Commit: a967c088f78e39819d4cc0bd349166501e00d74e https://github.com/galaxyproject/galaxy/commit/a967c088f78e39819d4cc0bd3491… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Avoid parsing default names of inputs to labels Commit: f652e9c778af3835de929cfa7823cf1f0a0aed8a https://github.com/galaxyproject/galaxy/commit/f652e9c778af3835de929cfa7823… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove hidden input parameters, attempt to identify label directly from previous state Commit: a3de5b042e8edae2f7beee6554ae78e18f5f115b https://github.com/galaxyproject/galaxy/commit/a3de5b042e8edae2f7beee6554ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py Log Message: ----------- Move backward compatibility handling of former names out of modules to the workflow manager Commit: 81f799c01f38bab0c584e9b39872d2a1dd7f0348 https://github.com/galaxyproject/galaxy/commit/81f799c01f38bab0c584e9b39872… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Revise comment Commit: afe2a6116a450fa69ae87705c14a4e43a7ef5830 https://github.com/galaxyproject/galaxy/commit/afe2a6116a450fa69ae87705c14a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-21 (Tue, 21 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Use label to connect workflow steps Commit: ae751adac8ae46d7f0eb2831666258143724bc0f https://github.com/galaxyproject/galaxy/commit/ae751adac8ae46d7f0eb28316662… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py M test/unit/workflows/test_modules.py Log Message: ----------- Adjust unit test to use labels instead of name through state Commit: 488c42aa4c3e3e903e0234804d3cd90277d9a930 https://github.com/galaxyproject/galaxy/commit/488c42aa4c3e3e903e0234804d3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Use constants to filter default naming of input modules Commit: dde9ba83acfbedd50a59ccb211cf9d352c86de97 https://github.com/galaxyproject/galaxy/commit/dde9ba83acfbedd50a59ccb211cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/datatypes/data.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-composite.js A test/functional/tools/mulled_example_multi_incomplete.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: 528b00667d4a053b3b8db4790323b0f655b18f9b https://github.com/galaxyproject/galaxy/commit/528b00667d4a053b3b8db4790323… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix comment Commit: 619bfeffd503681ab7d6072426f621fde7485fd5 https://github.com/galaxyproject/galaxy/commit/619bfeffd503681ab7d6072426f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Attempt to use fixed default name for unlabeled subworkflow inputs Commit: 007b6599c21a4927d58629210f103829e947011f https://github.com/galaxyproject/galaxy/commit/007b6599c21a4927d58629210f10… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix name handling in build module Commit: 198d36f77bb444572f03a34aec7c695d0adc52e1 https://github.com/galaxyproject/galaxy/commit/198d36f77bb444572f03a34aec7c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix step title in composite tool form Commit: 05687b8a19785c89772db499d6ede5a097ba47ce https://github.com/galaxyproject/galaxy/commit/05687b8a19785c89772db499d6ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-22 (Wed, 22 Feb 2017) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Strip debug output Commit: 820c46cf63602b788ed282f4277a19129d4b3dd8 https://github.com/galaxyproject/galaxy/commit/820c46cf63602b788ed282f4277a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Repack scripts Commit: 2f53b1d6d12457e0eaba5ca5da8b95321c69ff54 https://github.com/galaxyproject/galaxy/commit/2f53b1d6d12457e0eaba5ca5da8b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py M lib/galaxy/exceptions/error_codes.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/toolbox/base.py M scripts/bootstrap_history.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: b9ba754ce6eb2d4b23c54aa557cb6c0a512c4082 https://github.com/galaxyproject/galaxy/commit/b9ba754ce6eb2d4b23c54aa557cb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M static/maps/mvc/tool/tool-form-composite.js.map A static/maps/mvc/workflow/workflow-forms.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/mvc/tool/tool-form-composite.js A static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Fix repacked files Commit: c80380dc57305be36e615ec13d1d17aecd285114 https://github.com/galaxyproject/galaxy/commit/c80380dc57305be36e615ec13d1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M .ci/flake8_blacklist.txt M client/galaxy/scripts/mvc/grid/grid-view.js M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/webapps/galaxy/controllers/history.py M scripts/bootstrap_history.py M static/maps/mvc/grid/grid-view.js.map M static/scripts/mvc/grid/grid-view.js M templates/grid_base.mako M tools/data_source/upload.py Log Message: ----------- Merge branch 'dev' into unify_label_name_000 Commit: d3840c5c4140807297b22ad1e9b7da97eb1a6570 https://github.com/galaxyproject/galaxy/commit/d3840c5c4140807297b22ad1e9b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js R client/galaxy/scripts/mvc/tool/tool-form-workflow.js A client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/tool/tool-form-composite.js.map R static/maps/mvc/tool/tool-form-workflow.js.map A static/maps/mvc/workflow/workflow-forms.js.map M static/maps/mvc/workflow/workflow-view.js.map R static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/tool/tool-form-composite.js R static/scripts/mvc/tool/tool-form-workflow.js A static/scripts/mvc/workflow/workflow-forms.js M static/scripts/mvc/workflow/workflow-view.js M test/unit/workflows/test_modules.py Log Message: ----------- Merge pull request #3644 from guerler/unify_label_name_000 Introduce labels for all modules, remove name handling field for data inputs Compare: https://github.com/galaxyproject/galaxy/compare/0b4e52c8e93a...d3840c5c4140

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[galaxyproject/galaxy] d10f74: The user controller functions for changing informa...
by GitHub 01 Mar '17

01 Mar '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d10f740cff8e3520383c004a16830700b2789c9f https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality. Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915 https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here. Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Strip out unnecessary user address editing. Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452 https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Update docstring to explicitly mention this as a temporary endpoint. Commit: b46ac475a93fbf0da71272861677a00a3877b91b https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix verbiage in temporary method. Commit: 64036a441284151e1b1a3e9305537d526005ff3a https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-23 (Thu, 23 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge pull request #3656 from dannon/admin-userinfo-edit-fix [17.01] Admin user information editing Commit: 0636053901545a26662ed8f42a15bb67407f2231 https://github.com/galaxyproject/galaxy/commit/0636053901545a26662ed8f42a15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Use pgcalc when possible Commit: 895351cdf8e8867452d28dffb89a2067eabfadb3 https://github.com/galaxyproject/galaxy/commit/895351cdf8e8867452d28dffb89a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- initial working async recalc Commit: 45d75e3da55e43a4444c1a7982e1ea31e1aa5cb7 https://github.com/galaxyproject/galaxy/commit/45d75e3da55e43a4444c1a7982e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Encode userid in messages. Commit: c373bf27e79e48bc2e8ba983e9f08abde16db4df https://github.com/galaxyproject/galaxy/commit/c373bf27e79e48bc2e8ba983e9f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py Log Message: ----------- Change handling of declare in queue_async_task Commit: 00b1591f05af4743d8b16b7d1bbbbc99a3974adb https://github.com/galaxyproject/galaxy/commit/00b1591f05af4743d8b16b7d1bbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-24 (Fri, 24 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix inline doc Commit: 5a5dbb97f1e04dfe15fbf71c441eb50ae4b70b11 https://github.com/galaxyproject/galaxy/commit/5a5dbb97f1e04dfe15fbf71c441e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- improve 17.01 get galaxy release notes Commit: 53c00df805e7ae7e509c08374bc941d31d20000d https://github.com/galaxyproject/galaxy/commit/53c00df805e7ae7e509c08374bc9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-25 (Sat, 25 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Rename send_local_controL_task, add at least a tiny bit of documentation. Commit: d4b677bc38b221678bc991e0fddc43622accb928 https://github.com/galaxyproject/galaxy/commit/d4b677bc38b221678bc991e0fddc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-27 (Mon, 27 Feb 2017) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #3669 from dannon/logout-recalc-improvements [17.01] Logout recalc improvements Commit: 28875de584ac1967a8f2c0cdc8f5fa7b37e70f21 https://github.com/galaxyproject/galaxy/commit/28875de584ac1967a8f2c0cdc8f5… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M doc/source/releases/17.01_announce.rst Log Message: ----------- Merge pull request #3670 from martenson/fix-RN1701 [17.01] improve 17.01 get galaxy release notes Commit: 0997348a1c0a450986d376a96af024c73d4c7f37 https://github.com/galaxyproject/galaxy/commit/0997348a1c0a450986d376a96af0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix tool search idnex building for tools with / in id and not from TS Commit: c11cb3dd4572e7a4f1f814a31a45477f9ecd5ae9 https://github.com/galaxyproject/galaxy/commit/c11cb3dd4572e7a4f1f814a31a45… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- fix typo spotted by :beer: :eyes: Commit: 169b45b138685164010043be95cefe8148c6f713 https://github.com/galaxyproject/galaxy/commit/169b45b138685164010043be95ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix step name display for 17.01 Commit: e23facb966c9962bb5bd1fdd07bf6ee28d7d5930 https://github.com/galaxyproject/galaxy/commit/e23facb966c9962bb5bd1fdd07bf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-28 (Tue, 28 Feb 2017) Changed paths: M lib/galaxy/tools/search/__init__.py Log Message: ----------- Merge pull request #3680 from martenson/fix-id-indexing [17.01] fix tool search index building for tools with slash in id and not from TS Commit: 7824cd31fd7b9351efa1cf8274b89b2b9a0d811d https://github.com/galaxyproject/galaxy/commit/7824cd31fd7b9351efa1cf8274b8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #3681 from guerler/fix_name_display [17.01] Fix step name display for 17.01 Commit: 0b4e52c8e93aa5693f97ff1fc5d0a4c272f58b18 https://github.com/galaxyproject/galaxy/commit/0b4e52c8e93aa5693f97ff1fc5d0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-03-01 (Wed, 01 Mar 2017) Changed paths: M doc/source/releases/17.01_announce.rst M lib/galaxy/queue_worker.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py A templates/webapps/galaxy/user/manage_info.mako Log Message: ----------- Merge branch 'release_17.01' into dev Conflicts: lib/galaxy/managers/workflows.py Discarded all changes made to lib/galaxy/managers/workflows.py in https://github.com/galaxyproject/galaxy/pull/3681 Compare: https://github.com/galaxyproject/galaxy/compare/f0a26f309dd3...0b4e52c8e93a

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