Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 63e4663cc522d46f1749b08368c811108e73bb0d
https://github.com/galaxyproject/galaxy/commit/63e4663cc522d46f1749b08368c8…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-31 (Thu, 31 Jan 2019)
Changed paths:
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
Log Message:
-----------
Cleanup some log messages and one import
Commit: 498eba2e290c6026e2f65929bc7c796bd730de42
https://github.com/galaxyproject/galaxy/commit/498eba2e290c6026e2f65929bc7c…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-31 (Thu, 31 Jan 2019)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
Log Message:
-----------
Update all dependencies
with `make update-dependencies` using pipenv 2018.11.26 .
Commit: d5a406cef70029e0e16b27e093ef8576dfe56322
https://github.com/galaxyproject/galaxy/commit/d5a406cef70029e0e16b27e093ef…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-31 (Thu, 31 Jan 2019)
Changed paths:
M cron/add_manual_builds.py
M lib/galaxy/actions/library.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/jobs.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/util/hash_util.py
M test/api/test_workflows.py
M test/functional/test_toolbox.py
M tools/maf/maf_to_bed.py
M tools/phenotype_association/senatag.py
M tools/stats/gsummary.py
Log Message:
-----------
Fix errors reported by new flake8 3.7.3
Commit: 8c2066f07ac7bb48c59cf8378e5a852e6fb82a4e
https://github.com/galaxyproject/galaxy/commit/8c2066f07ac7bb48c59cf8378e5a…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2019-01-31 (Thu, 31 Jan 2019)
Changed paths:
M cron/add_manual_builds.py
M lib/galaxy/actions/library.py
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/jobs.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/util/hash_util.py
M test/api/test_workflows.py
M test/functional/test_toolbox.py
M tools/maf/maf_to_bed.py
M tools/phenotype_association/senatag.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge pull request #7285 from nsoranzo/update_deps
Update all dependencies
Compare: https://github.com/galaxyproject/galaxy/compare/ed4f1290e84b...8c2066f07ac7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 685af5f7e49d02396c213f355d40f64d706a0691
https://github.com/galaxyproject/galaxy/commit/685af5f7e49d02396c213f355d40…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2019-01-28 (Mon, 28 Jan 2019)
Changed paths:
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Handle subworkflows in view workflow mako
Otherwise displaying workflows with subworkflows via the "view"
button errors with
```
File 'lib/galaxy/web/framework/middleware/error.py', line 154 in __call__
app_iter = self.application(environ, sr_checker)
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py', line 85 in __call__
return self.application(environ, start_response)
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/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 143 in __call__
return self.handle_request(environ, start_response)
File 'lib/galaxy/web/framework/base.py', line 222 in handle_request
body = method(trans, **kwargs)
File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 233 in display_by_username_and_slug
return self._display(trans, stored_workflow)
File 'lib/galaxy/webapps/galaxy/controllers/workflow.py', line 269 in _display
user_item_rating=user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings)
File 'lib/galaxy/web/framework/webapp.py', line 940 in fill_template_mako
return template.render(**data)
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py', line 462 in render
return runtime._render(self, self.callable_, args, data)
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 838 in _render
**_kwargs_for_callable(callable_, data))
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 873 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/mako/runtime.py', line 899 in _exec_template
callable_(context, *args, **kwargs)
File '/data/users/mvandenb/galaxy/database/template_cache/base/base_panels.mako.py', line 122 in render_body
__M_writer(unicode(self.center_panel()))
File '/data/users/mvandenb/galaxy/database/template_cache/display_base.mako.py', line 152 in render_center_panel
__M_writer(unicode(self.render_content()))
File '/data/users/mvandenb/galaxy/database/template_cache/display_base.mako.py', line 116 in render_render_content
__M_writer(unicode(self.render_item( item, item_data )))
File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 123 in render_render_item
__M_writer(unicode(do_inputs( module.get_runtime_inputs(), step.state.inputs, "", step )))
File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 78 in do_inputs
return render_do_inputs(context,inputs,values,prefix,step,other_values)
File '/data/users/mvandenb/galaxy/database/template_cache/workflow/display.mako.py', line 153 in render_do_inputs
if input.type == "repeat":
AttributeError: 'InputProxy' object has no attribute 'type'
```
Also allows displaying subworkflows as a nested table.
Commit: 6630e6bd1ced92724808fbb5bf18069bd97fc0d8
https://github.com/galaxyproject/galaxy/commit/6630e6bd1ced92724808fbb5bf18…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-30 (Wed, 30 Jan 2019)
Changed paths:
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Merge pull request #7276 from mvdbeek/subworkflow_view
Handle subworkflows in view workflow mako
Compare: https://github.com/galaxyproject/galaxy/compare/1a61f31ec5fd...6630e6bd1ced
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 12128ad49d763ad725e5861ff0e1cd5aaeb5461e
https://github.com/galaxyproject/galaxy/commit/12128ad49d763ad725e5861ff0e1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2019-01-24 (Thu, 24 Jan 2019)
Changed paths:
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
Log Message:
-----------
Fix _.escape typo in toolshed group detail view
Commit: 8c93a914d86071968075a551ed307633ea68fbff
https://github.com/galaxyproject/galaxy/commit/8c93a914d86071968075a551ed30…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2019-01-24 (Thu, 24 Jan 2019)
Changed paths:
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
Log Message:
-----------
Merge pull request #7267 from dannon/toolshed-roup-detail-view-typo
[19.01] Fix _.escape typo in toolshed group detail view
Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694
https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-27 (Sun, 27 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Stop with tool migrations by default, they are not needed in modern Galaxies...
... and even problematic in some ways.
Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b
https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b2009791…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2019-01-29 (Tue, 29 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge pull request #7275 from jmchilton/1901_migrate_tools
[18.09] Stop tool migrations checking by default...
Commit: 152e0012c7c1cb037894b1b32ee040b619642863
https://github.com/galaxyproject/galaxy/commit/152e0012c7c1cb037894b1b32ee0…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-29 (Tue, 29 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge branch 'release_18.09' into release_19.01
Commit: d9dd2e3cf1ca8b50be1d17f0ee8218d9083555db
https://github.com/galaxyproject/galaxy/commit/d9dd2e3cf1ca8b50be1d17f0ee82…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-29 (Tue, 29 Jan 2019)
Changed paths:
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge branch 'release_19.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/884c7962ce48...d9dd2e3cf1ca
Branch: refs/heads/release_19.01
Home: https://github.com/galaxyproject/galaxy
Commit: d83db6a53796137c8ccc96efe3b40f3f3f88f694
https://github.com/galaxyproject/galaxy/commit/d83db6a53796137c8ccc96efe3b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2019-01-27 (Sun, 27 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Stop with tool migrations by default, they are not needed in modern Galaxies...
... and even problematic in some ways.
Commit: c8b3d5e4c415514ef626b2009791476d51f9cf9b
https://github.com/galaxyproject/galaxy/commit/c8b3d5e4c415514ef626b2009791…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2019-01-29 (Tue, 29 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge pull request #7275 from jmchilton/1901_migrate_tools
[18.09] Stop tool migrations checking by default...
Commit: 152e0012c7c1cb037894b1b32ee040b619642863
https://github.com/galaxyproject/galaxy/commit/152e0012c7c1cb037894b1b32ee0…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2019-01-29 (Tue, 29 Jan 2019)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge branch 'release_18.09' into release_19.01
Compare: https://github.com/galaxyproject/galaxy/compare/8c93a914d860...152e0012c7c1