Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 702870c17c9f27707db3c2f003356fe1b52529e0
https://github.com/galaxyproject/galaxy/commit/702870c17c9f27707db3c2f00335…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M scripts/common_startup_functions.sh
Log Message:
-----------
Allow starting Galaxy under gunicorn when using galaxy.ini
and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`.
Additional gunicorn cmdline arguments can be passed using
`GUNICORN_CMD_ARGS`. In a first pass this will allow
running planemo {server, test} under python 3, as Paste
has some problems under python 3:
```
galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
serve.run()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run
invoke(command, command_name, options, args[1:])
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
exit_code = runner.run(args)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run
result = self.command()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command
serve()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve
server(app)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
**context.local_conf)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
val = callable(*args, **kw)
File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner
for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
```
That said gunicorn is a nice pure-python alternative to paste going
forward.
Commit: 9f1e78d92f96499bc8409d7f5f1cfe0a652a1b92
https://github.com/galaxyproject/galaxy/commit/9f1e78d92f96499bc8409d7f5f1c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M client/gulpfile.js
Log Message:
-----------
Drop gulp plugin staging task from default (probably temporarily?), since it's all done in python at server start now.
Commit: b64c82921e02d3be5de21a8a971c44279650399c
https://github.com/galaxyproject/galaxy/commit/b64c82921e02d3be5de21a8a971c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M scripts/common_startup_functions.sh
Log Message:
-----------
Need quotes around export?
Commit: 7622d128094d16775c8eb426b6debace070193ad
https://github.com/galaxyproject/galaxy/commit/7622d128094d16775c8eb426b6de…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/gulpfile.js
Log Message:
-----------
Merge pull request #6808 from dannon/no_plugin_staging_gulp
[18.09] Drop gulp plugin staging task from default tasks
Commit: 176364ac80130ca439006c4b75fd393ac850681b
https://github.com/galaxyproject/galaxy/commit/176364ac80130ca439006c4b75fd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Move gunicorn to dev-requirements
Commit: 1a3e9ae17327f3d77fc6f64ec85c4165d4c680ef
https://github.com/galaxyproject/galaxy/commit/1a3e9ae17327f3d77fc6f64ec85c…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M scripts/common_startup_functions.sh
Log Message:
-----------
Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support
[18.09] Allow starting Galaxy under gunicorn when using galaxy.ini
Commit: 260e37f2bc317a4dc8685b84da5a831d6c4c164a
https://github.com/galaxyproject/galaxy/commit/260e37f2bc317a4dc8685b84da5a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/gulpfile.js
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M scripts/common_startup_functions.sh
Log Message:
-----------
Merge branch 'release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/55c90960e9a6...260e37f2bc31
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: 702870c17c9f27707db3c2f003356fe1b52529e0
https://github.com/galaxyproject/galaxy/commit/702870c17c9f27707db3c2f00335…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M scripts/common_startup_functions.sh
Log Message:
-----------
Allow starting Galaxy under gunicorn when using galaxy.ini
and starting Galaxy with `APP_WEBSERVER=gunicorn sh run.sh`.
Additional gunicorn cmdline arguments can be passed using
`GUNICORN_CMD_ARGS`. In a first pass this will allow
running planemo {server, test} under python 3, as Paste
has some problems under python 3:
```
galaxy.web.stack INFO 2018-09-29 22:16:00,216 Galaxy server instance 'main' is running
Traceback (most recent call last):
File "./scripts/paster.py", line 27, in <module>
serve.run()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1055, in run
invoke(command, command_name, options, args[1:])
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
exit_code = runner.run(args)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 226, in run
result = self.command()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 676, in command
serve()
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/serve.py", line 653, in serve
server(app)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
**context.local_conf)
File "/tmp/tmpv5tow6c8/galaxy-dev/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
val = callable(*args, **kw)
File "/home/travis/.planemo/gx_venv_3_release_18.09/lib/python3.6/site-packages/paste/httpserver.py", line 1353, in server_runner
for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
```
That said gunicorn is a nice pure-python alternative to paste going
forward.
Commit: b64c82921e02d3be5de21a8a971c44279650399c
https://github.com/galaxyproject/galaxy/commit/b64c82921e02d3be5de21a8a971c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M scripts/common_startup_functions.sh
Log Message:
-----------
Need quotes around export?
Commit: 176364ac80130ca439006c4b75fd393ac850681b
https://github.com/galaxyproject/galaxy/commit/176364ac80130ca439006c4b75fd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Move gunicorn to dev-requirements
Commit: 1a3e9ae17327f3d77fc6f64ec85c4165d4c680ef
https://github.com/galaxyproject/galaxy/commit/1a3e9ae17327f3d77fc6f64ec85c…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
M scripts/common_startup_functions.sh
Log Message:
-----------
Merge pull request #6805 from mvdbeek/gunicorn_run_sh_support
[18.09] Allow starting Galaxy under gunicorn when using galaxy.ini
Compare: https://github.com/galaxyproject/galaxy/compare/7622d128094d...1a3e9ae17327
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 106fb79c8b7bd8d2faa69f9bd007efe504183012
https://github.com/galaxyproject/galaxy/commit/106fb79c8b7bd8d2faa69f9bd007…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/style/scss/base.scss
Log Message:
-----------
Drop incorrect flex designation for panel inner; these are generally
single line styles with floats. Fixes header for "Published History"
view, etc.
Commit: 71df0e44652fca8755869248935dc2bdeba39208
https://github.com/galaxyproject/galaxy/commit/71df0e44652fca8755869248935d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/yarn.lock
M static/style/blue/base.css
Log Message:
-----------
New integrity hashes for yarn?
Typo, artifacts (which will be gone soon!)
Commit: d0b6bc6ddc7391527e98a4ece4e33396229c2d25
https://github.com/galaxyproject/galaxy/commit/d0b6bc6ddc7391527e98a4ece4e3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/style/scss/base.scss
M static/style/blue/base.css
M templates/webapps/galaxy/page/editor.mako
Log Message:
-----------
panel-body will always be full height
Commit: ab660686c26241ec4959711603919b80442d32a0
https://github.com/galaxyproject/galaxy/commit/ab660686c26241ec495971160391…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M test/api/test_tools.py
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add test for single and multi-input identifiers
test_identifier_map_over_input_in_conditional fails at the
moment (same issue as in https://github.com/galaxyproject/galaxy/issues/6182)
Commit: 73f8f3129b07cbe96c10da161a547bf2008706e2
https://github.com/galaxyproject/galaxy/commit/73f8f3129b07cbe96c10da161a54…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/tools/parameters/wrapped.py
Log Message:
-----------
Partially fix missing element identifier
This makes sure that any toplevel `|__identifier__` is passed on
to nested inputs.
Commit: f8d9a9e33a994a97c537ef15f1993fbe5d5866ea
https://github.com/galaxyproject/galaxy/commit/f8d9a9e33a994a97c537ef15f199…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Attempt to recover wrapper datasets
Otherwise we create new wrappers that lack the element identifier.
Commit: c6d915b8f2d470517dfa6504fa635c69cc546b64
https://github.com/galaxyproject/galaxy/commit/c6d915b8f2d470517dfa6504fa63…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Parse length to integer
When using the little up/down button we get strings instead of integers,
and those fail the rule validation. Fixes https://github.com/galaxyproject/galaxy/issues/6800
Commit: 2d78dbb9ec1d4d1ba7240d384b27bb6bb83c24b5
https://github.com/galaxyproject/galaxy/commit/2d78dbb9ec1d4d1ba7240d384b27…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Build client
Commit: 565f611389e434b6df57d39ad5c01ae037e46e76
https://github.com/galaxyproject/galaxy/commit/565f611389e434b6df57d39ad5c0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Fix remaining selenium py3 erorrs
Commit: 2e7adfbee4835f1374dffe7ba49760cfc19fdb0e
https://github.com/galaxyproject/galaxy/commit/2e7adfbee4835f1374dffe7ba497…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-09-29 (Sat, 29 Sep 2018)
Changed paths:
M lib/galaxy/web/framework/helpers/__init__.py
Log Message:
-----------
Cast to bytestring in md5 function
Commit: a47887639d50b2e5da55d9121b8d8e55509a9cd3
https://github.com/galaxyproject/galaxy/commit/a47887639d50b2e5da55d9121b8d…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/web/framework/helpers/__init__.py
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Merge pull request #6803 from mvdbeek/finish_py3_selenium
[18.09] Fix remaining selenium py3 errors
Commit: e226edc5ade76dd0ec2e3d8db2e799567e8c11d7
https://github.com/galaxyproject/galaxy/commit/e226edc5ade76dd0ec2e3d8db2e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-09-30 (Sun, 30 Sep 2018)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/util/__init__.py
M test/api/test_tools.py
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #6798 from mvdbeek/fix_element_identifier_for_non_multiple_true_mapover_in_conditionals
[18.09] Fix element identifier for non multiple true mapover in conditionals
Commit: d3ab953be3c553cfd71347322538c3adab6d7515
https://github.com/galaxyproject/galaxy/commit/d3ab953be3c553cfd71347322538…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/style/scss/base.scss
M client/yarn.lock
M static/style/blue/base.css
M templates/webapps/galaxy/page/editor.mako
Log Message:
-----------
Merge pull request #6791 from dannon/flex-style-fixes
[18.09] Flex-related style fixes
Commit: 2aad3b2ced20189ab4e500bd501797a876089ee9
https://github.com/galaxyproject/galaxy/commit/2aad3b2ced20189ab4e500bd5017…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Merge pull request #6802 from mvdbeek/fix_int_parsing_rules
[18.05] Cast rule.length to int when parsing rules
Commit: 87463f4be6334849b0e121bd534fada090aeb1d8
https://github.com/galaxyproject/galaxy/commit/87463f4be6334849b0e121bd534f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/galaxy/scripts/mvc/rules/rule-definitions.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.05' into release_18.09
Commit: 55c90960e9a69e8576489ffffba7a0c482748c60
https://github.com/galaxyproject/galaxy/commit/55c90960e9a69e8576489ffffba7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/rules/rule-definitions.js
M client/galaxy/style/scss/base.scss
M client/yarn.lock
M config/plugins/webhooks/demo/tour_generator/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/util/__init__.py
M lib/galaxy/web/framework/helpers/__init__.py
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/test_tools.py
A test/functional/tools/identifier_in_conditional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/4c0a20853c61...55c90960e9a6
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: 106fb79c8b7bd8d2faa69f9bd007efe504183012
https://github.com/galaxyproject/galaxy/commit/106fb79c8b7bd8d2faa69f9bd007…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/style/scss/base.scss
Log Message:
-----------
Drop incorrect flex designation for panel inner; these are generally
single line styles with floats. Fixes header for "Published History"
view, etc.
Commit: 71df0e44652fca8755869248935dc2bdeba39208
https://github.com/galaxyproject/galaxy/commit/71df0e44652fca8755869248935d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/yarn.lock
M static/style/blue/base.css
Log Message:
-----------
New integrity hashes for yarn?
Typo, artifacts (which will be gone soon!)
Commit: d0b6bc6ddc7391527e98a4ece4e33396229c2d25
https://github.com/galaxyproject/galaxy/commit/d0b6bc6ddc7391527e98a4ece4e3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-09-28 (Fri, 28 Sep 2018)
Changed paths:
M client/galaxy/style/scss/base.scss
M static/style/blue/base.css
M templates/webapps/galaxy/page/editor.mako
Log Message:
-----------
panel-body will always be full height
Commit: d3ab953be3c553cfd71347322538c3adab6d7515
https://github.com/galaxyproject/galaxy/commit/d3ab953be3c553cfd71347322538…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-01 (Mon, 01 Oct 2018)
Changed paths:
M client/galaxy/scripts/components/Sharing.vue
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/style/scss/base.scss
M client/yarn.lock
M static/style/blue/base.css
M templates/webapps/galaxy/page/editor.mako
Log Message:
-----------
Merge pull request #6791 from dannon/flex-style-fixes
[18.09] Flex-related style fixes
Compare: https://github.com/galaxyproject/galaxy/compare/e226edc5ade7...d3ab953be3c5
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.