Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bf3a487f2017d248317e9ea70e567f57a70d9cc9
https://github.com/galaxyproject/galaxy/commit/bf3a487f2017d248317e9ea70e56…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-01-16 (Mon, 16 Jan 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Fix import order and Python3 compatibility for lib/galaxy/tools/
xref. #1715
Commit: d2e019844471ee29f9b2433e0f90f53ea54a7b7f
https://github.com/galaxyproject/galaxy/commit/d2e019844471ee29f9b2433e0f90…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-17 (Tue, 17 Jan 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Merge pull request #3431 from nsoranzo/python3
Fix import order and Python3 compatibility for lib/galaxy/tools/
Compare: https://github.com/galaxyproject/galaxy/compare/910bbdfc54fe...d2e019844471
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2
https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component.
Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2
https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.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-view.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Swap form-view to use the new UnescapedMessage
Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8
https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Name function appropriately for Javascript instead of being stuck in Python.
Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24
https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-15 (Sun, 15 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.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-view.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge pull request #3416 from dannon/ui_misc_message_fixes
[16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html
Commit: 8cb61626811d51afef0f7e27e9713fa98e6b664a
https://github.com/galaxyproject/galaxy/commit/8cb61626811d51afef0f7e27e971…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-01-16 (Mon, 16 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.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-view.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge branch 'release_16.10' into dev
Conflicts:
static/maps/mvc/ui/ui-misc.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/ui/ui-misc.js
Compare: https://github.com/galaxyproject/galaxy/compare/ebf18440ac09...8cb61626811d
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: 68f5bc7a1ae092da266dae78adba5de8ebfd6eb2
https://github.com/galaxyproject/galaxy/commit/68f5bc7a1ae092da266dae78adba…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Reapply ui-misc.Message changes post-reversion. Following up with fixes to other uses of this component.
Commit: b798895af0c815783f741aa8c6278ed71ee6f0f2
https://github.com/galaxyproject/galaxy/commit/b798895af0c815783f741aa8c627…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.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-view.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Swap form-view to use the new UnescapedMessage
Commit: 08454cfa2a0ff2d02b3ec2a61740dd429c8a67f8
https://github.com/galaxyproject/galaxy/commit/08454cfa2a0ff2d02b3ec2a61740…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Name function appropriately for Javascript instead of being stuck in Python.
Commit: 02a8a7da0a0f2e3ff9c6d3cb7c5f2e1d56621a24
https://github.com/galaxyproject/galaxy/commit/02a8a7da0a0f2e3ff9c6d3cb7c5f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-15 (Sun, 15 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-misc.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-view.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge pull request #3416 from dannon/ui_misc_message_fixes
[16.10] Sanitize ui-misc.Message, implement UnescapedMessage for uses where we need html
Compare: https://github.com/galaxyproject/galaxy/compare/c94ccb3f28cd...02a8a7da0a0f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 537d6e645ae142962cdf59e6365299b8c99706bf
https://github.com/galaxyproject/galaxy/commit/537d6e645ae142962cdf59e63652…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix "exact" property for merged conda dependencies.
This was broken with there initial commit as part of #3391.
Commit: 2ed131d206dbf73a141b7baf76c5ffcce6fef206
https://github.com/galaxyproject/galaxy/commit/2ed131d206dbf73a141b7baf76c5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-01-14 (Sat, 14 Jan 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Fix display of repository dependency status
that broke with the introduction of the all-at-once dependency
resolution in #3391 and addresses in part #3398. I have only restored
the (collapsed) display of dependencies for all requirements in a
repository, so breaking the information out on a per tool basis remains
on the TODO list.
Commit: ebf18440ac09c364fa1fb6b1cdd1640808ffd593
https://github.com/galaxyproject/galaxy/commit/ebf18440ac09c364fa1fb6b1cdd1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-15 (Sun, 15 Jan 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #3427 from mvdbeek/fix_dependency_display_and_api
Fix dependency display and api
Compare: https://github.com/galaxyproject/galaxy/compare/b2cf773befd6...ebf18440ac09
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa
https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
A static/maps/libs/showdown.js.map
M static/maps/mvc/ui/ui-misc.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
A static/scripts/libs/showdown.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Swap the client's ui-misc.Message to escape by default.
Commit: e1083132b89f854e2ec824f97f187e925ba0abe6
https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own.
Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def
https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
Log Message:
-----------
Fix RStudio login
Thanks @shiltemann for reporting this
Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233
https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Export UnescapedMessage from ui-misc.
Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc
https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Formatting cleanup.
Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a
https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Reversion of ui-misc messagebox changes.
Commit: 2d69909218b287f8085a599e0a2a1214480330c9
https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js
Log Message:
-----------
Merge pull request #3415 from dannon/revert_uimisc
[16.10]Reversion of ui-misc messagebox changes.
Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50
https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
Log Message:
-----------
Merge pull request #3414 from erasche/fix-rstudio-login
[16.10] Fix RStudio login
Commit: b2cf773befd655ccae204c358703c9061916a32f
https://github.com/galaxyproject/galaxy/commit/b2cf773befd655ccae204c358703…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A static/maps/libs/showdown.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
A static/scripts/libs/showdown.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/1f9812b5d522...b2cf773befd6
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 422cf1917e97b612e972b3824fcf831c510dc535
https://github.com/galaxyproject/galaxy/commit/422cf1917e97b612e972b3824fcf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Switch to Miniconda3.
It is the platformed used by bioconda for testing and will be supported longer than the older Python 2 variant. This shouldn't require Python 3 be installed on the host running Galaxy.
Commit: d66d3a1a308a94dd548f29448b479c9d9b66a239
https://github.com/galaxyproject/galaxy/commit/d66d3a1a308a94dd548f29448b47…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Add a log message to explain long pause during startup.
When conda_auto_init is used.
Commit: 1f9812b5d522118f79a304e3c4f5f69e28661b05
https://github.com/galaxyproject/galaxy/commit/1f9812b5d522118f79a304e3c4f5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-01-13 (Fri, 13 Jan 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Merge pull request #3419 from jmchilton/conda_tweaks
Target Miniconda3 when installing Conda.
Compare: https://github.com/galaxyproject/galaxy/compare/e573826e02e8...1f9812b5d522