Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1383ced0bdf55d3355a2927db42b584d3b00b15f
https://github.com/galaxyproject/galaxy/commit/1383ced0bdf55d3355a2927db42b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/transform.py
M lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
flake8 lib/galaxy_utils/
Commit: cb1538588d8a7632dcb29232bbad1b299173a84c
https://github.com/galaxyproject/galaxy/commit/cb1538588d8a7632dcb29232bbad…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M .ci/flake8_blacklist.txt
M lib/galaxy_utils/sequence/fasta.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/sequence.py
M lib/galaxy_utils/sequence/transform.py
M lib/galaxy_utils/sequence/vcf.py
Log Message:
-----------
Merge pull request #604 from nsoranzo/flake8_fixes
flake8 lib/galaxy_utils/
Compare: https://github.com/galaxyproject/galaxy/compare/4459e9411b61...cb1538588d8a
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bf8d74da29ba02c08cc1debed38dbf63a13dd686
https://github.com/galaxyproject/galaxy/commit/bf8d74da29ba02c08cc1debed38d…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-30 (Thu, 30 Jul 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
UI, Histories: move unhide_datasets and delete_hidden_datasets to the client, remove them from the web controller
Commit: d20add4ff8abe54cbc15704edc0222935631c767
https://github.com/galaxyproject/galaxy/commit/d20add4ff8abe54cbc15704edc02…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-07-30 (Thu, 30 Jul 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/view.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
Log Message:
-----------
UI, Histories: use /history/view with current to replace /history, move history_as_xml to /history/as_xml
Commit: ff13fb85cc46cdf8399e3477ba8808dfc6078ed5
https://github.com/galaxyproject/galaxy/commit/ff13fb85cc46cdf8399e3477ba88…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-08-07 (Fri, 07 Aug 2015)
Changed paths:
M client/bower.json
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/farbtastic.js
A client/galaxy/scripts/libs/jquery.sparklines.js
M client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/libs/tracekit.js
M client/galaxy/scripts/mvc/form/form-select-content.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-panel-edit.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
A client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/history.less
A client/galaxy/style/less/reports.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
M config/galaxy.ini.sample
M config/plugins/visualizations/trackster/config/trackster.xml
A doc/source/api/guidelines.rst
M doc/source/api_doc.rst
M doc/source/index.rst
M doc/source/releases/_header.rst
A doc/source/ts_api_doc.rst
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/histories.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/output.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/util/basic_util.py
M scripts/tool_shed/build_ts_whoosh_index.py
M static/maps/libs/d3.js.map
M static/maps/libs/farbtastic.js.map
A static/maps/libs/jquery.sparklines.js.map
M static/maps/libs/jquery/jqtouch.js.map
M static/maps/libs/raven.js.map
M static/maps/libs/require.js.map
M static/maps/libs/tracekit.js.map
M static/maps/mvc/form/form-select-content.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-panel-edit.js.map
M static/maps/mvc/ui/ui-select-library.js.map
A static/maps/utils/query-string-parsing.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/trackster.js.map
M static/scripts/libs/d3.js
M static/scripts/libs/farbtastic.js
A static/scripts/libs/jquery.sparklines.js
M static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
M static/scripts/libs/tracekit.js
M static/scripts/mvc/form/form-select-content.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-panel-edit.js
M static/scripts/mvc/ui/ui-select-library.js
A static/scripts/utils/query-string-parsing.js
M static/scripts/utils/utils.js
M static/scripts/viz/trackster.js
M static/style/blue/base.css
A static/style/blue/reports.css
M templates/base.mako
M templates/display_base.mako
M templates/page_base.mako
M templates/search/index.mako
M templates/sorting_base.mako
A templates/spark_base.mako
M templates/webapps/galaxy/cloud/index.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/library/common/ldda_info.mako
M templates/webapps/galaxy/library/common/ldda_permissions.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/reports/index.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/registered_users_specified_month.mako
M templates/webapps/reports/requests_per_month_all.mako
M templates/webapps/reports/requests_per_user.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
A templates/webapps/reports/workflows_per_workflow.mako
M templates/webapps/reports/workflows_user_per_month.mako
R templates/webapps/tool_shed/message.mako
M test/functional/test_toolbox.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
A test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_list_of_pairs.xml
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
M test/functional/tools/samples_tool_conf.xml
M tools/extract/extract_genomic_dna.py
M tools/extract/extract_genomic_dna.xml
Log Message:
-----------
Merge conflicts
Commit: 971b96ddd6855e0e2fd61b89499a15d9e6fb3b93
https://github.com/galaxyproject/galaxy/commit/971b96ddd6855e0e2fd61b89499a…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
UI, Histories: when calling 'Delete hidden', both delete *and* unhide the datasets (preventing them from being both deleted and hidden)
Commit: 3e212507defb88e91799883754d4a1d1ae8c0876
https://github.com/galaxyproject/galaxy/commit/3e212507defb88e91799883754d4…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/root.py
M templates/webapps/galaxy/history/view.mako
Log Message:
-----------
UI, Histories: fix view.mako json ref, remove unused import in root
Commit: b0a8c6f52bfda10244e12b08ff3143c1f4ef0d45
https://github.com/galaxyproject/galaxy/commit/b0a8c6f52bfda10244e12b08ff31…
Author: Carl Eberhard <carlfeberhard(a)gmail.com>
Date: 2015-08-10 (Mon, 10 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
UI, Histories: use renderItems for batched changes in options menu
Commit: 4459e9411b610ea106fe2db74d20dfd27363aa23
https://github.com/galaxyproject/galaxy/commit/4459e9411b610ea106fe2db74d20…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-14 (Fri, 14 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/options-menu.js.map
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/options-menu.js
A templates/webapps/galaxy/history/as_xml.mako
M templates/webapps/galaxy/history/view.mako
R templates/webapps/galaxy/root/history.mako
R templates/webapps/galaxy/root/history_as_xml.mako
Log Message:
-----------
Merge pull request #578 from carlfeberhard/history.s-n-d
Remove more history UIController methods.
Compare: https://github.com/galaxyproject/galaxy/compare/d0a053608582...4459e9411b61
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 303597e48a8503aac09c33910aa5482a374f06a1
https://github.com/galaxyproject/galaxy/commit/303597e48a8503aac09c33910aa5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M client/galaxy/scripts/galaxy.menu.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M static/maps/galaxy.menu.js.map
M static/scripts/galaxy.menu.js
R templates/webapps/galaxy/cloud/index.mako
Log Message:
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Remove old cloudlaunch in favor of https://github.com/galaxyproject/cloudlaunch, at launch.usegalaxy.org
Commit: 635ef189df60e9a1ce6e0e8c177fdc3b136da9a1
https://github.com/galaxyproject/galaxy/commit/635ef189df60e9a1ce6e0e8c177f…
Author: Nitesh Turaga <nitesh.turaga(a)gmail.com>
Date: 2015-08-13 (Thu, 13 Aug 2015)
Changed paths:
M client/galaxy/scripts/galaxy.menu.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
R lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
M static/maps/galaxy.menu.js.map
M static/scripts/galaxy.menu.js
R templates/webapps/galaxy/cloud/index.mako
Log Message:
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Merge pull request #597 from dannon/no_more_cloudlaunch
Remove old cloudlaunch in favor of …
Compare: https://github.com/galaxyproject/galaxy/compare/369760aabe27...635ef189df60