- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4a61a4: UI, Histories: use links for file inputs shown in ...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4a61a4cb472f740ce98ead7fca44dcf82847c050 https://github.com/galaxyproject/galaxy/commit/4a61a4cb472f740ce98ead7fca44… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/list/list-view.js M templates/show_params.mako Log Message: ----------- UI, Histories: use links for file inputs shown in show_params (the 'i' button in the datasets of histories) that, when clicked, 1) scroll the history to the dataset shown and 2) open *that* datasets info/show_params in the center panel Commit: 017b97b7dc998151ec42c2dca919feb37d5a674d https://github.com/galaxyproject/galaxy/commit/017b97b7dc998151ec42c2dca919… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: 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 M static/scripts/bundled/login.bundled.js.map Log Message: ----------- (repack bundles) Commit: 1275dfd09955c254b801e7be2b741d8845fa4432 https://github.com/galaxyproject/galaxy/commit/1275dfd09955c254b801e7be2b74… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/list/list-view.js M static/maps/mvc/list/list-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 M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/list/list-view.js M templates/show_params.mako Log Message: ----------- Merge pull request #1561 from carlfeberhard/input-walking show_params input walking Compare: https://github.com/galaxyproject/galaxy/compare/a162f91447dc...1275dfd09955

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[galaxyproject/galaxy] 2b97a6: History manager: prototype history contents as a s...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b97a654558c95aa3ebfee4d9521c59212e67d09 https://github.com/galaxyproject/galaxy/commit/2b97a654558c95aa3ebfee4d9521… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History manager: prototype history contents as a separate manager - one that is a facade over the common/shared interfaces of the contained classes Commit: 7aace6dee0ddad8c0325b6ccc681f5b62035acb5 https://github.com/galaxyproject/galaxy/commit/7aace6dee0ddad8c0325b6ccc681… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/base.py M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: c9a5ce7c28ef778fb68ce714806ee0e4cc5a16b3 https://github.com/galaxyproject/galaxy/commit/c9a5ce7c28ef778fb68ce714806e… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-07-27 (Mon, 27 Jul 2015) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- History contents: remove HistoryAsContainer mixin Commit: 2c03d5330f0a45bb00c042b5553fa4fab9c3768b https://github.com/galaxyproject/galaxy/commit/2c03d5330f0a45bb00c042b5553f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: A .ci/check_controller.sh A .ci/check_mako.sh M .ci/flake8_blacklist.txt A .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh A .ci/py3_sources.txt M .gitignore A CODE_OF_CONDUCT.md M CONTRIBUTING.md M CONTRIBUTORS.md A Makefile M README.rst A client/.docker-build.sh A client/Dockerfile M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/tool-panel.js R client/galaxy/scripts/base.js R client/galaxy/scripts/galaxy-app-base.js R client/galaxy/scripts/galaxy.autocom_tagging.js R client/galaxy/scripts/galaxy.base.js R client/galaxy/scripts/galaxy.frame.js A client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js R client/galaxy/scripts/galaxy.masthead.js R client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.pages.js R client/galaxy/scripts/galaxy.panels.js R client/galaxy/scripts/galaxy.tools.js R client/galaxy/scripts/galaxy.ui.scrollPanel.js A client/galaxy/scripts/layout/masthead.js A client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/layout/modal.js A client/galaxy/scripts/layout/page.js A client/galaxy/scripts/layout/panel.js A client/galaxy/scripts/layout/scratchbook.js R client/galaxy/scripts/libs/IE/IE7.js R client/galaxy/scripts/libs/IE/IE8.js R client/galaxy/scripts/libs/IE/blank.gif R client/galaxy/scripts/libs/IE/excanvas.js R client/galaxy/scripts/libs/IE/ie7-recalc.js A client/galaxy/scripts/libs/backbone.js R client/galaxy/scripts/libs/backbone/backbone.js 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/jquery/jquery.dynatree.js M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/libs/raven.js M 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test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: fix tests Commit: 8e4d3845fdc6c535912d5cbca85646b367890362 https://github.com/galaxyproject/galaxy/commit/8e4d3845fdc6c535912d5cbca856… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: (an attempt to) clarify/simplify/clean up, re-implement default_order_by and respect it Commit: 28b8816f46d4619b396a13deb21f15135b020b7b https://github.com/galaxyproject/galaxy/commit/28b8816f46d4619b396a13deb21f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py Log Message: ----------- History contents manager: fully 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lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/pulsar/client/amqp_exchange.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M setup.cfg M static/maps/utils/utils.js.map 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/utils/utils.js M test/casperjs/casperjs_runner.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: bd237cd5863352faba908bbcf39529cd176601a0 https://github.com/galaxyproject/galaxy/commit/bd237cd5863352faba908bbcf395… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/managers/containers.py M lib/galaxy/managers/history_contents.py M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- History contents manager: add tests, fix order_by defaulting, clarify 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static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/layout/menu.js R static/scripts/libs/handlebars.runtime.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-view-edit.js M static/scripts/mvc/collection/collection-view.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/dataset/states.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M 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test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js A test/qunit/tests/ui_tests.html A test/qunit/tests/ui_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_execution.py M test/unit/unittest_utils/galaxy_mock.py A test/unit/web/framework/__init__.py A test/unit/web/framework/test_webapp.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into managers.history-contents Commit: 8ab1607b556b872ccedc6411790786f0a1b5db42 https://github.com/galaxyproject/galaxy/commit/8ab1607b556b872ccedc64117907… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryManager.py Log Message: ----------- Testing: remove unused imports in test_HistoryManager Commit: 48f45cb1853877f78eb917121c0da4fc7dc51c15 https://github.com/galaxyproject/galaxy/commit/48f45cb1853877f78eb917121c0d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M test/unit/managers/test_HistoryContentsManager.py Log Message: ----------- Testing: remove egg import from test_HistoryContentsManager Commit: a162f91447dc47f89df42246ce313de1e27acd35 https://github.com/galaxyproject/galaxy/commit/a162f91447dc47f89df42246ce31… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M lib/galaxy/managers/base.py M lib/galaxy/managers/containers.py M lib/galaxy/managers/histories.py A lib/galaxy/managers/history_contents.py A test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py Log Message: ----------- Merge pull request #1490 from carlfeberhard/managers.history-contents An attempt to add limit/offset to history contents Compare: https://github.com/galaxyproject/galaxy/compare/0f52600583e4...a162f91447dc

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[galaxyproject/galaxy] 5f175e: Update run_test_wrapper.sh
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5f175e35034d2a211264a2b37e9748998dc216e7 https://github.com/galaxyproject/galaxy/commit/5f175e35034d2a211264a2b37e97… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Update run_test_wrapper.sh Commit: 0f52600583e4a4776a46ad86db75fc5f56912bf2 https://github.com/galaxyproject/galaxy/commit/0f52600583e4a4776a46ad86db75… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #1566 from galaxyproject/upgrade_ts_db Update run_test_wrapper.sh to upgrade the toolshed database before running tests. Compare: https://github.com/galaxyproject/galaxy/compare/ce3f2b9cd18c...0f52600583e4

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[galaxyproject/galaxy] 5f175e: Update run_test_wrapper.sh
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/upgrade_ts_db Home: https://github.com/galaxyproject/galaxy Commit: 5f175e35034d2a211264a2b37e9748998dc216e7 https://github.com/galaxyproject/galaxy/commit/5f175e35034d2a211264a2b37e97… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M test/docker/base/run_test_wrapper.sh Log Message: ----------- Update run_test_wrapper.sh

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[galaxyproject/usegalaxy-playbook] 89cf99: update test to ce3f2b9cd18c0160ae198fe2482cd056c54...
by GitHub 22 Jan '16

22 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89cf999d529d4c7ce698952186eccc62a0d889f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/89cf999d529d4c7c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-22 (Fri, 22 Jan 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update test to ce3f2b9cd18c0160ae198fe2482cd056c5449e86

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[galaxyproject/galaxy] 8ceb4d: Force --skip-venv if we can detect that Python is ...
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 8ceb4d8ee495d21a664e3faece1e072a88048494 https://github.com/galaxyproject/galaxy/commit/8ceb4d8ee495d21a664e3faece1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Force --skip-venv if we can detect that Python is Conda Python. Commit: fe96255022f4fdf72f39be959a15993d014a0d38 https://github.com/galaxyproject/galaxy/commit/fe96255022f4fdf72f39be959a15… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1554 from natefoo/conda-interop [16.01] Force --skip-venv if we can detect that Python is Conda Python. Compare: https://github.com/galaxyproject/galaxy/compare/e48388ef6cca...fe96255022f4

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[galaxyproject/galaxy]
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/tags/v15.10.1 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] aad5d9: Bump 15.10 version to 15.10.1 (and apparently it h...
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: aad5d9a2e557e935bd88f725deb10d0ed82468d8 https://github.com/galaxyproject/galaxy/commit/aad5d9a2e557e935bd88f725deb1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Bump 15.10 version to 15.10.1 (and apparently it has been incorrectly set to 15.10.dev all this time). Commit: 868acc362f6ce8a8b3559fcb88ebb4c060321905 https://github.com/galaxyproject/galaxy/commit/868acc362f6ce8a8b3559fcb88eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #1555 from natefoo/release_15.10 [15.10] Bump 15.10 version to 15.10.1 Compare: https://github.com/galaxyproject/galaxy/compare/c13b1c088cfb...868acc362f6c

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[galaxyproject/galaxy] cd9563: Fix #1538.
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cd95635197eddaeee55be88f96543dc3a97e9343 https://github.com/galaxyproject/galaxy/commit/cd95635197eddaeee55be88f9654… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-20 (Wed, 20 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1538. Displaying subcollection mapping in tool forms was broken with #1308 - this fixes that I believe. Commit: e48388ef6cca6505d47b3daf3c2e0c4a5041b3f4 https://github.com/galaxyproject/galaxy/commit/e48388ef6cca6505d47b3daf3c2e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1545 from jmchilton/subcollection_mapping_problem [16.01] Fix #1538. Compare: https://github.com/galaxyproject/galaxy/compare/2fc982027cb3...e48388ef6cca

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[galaxyproject/galaxy] 1b43e8: Logging fix.
by GitHub 21 Jan '16

21 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 1b43e8d68ffd44780f552e2472010d02dbc274b6 https://github.com/galaxyproject/galaxy/commit/1b43e8d68ffd44780f552e247201… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Logging fix. Commit: 2fc982027cb3de555afbd1650b52dbd84897956a https://github.com/galaxyproject/galaxy/commit/2fc982027cb3de555afbd1650b52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: M lib/galaxy/tools/special_tools.py Log Message: ----------- Merge pull request #1553 from jmchilton/logging_fix [16.01] Logging fix. Compare: https://github.com/galaxyproject/galaxy/compare/17abd4a30d41...2fc982027cb3

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