- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b1f4a0: Fix initial conda version at 4.0.5
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1f4a0f61aeb8ddfec26c4b51bf92bdd50606c91 https://github.com/galaxyproject/galaxy/commit/b1f4a0f61aeb8ddfec26c4b51bf9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: ba6a0a36476cd5db46777e99b84b6440ec6073b0 https://github.com/galaxyproject/galaxy/commit/ba6a0a36476cd5db46777e99b84b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2869 from mvdbeek/upgrade_conda_instead_of_downgrading Fix initial conda version at 4.0.5 Compare: https://github.com/galaxyproject/galaxy/compare/0bd1ea108e7f...ba6a0a36476c

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[galaxyproject/galaxy] f6c1aa: Create a new trans method for getting the most rec...
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6c1aa0770508c552f074771078a4b7cc4cce400 https://github.com/galaxyproject/galaxy/commit/f6c1aa0770508c552f074771078a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Create a new trans method for getting the most recently touched history. Swap several uses of get_history (with create=True, only), to use this new functionality where it makes sense. Commit: 0bd1ea108e7f6000759583afd3e6d2d7daa3e7be https://github.com/galaxyproject/galaxy/commit/0bd1ea108e7f6000759583afd3e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #2870 from dannon/histories.most_recent_v_default Create a new trans method for getting the most recently touched history. Compare: https://github.com/galaxyproject/galaxy/compare/e64503697302...0bd1ea108e7f

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[galaxyproject/galaxy] d86ee3: Add the <conda_prefix> in 12. and fix typo
by GitHub 30 Aug '16

30 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d86ee3706089e59868c16a3352ce61e0257dbb40 https://github.com/galaxyproject/galaxy/commit/d86ee3706089e59868c16a3352ce… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Add the <conda_prefix> in 12. and fix typo I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda). And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``). Commit: 579ea41085501139eebbbeb5b3f72c9c04c03e4c https://github.com/galaxyproject/galaxy/commit/579ea41085501139eebbbeb5b3f7… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update Marius advice Commit: e6450369730230bc844db67d3df05f1cffd3cdad https://github.com/galaxyproject/galaxy/commit/e6450369730230bc844db67d3df0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2871 from remimarenco/patch-8 Add the <conda_prefix> in 12. and fix typo Compare: https://github.com/galaxyproject/galaxy/compare/dbde38c951cd...e64503697302

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[galaxyproject/galaxy] 040dd3: Fix typo
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 040dd33980668ecb74a44dfc9c4e39e1a1339cef https://github.com/galaxyproject/galaxy/commit/040dd33980668ecb74a44dfc9c4e… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Fix typo Commit: dbde38c951cdbb539def102ca55ddf5a4da3ced2 https://github.com/galaxyproject/galaxy/commit/dbde38c951cdbb539def102ca55d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M doc/source/admin/chat.rst Log Message: ----------- Merge pull request #2872 from remimarenco/patch-9 Fix typo Compare: https://github.com/galaxyproject/galaxy/compare/4ad0bee5523b...dbde38c951cd

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[galaxyproject/infrastructure-playbook] 308b9c: Only stratum 0s use the repo options
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 308b9c8862a75164b71d1465ef0b219e41997833 https://github.com/galaxyproject/infrastructure-playbook/commit/308b9c8862a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M roles/cvmfs/tasks/stratum0.yml Log Message: ----------- Only stratum 0s use the repo options Commit: dc0f1c9613afaa2a3b1096db53eedc7b62d83325 https://github.com/galaxyproject/infrastructure-playbook/commit/dc0f1c9613a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Node IPs were off by 1 Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/6e5c654c9d…

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[galaxyproject/infrastructure-playbook] 6e5c65: Relaunched all Jetstream @ TACC resources
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6e5c654c9d4eaa9b0a2b50b8f5834650fd6ed7f2 https://github.com/galaxyproject/infrastructure-playbook/commit/6e5c654c9d4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M galaxyenv/host_vars/cvmfs1-iu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/host_vars/cvmfs1-tacc0.galaxyproject.org.yml M jetstreamtaccenv/group_vars/all.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory M roles/cvmfs/tasks/stratum1.yml M roles/jetstream_nfs/tasks/server.yml Log Message: ----------- Relaunched all Jetstream @ TACC resources

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[galaxyproject/usegalaxy-playbook] 695d5f: Add gat2016 redirect
by GitHub 29 Aug '16

29 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 695d5f1841defb8424b145660401f30aef25864a https://github.com/galaxyproject/usegalaxy-playbook/commit/695d5f1841defb84… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Add gat2016 redirect

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[galaxyproject/usegalaxy-playbook] 86f45e: Update Test
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 86f45e53281aac412707fc132f735a33bdbc220e https://github.com/galaxyproject/usegalaxy-playbook/commit/86f45e53281aac41… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M stage/galaxy_version.yml Log Message: ----------- Update Test Commit: 18d381fee4580da464383ae64e7d0442680352ad https://github.com/galaxyproject/usegalaxy-playbook/commit/18d381fee4580da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M templates/nginx/galaxy_main_installer.j2 M templates/nginx/galaxy_test.j2 Log Message: ----------- Installer moved to docker on galaxy04 Commit: 053e1eeaca7ac558661f303b073ab09e87851060 https://github.com/galaxyproject/usegalaxy-playbook/commit/053e1eeaca7ac558… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/98a878e0e3b6...…

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[galaxyproject/galaxy] 4f3c44: Move the registration of the start function into t...
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Move the registration of the start function into the ToolConfWatcher itself so it doesn't have to be called by things that instantiate it. Fixes #2831. Commit: 6631367b7cd4f2049426f3554eef6da626b83837 https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Unused import, cleanup for #2856 Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- fix inclusion of release notes in announcement Commit: c98331eddd3f8a57cedca313249798e1e45a9555 https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca3132497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix [16.07] Postfork tool conf watcher test fix Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d217… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix [16.07] Unused import cleanup for #2856 Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge pull request #2859 from martenson/fix-notes-include [16.07] fix inclusion of release notes in the announcement Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4 https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2863 from martenson/release_16.07 [16.07] backport disable conda_auto_init Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Commit: 4ad0bee5523b1a05423eaa21624ebe146412d423 https://github.com/galaxyproject/galaxy/commit/4ad0bee5523b1a05423eaa21624e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M doc/source/releases/16.07.rst M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f9758f2871e3...4ad0bee5523b

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[galaxyproject/galaxy] 672414: Fix three conda bugs.
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6724146e7d09e5c0ac4f19d96e600d14831a8abe https://github.com/galaxyproject/galaxy/commit/6724146e7d09e5c0ac4f19d96e60… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix three conda bugs. - Don't attempt file lock if don't have write access for lock. - Set disabled to False if conda present and auto_init is False. - Use the correct parent path for conda_prefix (if default parent path is overridden). Commit: c01ce21e2cdb7b229dd8ced14e4e2c1c7fdf294c https://github.com/galaxyproject/galaxy/commit/c01ce21e2cdb7b229dd8ced14e4e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2864 from jmchilton/conda_fixes [16.07] Fix three conda bugs. Compare: https://github.com/galaxyproject/galaxy/compare/52768c0c4231...c01ce21e2cdb

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[galaxyproject/galaxy] d1821f: disable conda_auto_init
by GitHub 26 Aug '16

26 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d1821fed475a4261c007de3627cb3eeb42d53a1f https://github.com/galaxyproject/galaxy/commit/d1821fed475a4261c007de3627cb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- disable conda_auto_init Commit: 52768c0c42313c08f25ba07b47ccf2bed28248f4 https://github.com/galaxyproject/galaxy/commit/52768c0c42313c08f25ba07b47cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #2863 from martenson/release_16.07 [16.07] backport disable conda_auto_init Compare: https://github.com/galaxyproject/galaxy/compare/e891c5755f59...52768c0c4231

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[galaxyproject/galaxy] 4e5de5: alter release notes template
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e5de56b6341a693d877a6659eac703db67c025e https://github.com/galaxyproject/galaxy/commit/4e5de56b6341a693d877a6659eac… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- alter release notes template remove bitbucket distribution make github commands checkout the actual release instead of master Commit: f9758f2871e3b21b25d76f7b62bcc2aae99b9249 https://github.com/galaxyproject/galaxy/commit/f9758f2871e3b21b25d76f7b62bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2858 from martenson/rn_tweaks alter release notes template Compare: https://github.com/galaxyproject/galaxy/compare/75a3aecbbedd...f9758f2871e3

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[galaxyproject/galaxy] bcc3d7: Align chart form definitions, swap custom settings...
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bcc3d7fcddac1926af4f3d2192877071ea9b0db3 https://github.com/galaxyproject/galaxy/commit/bcc3d7fcddac1926af4f3d219287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M config/plugins/visualizations/charts/static/charts/types.js M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Align chart form definitions, swap custom settings form with regular form view Commit: b1fb1cff98f3a756bd02643459eda4468237ada8 https://github.com/galaxyproject/galaxy/commit/b1fb1cff98f3a756bd02643459ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js 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 Log Message: ----------- Match initial form values, remove settings customization Commit: fb075e15a9c7e73430ff049b33ee4e6543ab47f3 https://github.com/galaxyproject/galaxy/commit/fb075e15a9c7e73430ff049b33ee… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M config/plugins/visualizations/charts/static/charts/forms/default.js A config/plugins/visualizations/charts/static/charts/forms/inputs.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js M config/plugins/visualizations/charts/static/charts/types.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-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.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js Log Message: ----------- Use regular form definitions for all nvd3 charts Commit: 67b7516615fb785bcdd05e06827c329856918ccb https://github.com/galaxyproject/galaxy/commit/67b7516615fb785bcdd05e06827c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/forms/inputs.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-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.map M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-view.js Log Message: ----------- Revise groups form building Repack Commit: 4d81e6f3ebc8ac0e9c10f109796887b673d66702 https://github.com/galaxyproject/galaxy/commit/4d81e6f3ebc8ac0e9c10f1097968… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/types.js Log Message: ----------- Fix histogram configuration Commit: 118c397304802763d75b3289cb15071482b8d953 https://github.com/galaxyproject/galaxy/commit/118c397304802763d75b3289cb15… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M config/plugins/visualizations/charts/static/charts/forms/inputs.js M config/plugins/visualizations/charts/static/views/settings.js M static/maps/mvc/ui/ui-color-picker.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-color-picker.js Log Message: ----------- Revise color picker, fix settings form Commit: bda8ba737d3c60fae30541965165caab611cefbb 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config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js M config/plugins/visualizations/charts/static/views/editor.js M static/maps/mvc/ui/ui-color-picker.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-color-picker.js Log Message: ----------- Map settings when chart type changes Commit: 3f0cf73eba1341ba25a72ae424f26e99ccd02309 https://github.com/galaxyproject/galaxy/commit/3f0cf73eba1341ba25a72ae424f2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js Log Message: ----------- Revise error message Commit: 5ea8d035c9c3441f5314e9d281df53986af45d54 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config/plugins/visualizations/charts/static/app.js Log Message: ----------- Revise page viewing caller Commit: ff210c067763987bad2574a8996bbd8466c5485f https://github.com/galaxyproject/galaxy/commit/ff210c067763987bad2574a8996b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/storage.js Log Message: ----------- Refactor storage handler Commit: d952e876e5bf03c9fedfeff59e706d42decc21b6 https://github.com/galaxyproject/galaxy/commit/d952e876e5bf03c9fedfeff59e70… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M static/maps/mvc/form/form-data.js.map Log Message: ----------- Populate input states for settings and group forms Commit: b23b18c3027685ae8a44f1294152e839d01440c8 https://github.com/galaxyproject/galaxy/commit/b23b18c3027685ae8a44f1294152… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/utils/utils.js M config/plugins/visualizations/charts/static/models/chart.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/utils/utils.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/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/utils/utils.js Log Message: ----------- Populate input states for settings and group forms Commit: 183cbec3a6c1b2b25f4b11284f6d4c730de488a0 https://github.com/galaxyproject/galaxy/commit/183cbec3a6c1b2b25f4b11284f6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js Log Message: ----------- More config clean up Commit: 2fa3f2e801c59b8da08ba802eba599485cf217e6 https://github.com/galaxyproject/galaxy/commit/2fa3f2e801c59b8da08ba802eba5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/types.js Log Message: ----------- Reactivate chart types Commit: a78a398e57cecc67dc4a62f5fa23a06a0a0b146b https://github.com/galaxyproject/galaxy/commit/a78a398e57cecc67dc4a62f5fa23… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js Log Message: ----------- Fix precision handling in graph wrappers Commit: 9f4fc82a1442da4697fc8240320bf1bdb2cb8edc https://github.com/galaxyproject/galaxy/commit/9f4fc82a1442da4697fc8240320b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js Log Message: ----------- Cleanup wrappers Commit: 2cf0bb642b5264cd6be0dd214947f57597acd5a4 https://github.com/galaxyproject/galaxy/commit/2cf0bb642b5264cd6be0dd214947… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js Log Message: ----------- Adjust heatmap wrappers and configurations Commit: 972c5c0ce0ee1151b50d206f1edd8ef494090a23 https://github.com/galaxyproject/galaxy/commit/972c5c0ce0ee1151b50d206f1edd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/utils/utils.js M static/maps/utils/utils.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/utils.js Log Message: ----------- Revise cloning method Commit: 015b684ab076dc6e9712deb8f6dcd41d811b772c https://github.com/galaxyproject/galaxy/commit/015b684ab076dc6e9712deb8f6dc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js Log Message: ----------- Fix jqplot options Commit: e4000b1dc28458d75a751c00f3418ef292bdee96 https://github.com/galaxyproject/galaxy/commit/e4000b1dc28458d75a751c00f341… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js Log Message: ----------- Fix default label value, histogram color picker Commit: d370d56264763c1e9a36714caeb3ca936379e1aa https://github.com/galaxyproject/galaxy/commit/d370d56264763c1e9a36714caeb3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js Log Message: ----------- Fix heatmap panel option Commit: 322ebe0badc19766d50b58556dd682c3b425113d https://github.com/galaxyproject/galaxy/commit/322ebe0badc19766d50b58556dd6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Fix comments Commit: 48e3f3c4f7172ade82cf0c6d1f5464e163ec357e https://github.com/galaxyproject/galaxy/commit/48e3f3c4f7172ade82cf0c6d1f54… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/views/types.js M static/maps/mvc/form/form-data.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-data.js Log Message: ----------- Use libraries instead of data point sizes to filter list of visualization types Commit: 600a4177f00799ff6578005a5a8ae00427b45c21 https://github.com/galaxyproject/galaxy/commit/600a4177f00799ff6578005a5a8a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Add description for jqplots Commit: f4f82f61b0771ee5089d28ef0787a36748a3befa https://github.com/galaxyproject/galaxy/commit/f4f82f61b0771ee5089d28ef0787… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: A config/plugins/visualizations/charts/static/charts/overview.js M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Separate library overview dictionary Commit: 8f2bceebffc2fea12aa353320e5f21e61bf61e83 https://github.com/galaxyproject/galaxy/commit/8f2bceebffc2fea12aa353320e5f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-view.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/tools.js A config/plugins/visualizations/charts/static/charts/utilities.js M static/maps/mvc/form/form-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.map M static/scripts/mvc/form/form-view.js Log Message: ----------- Rename tools to utilities Commit: 38fc18f25f55e8693d057127a7764c5a48632e7c https://github.com/galaxyproject/galaxy/commit/38fc18f25f55e8693d057127a776… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/overview.js Log Message: ----------- Redirect to new browser tab when visiting 3rd party library links Commit: e385eec3b50df1ede7788e194667229a2450ff09 https://github.com/galaxyproject/galaxy/commit/e385eec3b50df1ede7788e194667… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Clean dataset handling Commit: 2ef4584487cf9f385d16670c2bbf6415af74ab76 https://github.com/galaxyproject/galaxy/commit/2ef4584487cf9f385d16670c2bbf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities.js Log Message: ----------- Clean utilities Commit: 6d3a9e60512f91fbe6f1261311ef7fb8f0feec46 https://github.com/galaxyproject/galaxy/commit/6d3a9e60512f91fbe6f1261311ef… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities.js Log Message: ----------- Fix spacing Commit: 5f292489d9ca60ed2a022ffa332219d93f2a735f https://github.com/galaxyproject/galaxy/commit/5f292489d9ca60ed2a022ffa3322… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/forms/default.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities.js M config/plugins/visualizations/charts/static/library/jobs.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Decouple dataset type from charts Commit: 171dbbcc25303fa374fec1ada2e424a15914b06c https://github.com/galaxyproject/galaxy/commit/171dbbcc25303fa374fec1ada2e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Revise group wrapper Commit: c61014515221bad676d9800936fe8ad2208b982b https://github.com/galaxyproject/galaxy/commit/c61014515221bad676d9800936fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/library/jobs.js Log Message: ----------- Revise job submission to charts tool Commit: 9bb7360dfbeb08a66a24b10593144c0cf441c70b https://github.com/galaxyproject/galaxy/commit/9bb7360dfbeb08a66a24b1059314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/library/jobs.js Log Message: ----------- Explicitly specify charts tool module within wrapper Commit: 12f87efb59c16fb6b011ba2a800cde11d29720d1 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Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities.js Log Message: ----------- Rename request dictionary builder Commit: 024122a778ca6005d2459799b957ad70cb8c3f7b https://github.com/galaxyproject/galaxy/commit/024122a778ca6005d2459799b957… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities.js Log Message: ----------- Add comment to panel helper Commit: f4f5abd9f7caaf3a958810107dac652a0b207314 https://github.com/galaxyproject/galaxy/commit/f4f5abd9f7caaf3a958810107dac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Use separate function to call dataset handler Commit: 97e0b7942814ee3979c8e546fa383330c125c1c8 https://github.com/galaxyproject/galaxy/commit/97e0b7942814ee3979c8e546fa38… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Revise data block fetching Commit: 46b9d21a2d886485efd147b24caf26477297c9fa https://github.com/galaxyproject/galaxy/commit/46b9d21a2d886485efd147b24caf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities.js M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Remove unused recursion and block caching features Commit: fbb65bfc3f4c196cc117ae73f26648dc027650ab https://github.com/galaxyproject/galaxy/commit/fbb65bfc3f4c196cc117ae73f266… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Fix log labels Commit: 9288b6b8a940b74bad19f572459b366dd25b9b92 https://github.com/galaxyproject/galaxy/commit/9288b6b8a940b74bad19f572459b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Remove unused variables Commit: 5275f71d68d894ebdbf8265546a11ff563b32b5d https://github.com/galaxyproject/galaxy/commit/5275f71d68d894ebdbf8265546a1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities.js M config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Clone result dictionary before filling column data Commit: 4683302479c153305e835bee5318237c4e331716 https://github.com/galaxyproject/galaxy/commit/4683302479c153305e835bee5318… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js Log Message: ----------- Align other executable chart types Commit: d1b0c4ddc10ff6a80c1953b98b9867f92d1ce4b9 https://github.com/galaxyproject/galaxy/commit/d1b0c4ddc10ff6a80c1953b98b98… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/library/datasets.js M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Remove dataset get caller Commit: 26351f1b1574fb65c69a25fdca3cf2a9de7f581f https://github.com/galaxyproject/galaxy/commit/26351f1b1574fb65c69a25fdca3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: R config/plugins/visualizations/charts/static/charts/forms/default.js R config/plugins/visualizations/charts/static/charts/forms/inputs.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/utilities.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-jobs.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/library/jobs.js Log Message: ----------- Move tabular specific features into utilities directory Commit: f43a5e373b717db5b7ae7ae65c6c8a07f15045d4 https://github.com/galaxyproject/galaxy/commit/f43a5e373b717db5b7ae7ae65c6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js R config/plugins/visualizations/charts/static/library/datasets.js Log Message: ----------- Move dataset handler to tabular specific location Commit: defb1bced431b44702c021449a973a45dd84f2c8 https://github.com/galaxyproject/galaxy/commit/defb1bced431b44702c021449a97… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js Log Message: ----------- Remove unused app parsing to utilities Commit: d9e47910684ea0da320aa82868ae705c489946f6 https://github.com/galaxyproject/galaxy/commit/d9e47910684ea0da320aa82868ae… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-jobs.js Log Message: ----------- Fix jqplot histogram wrapper Commit: 4b604bd1e1a8b8c102828917fb62e45aa0be6dfc https://github.com/galaxyproject/galaxy/commit/4b604bd1e1a8b8c102828917fb62… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/types.js Log Message: ----------- Add discrete history visualization for nvd3 Commit: b6eb08a418c2c0f5c5924991bc4e262c24c3e69e https://github.com/galaxyproject/galaxy/commit/b6eb08a418c2c0f5c5924991bc4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Fix message style, properly reject failed job submissions Commit: 2073114b68937ab7a02ab76dab85f7691ebd7725 https://github.com/galaxyproject/galaxy/commit/2073114b68937ab7a02ab76dab85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M static/maps/mvc/form/form-data.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-data.js Log Message: ----------- Generalize group forms Commit: 29b54a230d949cf944ba280934318346db453961 https://github.com/galaxyproject/galaxy/commit/29b54a230d949cf944ba28093431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities/tabular-jobs.js Log Message: ----------- Fix job submission Commit: 45a40186b77877980570a4b9e73e404372db564a https://github.com/galaxyproject/galaxy/commit/45a40186b77877980570a4b9e73e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Fix validation message for missing data columns Commit: 756f1a03df40775649e619f439bfff0c93016a7c https://github.com/galaxyproject/galaxy/commit/756f1a03df40775649e619f439bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js Log Message: ----------- Fix heatmap plugin Commit: d0efd5f797d37f49b7c028a48a7b514a7dd84947 https://github.com/galaxyproject/galaxy/commit/d0efd5f797d37f49b7c028a48a7b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js Log Message: ----------- Remove dataset limit Commit: 3e00f7a559d5a7e3d7ca19d72c6d2e431f2c3502 https://github.com/galaxyproject/galaxy/commit/3e00f7a559d5a7e3d7ca19d72c6d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.js A config/plugins/visualizations/charts/static/components/model.js A config/plugins/visualizations/charts/static/components/screenshot.js A config/plugins/visualizations/charts/static/components/storage.js R config/plugins/visualizations/charts/static/library/screenshot.js R config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/models/chart.js R config/plugins/visualizations/charts/static/models/config.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Remove unused config Commit: fdad129cbdb904aa599a3060d5642aefba780877 https://github.com/galaxyproject/galaxy/commit/fdad129cbdb904aa599a3060d564… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-21 (Sun, 21 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-jobs.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/templates/charts.mako Log Message: ----------- Remove global config dictionary, use Galaxy instead Commit: 9228213b989c7ae53c3f02e26f299eedfe4e61d3 https://github.com/galaxyproject/galaxy/commit/9228213b989c7ae53c3f02e26f29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js R config/plugins/visualizations/charts/static/charts/utilities/tabular-jobs.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js A config/plugins/visualizations/charts/static/components/jobs.js Log Message: ----------- Allow to execute any tool Commit: ebab021d3c7077e3b333b634521b45d6ad1ecedc https://github.com/galaxyproject/galaxy/commit/ebab021d3c7077e3b333b634521b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/components/jobs.js Log Message: ----------- Fix error message Commit: cab8f4c44f31ca9e8be984742a6961ce942bffea https://github.com/galaxyproject/galaxy/commit/cab8f4c44f31ca9e8be984742a69… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js Log Message: ----------- Make heatmap title font smaller Commit: 7325991e1569ac76559c7ca32e86ae073a4ff679 https://github.com/galaxyproject/galaxy/commit/7325991e1569ac76559c7ca32e86… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Add space between viewport top and portlet header Commit: 76d886ee97bfbd9e887eb68fdef8919dcc310723 https://github.com/galaxyproject/galaxy/commit/76d886ee97bfbd9e887eb68fdef8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/views/viewer.js Log Message: ----------- Fix message style, align view names Commit: 94d6d6f16fde5c2b5922cb3bd6d61a7a96636ec2 https://github.com/galaxyproject/galaxy/commit/94d6d6f16fde5c2b5922cb3bd6d6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js A config/plugins/visualizations/charts/static/charts/others/example/config.js A config/plugins/visualizations/charts/static/charts/others/example/logo.png A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/types.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/viewport.js M static/maps/mvc/ui/ui-tabs.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-tabs.js Log Message: ----------- Add developer example Commit: 5848a6202a1f9647ef6e54b7af656536e68ada3f https://github.com/galaxyproject/galaxy/commit/5848a6202a1f9647ef6e54b7af65… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/config.js Log Message: ----------- Fix example data labels Commit: afce76516c42e0cd549c7108d91c8190a512c263 https://github.com/galaxyproject/galaxy/commit/afce76516c42e0cd549c7108d91c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/example/config.js Log Message: ----------- Add multi-panel option to developer example Commit: 50dfd162c189f096a92b4e48f31ad5cdb80eac0c https://github.com/galaxyproject/galaxy/commit/50dfd162c189f096a92b4e48f31a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js Log Message: ----------- Use build in boolean input type instead of custom select definition Commit: 84e922c274713e07d14fd7ed991cb64a70a473d6 https://github.com/galaxyproject/galaxy/commit/84e922c274713e07d14fd7ed991c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Fix group refresh handling Commit: fbd81551a0f1bda6a388c0d03728058167a3650f https://github.com/galaxyproject/galaxy/commit/fbd81551a0f1bda6a388c0d03728… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/others/example/config.js M config/plugins/visualizations/charts/static/charts/others/example/logo.png M config/plugins/visualizations/charts/static/components/model.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewport.js Log Message: ----------- Display currently selected chart type details in settings and groups Commit: a1a264f79b2d84e7bffa3cf769e4cbdd24cd7e13 https://github.com/galaxyproject/galaxy/commit/a1a264f79b2d84e7bffa3cf769e4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css Log Message: ----------- Break long chart type descriptions Commit: 4efc4d2eed8c5aa7c2f61df99a08ec256cda763c https://github.com/galaxyproject/galaxy/commit/4efc4d2eed8c5aa7c2f61df99a08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css Log Message: ----------- Fix description styles Commit: 54be4b874c59ce90daa0025fd236a26140fa82df https://github.com/galaxyproject/galaxy/commit/54be4b874c59ce90daa0025fd236… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/groups.js Log Message: ----------- Remove unnecessary check Commit: f4510a089dff871583d8b3fab5aaa91fffd23dea https://github.com/galaxyproject/galaxy/commit/f4510a089dff871583d8b3fab5aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: A config/plugins/visualizations/charts/static/views/description.js Log Message: ----------- Add description view Commit: c2a0bc550940e73485738c78a253fcda94c34da9 https://github.com/galaxyproject/galaxy/commit/c2a0bc550940e73485738c78a253… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/description.js Log Message: ----------- Fix description change listener Commit: 8996b0a963abbcd1bd4ec3a2797b5ab9fe6f71e7 https://github.com/galaxyproject/galaxy/commit/8996b0a963abbcd1bd4ec3a2797b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/settings.js Log Message: ----------- Fix chart settings mapping and initialization Commit: e35520c13a91eb979abab524db0e5da829ffc4d4 https://github.com/galaxyproject/galaxy/commit/e35520c13a91eb979abab524db0e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js Log Message: ----------- Fix heatmap configuration Commit: d9b8a1674b3ba05e9076fdc85c494fbe1b2a736a https://github.com/galaxyproject/galaxy/commit/d9b8a1674b3ba05e9076fdc85c49… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-tabs.js M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/app.js M config/plugins/visualizations/charts/static/charts/types.js M config/plugins/visualizations/charts/static/components/storage.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/types.js M static/maps/mvc/ui/ui-tabs.js.map M static/scripts/mvc/ui/ui-tabs.js Log Message: ----------- Use tabs for chart type selector Commit: d921470fbd8217552e97b423c7f9104a537bd05c https://github.com/galaxyproject/galaxy/commit/d921470fbd8217552e97b423c7f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/app.css M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Fix spacing Commit: cece0b48edf8baff411d8667d2e7379335e7868a https://github.com/galaxyproject/galaxy/commit/cece0b48edf8baff411d8667d2e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/views/types.js Log Message: ----------- Remove unused library radio buttons Commit: a31640c7306a1d1de1187dd6c0df99805976ac3d https://github.com/galaxyproject/galaxy/commit/a31640c7306a1d1de1187dd6c0df… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/scripts/mvc/dataset/data.js M config/galaxy.ini.sample M config/reports.ini.sample M config/tool_shed.ini.sample M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/util/postfork.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M static/maps/mvc/dataset/data.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/dataset/data.js A test/api/test_api_batch.py A test/casperjs/api-batch-tests.js Log Message: ----------- Merge branch 'dev' into charts_revision Commit: 942c59bca4118e55df34743299f758fa3199f6fb https://github.com/galaxyproject/galaxy/commit/942c59bca4118e55df34743299f7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js Log Message: ----------- Fix data labels Commit: 68a3cb4f4326fcc5adb10d1d4a14aadde675e588 https://github.com/galaxyproject/galaxy/commit/68a3cb4f4326fcc5adb10d1d4a14… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js Log Message: ----------- Fix pie chart config Commit: 75a3aecbbeddf7124ab9e6d7b885bdd28765e0e0 https://github.com/galaxyproject/galaxy/commit/75a3aecbbeddf7124ab9e6d7b885… Author: 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config/plugins/visualizations/charts/static/charts/others/example/logo.png A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js A config/plugins/visualizations/charts/static/charts/overview.js R config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/charts/types.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js A config/plugins/visualizations/charts/static/components/jobs.js A config/plugins/visualizations/charts/static/components/model.js A config/plugins/visualizations/charts/static/components/screenshot.js A config/plugins/visualizations/charts/static/components/storage.js R config/plugins/visualizations/charts/static/library/datasets.js R config/plugins/visualizations/charts/static/library/jobs.js R config/plugins/visualizations/charts/static/library/screenshot.js R config/plugins/visualizations/charts/static/library/storage.js R config/plugins/visualizations/charts/static/models/chart.js R config/plugins/visualizations/charts/static/models/config.js A config/plugins/visualizations/charts/static/views/description.js M config/plugins/visualizations/charts/static/views/editor.js M config/plugins/visualizations/charts/static/views/groups.js M config/plugins/visualizations/charts/static/views/settings.js M config/plugins/visualizations/charts/static/views/types.js M config/plugins/visualizations/charts/static/views/viewer.js M config/plugins/visualizations/charts/static/views/viewport.js M config/plugins/visualizations/charts/templates/charts.mako M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/ui/ui-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.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/form/form-data.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/ui/ui-tabs.js M static/scripts/utils/utils.js Log Message: ----------- Merge pull request #2820 from guerler/charts_revision Charts revision, part 2 Compare: https://github.com/galaxyproject/galaxy/compare/d3c696f84671...75a3aecbbedd

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[galaxyproject/galaxy] 3e65a1: fix inclusion of release notes in announcement
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 3e65a165b722740b48ece5dab36a2a28cfa7681c https://github.com/galaxyproject/galaxy/commit/3e65a165b722740b48ece5dab36a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- fix inclusion of release notes in announcement Commit: e891c5755f59e8865cbee56cd4fcc8e5f4bbd0af https://github.com/galaxyproject/galaxy/commit/e891c5755f59e8865cbee56cd4fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge pull request #2859 from martenson/fix-notes-include [16.07] fix inclusion of release notes in the announcement Compare: https://github.com/galaxyproject/galaxy/compare/53a5b76ff2e4...e891c5755f59

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[galaxyproject/galaxy] 663136: Unused import, cleanup for #2856
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 6631367b7cd4f2049426f3554eef6da626b83837 https://github.com/galaxyproject/galaxy/commit/6631367b7cd4f2049426f3554eef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Unused import, cleanup for #2856 Commit: 53a5b76ff2e47bbf821845e0d2170240902a70eb https://github.com/galaxyproject/galaxy/commit/53a5b76ff2e47bbf821845e0d217… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #2860 from dannon/postfork-tool-conf-watcher-test-fix [16.07] Unused import cleanup for #2856 Compare: https://github.com/galaxyproject/galaxy/compare/c98331eddd3f...53a5b76ff2e4

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[galaxyproject/galaxy] 4f3c44: Move the registration of the start function into t...
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 4f3c44f3ad386a667f156f39d1af44bf23b7a8ab https://github.com/galaxyproject/galaxy/commit/4f3c44f3ad386a667f156f39d1af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Move the registration of the start function into the ToolConfWatcher itself so it doesn't have to be called by things that instantiate it. Fixes #2831. Commit: c98331eddd3f8a57cedca313249798e1e45a9555 https://github.com/galaxyproject/galaxy/commit/c98331eddd3f8a57cedca3132497… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Merge pull request #2856 from natefoo/postfork-tool-conf-watcher-test-fix [16.07] Postfork tool conf watcher test fix Compare: https://github.com/galaxyproject/galaxy/compare/e0aad7af4754...c98331eddd3f

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[galaxyproject/galaxy] 2c866e: Automate more of the release process...
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c866e38d63fb7560772eb5d2625374beb64c515 https://github.com/galaxyproject/galaxy/commit/2c866e38d63fb7560772eb5d2625… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Automate more of the release process... ... this has worked for a couple releases now - time for the computer to push these tags instead of error-prone humans. Commit: d3c696f84671b71fa8e4894c7c99d525c59f69b1 https://github.com/galaxyproject/galaxy/commit/d3c696f84671b71fa8e4894c7c99… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M Makefile M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #2857 from jmchilton/release_process_tweaks Automate more of the release process... Compare: https://github.com/galaxyproject/galaxy/compare/a14882f8720c...d3c696f84671

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[galaxyproject/galaxy]
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/tags/v16.07 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] f47ea8: initial curated release notes for 16.07
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb https://github.com/galaxyproject/galaxy/commit/f47ea88c236be2414d40ef933dd3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst Log Message: ----------- initial curated release notes for 16.07 Commit: 873f34f07953eaf194ec0338139a736d413c30c0 https://github.com/galaxyproject/galaxy/commit/873f34f07953eaf194ec0338139a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-20 (Sat, 20 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Inject HOME, so that conda doens't attempt to write to ~/.conda Commit: 53570e471e087fc92e0ef4befdd965703e4aeb14 https://github.com/galaxyproject/galaxy/commit/53570e471e087fc92e0ef4befdd9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Merge some entries, rephrasing and fixes Commit: 96bdde85bf259c2c821a7bbacc1c4aef60c3f3b7 https://github.com/galaxyproject/galaxy/commit/96bdde85bf259c2c821a7bbacc1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- add a highlight, update git commands Commit: 113999e5d574b29e1c197bcfe1bdef1777c5c507 https://github.com/galaxyproject/galaxy/commit/113999e5d574b29e1c197bcfe1bd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Tweaks to language of many of enhancements in 16.07 release notes. Commit: c82719f22d3d8971055fc9b833dc7fd2519fad22 https://github.com/galaxyproject/galaxy/commit/c82719f22d3d8971055fc9b833dc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst Log Message: ----------- drop subheaders, reorder, tweak to wording Commit: 9b96d9dbfa875375bc172451fb9c7e6993c62f41 https://github.com/galaxyproject/galaxy/commit/9b96d9dbfa875375bc172451fb9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- More user-focused language in release notes. Commit: e1060bd18fcf1bc69e5cd41f44adde37ba55ae1d https://github.com/galaxyproject/galaxy/commit/e1060bd18fcf1bc69e5cd41f44ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Spelling fix thanks to @nsoranzo. Commit: 04370845451da1cf839d75366d131325105698fe https://github.com/galaxyproject/galaxy/commit/04370845451da1cf839d75366d13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Another spelling fix thanks to @nsoranzo. Commit: 8f571bae7129b4ce07739ab8e4d9ddcef020af5e https://github.com/galaxyproject/galaxy/commit/8f571bae7129b4ce07739ab8e4d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- Wording fix thanks to @nsoranzo. Commit: f0ffa9c5947674d8e8731f36f00eb82b757b6558 https://github.com/galaxyproject/galaxy/commit/f0ffa9c5947674d8e8731f36f00e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- drop GRT reference Commit: 3d4300e5429b2b09b92cf5d9f55541643a0ff62b https://github.com/galaxyproject/galaxy/commit/3d4300e5429b2b09b92cf5d9f555… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07.rst Log Message: ----------- tweak wording of notes Commit: 26ceef668c57c0ef44f4072d3550472ff9582e29 https://github.com/galaxyproject/galaxy/commit/26ceef668c57c0ef44f4072d3550… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- announce conda as beta, link the IUC doc, link DTD wiki Commit: c33bf2a222a09cc7707bdf621c257e1a951f969a https://github.com/galaxyproject/galaxy/commit/c33bf2a222a09cc7707bdf621c25… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2825 from mvdbeek/conda_install_fix Inject HOME, so that conda doens't attempt to write to ~/.conda Commit: c6c646ead407ef29a42ff6a6de7182837a97a1f7 https://github.com/galaxyproject/galaxy/commit/c6c646ead407ef29a42ff6a6de71… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Document the Chat Server Commit: a1b2ec386e32f9fc357cb86836033a46084d8855 https://github.com/galaxyproject/galaxy/commit/a1b2ec386e32f9fc357cb8683603… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png M doc/source/admin/index.rst Log Message: ----------- Merge pull request #2843 from erasche/chat-docs [16.07] Document the Chat Server Commit: 4d19755c1313e8a014f873f1b011baf4f8d59310 https://github.com/galaxyproject/galaxy/commit/4d19755c1313e8a014f873f1b011… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst Log Message: ----------- add conda docs converted and modified from IUC googledoc Commit: 01a24f6560be2d6cc9c6aef43e9665f140fc3640 https://github.com/galaxyproject/galaxy/commit/01a24f6560be2d6cc9c6aef43e96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- rst problems Commit: 04f22b70a4ecd127e7990982c09db7278bf1cf98 https://github.com/galaxyproject/galaxy/commit/04f22b70a4ecd127e7990982c09d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix plural, split lines to prevent indentation Commit: e33f8fe5b623d38ec7b27c90279713a18807ee48 https://github.com/galaxyproject/galaxy/commit/e33f8fe5b623d38ec7b27c902797… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- replace apostrophes Commit: 453c98d8ad572b7d9154430f5f61123d7ca5fbc4 https://github.com/galaxyproject/galaxy/commit/453c98d8ad572b7d9154430f5f61… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- this one is even weirder than the ones before Commit: aedfdffafedd35a1ed52aec85dd373c76b7c3135 https://github.com/galaxyproject/galaxy/commit/aedfdffafedd35a1ed52aec85dd3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- add more literal includes Commit: e52dbde3e481a30c5980f1e0171b720c557ee72d https://github.com/galaxyproject/galaxy/commit/e52dbde3e481a30c5980f1e0171b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Conda/conda standardization Commit: b4495c1a8bb3e184bf35a9ebc4e795b7da3aadbb https://github.com/galaxyproject/galaxy/commit/b4495c1a8bb3e184bf35a9ebc4e7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #17 from dannon/docs_conda Conda/conda standardization Commit: 3d0bf645ab03585e316d673cd6b073e706fb616d https://github.com/galaxyproject/galaxy/commit/3d0bf645ab03585e316d673cd6b0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- fix tiny things in docs Commit: 779c357dcac2940f9bdaacf8de5259fe632ada1c https://github.com/galaxyproject/galaxy/commit/779c357dcac2940f9bdaacf8de52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge branch 'docs_conda' of https://github.com/martenson/galaxy into docs_conda Commit: 124d546be6e789a288f19c21adb229e149e9d7d2 https://github.com/galaxyproject/galaxy/commit/124d546be6e789a288f19c21adb2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst Log Message: ----------- Merge pull request #2844 from martenson/docs_conda [16.07] add conda docs converted and modified from IUC googledoc Commit: 7326498335804560d0376c555524b096c69720ce https://github.com/galaxyproject/galaxy/commit/7326498335804560d0376c555524… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- improve conda doc to include TOC Commit: 08b2bda13bd4622d9e492aaa256d7c9bba5790aa https://github.com/galaxyproject/galaxy/commit/08b2bda13bd4622d9e492aaa256d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/releases/16.07_announce.rst Log Message: ----------- change links to target official docs Commit: df47bd2007365f22921375fd0eb757f0ec749473 https://github.com/galaxyproject/galaxy/commit/df47bd2007365f22921375fd0eb7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst Log Message: ----------- Merge pull request #2821 from martenson/16.07_release_notes [16.07] curated release notes for 16.07 Commit: 3248b679ac91fbb2275fd3cd47d2fb2ea96e5a2e https://github.com/galaxyproject/galaxy/commit/3248b679ac91fbb2275fd3cd47d2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2850 from martenson/docs_conda [16.07] conda docs - add TOC Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9 https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca53309… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Acquire lock before attempting to install conda Commit: a2f234d5661f88263e1e6c5e8edef1e521b55359 https://github.com/galaxyproject/galaxy/commit/a2f234d5661f88263e1e6c5e8ede… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Create default tool_dependency dir if it doesn't exist Commit: e9d81500caa3526200b204270aca175839f36f56 https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- shorten Conda environment names Commit: fad13d50c344112c8ab637e3c568e43d863730bd https://github.com/galaxyproject/galaxy/commit/fad13d50c344112c8ab637e3c568… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2851 from martenson/backport_2794_2826 [16.07] Backport conda fixes Commit: e5a1cabe8e4268813bf20156690202973fb07207 https://github.com/galaxyproject/galaxy/commit/e5a1cabe8e4268813bf201566902… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- unicodify time on shed counter to prevent problems with dates that contain non-ascii Commit: 992cd51ac3aaa284478813196ef8aa0cb2c16246 https://github.com/galaxyproject/galaxy/commit/992cd51ac3aaa284478813196ef8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge pull request #2855 from martenson/fix-ts-unicodify [16.07] unicodify TS main template Commit: 99fca272708ac07bb6bc3b3b649865249c3a6f04 https://github.com/galaxyproject/galaxy/commit/99fca272708ac07bb6bc3b3b6498… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: A doc/source/admin/chat-0.png A doc/source/admin/chat-1.png A doc/source/admin/chat-2.png A doc/source/admin/chat-3.png A doc/source/admin/chat-4.png A doc/source/admin/chat.rst A doc/source/admin/communication_server.png A doc/source/admin/communication_server_rooms.png A doc/source/admin/conda_faq.rst M doc/source/admin/index.rst A doc/source/releases/16.07.rst M doc/source/releases/16.07_announce.rst A doc/source/releases/16.10_announce.rst M lib/galaxy/tools/deps/conda_util.py M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge branch 'release_16.07' into dev Commit: e0aad7af47547c04013dffe3874e757c905b2021 https://github.com/galaxyproject/galaxy/commit/e0aad7af47547c04013dffe3874e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07 Commit: a14882f8720ce9eedb3119c5ae16d177018e918e https://github.com/galaxyproject/galaxy/commit/a14882f8720ce9eedb3119c5ae16… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7ac7e48ca86c...a14882f8720c

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[galaxyproject/galaxy] e0aad7: Update version to 16.07
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: e0aad7af47547c04013dffe3874e757c905b2021 https://github.com/galaxyproject/galaxy/commit/e0aad7af47547c04013dffe3874e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.07

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[galaxyproject/galaxy] e5a1ca: unicodify time on shed counter
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: e5a1cabe8e4268813bf20156690202973fb07207 https://github.com/galaxyproject/galaxy/commit/e5a1cabe8e4268813bf201566902… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- unicodify time on shed counter to prevent problems with dates that contain non-ascii Commit: 992cd51ac3aaa284478813196ef8aa0cb2c16246 https://github.com/galaxyproject/galaxy/commit/992cd51ac3aaa284478813196ef8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M templates/webapps/tool_shed/index.mako Log Message: ----------- Merge pull request #2855 from martenson/fix-ts-unicodify [16.07] unicodify TS main template Compare: https://github.com/galaxyproject/galaxy/compare/fad13d50c344...992cd51ac3aa

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[galaxyproject/usegalaxy-playbook] 686959: merge upstream disposable domains list
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/upstream-merge Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6869590f32208080f61dc800ffcdeb56530b8d8d https://github.com/galaxyproject/usegalaxy-playbook/commit/6869590f32208080… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: M files/galaxy/common/config/disposable_email_blacklist.conf Log Message: ----------- merge upstream disposable domains list

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[galaxyproject/usegalaxy-playbook] 98a878: move the disposable_blacklist out of secret vars. ...
by GitHub 25 Aug '16

25 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98a878e0e3b630a7de10dce7c656bae97dda466d https://github.com/galaxyproject/usegalaxy-playbook/commit/98a878e0e3b630a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-25 (Thu, 25 Aug 2016) Changed paths: A files/galaxy/common/config/disposable_email_blacklist.conf A files/galaxy/test.galaxyproject.org/config/disposable_email_blacklist.conf A files/galaxy/usegalaxy.org/config/disposable_email_blacklist.conf M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml R templates/galaxy/common/config/disposable_email_blacklist.conf.j2 R templates/galaxy/test.galaxyproject.org/config/disposable_email_blacklist.c… R templates/galaxy/usegalaxy.org/config/disposable_email_blacklist.conf.j2 Log Message: ----------- move the disposable_blacklist out of secret vars. closes #20

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[galaxyproject/galaxy] 8b67dd: Acquire lock before attempting to install conda
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 8b67ddfa37f82081791bcca5330983a2dd1301f9 https://github.com/galaxyproject/galaxy/commit/8b67ddfa37f82081791bcca53309… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Acquire lock before attempting to install conda Commit: a2f234d5661f88263e1e6c5e8edef1e521b55359 https://github.com/galaxyproject/galaxy/commit/a2f234d5661f88263e1e6c5e8ede… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Create default tool_dependency dir if it doesn't exist Commit: e9d81500caa3526200b204270aca175839f36f56 https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- shorten Conda environment names Commit: fad13d50c344112c8ab637e3c568e43d863730bd https://github.com/galaxyproject/galaxy/commit/fad13d50c344112c8ab637e3c568… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2851 from martenson/backport_2794_2826 [16.07] Backport conda fixes Compare: https://github.com/galaxyproject/galaxy/compare/3248b679ac91...fad13d50c344

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[galaxyproject/galaxy] ffef28: shorten Conda environment names
by GitHub 24 Aug '16

24 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ffef288e4fd85261d4bd4c3e8c3abd3450fca859 https://github.com/galaxyproject/galaxy/commit/ffef288e4fd85261d4bd4c3e8c3a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- shorten Conda environment names Commit: 7ac7e48ca86c8869fc3db7361fedd1fedd1c03ca https://github.com/galaxyproject/galaxy/commit/7ac7e48ca86c8869fc3db7361fed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2794 from bgruening/shorten_conda_envs shorten Conda environment names Compare: https://github.com/galaxyproject/galaxy/compare/57937933fb97...7ac7e48ca86c

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