January 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 3ee94d: catch Exception and properly log errors
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 3ee94d58e0f24d3812ac59ef91b43e24856db45b https://github.com/galaxyproject/galaxy/commit/3ee94d58e0f24d3812ac59ef91b4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- catch Exception and properly log errors Commit: 12445a0524510dbafffa4c7908e243f70c55f154 https://github.com/galaxyproject/galaxy/commit/12445a0524510dbafffa4c7908e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- use log.exception instead of log.error to retain the stacktrace Commit: 3d1ad5ad8dab30aa6c6372fbe85a0c3c7d198d61 https://github.com/galaxyproject/galaxy/commit/3d1ad5ad8dab30aa6c6372fbe85a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1511 from martenson/log-user-exceptions-properly [16.01] catch Exception and properly log errors Compare: https://github.com/galaxyproject/galaxy/compare/e397ebba585e...3d1ad5ad8dab

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[galaxyproject/usegalaxy-playbook] b05d6f: Update Main, re-enable activation (fixed in update...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b05d6ff5aae0808541d911727f8fb47300222d62 https://github.com/galaxyproject/usegalaxy-playbook/commit/b05d6ff5aae08085… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M production/group_vars/all.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main, re-enable activation (fixed in update)

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[galaxyproject/galaxy] 95d00b: Fix MIMEText usage in galaxy.util
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 95d00b4174efd23b0ad9c350d3463bf9d696d8cc https://github.com/galaxyproject/galaxy/commit/95d00b4174efd23b0ad9c350d346… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Fix MIMEText usage in galaxy.util Commit: e397ebba585ed578798645ee9352b891e3055372 https://github.com/galaxyproject/galaxy/commit/e397ebba585ed578798645ee9352… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1509 from dannon/release_16.01 Fix MIMEText usage in galaxy.util Compare: https://github.com/galaxyproject/galaxy/compare/be4ddb26d4c4...e397ebba585e

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[galaxyproject/galaxy] ba592a: Fix Python 3.4 problem causing Travis failure of d...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ba592a79fe75692a75b9786903bc47b7faea5ea0 https://github.com/galaxyproject/galaxy/commit/ba592a79fe75692a75b9786903bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Fix Python 3.4 problem causing Travis failure of dev. Commit: 669d65c32708a790a7c62f4ddd6488d79b7c7335 https://github.com/galaxyproject/galaxy/commit/669d65c32708a790a7c62f4ddd64… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #1505 from jmchilton/dev_merge_0 Fix Python 3 problem causing Travis failure of dev. Compare: https://github.com/galaxyproject/galaxy/compare/be7c0dfcbf2e...669d65c32708

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[galaxyproject/galaxy] 944436: Cleanup settings view
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 94443625d8b52b8b2cc7607933e7f627f27ee412 https://github.com/galaxyproject/galaxy/commit/94443625d8b52b8b2cc7607933e7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/upload.less M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.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/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js Log Message: ----------- Cleanup settings view Commit: b38bc293d7f83bf8510eca77de5e11d70d79ecee https://github.com/galaxyproject/galaxy/commit/b38bc293d7f83bf8510eca77de5e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: A config/plugins/tours/core.scratchbook.yaml Log Message: ----------- Add Scratchbook tour Commit: 0ccb72160a922d41ba46c5c9c4570edc31cf7a4a https://github.com/galaxyproject/galaxy/commit/0ccb72160a922d41ba46c5c9c457… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Refactor masthead render to improve readibility Commit: 30c472a3883884a3c586b14d6f908f0ba8ed1590 https://github.com/galaxyproject/galaxy/commit/30c472a3883884a3c586b14d6f90… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-repeat.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-input.js M static/scripts/mvc/form/form-repeat.js Log Message: ----------- Add flat id attribute to form parameters Commit: e52626b279f3edd5ebab2b48fa1ab1f86f963777 https://github.com/galaxyproject/galaxy/commit/e52626b279f3edd5ebab2b48fa1a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Apply fix from 16.01 Commit: be7c0dfcbf2eb8b88a340380804a3e1af5850749 https://github.com/galaxyproject/galaxy/commit/be7c0dfcbf2eb8b88a340380804a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/style/less/upload.less A config/plugins/tours/core.scratchbook.yaml M static/maps/layout/menu.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/upload/default/default-row.js.map M static/maps/mvc/upload/upload-settings.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/layout/menu.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/upload/default/default-row.js M static/scripts/mvc/upload/upload-settings.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1463 from guerler/tour_000 Scratchbook tour Compare: https://github.com/galaxyproject/galaxy/compare/aeafcb1d6d38...be7c0dfcbf2e

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[galaxyproject/galaxy] 55677f: Fix to ensure integrity of tool_script.sh also.
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55677f2d3db723c023540b8d640563a9f3ca04c5 https://github.com/galaxyproject/galaxy/commit/55677f2d3db723c023540b8d6405… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Fix to ensure integrity of tool_script.sh also. Previously the job script underwent these checks and I had assumed since that got written later it would never be the case that tool_script.sh wouldn't be synchronized by the job script was - turns out file systems are more creative and less logical than one might expected. Also increases the count for the number of syncs that will execute because 15 on rare occasion proved not to be enough as well as making both the count and sleep time configurable. Commit: 37f8038d63f8243151e817e9d564f90c58772c1f https://github.com/galaxyproject/galaxy/commit/37f8038d63f8243151e817e9d564… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Undo user icon in masthead Commit: 9d91be8dd3b84a5b37b6010cbb31df7070fb6170 https://github.com/galaxyproject/galaxy/commit/9d91be8dd3b84a5b37b6010cbb31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Pin release wheel verisons. pinned-requirements.txt renamed to pinned-hashed-requirements.txt as unfortunately even Galaxy pip does not support --hash Commit: 0bcfa74ea1e0eb57927bd1850feb9331489af6bc https://github.com/galaxyproject/galaxy/commit/0bcfa74ea1e0eb57927bd1850feb… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Fixes the issue of losing newlines and actual spacing (i.e. do not treat as html). Commit: f78756cb79f294689227e0222c8b75f3100047b5 https://github.com/galaxyproject/galaxy/commit/f78756cb79f294689227e0222c8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix a few problems discovered through planemo. Including 'TypeError: _get_config_option() got multiple values for keyword argument 'prefix' and problem when planemo's cwltool is installed in Galaxy's virtualenv. Commit: 9d52a4a31dd9e660855bf1e12bd07d3c49b73fd9 https://github.com/galaxyproject/galaxy/commit/9d52a4a31dd9e660855bf1e12bd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1493 from guerler/undo_user_000 [16.01] Undo user icon in masthead Commit: 4b5b970d7898a33faca5557b4382ddc9d3923ae6 https://github.com/galaxyproject/galaxy/commit/4b5b970d7898a33faca5557b4382… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Fix disabled css Commit: 2e62388b2f34ad83f215bb3eff4c6ae5b1efd7b7 https://github.com/galaxyproject/galaxy/commit/2e62388b2f34ad83f215bb3eff4c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Merge pull request #1494 from jmchilton/tool_command_integrity [16.01] Fix to ensure integrity of tool_script.sh also. Commit: 3e47aa23b8426e21f5dac573f6eb96bfeac550b6 https://github.com/galaxyproject/galaxy/commit/3e47aa23b8426e21f5dac573f6eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Switch to bash as default shell (for conda resolver). I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now. Commit: e69638277fc4e0c56347e51ed77f93c1f9261ecf https://github.com/galaxyproject/galaxy/commit/e69638277fc4e0c56347e51ed77f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M test/functional/tools/output_action_change_format.xml Log Message: ----------- Fix tab problem in test tool. dash will convert the literal characters \t to a tab, bash doesn't seem to do this. Use portable printf as suggested by nicola. Commit: 602dc7f6649d96086b85ed0d309eef7c4ed73a13 https://github.com/galaxyproject/galaxy/commit/602dc7f6649d96086b85ed0d309e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Switch default job shell back to /bin/sh for 16.01. Commit: f2c3eaaf64041021abb39ea4595e3619658554e1 https://github.com/galaxyproject/galaxy/commit/f2c3eaaf64041021abb39ea4595e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge branch 'release_16.01' into dev_merge_0 Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: 0902c23f3491b4840b649a203315939d0c7caa8c https://github.com/galaxyproject/galaxy/commit/0902c23f3491b4840b649a203315… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/qunit/tests/masthead_tests.js Log Message: ----------- Merge pull request #1501 from guerler/fix_disabled_000 [16.01] Fix disabled css Commit: eb3fc642fc1bddaeb5aaec3d4dbba8efd0ab398d https://github.com/galaxyproject/galaxy/commit/eb3fc642fc1bddaeb5aaec3d4dbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1498 from blankenberg/tab_mime [16.01] Set mime type when previewing tabular data that has > 50 columns, but < 1000000 bytes. Commit: 7de3bcdd7e4ecfbe4202bff1ad69a0d8b6b716cc https://github.com/galaxyproject/galaxy/commit/7de3bcdd7e4ecfbe4202bff1ad69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Merge pull request #1495 from natefoo/pin-release-wheels [16.01] Pin release wheel versions Commit: 1dac5f3bb63f7b34e7a84ae79d3eb60089712d0b https://github.com/galaxyproject/galaxy/commit/1dac5f3bb63f7b34e7a84ae79d3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1502 from jmchilton/planemo_fix [16.01] Fix a few problems discovered through planemo. Commit: be4ddb26d4c448bee8f797b9972360c93cae33fc https://github.com/galaxyproject/galaxy/commit/be4ddb26d4c448bee8f797b99723… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/functional/tools/output_action_change_format.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1473 from jmchilton/job_shell [16.01] Allow override of job shell (for conda resolver). Commit: 793fbdbedc3e59140ece9aa2caed11d69815069b https://github.com/galaxyproject/galaxy/commit/793fbdbedc3e59140ece9aa2caed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M requirements.txt M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_16.01' into dev_merge_0 Conflicts: static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Commit: aeafcb1d6d389401e9c24267da75fa297375a2e4 https://github.com/galaxyproject/galaxy/commit/aeafcb1d6d389401e9c24267da75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M requirements.txt M static/maps/layout/menu.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M test/functional/tools/output_action_change_format.xml M test/qunit/tests/masthead_tests.js M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1504 from jmchilton/dev_merge_0 Merge release 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/33a3ae4562ce...aeafcb1d6d38

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[galaxyproject/galaxy] 487ece: Fix all E731 "errors".
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 487ece0f409ac0ef16a750511b53617fa465c970 https://github.com/galaxyproject/galaxy/commit/487ece0f409ac0ef16a750511b53… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/framework/openid_manager.py M setup.cfg M test/api/helpers.py M test/casperjs/casperjs_runner.py M test/functional/test_toolbox.py M test/unit/tools/test_execution.py Log Message: ----------- Fix all E731 "errors". Commit: 33a3ae4562ce83f8dab2fa06e1e0f089afa9e601 https://github.com/galaxyproject/galaxy/commit/33a3ae4562ce83f8dab2fa06e1e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/test.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/wrappers.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/framework/openid_manager.py M setup.cfg M test/api/helpers.py M test/casperjs/casperjs_runner.py M test/functional/test_toolbox.py M test/unit/tools/test_execution.py Log Message: ----------- Merge pull request #1489 from nsoranzo/flake8_fixes Fix all E731 "errors". Compare: https://github.com/galaxyproject/galaxy/compare/f41550f69f05...33a3ae4562ce

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[galaxyproject/galaxy] 3e47aa: Switch to bash as default shell (for conda resolve...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 3e47aa23b8426e21f5dac573f6eb96bfeac550b6 https://github.com/galaxyproject/galaxy/commit/3e47aa23b8426e21f5dac573f6eb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Switch to bash as default shell (for conda resolver). I'm making more things configurable in case someday the BSD user wants to use Galaxy - the default shell for jobs can be configured at the galaxy or job destination level now. Commit: e69638277fc4e0c56347e51ed77f93c1f9261ecf https://github.com/galaxyproject/galaxy/commit/e69638277fc4e0c56347e51ed77f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M test/functional/tools/output_action_change_format.xml Log Message: ----------- Fix tab problem in test tool. dash will convert the literal characters \t to a tab, bash doesn't seem to do this. Use portable printf as suggested by nicola. Commit: 602dc7f6649d96086b85ed0d309eef7c4ed73a13 https://github.com/galaxyproject/galaxy/commit/602dc7f6649d96086b85ed0d309e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Switch default job shell back to /bin/sh for 16.01. Commit: be4ddb26d4c448bee8f797b9972360c93cae33fc https://github.com/galaxyproject/galaxy/commit/be4ddb26d4c448bee8f797b99723… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M test/functional/tools/output_action_change_format.xml M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1473 from jmchilton/job_shell [16.01] Allow override of job shell (for conda resolver). Compare: https://github.com/galaxyproject/galaxy/compare/1dac5f3bb63f...be4ddb26d4c4

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[galaxyproject/galaxy] f78756: Fix a few problems discovered through planemo.
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f78756cb79f294689227e0222c8b75f3100047b5 https://github.com/galaxyproject/galaxy/commit/f78756cb79f294689227e0222c8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix a few problems discovered through planemo. Including 'TypeError: _get_config_option() got multiple values for keyword argument 'prefix' and problem when planemo's cwltool is installed in Galaxy's virtualenv. Commit: 1dac5f3bb63f7b34e7a84ae79d3eb60089712d0b https://github.com/galaxyproject/galaxy/commit/1dac5f3bb63f7b34e7a84ae79d3e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #1502 from jmchilton/planemo_fix [16.01] Fix a few problems discovered through planemo. Compare: https://github.com/galaxyproject/galaxy/compare/7de3bcdd7e4e...1dac5f3bb63f

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[galaxyproject/galaxy] 9d91be: Pin release wheel verisons. pinned-requirements.tx...
by GitHub 14 Jan '16

14 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9d91be8dd3b84a5b37b6010cbb31df7070fb6170 https://github.com/galaxyproject/galaxy/commit/9d91be8dd3b84a5b37b6010cbb31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Pin release wheel verisons. pinned-requirements.txt renamed to pinned-hashed-requirements.txt as unfortunately even Galaxy pip does not support --hash Commit: 7de3bcdd7e4ecfbe4202bff1ad69a0d8b6b716cc https://github.com/galaxyproject/galaxy/commit/7de3bcdd7e4ecfbe4202bff1ad69… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-14 (Thu, 14 Jan 2016) Changed paths: A lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M requirements.txt Log Message: ----------- Merge pull request #1495 from natefoo/pin-release-wheels [16.01] Pin release wheel versions Compare: https://github.com/galaxyproject/galaxy/compare/eb3fc642fc1b...7de3bcdd7e4e

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