July 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f8281c: py3 compat
by GitHub 03 Jul '18

03 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8281cf67f40eab30dc00099b757416f48d7fa78 https://github.com/galaxyproject/galaxy/commit/f8281cf67f40eab30dc00099b757… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py M test/unit/tools/test_tool_deps.py Log Message: ----------- py3 compat Commit: fe003da510d71ad001bb63ed40e6ce45f4ca23c2 https://github.com/galaxyproject/galaxy/commit/fe003da510d71ad001bb63ed40e6… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- fix linting errors Commit: 561330fea9eb1a79a52aa48d986218e1b89d8800 https://github.com/galaxyproject/galaxy/commit/561330fea9eb1a79a52aa48d9862… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- rewind change Commit: cc0022d5d1cc985b23644b6ff6b3e60c29d9caa6 https://github.com/galaxyproject/galaxy/commit/cc0022d5d1cc985b23644b6ff6b3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #6434 from caleb-easterly/test_tool_deps_py3 py3 compat Compare: https://github.com/galaxyproject/galaxy/compare/f65c77d38530...cc0022d5d1cc **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a1bedf: Lint doctests
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1bedf4be8835f84a14df9cc5e1231dd585302d5 https://github.com/galaxyproject/galaxy/commit/a1bedf4be8835f84a14df9cc5e12… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Lint doctests Commit: 256d901df20e6703094cf98f693b19ff79384c3e https://github.com/galaxyproject/galaxy/commit/256d901df20e6703094cf98f693b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/checkers.py Log Message: ----------- Use `with` statement Commit: c03dd53520a4b581af208c1e592ea135a4340016 https://github.com/galaxyproject/galaxy/commit/c03dd53520a4b581af208c1e592e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Correctly handle `bytearray`s in `smart_str()` Also: - Use `assert` in doctests - Speed up `unicodify()` on Unicode strings Commit: 7195c224321b0826a9b2297166ea6fa6ce1de007 https://github.com/galaxyproject/galaxy/commit/7195c224321b0826a9b2297166ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Encode chunk before comparing with gzip_magic Since commit 8d8299a19315aef2f2daef278a5e8d8c47da63bb , `text_type(util.gzip_magic)` generates the following exception: ``` UnicodeDecodeError: 'ascii' codec can't decode byte 0x8b in position 1: ordinal not in range(128) ``` Commit: 82028d95d0d58532821816d526e2b932ea8ee5ec https://github.com/galaxyproject/galaxy/commit/82028d95d0d58532821816d526e2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove needless check The `filename` file is the destination file and is always empty at this point. Introduced in commit 85ea42b79dcfc30622a55f1b9fc507bc822ae325 . Commit: 64c591a6069c43067ad1871dca06cc3c5a581903 https://github.com/galaxyproject/galaxy/commit/64c591a6069c43067ad1871dca06… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- More proper fix for some test_tool_deps.py unit tests Follow up to https://github.com/galaxyproject/galaxy/pull/6436/files#r199368686 Commit: f65c77d385303703d1cfcd47140f84d56fadec2b https://github.com/galaxyproject/galaxy/commit/f65c77d385303703d1cfcd47140f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-07-03 (Tue, 03 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #6455 from nsoranzo/python3 Various Python 3 fixes Compare: https://github.com/galaxyproject/galaxy/compare/59cc94256ca0...f65c77d38530 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 7b0872: Run workflows from published workflows menu
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7b08728c348c9fa4767683b98632ec763420b39e https://github.com/galaxyproject/galaxy/commit/7b08728c348c9fa4767683b98632… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-30 (Sat, 30 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Run workflows from published workflows menu Just needed to generate the right URL. Commit: 59cc94256ca011ab68e25d3a9423166c3ad4ec1c https://github.com/galaxyproject/galaxy/commit/59cc94256ca011ab68e25d3a9423… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #6428 from mvdbeek/run_published_workflows Run workflows from published workflows menu Compare: https://github.com/galaxyproject/galaxy/compare/b46d7c6276d0...59cc94256ca0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9eb1bf: Fix droptarget:drop trigger (wasn't passing the pa...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9eb1bfe3ff0a17629922156a0465694c3a31b88e https://github.com/galaxyproject/galaxy/commit/9eb1bfe3ff0a17629922156a0465… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Fix droptarget:drop trigger (wasn't passing the panel) Commit: b46d7c6276d09c160f37f22df8ed64461a96b407 https://github.com/galaxyproject/galaxy/commit/b46d7c6276d09c160f37f22df8ed… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js Log Message: ----------- Merge pull request #6451 from dannon/fixdragdrop Fix droptarget:drop trigger (drag/drop in the multiview) Compare: https://github.com/galaxyproject/galaxy/compare/9957d39b043d...b46d7c6276d0 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1eae38: py3: replace e.message with str(e)
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1eae38854b53433a367ec2038e74e30ffa4bfab1 https://github.com/galaxyproject/galaxy/commit/1eae38854b53433a367ec2038e74… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- py3: replace e.message with str(e) Commit: 9957d39b043dd9bc17b7e0c56c5e116ddc45f94f https://github.com/galaxyproject/galaxy/commit/9957d39b043dd9bc17b7e0c56c5e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/users.py Log Message: ----------- Merge pull request #6454 from caleb-easterly/exceptions py3: replace e.message with str(e) Compare: https://github.com/galaxyproject/galaxy/compare/19e70b8aeb0c...9957d39b043d **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] dc6774: CI - ignore node_modules anywhere, since we use th...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc6774b7b2d0bd90705f289fe6cd82ba9e8eed9e https://github.com/galaxyproject/galaxy/commit/dc6774b7b2d0bd90705f289fe6cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- CI - ignore node_modules anywhere, since we use them in multiple places and not always 'client' Commit: 19e70b8aeb0c8d08b70d050b1dcf2d4d00480b4f https://github.com/galaxyproject/galaxy/commit/19e70b8aeb0c8d08b70d050b1dcf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M .ci/flake8_blacklist.txt Log Message: ----------- Merge pull request #6449 from dannon/node_modules_blacklist CI - ignore node_modules anywhere Compare: https://github.com/galaxyproject/galaxy/compare/5ad321e08540...19e70b8aeb0c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 72f9e9: py3: fixes test_DatasetManager.py:DatasetManagerTe...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 72f9e9c587e043982a296f4885a88077a720fb1f https://github.com/galaxyproject/galaxy/commit/72f9e9c587e043982a296f4885a8… Author: caleb <caleb.easterly(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- py3: fixes test_DatasetManager.py:DatasetManagerTestCase Commit: 6d2ff7bad295d9850f2690e4cb81e06f851cc451 https://github.com/galaxyproject/galaxy/commit/6d2ff7bad295d9850f2690e4cb81… Author: Caleb Easterly <easte080(a)umn.edu> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- linting fix Commit: 5ad321e08540f6c1a046f397a5c18db16d240c56 https://github.com/galaxyproject/galaxy/commit/5ad321e08540f6c1a046f397a5c1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/managers/rbac_secured.py Log Message: ----------- Merge pull request #6452 from caleb-easterly/test_dataset_manager py3: fixes test_DatasetManager.py:DatasetManagerTestCase Compare: https://github.com/galaxyproject/galaxy/compare/f7e43aa22120...5ad321e08540 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] e39881: Drop fix_json, doesn't seem to be necessary and fi...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e398818ab6329888f8855cde7ffc9ebfd18a9abc https://github.com/galaxyproject/galaxy/commit/e398818ab6329888f8855cde7ffc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Drop fix_json, doesn't seem to be necessary and fixes workflow unit tests Commit: f7e43aa2212090f08e94ba9ad65ad7afbf4fcfd4 https://github.com/galaxyproject/galaxy/commit/f7e43aa2212090f08e94ba9ad65a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/util/json.py Log Message: ----------- Merge pull request #6446 from mvdbeek/drop_json_fix Python3: Drop fix_json, doesn't seem to be necessary and fixes workflow unit t… Compare: https://github.com/galaxyproject/galaxy/compare/75511506a882...f7e43aa22120 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 8b90cd: Encode JSON encoder output
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b90cd997fb485045ab4384d96149e89891b29aa https://github.com/galaxyproject/galaxy/commit/8b90cd997fb485045ab4384d9614… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Encode JSON encoder output Commit: 44300668d4e479b3f7f6e6928fd82c5517f1c556 https://github.com/galaxyproject/galaxy/commit/44300668d4e479b3f7f6e6928fd8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M test/unit/test_galaxy_mapping.py Log Message: ----------- Fix registry import in test_galaxy_mapping.py Commit: f93b3e09862bbda6d7a7c358f414d847bd6c2238 https://github.com/galaxyproject/galaxy/commit/f93b3e09862bbda6d7a7c358f414… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Unicodify _sniffnfix_pg9_hex output Commit: 75511506a8828e922c8b12f91af4637c5db3b778 https://github.com/galaxyproject/galaxy/commit/75511506a8828e922c8b12f91af4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M lib/galaxy/model/custom_types.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge pull request #6439 from mvdbeek/py3_db_interaction Python3: Encode return values of JSON encoder Compare: https://github.com/galaxyproject/galaxy/compare/a51ad0fc5204...75511506a882 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 590607: replace the administration header in admin menu wi...
by GitHub 02 Jul '18

02 Jul '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 59060783a9e169496548ae38766f04cd94eb54a3 https://github.com/galaxyproject/galaxy/commit/59060783a9e169496548ae38766f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-07-01 (Sun, 01 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- replace the administration header in admin menu with version closes #1201 Commit: 9b2101e948942f6b239a2c45892c4535a13ec9f9 https://github.com/galaxyproject/galaxy/commit/9b2101e948942f6b239a2c45892c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js Log Message: ----------- Merge remote-tracking branch 'martenson/show-version-admin' into dev Commit: a51ad0fc5204ae138d024c19358be720359f09ab https://github.com/galaxyproject/galaxy/commit/a51ad0fc5204ae138d024c19358b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-07-02 (Mon, 02 Jul 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-connector.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Client format and build from several upstream changes Compare: https://github.com/galaxyproject/galaxy/compare/ee267e956116...a51ad0fc5204 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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