January 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f854a8: Fix upload to respect explicit name override on pa...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f854a8b01cef74369bd3049dfb5d981a5310d21a https://github.com/galaxyproject/galaxy/commit/f854a8b01cef74369bd3049dfb5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: d9ffbc433ef417c08d5d040b27a6d3d626d54872 https://github.com/galaxyproject/galaxy/commit/d9ffbc433ef417c08d5d040b27a6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test cases for renaming datasets based on tool input datasets. Includes test cases for #3197 and #662. Commit: a18b24e0679016da159703a4e6b873f0ae95cf4e https://github.com/galaxyproject/galaxy/commit/a18b24e0679016da159703a4e6b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py M test/functional/tools/for_workflows/mapper2.xml Log Message: ----------- Allow rename PJA to target input collections. Implements #2346 w/test case. Commit: dad4c60d852d3c2cd06d4327c20f2b2ee516c9cf https://github.com/galaxyproject/galaxy/commit/dad4c60d852d3c2cd06d4327c20f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/jobs/actions/post.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py M test/api/helpers.py M test/api/test_workflows.py A test/functional/tools/for_workflows/mapper2.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3381 from jmchilton/rename_improvements Test cases & small enhancement to workflow renaming PJAs. Compare: https://github.com/galaxyproject/galaxy/compare/690b512dbded...dad4c60d852d

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[galaxyproject/galaxy] eefd71: Migrate more CasperJS API tests to the API test fr...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eefd716f1f86e8c964f54d133b91db2a0a575b44 https://github.com/galaxyproject/galaxy/commit/eefd716f1f86e8c964f54d133b91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-08 (Thu, 08 Dec 2016) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Migrate more CasperJS API tests to the API test framework. - Replace visualization tests (api-visualizations-tests.js -> test_visualizations.py). - Replace dataset API tests (api-dataset-tests.js -> test_datasets.py). - Start work on migrating history dataset API tests (api-hda-tests.js -> test_history_contents.py). Commit: 690b512dbded1989fa3c98af3b7733d258ec3f97 https://github.com/galaxyproject/galaxy/commit/690b512dbded1989fa3c98af3b77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M test/api/test_datasets.py M test/api/test_history_contents.py A test/api/test_visualizations.py R test/casperjs/api-dataset-tests.js R test/casperjs/api-visualizations-tests.js Log Message: ----------- Merge pull request #3288 from jmchilton/casper2api_0 Migrate more CasperJS API tests to the API test framework. Compare: https://github.com/galaxyproject/galaxy/compare/bb5d450b32af...690b512dbded

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[galaxyproject/galaxy] 50257a: Add re-submission info to job_conf.xml.sample_adva...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50257aac80c7aedf41ad436d475640d586ca732c https://github.com/galaxyproject/galaxy/commit/50257aac80c7aedf41ad436d4756… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Add re-submission info to job_conf.xml.sample_advanced. Commit: 34f0b0fe8911c01562c7dfc0e83e0d56df50f66c https://github.com/galaxyproject/galaxy/commit/34f0b0fe8911c01562c7dfc0e83e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-04 (Wed, 04 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Implement a Galaxy config option for default job re-submission conditions. Commit: bb5d450b32afca22b666095e9ea4482f08647e3d https://github.com/galaxyproject/galaxy/commit/bb5d450b32afca22b666095e9ea4… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py A test/integration/resubmission_default_job_conf.xml M test/integration/resubmission_runners.py M test/integration/test_job_resubmission.py M test/unit/jobs/test_job_configuration.py Log Message: ----------- Merge pull request #3319 from jmchilton/job_resubmission_refinement_0 Make it easier to use job re-submission conditions. Compare: https://github.com/galaxyproject/galaxy/compare/9843e404b70b...bb5d450b32af

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[galaxyproject/galaxy] 06cc5f: Fix implicit conversion for sessionless tool API c...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 06cc5f58288fbd6e3762a91fdd8e76b715f7c4e6 https://github.com/galaxyproject/galaxy/commit/06cc5f58288fbd6e3762a91fdd8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-27 (Tue, 27 Dec 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Fix implicit conversion for sessionless tool API calls. Also fixes it for backgrounded workflow invocations (fixes #3268 reported by @guerler). Includes a new test tool w/test definition that exercises this functionality. This tool fails without these changes. Commit: 41f5ff48ed848f4fe111f78c8f364e32abdfe405 https://github.com/galaxyproject/galaxy/commit/41f5ff48ed848f4fe111f78c8f36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/implicit_conversion.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3375 from jmchilton/fix_3268 [16.10] Fix implicit conversion for sessionless tool API calls. Compare: https://github.com/galaxyproject/galaxy/compare/4d73dfc2e03d...41f5ff48ed84

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[galaxyproject/galaxy] 91c5b7: Fix upload to respect explicit name override on pa...
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91c5b76667f28523bddde96171cd38af5f1ca2ba https://github.com/galaxyproject/galaxy/commit/91c5b76667f28523bddde96171cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-31 (Sat, 31 Dec 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Fix upload to respect explicit name override on pasted uploads. Commit: 9843e404b70b58616e55cf26e8a514a8df628771 https://github.com/galaxyproject/galaxy/commit/9843e404b70b58616e55cf26e8a5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/grouping.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3377 from jmchilton/upload_fix Fix upload to respect explicit name override on pasted uploads. Compare: https://github.com/galaxyproject/galaxy/compare/5a1caa5912a5...9843e404b70b

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[galaxyproject/galaxy] a78ae1: Fix tool shed pre-population against current dev.
by GitHub 08 Jan '17

08 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a78ae1bb7149199122f7dd2f8fd6b09599eb3ca4 https://github.com/galaxyproject/galaxy/commit/a78ae1bb7149199122f7dd2f8fd6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Fix tool shed pre-population against current dev. I don't know how this ever worked to be honest - but these changes make a lot of sense. I think there was another bug somewhere that prevented this bug from exhibiting itself. Commit: b75ee68d9f6305646a55d816fb1173210e36eab9 https://github.com/galaxyproject/galaxy/commit/b75ee68d9f6305646a55d816fb11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/run_test_wrapper.sh Log Message: ----------- Run Galaxy tests in --dockerize mode as UID of tester. Fixes #1541 and should really help Jenkins clean up after itself. Commit: 5a1caa5912a515b35257a2e8b911293c2eb7aad1 https://github.com/galaxyproject/galaxy/commit/5a1caa5912a515b35257a2e8b911… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-08 (Sun, 08 Jan 2017) Changed paths: M run_tests.sh M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh Log Message: ----------- Merge pull request #3387 from jmchilton/docker_fix Docker Testing Fixes (for Jenkins for instance) Compare: https://github.com/galaxyproject/galaxy/compare/387c08b39b63...5a1caa5912a5

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[galaxyproject/galaxy] 8b7530: Merge pull request #3351 from jmchilton/galaxy_env...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: 387c08b39b63b9e3abf738b67267b04baf949a67 https://github.com/galaxyproject/galaxy/commit/387c08b39b63b9e3abf738b67267… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9a876e659b3...387c08b39b63

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Commit: 05cd16f11cb523345894816ab6cc8165ebe71559 https://github.com/galaxyproject/galaxy/commit/05cd16f11cb523345894816ab6cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-20 (Tue, 20 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Fix explicit Docker container resolution. Fix thanks to @stevecassidy. Fixes #3207. Broken with introduction of container resolution stradegies in #2986. Commit: fe2a1d8ade4fbda158ae035c78133258d7fec099 https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Do not replace Galaxy's Python environment for select tools. This has never happened in my testing, but there have been multiple reports of Conda crafting environments for the set metadata tool that include Python. When this happens Galaxy's Python environment is lost and the tool cannot function properly. Fixes #3238. Fixes #3224. Fixes https://biostar.usegalaxy.org/p/20865/. Rebased to add a comment as suggested by @nsoranzo. Commit: 4969c4a308fd5bfc8bc52739b024765147af49e8 https://github.com/galaxyproject/galaxy/commit/4969c4a308fd5bfc8bc52739b024… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge 16.07 conda fix from #3351 into 16.10. Tricky merge - please review. Conflicts: lib/galaxy/tools/deps/resolvers/conda.py Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 14549d0f1b202a720dfc2dbb1f6501fc2cd8fd49 https://github.com/galaxyproject/galaxy/commit/14549d0f1b202a720dfc2dbb1f65… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3354 from jmchilton/1610_conda_fixes [16.10] Merge forward #3351. Commit: 17a752d1f2fbc19fdccbd9dd24ca1bdfd26aae5e https://github.com/galaxyproject/galaxy/commit/17a752d1f2fbc19fdccbd9dd24ca… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py Log Message: ----------- Merge pull request #3346 from jmchilton/docker_tools_fix [16.10] Fix explicit Docker container resolution. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: 3d155f0be0c91dbfe891394261c08922f75f3f17 https://github.com/galaxyproject/galaxy/commit/3d155f0be0c91dbfe891394261c0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Fix history list selector Commit: b57a961f250968d6d62eff142b4ee6e046085fda https://github.com/galaxyproject/galaxy/commit/b57a961f250968d6d62eff142b4e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge changes fixing tour from dev commit 10720fa4f9e26b3feec1a90468f4ecc726a99c05 Cannot do a full cherry-pick because the test modified did not exist in 16.10. Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: 4d84b3faa17872d1ebe22a1b8c622aa60a8a4324 https://github.com/galaxyproject/galaxy/commit/4d84b3faa17872d1ebe22a1b8c62… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3357 from jmchilton/backport_3185 [16.10] Backport #3185 Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Commit: 8b538f17feb17eba11b3025a2dfb3ba35414a78e https://github.com/galaxyproject/galaxy/commit/8b538f17feb17eba11b3025a2dfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M config/plugins/tours/core.history.yaml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/parameters/output_collect.py M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js M test/api/test_tools.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge branch 'release_16.10' Compare: https://github.com/galaxyproject/galaxy/compare/378ed53a33ee...8b538f17feb1

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[galaxyproject/galaxy] 8b7530: Merge pull request #3351 from jmchilton/galaxy_env...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 8b75305c49c3e9fe3fb4665177af977cdfc9a582 https://github.com/galaxyproject/galaxy/commit/8b75305c49c3e9fe3fb4665177af… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3351 from jmchilton/galaxy_environment_fixes [16.07] Do not allow Conda to replace Galaxy's Python environment for select tools. Commit: 42a461353bc2dd07f60daf33a42e6d45ec7c86a8 https://github.com/galaxyproject/galaxy/commit/42a461353bc2dd07f60daf33a42e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of 16.07 broken with security patches. Commit: 69fe5ae83ae53cb84a2d0bdd9ea53389b8af5a3a https://github.com/galaxyproject/galaxy/commit/69fe5ae83ae53cb84a2d0bdd9ea5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-21 (Wed, 21 Dec 2016) Changed paths: M tox.ini Log Message: ----------- Fix 16.07 linting of imports broken with release of flake8-import-order 0.11. This is pinned to 0.11 in release_16.10 and unpinned in dev, when merging forward keep these "forward" branches the same (i.e. do not revert to flake8-import-order 0.10). Commit: b400a15c78faba3b873ecf1ce2237c36bc24f440 https://github.com/galaxyproject/galaxy/commit/b400a15c78faba3b873ecf1ce223… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-23 (Fri, 23 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tox.ini Log Message: ----------- Merge pull request #3352 from jmchilton/1607_lintfixes [16.07] Attempt to fix TravisCI for release 16.07. Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Commit: 4d73dfc2e03de4c7eaabfd2f6fadd2ca4eff62f8 https://github.com/galaxyproject/galaxy/commit/4d73dfc2e03de4c7eaabfd2f6fad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'upstream/release_16.07' into release_16.10 Compare: https://github.com/galaxyproject/galaxy/compare/4d84b3faa178...4d73dfc2e03d

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[galaxyproject/galaxy] c36871: Set metadata on HDAs from dynamically discovered c...
by GitHub 06 Jan '17

06 Jan '17

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c3687114d6f2f14df49af9a3fee6dbebe08aa7e5 https://github.com/galaxyproject/galaxy/commit/c3687114d6f2f14df49af9a3fee6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-05 (Thu, 05 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Set metadata on HDAs from dynamically discovered collections. With test case that previously failed. Fixes #3267. Commit: 5b3debc510888bd44ae55700fad8e03f2cdc2bdc https://github.com/galaxyproject/galaxy/commit/5b3debc510888bd44ae55700fad8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-06 (Fri, 06 Jan 2017) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/api/test_tools.py Log Message: ----------- Merge pull request #3386 from jmchilton/discovered_collection_metadata_1607 [16.07] Fix metadata on HDAs in dynamically discovered collections. Compare: https://github.com/galaxyproject/galaxy/compare/b400a15c78fa...5b3debc51088

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