Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 57f5b42974929d4090429df87aca9973faae869f https://github.com/galaxyproject/galaxy/commit/57f5b42974929d4090429df87aca9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/workflows/test_extract_summary.py Log Message: ----------- py3: fix workflow extract summary Commit: af6b572eac2e2571e5f6f0b46945f7f76fce685b https://github.com/galaxyproject/galaxy/commit/af6b572eac2e2571e5f6f0b46945f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_history_imp_exp.py Log Message: ----------- py3: Fix history/import export Commit: 048f7737dda50c8dc64fc211a5e59c971aa92041 https://github.com/galaxyproject/galaxy/commit/048f7737dda50c8dc64fc211a5e59... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix job disocvery Commit: c52d1476122adf82b62e6e1045cd7155f34bb9f7 https://github.com/galaxyproject/galaxy/commit/c52d1476122adf82b62e6e1045cd7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- No need to explicitly compare to bytestring Commit: 492ee207e0ac9884178249251f1047181148c458 https://github.com/galaxyproject/galaxy/commit/492ee207e0ac9884178249251f104... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cast odict.items() and odict.values() to list Commit: b773aedfa7670ee7fe13d43618f956a4bea3d5da https://github.com/galaxyproject/galaxy/commit/b773aedfa7670ee7fe13d43618f95... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- py3: open job script in text mode Commit: c03a86caea4f7cb945a5a8ae539cb7d8ea3ccce8 https://github.com/galaxyproject/galaxy/commit/c03a86caea4f7cb945a5a8ae539cb... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M test/unit/tools/test_collect_primary_datasets.py Log Message: ----------- py3: fix test_job_param unit test Commit: 3af3591e626ddb7204cb958ef414e1fba203e843 https://github.com/galaxyproject/galaxy/commit/3af3591e626ddb7204cb958ef414e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/rule_helper.py Log Message: ----------- py3: fix rule-helper Commit: 25b93c78b6d2a68917bd0aad1e27f155f9d5600c https://github.com/galaxyproject/galaxy/commit/25b93c78b6d2a68917bd0aad1e27f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/config.py M test/unit/web/framework/test_webapp.py Log Message: ----------- Fix CORS unit test Commit: 05f8f2063a69e682bc5349933e44d751b2c9e477 https://github.com/galaxyproject/galaxy/commit/05f8f2063a69e682bc5349933e44d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Fix output collection unit test Commit: e649f7876fc7753ec76d356e04992169476d619d https://github.com/galaxyproject/galaxy/commit/e649f7876fc7753ec76d356e04992... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Fix recheck_missing_job_retries by casting retries to integer Commit: 0e9adcca823dc0b0a273486ef3137cc030d54db3 https://github.com/galaxyproject/galaxy/commit/0e9adcca823dc0b0a273486ef3137... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/rules_dsl.py Log Message: ----------- Fix rules_dsl comparison by converting to key-style sort function Commit: 37e112323ec8b7e17d11921a781b6b49f2bf05a2 https://github.com/galaxyproject/galaxy/commit/37e112323ec8b7e17d11921a781b6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/security/__init__.py Log Message: ----------- Fix MAXIMUM_ID_SECRET_LENGTH constant Commit: 192633b0b200130b9f718f25c9070deea34981ad https://github.com/galaxyproject/galaxy/commit/192633b0b200130b9f718f25c9070... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml Log Message: ----------- Remove py34-unit from allowed failures Commit: 71b9024769d2ba008740e9e071eac46139258987 https://github.com/galaxyproject/galaxy/commit/71b9024769d2ba008740e9e071eac... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_collection_def.py Log Message: ----------- Flake8 fix Commit: db10b5b679217c36414dcf2a80189e46ef9cc680 https://github.com/galaxyproject/galaxy/commit/db10b5b679217c36414dcf2a80189... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: Fix has_limit Commit: cde7784606947eb452d1b3c98ca3eaca99b25ea8 https://github.com/galaxyproject/galaxy/commit/cde7784606947eb452d1b3c98ca3e... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- py3: Fix metadata setting Commit: 84dc5cd02ff0ceab8529cd9e11f825eaed2e3633 https://github.com/galaxyproject/galaxy/commit/84dc5cd02ff0ceab8529cd9e11f82... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- py3: Get unicode strings from ElementTree on py3 Commit: c8f720d71c3d14c2e90d5ebcf0fa41d7bb2726b5 https://github.com/galaxyproject/galaxy/commit/c8f720d71c3d14c2e90d5ebcf0fa4... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/decorators.py Log Message: ----------- py3: don't case payload to bytestring. Doesn't seem to affect py2 either Commit: f29ebb7389a8e695020e11ec4c4c759e89c0a062 https://github.com/galaxyproject/galaxy/commit/f29ebb7389a8e695020e11ec4c4c7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- py3: fix generting conda env hash Commit: c16d8531b9948f71d9861692b40a005e7d8c2a21 https://github.com/galaxyproject/galaxy/commit/c16d8531b9948f71d9861692b40a0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- py3: fix StringFunctionFilter Commit: 7e29d5d83b55846e0bbe5ec43ced2870b7bb1913 https://github.com/galaxyproject/galaxy/commit/7e29d5d83b55846e0bbe5ec43ced2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- py3: fix paramiko shell runner by casting to unicode Commit: 962b1fe176e1120d5a093726d74271fda860884f https://github.com/galaxyproject/galaxy/commit/962b1fe176e1120d5a093726d7427... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- py3: fix check_limits Commit: 6bad1027a7b22c833ca241214c93090badc66d37 https://github.com/galaxyproject/galaxy/commit/6bad1027a7b22c833ca241214c930... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- py3: fix collection mapping over Commit: 9d547dd5e439ea67193e94242b8354b5e6ec1b92 https://github.com/galaxyproject/galaxy/commit/9d547dd5e439ea67193e94242b835... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix 'saved histories' menu Commit: e08c2b347e8e2c625c97f719bc6048e5e956ca9d https://github.com/galaxyproject/galaxy/commit/e08c2b347e8e2c625c97f719bc604... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py Log Message: ----------- Fix some datatype sniffers and `guess_ext()` doctests Commit: 09e39e90794234ae2cbcc2ea6b747888a5075dcd https://github.com/galaxyproject/galaxy/commit/09e39e90794234ae2cbcc2ea6b747... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- py3: Fix mako template rendering in multiple history view and workflow editor Commit: ea440345facd8c9e1cb6c6636970cacfa0544a6f https://github.com/galaxyproject/galaxy/commit/ea440345facd8c9e1cb6c6636970c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py M templates/tagging_common.mako Log Message: ----------- py3: fix published workflows grid Commit: 252913b84a4de19d61294790d10ffca93944e520 https://github.com/galaxyproject/galaxy/commit/252913b84a4de19d61294790d10ff... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix SafeConfigParser import for Python 3 Commit: e9f3afa0f3d6451116283a592c680c47a986bbef https://github.com/galaxyproject/galaxy/commit/e9f3afa0f3d6451116283a592c680... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- py3: fix tool_shed.util.web_util.escape doctest Commit: 7cf76bc66aa9c8b95a74f699a934c4dd81debd57 https://github.com/galaxyproject/galaxy/commit/7cf76bc66aa9c8b95a74f699a934c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/dynamic_tool_destination.py Log Message: ----------- Fix documentation Commit: d5d245ff65841a33c8cb8a32a146a63b14663a7a https://github.com/galaxyproject/galaxy/commit/d5d245ff65841a33c8cb8a32a146a... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- py3: Fix job_script writing Commit: 0c3a447f25d74132f5b449cac4c744f57af48198 https://github.com/galaxyproject/galaxy/commit/0c3a447f25d74132f5b449cac4c74... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Import docker.types Might fix the last failing unit test? Commit: 84af674f9c84182094803a81091ff932873d80a5 https://github.com/galaxyproject/galaxy/commit/84af674f9c84182094803a81091ff... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/web/framework/decorators.py Log Message: ----------- Fix loading workflow in the editor under Python 3 Commit: a177fc6240c90985183807fc141b18e06e436cda https://github.com/galaxyproject/galaxy/commit/a177fc6240c90985183807fc141b1... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix login under Python 3 Commit: b49c4be21c6c090448d899857e53c1fed8be5d5a https://github.com/galaxyproject/galaxy/commit/b49c4be21c6c090448d899857e53c... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/tool_shed/util/readme_util.py Log Message: ----------- Misc Python 3 fixes Commit: d15b6cc7360d3e00780dc1b9ee39353707ba786f https://github.com/galaxyproject/galaxy/commit/d15b6cc7360d3e00780dc1b9ee393... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Code clarifications Commit: e33427a3b79073b1f78a91e848a154f27798ec6c https://github.com/galaxyproject/galaxy/commit/e33427a3b79073b1f78a91e848a15... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-05 (Thu, 05 Jul 2018) Changed paths: M .travis.yml M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/triples.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/output_actions.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/web_util.py M templates/tagging_common.mako M test/unit/test_remote_shell.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_history_imp_exp.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py Log Message: ----------- Merge pull request #6450 from mvdbeek/py3_workflow_and_tool_unit_fixes Fix all remaining unit tests under Python 3 Compare: https://github.com/galaxyproject/galaxy/compare/9a06474a30cb...e33427a3b790 **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.