Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1939154622db826d3e91f6bf51573b2947308181 https://github.com/galaxyproject/galaxy/commit/1939154622db826d3e91f6bf51573... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh Log Message: ----------- Update all dependencies with `make update-dependencies` using pipenv 2018.10.13 . Also remove `python_version` pin for `monotonic` and `python-dateutil` packages. Commit: f4203ca051b385a449fec5273b9777de51fd3c6e https://github.com/galaxyproject/galaxy/commit/f4203ca051b385a449fec5273b977... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/search.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_util.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M test/functional/webhooks/phdcomics/__init__.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Fix errors reported by flake8 3.6.0 Ignore W504. Commit: a38a0add24a4602fa4ac58e59d9276c85955013d https://github.com/galaxyproject/galaxy/commit/a38a0add24a4602fa4ac58e59d927... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-10-25 (Thu, 25 Oct 2018) Changed paths: M lib/galaxy/datatypes/isa.py Log Message: ----------- Fix Python3 compatibility for ISA datatype Follow-up on https://github.com/galaxyproject/galaxy/pull/5787 . xref. https://github.com/galaxyproject/galaxy/issues/1715 Commit: 2be4f3b2a145136aeea49b93482c0ba5c06b2c84 https://github.com/galaxyproject/galaxy/commit/2be4f3b2a145136aeea49b93482c0... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/containers/docker.py M lib/galaxy/containers/docker_model.py M lib/galaxy/containers/docker_swarm.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/isa.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/instrumenters/env.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/rbac_secured.py M lib/galaxy/managers/sharable.py M lib/galaxy/managers/tags.py M lib/galaxy/model/search.py M lib/galaxy/security/validate_user_input.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/brew_exts.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/views.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/inflection.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/webapps/galaxy/api/uploads.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/repository_util.py M scripts/bootstrap_history.py M scripts/check_python.py M scripts/runtime_stats.py M scripts/summarize_timings.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/transfer.py M setup.cfg M test/functional/webhooks/phdcomics/__init__.py M test/selenium_tests/test_uploads.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py M test/unit/web/framework/test_webapp.py M tools/data_source/upload.py M tools/extract/extract_genomic_dna.py M tools/filters/convert_characters.py M tools/filters/grep.py M tools/filters/uniq.py M tools/stats/filtering.py M tools/stats/gsummary.py Log Message: ----------- Merge pull request #6921 from nsoranzo/dependencies_update Update all dependencies Compare: https://github.com/galaxyproject/galaxy/compare/79da3e554c94...2be4f3b2a145 **NOTE:** This service has 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.