[galaxy-commits] [galaxyproject/galaxy] d6b934: Extend import order linting to all of galaxy-lib w...

GitHub noreply at github.com
Wed Sep 7 13:58:40 EDT 2016


  Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: d6b9348f377d48f85286fdf57b826ec99e29a856
      https://github.com/galaxyproject/galaxy/commit/d6b9348f377d48f85286fdf57b826ec99e29a856
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-07 (Wed, 07 Sep 2016)

  Changed paths:
    M .ci/flake8_lint_include_list.txt
    M lib/galaxy/exceptions/error_codes.py
    M lib/galaxy/jobs/metrics/__init__.py
    M lib/galaxy/jobs/metrics/collectl/cli.py
    M lib/galaxy/jobs/metrics/collectl/processes.py
    M lib/galaxy/jobs/metrics/instrumenters/__init__.py
    M lib/galaxy/jobs/metrics/instrumenters/collectl.py
    M lib/galaxy/jobs/metrics/instrumenters/core.py
    M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
    M lib/galaxy/jobs/metrics/instrumenters/env.py
    M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/objectstore/rods.py
    M lib/galaxy/objectstore/s3.py
    M lib/galaxy/tools/cwl/__init__.py
    M lib/galaxy/tools/cwl/representation.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/brew_exts.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/dockerfiles.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
    M lib/galaxy/tools/deps/resolvers/modules.py
    M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
    M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
    M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
    M lib/galaxy/tools/loader.py
    M lib/galaxy/tools/parser/__init__.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/output_actions.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/tools/toolbox/__init__.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/__init__.py
    M lib/galaxy/tools/toolbox/lineages/factory.py
    M lib/galaxy/tools/toolbox/panel.py
    M lib/galaxy/tools/toolbox/parser.py
    M lib/galaxy/tools/toolbox/tags.py
    M lib/galaxy/tools/verify/asserts/xml.py
    M lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/biostar.py
    M lib/galaxy/util/checkers.py
    M lib/galaxy/util/hash_util.py
    M lib/galaxy/util/heartbeat.py
    M lib/galaxy/util/json.py
    M lib/galaxy/util/lazy_process.py
    M lib/galaxy/util/none_like.py
    M lib/galaxy/util/object_wrapper.py
    M lib/galaxy/util/pastescript/loadwsgi.py
    M lib/galaxy/util/pastescript/serve.py
    M lib/galaxy/util/permutations.py
    M lib/galaxy/util/properties.py
    M lib/galaxy/util/sanitize_html.py
    M lib/galaxy/util/sockets.py
    M lib/galaxy/util/sqlite.py
    M lib/galaxy/util/streamball.py
    M lib/galaxy/util/submodules.py
    M lib/galaxy/util/topsort.py
    M lib/galaxy/util/validation.py
    M lib/galaxy/util/xml_macros.py
    M setup.cfg
    M test/unit/test_objectstore.py
    M test/unit/tools/test_parsing.py
    M test/unit/tools/test_tool_deps.py
    M test/unit/tools/test_tool_loader.py
    M test/unit/tools/test_toolbox.py
    M test/unit/tools/test_toolbox_filters.py
    M test/unit/tools/test_watcher.py
    M test/unit/tools/test_wrappers.py

  Log Message:
  -----------
  Extend import order linting to all of galaxy-lib w/fixes.

Includes a bit linting of order for galaxy.util.


  Commit: 825c7287a57dabe465f86bb5b66730aba080d000
      https://github.com/galaxyproject/galaxy/commit/825c7287a57dabe465f86bb5b66730aba080d000
  Author: John Chilton <jmchilton at gmail.com>
  Date:   2016-09-07 (Wed, 07 Sep 2016)

  Changed paths:
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/util/topsort.py

  Log Message:
  -----------
  Lint fixes thanks to @nsoranzo's eagle eyes.


  Commit: 69ee5afaeca5dce6acb814cf292a009e9fd2f0c5
      https://github.com/galaxyproject/galaxy/commit/69ee5afaeca5dce6acb814cf292a009e9fd2f0c5
  Author: Martin Cech <cech.marten at gmail.com>
  Date:   2016-09-07 (Wed, 07 Sep 2016)

  Changed paths:
    M .ci/flake8_lint_include_list.txt
    M lib/galaxy/exceptions/error_codes.py
    M lib/galaxy/jobs/metrics/__init__.py
    M lib/galaxy/jobs/metrics/collectl/cli.py
    M lib/galaxy/jobs/metrics/collectl/processes.py
    M lib/galaxy/jobs/metrics/instrumenters/__init__.py
    M lib/galaxy/jobs/metrics/instrumenters/collectl.py
    M lib/galaxy/jobs/metrics/instrumenters/core.py
    M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
    M lib/galaxy/jobs/metrics/instrumenters/env.py
    M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
    M lib/galaxy/objectstore/__init__.py
    M lib/galaxy/objectstore/azure_blob.py
    M lib/galaxy/objectstore/rods.py
    M lib/galaxy/objectstore/s3.py
    M lib/galaxy/tools/cwl/__init__.py
    M lib/galaxy/tools/cwl/representation.py
    M lib/galaxy/tools/cwl/schema.py
    M lib/galaxy/tools/deps/__init__.py
    M lib/galaxy/tools/deps/brew_exts.py
    M lib/galaxy/tools/deps/conda_util.py
    M lib/galaxy/tools/deps/containers.py
    M lib/galaxy/tools/deps/dockerfiles.py
    M lib/galaxy/tools/deps/resolvers/__init__.py
    M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
    M lib/galaxy/tools/deps/resolvers/conda.py
    M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
    M lib/galaxy/tools/deps/resolvers/modules.py
    M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
    M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
    M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
    M lib/galaxy/tools/loader.py
    M lib/galaxy/tools/parser/__init__.py
    M lib/galaxy/tools/parser/cwl.py
    M lib/galaxy/tools/parser/factory.py
    M lib/galaxy/tools/parser/output_actions.py
    M lib/galaxy/tools/parser/xml.py
    M lib/galaxy/tools/parser/yaml.py
    M lib/galaxy/tools/toolbox/__init__.py
    M lib/galaxy/tools/toolbox/base.py
    M lib/galaxy/tools/toolbox/filters/__init__.py
    M lib/galaxy/tools/toolbox/lineages/factory.py
    M lib/galaxy/tools/toolbox/panel.py
    M lib/galaxy/tools/toolbox/parser.py
    M lib/galaxy/tools/toolbox/tags.py
    M lib/galaxy/tools/verify/asserts/xml.py
    M lib/galaxy/tools/verify/test_data.py
    M lib/galaxy/util/__init__.py
    M lib/galaxy/util/biostar.py
    M lib/galaxy/util/checkers.py
    M lib/galaxy/util/hash_util.py
    M lib/galaxy/util/heartbeat.py
    M lib/galaxy/util/json.py
    M lib/galaxy/util/lazy_process.py
    M lib/galaxy/util/none_like.py
    M lib/galaxy/util/object_wrapper.py
    M lib/galaxy/util/pastescript/loadwsgi.py
    M lib/galaxy/util/pastescript/serve.py
    M lib/galaxy/util/permutations.py
    M lib/galaxy/util/properties.py
    M lib/galaxy/util/sanitize_html.py
    M lib/galaxy/util/sockets.py
    M lib/galaxy/util/sqlite.py
    M lib/galaxy/util/streamball.py
    M lib/galaxy/util/submodules.py
    M lib/galaxy/util/topsort.py
    M lib/galaxy/util/validation.py
    M lib/galaxy/util/xml_macros.py
    M setup.cfg
    M test/unit/test_objectstore.py
    M test/unit/tools/test_parsing.py
    M test/unit/tools/test_tool_deps.py
    M test/unit/tools/test_tool_loader.py
    M test/unit/tools/test_toolbox.py
    M test/unit/tools/test_toolbox_filters.py
    M test/unit/tools/test_watcher.py
    M test/unit/tools/test_wrappers.py

  Log Message:
  -----------
  Merge pull request #2889 from jmchilton/import-order-linting

Extend import order linting to all of galaxy-lib w/fixes.


Compare: https://github.com/galaxyproject/galaxy/compare/cbd55b20d373...69ee5afaeca5


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