[galaxy-commits] [galaxyproject/galaxy] 93348e: Fix the remaining 1334 flake8 errors in scripts/ ....

25 Feb 2016


      Branch: refs/heads/dev
  Home:   https://github.com/galaxyproject/galaxy
  Commit: 93348e7199a2e35ee85607b948d2ca4ced951c86
      https://github.com/galaxyproject/galaxy/commit/93348e7199a2e35ee85607b948d2c...
  Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk
  Date:   2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
    M .ci/flake8_blacklist.txt
    M scripts/api/common.py
    M scripts/api/copy_hda_to_library_folder.py
    M scripts/api/create.py
    M scripts/api/data_manager_example_execute.py
    M scripts/api/delete.py
    M scripts/api/display.py
    M scripts/api/example_watch_folder.py
    M scripts/api/form_create_from_xml.py
    M scripts/api/history_create_history.py
    M scripts/api/history_delete_history.py
    M scripts/api/import_library_dataset_to_history.py
    M scripts/api/import_workflows_from_installed_tool_shed_repository.py
    M scripts/api/install_tool_shed_repositories.py
    M scripts/api/library_create_folder.py
    M scripts/api/library_create_library.py
    M scripts/api/library_upload_dir.py
    M scripts/api/library_upload_from_import_dir.py
    M scripts/api/load_data_with_metadata.py
    M scripts/api/repair_tool_shed_repository.py
    M scripts/api/request_type_create_from_xml.py
    M scripts/api/requests_update_state.py
    M scripts/api/reset_metadata_on_installed_repositories.py
    M scripts/api/sample_dataset_update_status.py
    M scripts/api/sample_update_state.py
    M scripts/api/search.py
    M scripts/api/sequencer_configuration_create.py
    M scripts/api/update.py
    M scripts/api/upload_to_history.py
    M scripts/api/workflow_delete.py
    M scripts/api/workflow_execute.py
    M scripts/api/workflow_execute_parameters.py
    M scripts/api/workflow_import.py
    M scripts/api/workflow_import_from_file_rpark.py
    M scripts/check_galaxy.py
    M scripts/data_libraries/build_lucene_index.py
    M scripts/data_libraries/build_whoosh_index.py
    M scripts/galaxy-main
    M scripts/get_platforms.py
    M scripts/loc_files/create_all_fasta_loc.py
    M scripts/microbes/BeautifulSoup.py
    M scripts/microbes/create_bacteria_loc_file.py
    M scripts/microbes/create_bacteria_table.py
    M scripts/microbes/create_nib_seq_loc_file.py
    M scripts/microbes/get_builds_lengths.py
    M scripts/microbes/harvest_bacteria.py
    M scripts/microbes/ncbi_to_ucsc.py
    M scripts/microbes/util.py
    M scripts/others/incorrect_gops_jobs.py
    M scripts/others/incorrect_gops_join_jobs.py
    M scripts/tool_shed/check_download_urls.py
    M scripts/tool_shed/migrate_tools_to_repositories.py
    M scripts/tools/maf/check_loc_file.py
    M scripts/tools/re_escape_output.py
    M scripts/transfer.py
Log Message:
  -----------
  Fix the remaining 1334 flake8 errors in scripts/ . Close #391.
Commit: 196d174716b54593735ce7ca73d80dc48ed58470
      https://github.com/galaxyproject/galaxy/commit/196d174716b54593735ce7ca73d80...
  Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk
  Date:   2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
    M .ci/py3_sources.txt
    M scripts/api/common.py
    M scripts/api/display.py
    M scripts/api/workflow_execute_parameters.py
Log Message:
  -----------
  Python 3 support for 3 files.
Commit: d85db9daa6601ab8b1a086d43ea55b46dbe6609a
      https://github.com/galaxyproject/galaxy/commit/d85db9daa6601ab8b1a086d43ea55...
  Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk
  Date:   2016-02-18 (Thu, 18 Feb 2016)
Changed paths:
    M scripts/api/copy_hda_to_library_folder.py
    M scripts/api/create.py
    M scripts/api/data_manager_example_execute.py
    M scripts/api/delete.py
    M scripts/api/display.py
    M scripts/api/example_watch_folder.py
    M scripts/api/form_create_from_xml.py
    M scripts/api/history_create_history.py
    M scripts/api/history_delete_history.py
    M scripts/api/import_library_dataset_to_history.py
    M scripts/api/import_workflows_from_installed_tool_shed_repository.py
    M scripts/api/install_tool_shed_repositories.py
    M scripts/api/library_create_folder.py
    M scripts/api/library_create_library.py
    M scripts/api/library_upload_from_import_dir.py
    M scripts/api/load_data_with_metadata.py
    M scripts/api/repair_tool_shed_repository.py
    M scripts/api/request_type_create_from_xml.py
    M scripts/api/requests_update_state.py
    M scripts/api/reset_metadata_on_installed_repositories.py
    M scripts/api/sample_dataset_update_status.py
    M scripts/api/sample_update_state.py
    M scripts/api/sequencer_configuration_create.py
    M scripts/api/update.py
    M scripts/api/workflow_delete.py
    M scripts/api/workflow_execute.py
    M scripts/api/workflow_execute_parameters.py
    M scripts/api/workflow_import.py
    M scripts/api/workflow_import_from_file_rpark.py
    M scripts/cleanup_datasets/cleanup_datasets.py
    M scripts/cleanup_datasets/pgcleanup.py
    M scripts/cleanup_datasets/update_metadata.py
    M scripts/create_db.py
    M scripts/data_libraries/build_lucene_index.py
    M scripts/data_libraries/build_whoosh_index.py
    M scripts/db_shell.py
    M scripts/edam_mapping.py
    M scripts/extract_dataset_part.py
    M scripts/functional_tests.py
    M scripts/helper.py
    M scripts/manage_db.py
    M scripts/manage_tools.py
    M scripts/migrate_tools/migrate_tools.py
    M scripts/paster.py
    M scripts/set_dataset_sizes.py
    M scripts/set_user_disk_usage.py
    M scripts/tool_shed/build_ts_whoosh_index.py
    M scripts/tool_shed/migrate_tools_to_repositories.py
    M scripts/transfer.py
    M scripts/update_shed_config_path.py
Log Message:
  -----------
  Use __file__ when adding paths to sys.path instead of os.getcwd() .
Also insert additional paths in position 1 unless strictly necessary.
Commit: 94f847b3b2478d92019237402012a719b1c62c49
      https://github.com/galaxyproject/galaxy/commit/94f847b3b2478d92019237402012a...
  Author: John Chilton jmchilton@gmail.com
  Date:   2016-02-25 (Thu, 25 Feb 2016)
Changed paths:
    M .ci/flake8_blacklist.txt
    M .ci/py3_sources.txt
    M scripts/api/common.py
    M scripts/api/copy_hda_to_library_folder.py
    M scripts/api/create.py
    M scripts/api/data_manager_example_execute.py
    M scripts/api/delete.py
    M scripts/api/display.py
    M scripts/api/example_watch_folder.py
    M scripts/api/form_create_from_xml.py
    M scripts/api/history_create_history.py
    M scripts/api/history_delete_history.py
    M scripts/api/import_library_dataset_to_history.py
    M scripts/api/import_workflows_from_installed_tool_shed_repository.py
    M scripts/api/install_tool_shed_repositories.py
    M scripts/api/library_create_folder.py
    M scripts/api/library_create_library.py
    M scripts/api/library_upload_dir.py
    M scripts/api/library_upload_from_import_dir.py
    M scripts/api/load_data_with_metadata.py
    M scripts/api/repair_tool_shed_repository.py
    M scripts/api/request_type_create_from_xml.py
    M scripts/api/requests_update_state.py
    M scripts/api/reset_metadata_on_installed_repositories.py
    M scripts/api/sample_dataset_update_status.py
    M scripts/api/sample_update_state.py
    M scripts/api/search.py
    M scripts/api/sequencer_configuration_create.py
    M scripts/api/update.py
    M scripts/api/upload_to_history.py
    M scripts/api/workflow_delete.py
    M scripts/api/workflow_execute.py
    M scripts/api/workflow_execute_parameters.py
    M scripts/api/workflow_import.py
    M scripts/api/workflow_import_from_file_rpark.py
    M scripts/check_galaxy.py
    M scripts/cleanup_datasets/cleanup_datasets.py
    M scripts/cleanup_datasets/pgcleanup.py
    M scripts/cleanup_datasets/update_metadata.py
    M scripts/create_db.py
    M scripts/data_libraries/build_lucene_index.py
    M scripts/data_libraries/build_whoosh_index.py
    M scripts/db_shell.py
    M scripts/edam_mapping.py
    M scripts/extract_dataset_part.py
    M scripts/functional_tests.py
    M scripts/galaxy-main
    M scripts/get_platforms.py
    M scripts/helper.py
    M scripts/loc_files/create_all_fasta_loc.py
    M scripts/manage_db.py
    M scripts/manage_tools.py
    M scripts/microbes/BeautifulSoup.py
    M scripts/microbes/create_bacteria_loc_file.py
    M scripts/microbes/create_bacteria_table.py
    M scripts/microbes/create_nib_seq_loc_file.py
    M scripts/microbes/get_builds_lengths.py
    M scripts/microbes/harvest_bacteria.py
    M scripts/microbes/ncbi_to_ucsc.py
    M scripts/microbes/util.py
    M scripts/migrate_tools/migrate_tools.py
    M scripts/others/incorrect_gops_jobs.py
    M scripts/others/incorrect_gops_join_jobs.py
    M scripts/paster.py
    M scripts/set_dataset_sizes.py
    M scripts/set_user_disk_usage.py
    M scripts/tool_shed/build_ts_whoosh_index.py
    M scripts/tool_shed/check_download_urls.py
    M scripts/tool_shed/migrate_tools_to_repositories.py
    M scripts/tools/maf/check_loc_file.py
    M scripts/tools/re_escape_output.py
    M scripts/transfer.py
    M scripts/update_shed_config_path.py
Log Message:
  -----------
  Merge pull request #1755 from nsoranzo/flake8_fixes
Fix the remaining 1334 flake8 errors in scripts/ .
Compare: https://github.com/galaxyproject/galaxy/compare/5370f2d1cdb3...94f847b3b247

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[galaxy-commits] [galaxyproject/galaxy] 93348e: Fix the remaining 1334 flake8 errors in scripts/ ....