Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a77e3ff6607a86a85a30bfa552402e57602ab0e2 https://github.com/galaxyproject/galaxy/commit/a77e3ff6607a86a85a30bfa552402... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M tox.ini

Log Message: ----------- Add tox.ini config params for python3.5

Commit: c9cbcf6f79b8d6ae3fa6fa6178c0d59440b8545b https://github.com/galaxyproject/galaxy/commit/c9cbcf6f79b8d6ae3fa6fa6178c0d... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M lib/galaxy/security/passwords.py

Log Message: ----------- Python3: fix passwords.py

Commit: bd92dc17fc8314806db39354c1c6d07286a97550 https://github.com/galaxyproject/galaxy/commit/bd92dc17fc8314806db39354c1c6d... Author: Xiaoqian Jiang jxq198409@hotmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/unit/managers/base.py M tox.ini

Log Message: ----------- Python3: test/unit/managers/base.py

Commit: dd931f9691f2599b4c6642015c95bc10a7f6590a https://github.com/galaxyproject/galaxy/commit/dd931f9691f2599b4c6642015c95b... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/unit/test_galaxy_mapping.py

Log Message: ----------- Python3: test/unit/test_galaxy_mapping.py

Commit: dba8d0bb0a717427a9f3647f9f32935f60c5f063 https://github.com/galaxyproject/galaxy/commit/dba8d0bb0a717427a9f3647f9f329... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M tools/stats/aggregate_scores_in_intervals.py

Log Message: ----------- Python3: tools/stats/aggregate_scores_in_intervals.py

Commit: 17fc7ac5bc8b3a2f973fd2ed8337682223d514c6 https://github.com/galaxyproject/galaxy/commit/17fc7ac5bc8b3a2f973fd2ed83376... Author: Xiaoqian Jiang jxq198409@hotmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_DatasetManager.py

Log Message: ----------- Python3: test/unit/managers/test_DatasetManager.py

Commit: 2fd84dd4995c03f966dbdd1df26dc984e3bbd975 https://github.com/galaxyproject/galaxy/commit/2fd84dd4995c03f966dbdd1df26dc... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/interval_to_coverage.py

Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_coverage.py

Commit: ac07c6238136bf2e2a90fd259dcd6d7312786e90 https://github.com/galaxyproject/galaxy/commit/ac07c6238136bf2e2a90fd259dcd6... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_DatasetManager.py

Log Message: ----------- Merge branch 'python3' of github.com:bxlab/galaxy_hackathon into python3

Commit: 7d7396f18f65e393ff330cdb9f509fd7036eb804 https://github.com/galaxyproject/galaxy/commit/7d7396f18f65e393ff330cdb9f509... Author: Junzhou Wang junzhouwang@gmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py

Log Message: ----------- Python3: test/api/

Commit: 5939c5fc2666ecd649ab033c23d432f6572eb7b1 https://github.com/galaxyproject/galaxy/commit/5939c5fc2666ecd649ab033c23d43... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/dataset_collections/structure.py M lib/galaxy/security/__init__.py

Log Message: ----------- Python3: lib/galaxy/dataset_collections/ and lib/galaxy/security/

Commit: 1fadc336a0bb228c9b96f3826e44fec327261740 https://github.com/galaxyproject/galaxy/commit/1fadc336a0bb228c9b96f3826e44f... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/binary.py

Log Message: ----------- Python3: lib/galaxy/datatypes/binary.py

Commit: c9ad6e31ba5a29d1c7d23842ea23fb6d222738c1 https://github.com/galaxyproject/galaxy/commit/c9ad6e31ba5a29d1c7d23842ea23f... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

Commit: 578ed609b7f836733c7225e5ee44a09536a39160 https://github.com/galaxyproject/galaxy/commit/578ed609b7f836733c7225e5ee44a... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M lib/galaxy/datatypes/converters/interval_to_bed_converter.py

Log Message: ----------- Python3: lib/galaxy/datatypes/converters/interval_to_bed_converter.py

Commit: 4b9f433f2d9b63b04477063e7321a8ac19fc370c https://github.com/galaxyproject/galaxy/commit/4b9f433f2d9b63b04477063e7321a... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt

Log Message: ----------- Forgot py3_sources.txt for prev commit

Commit: a04f6589eae995352e5bbcc9c0a73481a3abe8a8 https://github.com/galaxyproject/galaxy/commit/a04f6589eae995352e5bbcc9c0a73... Author: Junzhou Wang junzhouwang@gmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M scripts/api/data_manager_example_execute.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py

Log Message: ----------- Python3: test/shed_functional/ and test/unit/

Commit: 44d895ae500b1d20ec615aa839cfd2f56efc6d30 https://github.com/galaxyproject/galaxy/commit/44d895ae500b1d20ec615aa839cfd... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/sequence.py

Log Message: ----------- Python3: lib/galaxy/datatypes/sequence.py

Commit: f01c98bdccb8f4215f3beb525a7dc5e43bc061b4 https://github.com/galaxyproject/galaxy/commit/f01c98bdccb8f4215f3beb525a7dc... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py

Log Message: ----------- Python3: more lib/galaxy/datatypes/converters/

lib/galaxy/datatypes/converters/fastq_to_fqtoc.py lib/galaxy/datatypes/converters/gff_to_bed_converter.py

Commit: dc37a5f19c456376a8f9d996a5a73fbd1c42e212 https://github.com/galaxyproject/galaxy/commit/dc37a5f19c456376a8f9d996a5a73... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M tox.ini

Log Message: ----------- flake8 2.6.2 released

Commit: 9c3e8e5f95b64fcbb764578fa45b3aaf26832dbc https://github.com/galaxyproject/galaxy/commit/9c3e8e5f95b64fcbb764578fa45b3... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M tox.ini

Log Message: ----------- Merge branch 'python3' of github.com:bxlab/galaxy_hackathon into python3

Commit: 6ea74e2c1f272dc7c71e480a98b6c125a6fafde6 https://github.com/galaxyproject/galaxy/commit/6ea74e2c1f272dc7c71e480a98b6c... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Python3: lib/galaxy/datatypes/sniff.py

Commit: 9fd77057339260e3c0c2cba802510e93db761c6f https://github.com/galaxyproject/galaxy/commit/9fd77057339260e3c0c2cba802510... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/bed_to_gff_converter.py

Log Message: ----------- Python3: lib/galaxy/datatypes/converters/bed_to_gff_converter.py

Commit: 3f4f7af2f147ef534372e903b68e1877e86fc8cb https://github.com/galaxyproject/galaxy/commit/3f4f7af2f147ef534372e903b68e1... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/tabular.py

Log Message: ----------- Python3: lib/galaxy/datatypes/tabular.py

Commit: e45f8abb54a3008e11eb22a478c0521d39626629 https://github.com/galaxyproject/galaxy/commit/e45f8abb54a3008e11eb22a478c05... Author: Junzhou Wang junzhouwang@gmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt 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/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/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/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py

Log Message: ----------- Python3:script/api/

Commit: 3b31f02d07834882a46ebcd2ff82423c2f4b5df2 https://github.com/galaxyproject/galaxy/commit/3b31f02d07834882a46ebcd2ff824... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py

Log Message: ----------- Python 3: more lib/galaxy/datatypes/converters/

lib/galaxy/datatypes/converters/lped_to_fped_converter.py lib/galaxy/datatypes/converters/lped_to_pbed_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py

Commit: ef335721679618b9c53b6024610d6bc024129774 https://github.com/galaxyproject/galaxy/commit/ef335721679618b9c53b6024610d6... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/util/gff_util.py

Log Message: ----------- Python3: lib/galaxy/datatypes/dataproviders/

Commit: 86a54452b32008b91b400aa06213fe3d394730c3 https://github.com/galaxyproject/galaxy/commit/86a54452b32008b91b400aa06213f... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M test/unit/managers/base.py

Log Message: ----------- Revert change to callable(), it has been brought back in Python 3.2

Commit: 31c61caba371507c3ad33cffaab1e05d4c1684c1 https://github.com/galaxyproject/galaxy/commit/31c61caba371507c3ad33cffaab1e... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt

Log Message: ----------- Simplify .ci/py3_sources.txt

Commit: f68a8198da85101f241f0c8d8935b06b03019ebe https://github.com/galaxyproject/galaxy/commit/f68a8198da85101f241f0c8d8935b... Author: Junzhou Wang junzhouwang@gmail.com Date: 2016-06-25 (Sat, 25 Jun 2016)

Changed paths: M .ci/py3_sources.txt M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py

Log Message: ----------- Python3: scripts/cleanup_datasets scripts/data_libraries

Commit: 440c9f66d73baf83bf8dd277608dfb55358edfe3 https://github.com/galaxyproject/galaxy/commit/440c9f66d73baf83bf8dd277608df... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py

Log Message: ----------- Python3: lib/galaxy/managers/

Commit: cd134239535a94d5a2f4f7822f7c29e79208c5d6 https://github.com/galaxyproject/galaxy/commit/cd134239535a94d5a2f4f7822f7c2... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py M scripts/bootstrap_history.py M scripts/cleanup_datasets/pgcleanup.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M test/api/test_workflows.py M test/shed_functional/base/twilltestcase.py

Log Message: ----------- Python3: small fixes to previous commits

Commit: 693e18cdc24f8b13bb0d80fdf985e0fa3ddbf245 https://github.com/galaxyproject/galaxy/commit/693e18cdc24f8b13bb0d80fdf985e... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M lib/galaxy/datatypes/converters/interval_to_coverage.py

Log Message: ----------- Fix the fix

Commit: a8ac700318a48b5ebc2787eb81c13e9e6927db8d https://github.com/galaxyproject/galaxy/commit/a8ac700318a48b5ebc2787eb81c13... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/__init__.py M lib/galaxy/security/__init__.py

Log Message: ----------- Python3: lib/galaxy/model/__init__.py

Commit: 1fd6efcb0c8664551ca61b00e239263776526fa1 https://github.com/galaxyproject/galaxy/commit/1fd6efcb0c8664551ca61b00e2392... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

Log Message: ----------- Python3: the rest of lib/galaxy/datatypes/converters/

lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/pbed_to_lped_converter.py lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

Commit: 1b06c52e8d62c864e9a4f45a038cd3482db9f9d6 https://github.com/galaxyproject/galaxy/commit/1b06c52e8d62c864e9a4f45a038cd... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt

Log Message: ----------- Python3: sort, remove dup in .ci/py3_sources.txt

Commit: 2c67f1e7e59939d17fd91ca13c8d898ae887a8b7 https://github.com/galaxyproject/galaxy/commit/2c67f1e7e59939d17fd91ca13c8d8... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py

Log Message: ----------- Python3: lib/galaxy/model/migrate/versions/0006..0013

lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py lib/galaxy/model/migrate/versions/0007_sharing_histories.py lib/galaxy/model/migrate/versions/0008_galaxy_forms.py lib/galaxy/model/migrate/versions/0009_request_table.py lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py lib/galaxy/model/migrate/versions/0012_user_address.py lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py

Commit: de99c7efe2d6c540d6388206ae7673a54204d85d https://github.com/galaxyproject/galaxy/commit/de99c7efe2d6c540d6388206ae767... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py

Log Message: ----------- Python3: lib/galaxy/visualization/

Commit: 005429acbb2c9e09b4b653dc93b4eff2ee883a77 https://github.com/galaxyproject/galaxy/commit/005429acbb2c9e09b4b653dc93b4e... Author: Timur Shtatland shtatland@neb.com Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py

Log Message: ----------- Python3: lib/galaxy/model/migrate/versions/0014..0023

lib/galaxy/model/migrate/versions/0014_pages.py lib/galaxy/model/migrate/versions/0015_tagging.py lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py lib/galaxy/model/migrate/versions/0017_library_item_indexes.py lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py lib/galaxy/model/migrate/versions/0019_request_library_folder.py lib/galaxy/model/migrate/versions/0020_library_upload_job.py lib/galaxy/model/migrate/versions/0021_user_prefs.py lib/galaxy/model/migrate/versions/0022_visualization_tables.py lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py

Commit: 9ad9c0c80a1521abec0404e319ef41d89d5a9c50 https://github.com/galaxyproject/galaxy/commit/9ad9c0c80a1521abec0404e319ef4... Author: Eric Enns eric.enns@phac-aspc.gc.ca Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py

Log Message: ----------- Python 3: remaining model migrations

Commit: 6a870a7345353d2ad24b0d9280d87dcd3770325e https://github.com/galaxyproject/galaxy/commit/6a870a7345353d2ad24b0d9280d87... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-26 (Sun, 26 Jun 2016)

Changed paths: M .ci/py3_sources.txt

Log Message: ----------- Simplify .ci/py3_sources.txt

Commit: 5feefc73b367c09be6775c1372f0872830ce448d https://github.com/galaxyproject/galaxy/commit/5feefc73b367c09be6775c1372f08... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-27 (Mon, 27 Jun 2016)

Changed paths: M .ci/py3_sources.txt

Log Message: ----------- Simplify .ci/py3_sources.txt

Commit: 40f85f291327c217d7603f59c5454f38016d1e71 https://github.com/galaxyproject/galaxy/commit/40f85f291327c217d7603f59c5454... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-27 (Mon, 27 Jun 2016)

Changed paths: M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M test/api/test_workflows.py

Log Message: ----------- Python3: add missing print_function imports

Commit: 9a97a2952f3c33a496157e86719fc41e10d32382 https://github.com/galaxyproject/galaxy/commit/9a97a2952f3c33a496157e86719fc... Author: Nicola Soranzo nicola.soranzo@tgac.ac.uk Date: 2016-06-29 (Wed, 29 Jun 2016)

Changed paths: M .ci/py3_sources.txt M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py

Log Message: ----------- Python3: test/unit/

Commit: a946b04316802f56f493b867d0755692a4f9753f https://github.com/galaxyproject/galaxy/commit/a946b04316802f56f493b867d0755... Author: Dannon Baker dannon.baker@gmail.com Date: 2016-07-05 (Tue, 05 Jul 2016)

Changed paths: M .ci/py3_sources.txt M lib/galaxy/dataset_collections/structure.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bed_converter.py M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py M lib/galaxy/datatypes/converters/interval_to_coverage.py M lib/galaxy/datatypes/converters/lped_to_fped_converter.py M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py M lib/galaxy/datatypes/converters/maf_to_interval_converter.py M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/managers/base.py M lib/galaxy/managers/context.py M lib/galaxy/model/__init__.py M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py M lib/galaxy/model/migrate/versions/0007_sharing_histories.py M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py M lib/galaxy/model/migrate/versions/0009_request_table.py M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0012_user_address.py M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py M lib/galaxy/model/migrate/versions/0014_pages.py M lib/galaxy/model/migrate/versions/0015_tagging.py M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py M lib/galaxy/model/migrate/versions/0019_request_library_folder.py M lib/galaxy/model/migrate/versions/0020_library_upload_job.py M lib/galaxy/model/migrate/versions/0021_user_prefs.py M lib/galaxy/model/migrate/versions/0022_visualization_tables.py M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py M lib/galaxy/model/migrate/versions/0025_user_info.py M lib/galaxy/model/migrate/versions/0026_cloud_tables.py M lib/galaxy/model/migrate/versions/0027_request_events.py M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py M lib/galaxy/model/migrate/versions/0029_user_actions.py M lib/galaxy/model/migrate/versions/0030_history_slug_column.py M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0037_samples_library.py M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py M lib/galaxy/model/migrate/versions/0040_page_annotations.py M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py M lib/galaxy/model/migrate/versions/0046_post_job_actions.py M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0049_api_keys_table.py M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py M lib/galaxy/model/migrate/versions/0053_item_ratings.py M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py M lib/galaxy/model/migrate/versions/0057_request_notify.py M lib/galaxy/model/migrate/versions/0058_history_import_export.py M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py M lib/galaxy/model/migrate/versions/0060_history_archive_import.py M lib/galaxy/model/migrate/versions/0061_tasks.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0063_sequencer_table.py M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py M lib/galaxy/model/migrate/versions/0080_quota_tables.py M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py M lib/galaxy/model/migrate/versions/0085_add_task_info.py M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py M lib/galaxy/model/migrate/versions/0095_hda_subsets.py M lib/galaxy/model/migrate/versions/0096_openid_provider.py M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py M lib/galaxy/model/migrate/versions/0117_add_user_activation.py M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/security/__init__.py M lib/galaxy/security/passwords.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/genomes.py M scripts/api/data_manager_example_execute.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/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/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/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/bootstrap_history.py M scripts/build_toolbox.py M scripts/check_galaxy.py M scripts/check_python.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py M scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_runner.py M scripts/fetch_eggs.py M test/api/helpers.py M test/api/test_datasets.py M test/api/test_tool_data.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/shed_functional/base/twilltestcase.py M test/shed_functional/functional_tests.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py M test/unit/managers/base.py M test/unit/managers/test_DatasetManager.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HDCAManager.py M test/unit/managers/test_HistoryContentsManager.py M test/unit/managers/test_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/test_galaxy_mapping.py M test/unit/tools/test_toolbox.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/base/test_HookPluginManager.py M test/unit/web/base/test_PageServingPluginManager.py M test/unit/web/base/test_PluginManager.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini

Log Message: ----------- Merge pull request #2574 from bxlab/python3

Python3: port 215 files

Compare: https://github.com/galaxyproject/galaxy/compare/6c995f73fb5b...a946b0431680