Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 633061f3e0e95041383901378e33f8b41b83717e https://github.com/galaxyproject/galaxy/commit/633061f3e0e95041383901378e33f... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-04 (Sat, 04 Jul 2015)
Changed paths: M lib/galaxy/__init__.py M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py A lib/galaxy/wheels.py R lib/pkg_resources.py M run.sh R scripts/check_eggs.py M scripts/common_startup.sh R scripts/dist-scramble.py R scripts/fetch_eggs.py R scripts/make_egg_packager.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py R scripts/test_dist_egg.py
Log Message: ----------- WIP: Stop using eggs, start using prebuilt wheels.
Commit: a24134c447818fc8f55e0f7b7a0f33690155444b https://github.com/galaxyproject/galaxy/commit/a24134c447818fc8f55e0f7b7a0f3... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-05 (Sun, 05 Jul 2015)
Changed paths: M scripts/common_startup.sh
Log Message: ----------- Install modified pip for fetching Linux wheels, fetch wheels from wheels.galaxyproject.org
Commit: 0de745188e28b5b53097b7cb1d69454bf681f523 https://github.com/galaxyproject/galaxy/commit/0de745188e28b5b53097b7cb1d694... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-05 (Sun, 05 Jul 2015)
Changed paths: R dist-eggs.ini R eggs.ini
Log Message: ----------- Remove (dist-)eggs.ini.
Commit: 33095318f777bf55fcf01cff4fe9d00910ff2868 https://github.com/galaxyproject/galaxy/commit/33095318f777bf55fcf01cff4fe9d... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-05 (Sun, 05 Jul 2015)
Changed paths: M lib/galaxy/wheels.py
Log Message: ----------- Fix problems in wheels.py found by flake8
Commit: 55019173466628c117a8a41eb068a605c1282f06 https://github.com/galaxyproject/galaxy/commit/55019173466628c117a8a41eb068a... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-05 (Sun, 05 Jul 2015)
Changed paths: M scripts/common_startup.sh
Log Message: ----------- Install modified pip in develop/edit mode so it won't be reinstalled every time (courtesy @jxtx).
Commit: e6446b05d35e7950675f4bcd95cf8c9e1c89ef1d https://github.com/galaxyproject/galaxy/commit/e6446b05d35e7950675f4bcd95cf8... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-05 (Sun, 05 Jul 2015)
Changed paths: M requirements.txt
Log Message: ----------- Add nose to requirements.txt.
Commit: 033b1e88da99b86ffbd33321374aa59d1d72484c https://github.com/galaxyproject/galaxy/commit/033b1e88da99b86ffbd33321374aa... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-13 (Mon, 13 Jul 2015)
Changed paths: M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_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/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_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/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/lwr_client/config_util.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/hg_util.py
Log Message: ----------- Remove all imports of `galaxy.eggs` and all calls to `{eggs,pkg_resources}.require`. Probably broke some stuff where we were trying to be smart about whether a particular egg was available, but Galaxy does at least start.
Commit: 431ebf93bd75437fb5f5c41e40791c5c9e6e9aad https://github.com/galaxyproject/galaxy/commit/431ebf93bd75437fb5f5c41e40791... Author: Nate Coraor nate@bx.psu.edu Date: 2015-07-15 (Wed, 15 Jul 2015)
Changed paths: M requirements.txt
Log Message: ----------- Updating requirements.txt as I get wheels ready. TODO: automate OS X wheels.
Commit: 90279909209983fc620e26c6d7fabb6031d57dfd https://github.com/galaxyproject/galaxy/commit/90279909209983fc620e26c6d7fab... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M requirements.txt
Log Message: ----------- Pin requirements
Commit: 40bde6e102ae7bd66973a9f81b79fa9a08836c55 https://github.com/galaxyproject/galaxy/commit/40bde6e102ae7bd66973a9f81b79f... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M lib/galaxy/wheels.py M scripts/common_startup.sh
Log Message: ----------- Install required dependencies from requirements.txt rather than convoluted galaxy.wheels method. Not sure why I was doing that. Hackathons are dangerous places.
Commit: 97ad53f570800fc2518925555dc99f5a56356bdc https://github.com/galaxyproject/galaxy/commit/97ad53f570800fc2518925555dc99... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: A .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh R .ci/pep8_sources.txt A CODE_OF_CONDUCT.md M CONTRIBUTING.md M README.rst M client/GruntFile.js M client/README.md M client/bower.json M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.menu.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/farbtastic.js M client/galaxy/scripts/libs/handlebars.runtime.js A client/galaxy/scripts/libs/jquery.sparklines.js M client/galaxy/scripts/libs/jquery/jqtouch.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/libs/tracekit.js A client/galaxy/scripts/mvc/app/app-analysis.js A client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js A client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-panel-edit.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-form.js R client/galaxy/scripts/mvc/ui/ui-button-check.js R client/galaxy/scripts/mvc/ui/ui-button-menu.js A client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/upload/composite/composite-row.js A client/galaxy/scripts/mvc/upload/composite/composite-view.js A client/galaxy/scripts/mvc/upload/default/default-row.js A client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-ftp.js M client/galaxy/scripts/mvc/upload/upload-model.js R client/galaxy/scripts/mvc/upload/upload-row.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js A client/galaxy/scripts/reports_webapp/run_stats.js R client/galaxy/scripts/templates/compile_templates.py M client/galaxy/scripts/templates/compiled/panel_section.js M client/galaxy/scripts/templates/compiled/tool_form.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/compiled/tool_search.js M client/galaxy/scripts/utils/config.js A client/galaxy/scripts/utils/query-string-parsing.js M client/galaxy/scripts/utils/uploadbox.js M client/galaxy/scripts/utils/utils.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/style/less/base.less M client/galaxy/style/less/galaxy_bootstrap/variables.less M client/galaxy/style/less/history.less A client/galaxy/style/less/reports.less M client/galaxy/style/less/trackster.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M client/galaxy/style/source_material/circle.py M client/grunt-tasks/install-libs.js M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js A client/grunt-tasks/templates.js M client/package.json M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/visualizations/trackster/config/trackster.xml M config/tool_data_table_conf.xml.sample M contrib/galaxy_config_merger.py M contrib/nagios/check_galaxy.py M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M cron/parse_builds_3_sites.py M doc/patch.py A doc/source/api/guidelines.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/conf.py A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst M doc/source/project/organization.rst A doc/source/releases/15.07.rst M doc/source/releases/15.07_announce.rst A doc/source/releases/15.10_announce.rst M doc/source/releases/_header.rst M doc/source/releases/index.rst A doc/source/ts_api_doc.rst M lib/galaxy/actions/admin.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py A lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/dataset_collections/builder.py M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/dataset_collections/types/__init__.py M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/checkers.py M lib/galaxy/datatypes/chrominfo.py M lib/galaxy/datatypes/converters/bed_to_gff_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/fasta_to_len.py M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py M lib/galaxy/datatypes/converters/fastq_to_fqtoc.py M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py M lib/galaxy/datatypes/converters/gff_to_bed_converter.py M lib/galaxy/datatypes/converters/gff_to_interval_index_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/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_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/picard_interval_list_to_bed6_converter.py M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/__init__.py M lib/galaxy/datatypes/dataproviders/base.py M lib/galaxy/datatypes/dataproviders/chunk.py M lib/galaxy/datatypes/dataproviders/column.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/dataproviders/decorators.py M lib/galaxy/datatypes/dataproviders/exceptions.py M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/datatypes/dataproviders/hierarchy.py M lib/galaxy/datatypes/dataproviders/line.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/display_applications/parameters.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/genetics.py M lib/galaxy/datatypes/graph.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/ngsindex.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py A lib/galaxy/datatypes/test/oxli_countgraph.oxlicg A lib/galaxy/datatypes/test/oxli_graphlabels.oxligl A lib/galaxy/datatypes/test/oxli_nodegraph.oxling A lib/galaxy/datatypes/test/oxli_stoptags.oxlist A lib/galaxy/datatypes/test/oxli_subset.oxliss A lib/galaxy/datatypes/test/oxli_tagset.oxlits M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/datatypes/util/image_util.py M lib/galaxy/datatypes/xml.py M lib/galaxy/eggs/__init__.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/external_services/__init__.py M lib/galaxy/external_services/actions.py M lib/galaxy/external_services/parameters.py M lib/galaxy/external_services/result_handlers/__init__.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/external_services/service.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/datasets.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/deferred/data_transfer.py M lib/galaxy/jobs/deferred/manual_data_transfer.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/mapper.py M lib/galaxy/jobs/metrics/formatting.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py M lib/galaxy/jobs/output_checker.py M 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tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/stats/grouping.py
Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into smash_eggs
Conflicts: eggs.ini lib/galaxy/__init__.py lib/galaxy/datatypes/binary.py lib/galaxy/datatypes/converters/bgzip.py lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py lib/galaxy/datatypes/converters/interval_to_coverage.py lib/galaxy/datatypes/converters/interval_to_fli.py lib/galaxy/datatypes/converters/interval_to_tabix_converter.py lib/galaxy/datatypes/converters/maf_to_fasta_converter.py lib/galaxy/datatypes/converters/maf_to_interval_converter.py lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py lib/galaxy/datatypes/coverage.py lib/galaxy/eggs/__init__.py lib/galaxy/eggs/dist.py lib/galaxy/eggs/scramble.py lib/galaxy/exceptions/__init__.py lib/galaxy/jobs/runners/pbs.py lib/galaxy/jobs/transfer_manager.py lib/galaxy/model/__init__.py lib/galaxy/model/migrate/check.py lib/galaxy/model/orm/__init__.py lib/galaxy/model/tool_shed_install/migrate/check.py lib/galaxy/web/framework/__init__.py lib/galaxy/web/framework/helpers/__init__.py lib/galaxy/web/framework/middleware/sentry.py lib/galaxy/web/framework/openid_manager.py lib/galaxy/web/framework/webapp.py lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py lib/galaxy/webapps/galaxy/controllers/dataset.py lib/galaxy/webapps/galaxy/controllers/library_common.py lib/galaxy/webapps/reports/controllers/workflows.py lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/search/repo_search.py lib/galaxy/webapps/tool_shed/search/tool_search.py lib/galaxy_ext/metadata/set_metadata.py lib/pulsar/client/config_util.py lib/tool_shed/galaxy_install/install_manager.py lib/tool_shed/galaxy_install/migrate/check.py lib/tool_shed/grids/admin_grids.py lib/tool_shed/grids/repository_grids.py lib/tool_shed/repository_types/repository_suite_definition.py lib/tool_shed/repository_types/tool_dependency_definition.py lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py lib/tool_shed/scripts/check_repositories_for_functional_tests.py lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py lib/tool_shed/util/basic_util.py lib/tool_shed/util/encoding_util.py lib/tool_shed/util/hg_util.py scripts/check_eggs.py scripts/dist-scramble.py scripts/fetch_eggs.py scripts/make_egg_packager.py scripts/scramble.py scripts/scramble/lib/scramble_lib.py scripts/scramble/scripts/DRMAA_python-macosx.py scripts/scramble/scripts/DRMAA_python-solaris.py scripts/scramble/scripts/DRMAA_python.py scripts/scramble/scripts/MySQL_python-solaris.py scripts/scramble/scripts/MySQL_python.py scripts/scramble/scripts/PyRods.py scripts/scramble/scripts/bx_python-solaris.py scripts/scramble/scripts/generic.py scripts/scramble/scripts/pbs_python.py scripts/scramble/scripts/psycopg2-linux.py scripts/scramble/scripts/psycopg2-macosx.py scripts/scramble/scripts/psycopg2-solaris.py scripts/scramble/scripts/psycopg2.py scripts/scramble/scripts/pysam-solaris.py scripts/scramble/scripts/pysqlite.py scripts/test_dist_egg.py
Commit: 975fddeb4092097c5f6eb02f36cac65dcddf0d6a https://github.com/galaxyproject/galaxy/commit/975fddeb4092097c5f6eb02f36cac... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/wheels.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py
Log Message: ----------- Fix linting errors
Commit: 0469ed29e064a4aed213dcc0230e8a06e711fc24 https://github.com/galaxyproject/galaxy/commit/0469ed29e064a4aed213dcc0230e8... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M scripts/api/common.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py M scripts/functional_tests.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/summarize_timings.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py
Log Message: ----------- Remove egg cruft from scripts/
Commit: b727174326292fcc713adc79471065d483ce42a8 https://github.com/galaxyproject/galaxy/commit/b727174326292fcc713adc7947106... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M tox.ini
Log Message: ----------- tox: Install nose and NoseHTML for unit tests.
Commit: 93410ecf2538e32bdac7bed45367dbd6c993fb04 https://github.com/galaxyproject/galaxy/commit/93410ecf2538e32bdac7bed45367d... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M scripts/nosetests.py M scripts/summarize_timings.py
Log Message: ----------- Fix additional lint errors created by modifying stuff in scripts/
Commit: 165d6bdc9ded10c751e4eecbcca4390d231875ee https://github.com/galaxyproject/galaxy/commit/165d6bdc9ded10c751e4eecbcca43... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
Log Message: ----------- Fix ctabix import errors (would these converters ever have worked?)
Commit: 222bb4294a3dd9c9c58ae9f0785a10eb361c1e77 https://github.com/galaxyproject/galaxy/commit/222bb4294a3dd9c9c58ae9f0785a1... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-21 (Mon, 21 Sep 2015)
Changed paths: M lib/galaxy/objectstore/rods.py
Log Message: ----------- Conditional import for irods
Commit: bf50d44ee50f5ace7d34db3e69c39779283167c7 https://github.com/galaxyproject/galaxy/commit/bf50d44ee50f5ace7d34db3e69c39... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-22 (Tue, 22 Sep 2015)
Changed paths: M lib/galaxy/util/log/fluent_log.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/wheels.py
Log Message: ----------- Conditional imports for optional dependencies.
Commit: f33476462722ec17947522d0a88661c88b688438 https://github.com/galaxyproject/galaxy/commit/f33476462722ec17947522d0a8866... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-22 (Tue, 22 Sep 2015)
Changed paths: M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.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_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini
Log Message: ----------- Egg cleaning in test/
Commit: a44b2c2170c9c326a2d5e1fec35beb44fd9834df https://github.com/galaxyproject/galaxy/commit/a44b2c2170c9c326a2d5e1fec35be... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-22 (Tue, 22 Sep 2015)
Changed paths: A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/requirements.txt R lib/galaxy/wheels.py M requirements.txt M run.sh M scripts/common_startup.sh
Log Message: ----------- Rename galaxy.wheels to the more generalized galaxy.dependencies (since technically we don't care whether they are wheels), handle optional deps more correctly. Add error handling to common_startup.sh.
Commit: c0cb01c2f65ccf94e96120b080eb7b5aa06bf31b https://github.com/galaxyproject/galaxy/commit/c0cb01c2f65ccf94e96120b080eb7... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-22 (Tue, 22 Sep 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt
Log Message: ----------- Fixes for job_conf.xml conditional dependencies
Commit: e6337269b6fcd2b6c9d76045ff068a22d1dc39f8 https://github.com/galaxyproject/galaxy/commit/e6337269b6fcd2b6c9d76045ff068... Author: Nate Coraor nate@bx.psu.edu Date: 2015-09-22 (Tue, 22 Sep 2015)
Changed paths: M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/util/gff_util.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/users.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/template.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message: ----------- Remove pkg_resources.requires from lib/
Commit: 7c9c0cecdc3c31b9e86356470611ad1c7c0e87f4 https://github.com/galaxyproject/galaxy/commit/7c9c0cecdc3c31b9e86356470611a... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Add missing WebError requirement
Commit: 95b102371b5a2cdf617f988ab0d9e3bebcd03ebe https://github.com/galaxyproject/galaxy/commit/95b102371b5a2cdf617f988ab0d9e... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Add Pygments as a dependency of WebError and update SQLAlchemy version
Commit: 02aed9c79e9f886990d2f5b747b35183f64a2cf7 https://github.com/galaxyproject/galaxy/commit/02aed9c79e9f886990d2f5b747b35... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Update Mercurial to 3.5
Commit: 2955ac414ac572a0c7a32c8b7ae61e0707d90524 https://github.com/galaxyproject/galaxy/commit/2955ac414ac572a0c7a32c8b7ae61... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional_requirements.txt
Log Message: ----------- pysqlite is not a dependency (we expect Python's sqlite module to exist)
Commit: 665c4c299d93b8a028b92ec34988371ac8171617 https://github.com/galaxyproject/galaxy/commit/665c4c299d93b8a028b92ec349883... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M scripts/common_startup.sh
Log Message: ----------- Handle the case where there are no conditional (heh) requirements
Commit: 94a6f4c1704e30b839ba0de8abedff04155db5d2 https://github.com/galaxyproject/galaxy/commit/94a6f4c1704e30b839ba0de8abedf... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-01 (Thu, 01 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- psycopg2 is not a hard requirement
Commit: 4a4bfb55ec6a721f4b915ea1a7023d0ff945557d https://github.com/galaxyproject/galaxy/commit/4a4bfb55ec6a721f4b915ea1a7023... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-02 (Fri, 02 Oct 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py
Log Message: ----------- Slurm runner is a subclass of DRMAA so its use should trigger the conditional dependency code for the drmaa wheel.
Commit: 5994311d8274d8b946f51d28efcca17d31a05bbc https://github.com/galaxyproject/galaxy/commit/5994311d8274d8b946f51d28efcca... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-02 (Fri, 02 Oct 2015)
Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message: ----------- Pass Galaxy's virtualenv to jobs (local and remote) if a venv is not set. Can be overridden with <env file="/path/to/activate"/> on the destination.
Commit: 7df95d15ab67dd5e1f22107a200913d1b874749e https://github.com/galaxyproject/galaxy/commit/7df95d15ab67dd5e1f22107a20091... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-13 (Tue, 13 Oct 2015)
Changed paths: M lib/galaxy/jobs/runners/__init__.py
Log Message: ----------- Fix flake8 error
Commit: 6449db2a4ccc78e35193d7c14d315b4686f12532 https://github.com/galaxyproject/galaxy/commit/6449db2a4ccc78e35193d7c14d315... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-13 (Tue, 13 Oct 2015)
Changed paths: M test/unit/jobs/test_runner_local.py
Log Message: ----------- Fix broken unit test caused by addition of the job wrapper's galaxy_virtual_env attribute
Commit: 744835bbfe8bb07041600326af2f2f5d203365f5 https://github.com/galaxyproject/galaxy/commit/744835bbfe8bb07041600326af2f2... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-13 (Tue, 13 Oct 2015)
Changed paths: M run_tests.sh M scripts/common_startup.sh M tox.ini
Log Message: ----------- Allow the use of common_startup.sh's --skip-eggs from run_tests.sh, and have tox pass this flag (so that dependencies are installed in the tox envs)
Commit: 433b79de2b001369a62d4da3b8cc46f75dac86bb https://github.com/galaxyproject/galaxy/commit/433b79de2b001369a62d4da3b8cc4... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-13 (Tue, 13 Oct 2015)
Changed paths: M .ci/flake8_blacklist.txt M .gitignore M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/grunt-tasks/scripts.js M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako A config/plugins/visualizations/graphviz/README.md A config/plugins/visualizations/graphviz/config/graphviz.xml A config/plugins/visualizations/graphviz/static/css/style.css A config/plugins/visualizations/graphviz/static/img/15xvbd5.png A config/plugins/visualizations/graphviz/static/img/lite-blue-check.png A config/plugins/visualizations/graphviz/static/js/collapse.js A config/plugins/visualizations/graphviz/static/js/cytoscape.min.js A config/plugins/visualizations/graphviz/static/js/graphVis.js A config/plugins/visualizations/graphviz/static/js/jquery.qtip.js A config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js A config/plugins/visualizations/graphviz/static/js/tip_followscroll.js A config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js A config/plugins/visualizations/graphviz/static/js/wz_tooltip.js A config/plugins/visualizations/graphviz/templates/graphviz.mako A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A 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test/api/test_workflows.py M test/base/interactor.py M test/base/test_data.py M test/base/twilltestcase.py M test/casperjs/casperjs_runner.py M test/docker/base/Dockerfile M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/multi_data_param.xml M test/functional/tools/multi_output_configured.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/tool_shed/functional/test_1140_tool_help_images.py M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_execution.py M test/unit/tools/test_parsing.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample M tools/data_source/biomart.xml M tools/data_source/biomart_test.xml R tools/data_source/echo.py R tools/data_source/echo.xml R tools/data_source/ucsc_archaea.xml R tools/data_source/ucsc_filter.py R tools/data_source/ucsc_proxy.py R tools/data_source/ucsc_proxy.xml M tools/data_source/ucsc_tablebrowser.xml M tools/data_source/ucsc_tablebrowser_archaea.xml M tools/data_source/ucsc_tablebrowser_test.xml R tools/data_source/ucsc_testproxy.xml M tools/filters/gff/gff_filter_by_attribute.xml M tools/sr_mapping/bfast_wrapper.xml M tools/sr_mapping/fastq_statistics.xml M tools/sr_mapping/mosaik.xml M tools/sr_mapping/srma_wrapper.xml M tools/visualization/LAJ.xml
Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
Commit: d92787557a56fbf542a488c795a33f43b54b325f https://github.com/galaxyproject/galaxy/commit/d92787557a56fbf542a488c795a33... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-15 (Thu, 15 Oct 2015)
Changed paths: M scripts/common_startup.sh
Log Message: ----------- Move vvers and vurl vars to a more relevant scope.
Commit: 735e1c1bb0ea6ee857d04cd1f137c696303af5b0 https://github.com/galaxyproject/galaxy/commit/735e1c1bb0ea6ee857d04cd1f137c... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-15 (Thu, 15 Oct 2015)
Changed paths: M lib/pulsar/client/config_util.py
Log Message: ----------- Fix a bad merge in pulsar client lib caught (as always) by @nsoranzo
Commit: 22297e3b839f1985b70944088eeb02c1bf9f26e0 https://github.com/galaxyproject/galaxy/commit/22297e3b839f1985b70944088eeb0... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-15 (Thu, 15 Oct 2015)
Changed paths: M lib/pulsar/client/config_util.py
Log Message: ----------- Missed the rest of the bad merge in the previous commit
Commit: b6fde86369bcd715c976e6d8bd3002ffa25a2136 https://github.com/galaxyproject/galaxy/commit/b6fde86369bcd715c976e6d8bd300... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-15 (Thu, 15 Oct 2015)
Changed paths: M lib/galaxy/util/plugin_config.py
Log Message: ----------- More graceful handling of failure to import yaml (a la Pulsar)
Commit: f22ab8a60b06512596d68080b1bae4011110f4f1 https://github.com/galaxyproject/galaxy/commit/f22ab8a60b06512596d68080b1bae... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-15 (Thu, 15 Oct 2015)
Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py
Log Message: ----------- Conditional boto import in s3_multipart_upload.py
Commit: 367ceae2560efac06e85018f9822207011240bd6 https://github.com/galaxyproject/galaxy/commit/367ceae2560efac06e85018f98222... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-16 (Fri, 16 Oct 2015)
Changed paths: M create_db.sh M manage_db.sh M manage_tools.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M set_metadata.sh M test/docker/base/run_test_wrapper.sh
Log Message: ----------- Dockerized tests need to create and activate .venv if it does not exist. Do this by calling common_startup.sh prior to manage_db.sh in run_test_wrapper.sh. Will require a rebuild of the testing-base image.
Also, have scripts in Galaxy root activate .venv if it exists.
Commit: f7d0d76c509a8d468f29cb07a4fbd98ad1640d8f https://github.com/galaxyproject/galaxy/commit/f7d0d76c509a8d468f29cb07a4fbd... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-16 (Fri, 16 Oct 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Add boto as an explicit requirement (as a dependency of bioblend)
Commit: c893afda008f4c47550f9bc94feb1a1256c470e7 https://github.com/galaxyproject/galaxy/commit/c893afda008f4c47550f9bc94feb1... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/constructive_solid_geometry.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/version.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run_tests.sh M scripts/cleanup_datasets/cleanup_datasets.py M templates/webapps/galaxy/workflow/editor.mako M test/api/test_tools.py M test/docker/base/run_test_wrapper.sh M test/unit/test_galaxy_mapping.py
Log Message: ----------- Merge branch 'dev' into smash_eggs
Commit: 26f78a5870a551630a5f4b91533b07b64bd3cb10 https://github.com/galaxyproject/galaxy/commit/26f78a5870a551630a5f4b91533b0... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths: M run_tests.sh
Log Message: ----------- Bump docker test image to 15.10.1
Commit: 6aea26caf307d9931c9f8349c324ed1a90c1a5d7 https://github.com/galaxyproject/galaxy/commit/6aea26caf307d9931c9f8349c324e... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Add requests as a dependency of bioblend
Commit: 6e00db2d35be741247fbd43d154f107585bb81c3 https://github.com/galaxyproject/galaxy/commit/6e00db2d35be741247fbd43d154f1... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py
Log Message: ----------- Make galaxy.dependencies env-config-var-aware.
Commit: 50bfed49f55a7d9c39308f46648616906ce20eb4 https://github.com/galaxyproject/galaxy/commit/50bfed49f55a7d9c39308f4664861... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-19 (Mon, 19 Oct 2015)
Changed paths: M lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt R lib/galaxy/dependencies/conditional_requirements.txt A lib/galaxy/dependencies/dev-requirements.txt
Log Message: ----------- Rename conditional_requirements.txt ('_' -> '-'), add dev-requirements.txt, fix a flake8 violation that doesn't violate PEP-8. =P
Commit: 4a05d5ea12142046eac2d4593030f4d4dcd3c4b1 https://github.com/galaxyproject/galaxy/commit/4a05d5ea12142046eac2d4593030f... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-20 (Tue, 20 Oct 2015)
Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/style/less/base.less M doc/source/admin/index.rst A doc/source/admin/useful_scripts.rst M doc/source/dev/faq.rst M lib/galaxy/tools/loader_directory.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/library_upload_dir.py M scripts/functional_tests.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js M static/style/blue/base.css M test/casperjs/anon-history-tests.js M test/casperjs/api-hda-tests.js M test/casperjs/api-history-tests.js M test/casperjs/hda-state-tests.js M test/casperjs/history-panel-tests.js M test/casperjs/modules/historypanel.js M test/docker/base/run_test_wrapper.sh
Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
Commit: 2b48f5676527a83b76cb4205950670cf16c4b2cb https://github.com/galaxyproject/galaxy/commit/2b48f5676527a83b76cb420595067... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-20 (Tue, 20 Oct 2015)
Changed paths: M lib/galaxy/dependencies/dev-requirements.txt
Log Message: ----------- Add lxml as a dev requirement for twill
Commit: 5098b7cb27f2c64603c57ee9991bd9516e0d25bb https://github.com/galaxyproject/galaxy/commit/5098b7cb27f2c64603c57ee9991bd... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-20 (Tue, 20 Oct 2015)
Changed paths: M lib/galaxy/dependencies/dev-requirements.txt
Log Message: ----------- Downgrade twill to 0.9.1 so we don't have to install lxml, which won't compile because libxml-dev isn't installed in the testing image, so we'd have to rebuild it yet again...
Commit: af89922aee11a8dffbdeabbc36cf1003828f3a73 https://github.com/galaxyproject/galaxy/commit/af89922aee11a8dffbdeabbc36cf1... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- Update the BAM datatype for pysam API changes. index_file also no longer exists (the index must be filename + b".bai" or filename[:-4] + b".bai") =/. Removing it here is okay since the impact is that we can't fetch() random regions or use .pileup(), neither of which are done here. But it might be a problem for galaxy.visualization.data_providers.genome.
Commit: 048f0be1bebb233edfb47a3625e8e0a9f751a696 https://github.com/galaxyproject/galaxy/commit/048f0be1bebb233edfb47a3625e8e... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- Talked to Dan, who corrected me on a few things. Also, forgot that the whole reason we use a modified pysam is for the index_filename param...
Commit: 7e372d3cd0e18e3a533d2b36fadc5ab9c755d2ca https://github.com/galaxyproject/galaxy/commit/7e372d3cd0e18e3a533d2b36fadc5... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M lib/galaxy/visualization/data_providers/genome.py
Log Message: ----------- Updates to vis data providers for pysam API changes
Commit: 0cbaf3b8c57138d694f8e1e06e353d97b211215f https://github.com/galaxyproject/galaxy/commit/0cbaf3b8c57138d694f8e1e06e353... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M lib/galaxy/dependencies/requirements.txt
Log Message: ----------- Use proper PEP-440 local version identifiers for modified dependencies.
Commit: 4a5f5f44dc09be5194c9ee4ebc6b0b6a4a057480 https://github.com/galaxyproject/galaxy/commit/4a5f5f44dc09be5194c9ee4ebc6b0... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M scripts/common_startup.sh
Log Message: ----------- Install our modified pip as a wheel from wheels.galaxyproject.org rather than an editable directly from github.
Also, use `set -e` in scripts/common_startup.sh to fail if anything fails, rather than chaining a bunch of things with `&&` but not properly handling failure cases.
Commit: 737596413f88174edc24345282aee9a1c1b53cac https://github.com/galaxyproject/galaxy/commit/737596413f88174edc24345282aee... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M run.sh
Log Message: ----------- Pass relevant args from run.sh to common_startup.sh.
Commit: 88683c3c40821581d80b3e984da486032c746c06 https://github.com/galaxyproject/galaxy/commit/88683c3c40821581d80b3e984da48... Author: Nate Coraor nate@bx.psu.edu Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M run.sh M scripts/common_startup.sh
Log Message: ----------- Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is provided.
Commit: e423ab6246088fec6a41c31fb67bc34c0ff40a89 https://github.com/galaxyproject/galaxy/commit/e423ab6246088fec6a41c31fb67bc... Author: Dannon Baker dannon.baker@gmail.com Date: 2015-10-22 (Thu, 22 Oct 2015)
Changed paths: M create_db.sh R dist-eggs.ini R eggs.ini M lib/galaxy/__init__.py M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py M lib/galaxy/datatypes/converters/bgzip.py M lib/galaxy/datatypes/converters/gff_to_interval_index_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/interval_to_fli.py M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py M lib/galaxy/datatypes/converters/interval_to_tabix_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/pileup_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py M lib/galaxy/datatypes/coverage.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/util.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/metadata.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/util/gff_util.py A lib/galaxy/dependencies/__init__.py A lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/dependencies/dev-requirements.txt A lib/galaxy/dependencies/requirements.txt M lib/galaxy/eggs/__init__.py R lib/galaxy/eggs/dist.py R lib/galaxy/eggs/scramble.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/managers/base.py M lib/galaxy/managers/citations.py M lib/galaxy/managers/histories.py M lib/galaxy/managers/libraries.py M lib/galaxy/managers/users.py M lib/galaxy/model/__init__.py M lib/galaxy/model/custom_types.py M lib/galaxy/model/mapping.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/orm/__init__.py M lib/galaxy/model/orm/engine_factory.py M lib/galaxy/model/orm/logging_connection_proxy.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/search.py M lib/galaxy/model/tool_shed_install/migrate/check.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/util/maf_utilities.py M lib/galaxy/util/__init__.py M lib/galaxy/util/log/fluent_log.py M lib/galaxy/util/plugin_config.py M lib/galaxy/util/template.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/plugins/plugin.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/web/base/pluginframework.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/requests.py M lib/galaxy/webapps/galaxy/api/roles.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/tool_runner.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/userskeys.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/home.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/query.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/system.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/repository_revisions.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/galaxy/webapps/tool_shed/model/mapping.py M lib/galaxy/webapps/tool_shed/model/migrate/check.py M lib/galaxy/webapps/tool_shed/search/repo_search.py M lib/galaxy/webapps/tool_shed/search/tool_search.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/util.py M lib/galaxy/workflow/render.py M lib/galaxy_ext/metadata/set_metadata.py R lib/pkg_resources.py M lib/pulsar/client/config_util.py M lib/pulsar/client/transport/poster.py M lib/pulsar/client/transport/requests.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/installed_repository_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/migrate/check.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/managers/groups.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/repository_types/metadata.py M lib/tool_shed/repository_types/repository_suite_definition.py M lib/tool_shed/repository_types/tool_dependency_definition.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/check_repositories_for_functional_tests.py M lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py M lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py M lib/tool_shed/scripts/deprecate_repositories_without_metadata.py M lib/tool_shed/tools/tool_version_manager.py M lib/tool_shed/util/basic_util.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/review_util.py M lib/tool_shed/util/search_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.py M manage_db.sh M manage_tools.sh M requirements.txt M run.sh M run_reports.sh M run_tests.sh M run_tool_shed.sh M scripts/api/common.py R scripts/check_eggs.py M scripts/check_galaxy.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/common_startup.sh M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py R scripts/dist-scramble.py M scripts/drmaa_external_killer.py M scripts/drmaa_external_runner.py R scripts/egg_packager_template.py R scripts/fetch_eggs.py M scripts/functional_tests.py R scripts/make_egg_packager.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/nosetests.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py R scripts/scramble.py R scripts/scramble/lib/scramble_lib.py R scripts/scramble/patches/Cheetah/SetupConfig.py R scripts/scramble/patches/MySQL_python/site.cfg R scripts/scramble/patches/PasteScript/setup.py R scripts/scramble/patches/python_daemon/setup.py R scripts/scramble/scripts/DRMAA_python-macosx.py R scripts/scramble/scripts/DRMAA_python-solaris.py R scripts/scramble/scripts/DRMAA_python.py R scripts/scramble/scripts/MySQL_python-solaris.py R scripts/scramble/scripts/MySQL_python.py R scripts/scramble/scripts/PyRods.py R scripts/scramble/scripts/bx_python-solaris.py R scripts/scramble/scripts/generic.py R scripts/scramble/scripts/pbs_python.py R scripts/scramble/scripts/psycopg2-linux.py R scripts/scramble/scripts/psycopg2-macosx.py R scripts/scramble/scripts/psycopg2-solaris.py R scripts/scramble/scripts/psycopg2.py R scripts/scramble/scripts/pysam-solaris.py R scripts/scramble/scripts/pysqlite.py M scripts/summarize_timings.py R scripts/test_dist_egg.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/transfer.py M scripts/update_shed_config_path.py M set_metadata.sh M test/base/instrument.py M test/base/interactor.py M test/base/nose_util.py M test/base/test_db_util.py M test/base/twilltestcase.py M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M test/functional/test_metadata_editing.py M test/install_and_test_tool_shed_repositories/base/test_db_util.py M test/install_and_test_tool_shed_repositories/base/twilltestcase.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/base/test_db_util.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional_tests.py M test/unit/jobs/test_runner_local.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_HistoryManager.py M test/unit/managers/test_UserManager.py M test/unit/tools/test_execution.py M test/unit/workflows/test_modules.py M tox.ini
Log Message: ----------- Merge pull request #428 from natefoo/smash_eggs
Replace eggs with wheels
Compare: https://github.com/galaxyproject/galaxy/compare/112c0390d586...e423ab624608