April 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 4c216f: Adjust testing directories so no python root is ev...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c216f1077f4f44b459397f085c26a54c2da547b https://github.com/galaxyproject/galaxy/commit/4c216f1077f4f44b459397f085c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M run_tests.sh A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0450_skip_tool_tests.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py A test/shed_functional/functional/test_0530_repository_admin_feature.py A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_1000_install_basic_repository.py A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_1060_install_repository_with_workflow.py A test/shed_functional/functional/test_1070_invalid_tool.py A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1300_reset_all_metadata.py A test/shed_functional/functional/test_1400_review_migration_stages.py A test/shed_functional/functional/test_1410_update_manager.py A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py A test/shed_functional/functional/test_1430_repair_installed_repository.py A test/shed_functional/functional/test_1440_missing_env_sh_files.py A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py A test/shed_functional/functional/test_1460_data_managers.py A test/shed_functional/functional/test_1470_updating_installed_repositories.py A test/shed_functional/functional_tests.py A test/shed_functional/test_data/0460_files/repository_dependencies.xml A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar A test/shed_functional/test_data/0460_files/tool_dependencies.xml A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar A test/shed_functional/test_data/0480_files/tool_dependencies.xml A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar A test/shed_functional/test_data/bismark/bismark.tar A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml A test/shed_functional/test_data/blast/blast_datatypes.tar A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar A test/shed_functional/test_data/bwa/bwa_base.tar A test/shed_functional/test_data/bwa/bwa_color.tar A test/shed_functional/test_data/bwa/complex/bwa_base.tar A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml A test/shed_functional/test_data/column_maker/column_maker.tar A test/shed_functional/test_data/convert_chars/convert_chars.tar A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/shed_functional/test_data/emboss/emboss.tar A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/filtering/README A test/shed_functional/test_data/filtering/filtering_0000.txt A test/shed_functional/test_data/filtering/filtering_1.1.0.tar A test/shed_functional/test_data/filtering/filtering_2.2.0.tar A test/shed_functional/test_data/filtering/filtering_test_data.tar A test/shed_functional/test_data/filtering/readme.txt A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga A test/shed_functional/test_data/freebayes/freebayes.tar A test/shed_functional/test_data/freebayes/freebayes.xml A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample A test/shed_functional/test_data/freebayes/tool_dependencies.xml A test/shed_functional/test_data/htseq_count/htseq_count.tar A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R 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test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar R 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test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py Log Message: ----------- Adjust testing directories so no python root is ever "tool_shed". We have a tool_shed directory in lib, so if we enter a test case from some path and test/tool_shed happens to be a valid python top-level module - it blocks out lib/tool_shed and Galaxy doesn't work properly in the test. A similar problem was encountered with unit tests and fixed with https://github.com/galaxyproject/galaxy/commit/df442a06382f23bdf0401bdd632b… - but I have decided that directory name was a bit log and so this commit unifies the approach to unit and functional test names for tool shed tests. Commit: 27f99cdf4014dbf1d70d6cb2a98a957fe38d7a42 https://github.com/galaxyproject/galaxy/commit/27f99cdf4014dbf1d70d6cb2a98a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Fix test data path. Commit: c04d200dc77ecc67d85ae1a41f709cfcf84cfaae https://github.com/galaxyproject/galaxy/commit/c04d200dc77ecc67d85ae1a41f70… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M test/base/driver_util.py Log Message: ----------- Merge pull request #46 from davebx/shed_tests Fix test data path. Commit: e02e97dc798dcb3c153ae46ece382ddd44917b8a https://github.com/galaxyproject/galaxy/commit/e02e97dc798dcb3c153ae46ece38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M run_tests.sh M test/base/driver_util.py A test/shed_functional/__init__.py A test/shed_functional/base/__init__.py A test/shed_functional/base/common.py A test/shed_functional/base/test_db_util.py A test/shed_functional/base/twilltestcase.py A test/shed_functional/functional/__init__.py A test/shed_functional/functional/test_0000_basic_repository_features.py A test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py A test/shed_functional/functional/test_0020_basic_repository_dependencies.py A test/shed_functional/functional/test_0030_repository_dependency_revisions.py A test/shed_functional/functional/test_0040_repository_circular_dependencies.py A test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_0060_workflows.py A test/shed_functional/functional/test_0070_invalid_tool.py A test/shed_functional/functional/test_0080_advanced_circular_dependencies.py A test/shed_functional/functional/test_0090_tool_search.py A test/shed_functional/functional/test_0100_complex_repository_dependencies.py A test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py A test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_0130_datatype_converters.py A test/shed_functional/functional/test_0140_tool_help_images.py A test/shed_functional/functional/test_0150_prior_installation_required.py A test/shed_functional/functional/test_0160_circular_prior_installation_required.py A test/shed_functional/functional/test_0170_complex_prior_installation_required.py A test/shed_functional/functional/test_0300_reset_all_metadata.py A test/shed_functional/functional/test_0310_hg_api_features.py A test/shed_functional/functional/test_0400_repository_component_reviews.py A test/shed_functional/functional/test_0410_repository_component_review_access_control.py A test/shed_functional/functional/test_0420_citable_urls_for_repositories.py A test/shed_functional/functional/test_0430_browse_utilities.py A test/shed_functional/functional/test_0440_deleting_dependency_definitions.py A test/shed_functional/functional/test_0450_skip_tool_tests.py A test/shed_functional/functional/test_0460_upload_to_repository.py A test/shed_functional/functional/test_0470_tool_dependency_repository_type.py A test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py A test/shed_functional/functional/test_0490_export_import_repositories.py A test/shed_functional/functional/test_0500_export_repository_simple_dependency.py A test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py A test/shed_functional/functional/test_0520_import_export_circular_dependencies.py A test/shed_functional/functional/test_0530_repository_admin_feature.py A test/shed_functional/functional/test_0540_get_all_metadata_from_api.py A test/shed_functional/functional/test_1000_install_basic_repository.py A test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py A test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py A test/shed_functional/functional/test_1060_install_repository_with_workflow.py A test/shed_functional/functional/test_1070_invalid_tool.py A test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py A test/shed_functional/functional/test_1090_repository_dependency_handling.py A test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py A test/shed_functional/functional/test_1110_install_tool_from_tool_search.py A test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py A test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py A test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A test/shed_functional/functional/test_1150_datatype_converters.py A test/shed_functional/functional/test_1160_tool_help_images.py A test/shed_functional/functional/test_1170_prior_installation_required.py A test/shed_functional/functional/test_1180_circular_prior_installation_required.py A test/shed_functional/functional/test_1190_complex_prior_installation_required.py A test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py A test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py A test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py A test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py A test/shed_functional/functional/test_1300_reset_all_metadata.py A test/shed_functional/functional/test_1400_review_migration_stages.py A test/shed_functional/functional/test_1410_update_manager.py A test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py A test/shed_functional/functional/test_1430_repair_installed_repository.py A test/shed_functional/functional/test_1440_missing_env_sh_files.py A test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py A test/shed_functional/functional/test_1460_data_managers.py A test/shed_functional/functional/test_1470_updating_installed_repositories.py A test/shed_functional/functional_tests.py A test/shed_functional/test_data/0460_files/repository_dependencies.xml A test/shed_functional/test_data/0460_files/repository_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/repository_dependencies_in_subfolder.tar A test/shed_functional/test_data/0460_files/tool_dependencies.xml A test/shed_functional/test_data/0460_files/tool_dependencies_in_root.tar A test/shed_functional/test_data/0460_files/tool_dependencies_in_subfolder.tar A test/shed_functional/test_data/0480_files/tool_dependencies.xml A test/shed_functional/test_data/0540_files/column_maker/column_maker.tar A test/shed_functional/test_data/0540_files/column_maker/repository_dependencies.xml A test/shed_functional/test_data/0540_files/convert_chars/convert_chars.tar A test/shed_functional/test_data/0540_files/convert_chars/tool_dependencies.xml A test/shed_functional/test_data/0540_files/package_bwa/tool_dependencies.xml A test/shed_functional/test_data/1420_files/binary_tarballs/atlas.tar A test/shed_functional/test_data/1420_files/binary_tarballs/boost.tar A test/shed_functional/test_data/1420_files/binary_tarballs/bzlib.tar A test/shed_functional/test_data/1420_files/binary_tarballs/lapack.tar A test/shed_functional/test_data/1420_files/binary_tarballs/numpy.tar A test/shed_functional/test_data/1420_files/binary_tarballs/rdkit.tar A test/shed_functional/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml A test/shed_functional/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml A test/shed_functional/test_data/1440_files/complex_dependency/tool_dependencies.xml A test/shed_functional/test_data/1440_files/dependency_definition/tool_dependencies.xml A test/shed_functional/test_data/1460_files/data_manager_files/test_data_manager.tar A test/shed_functional/test_data/bed_to_gff_converter/bed_to_gff_converter.tar A test/shed_functional/test_data/bismark/bismark.tar A test/shed_functional/test_data/bismark/bismark_methylation_extractor.xml A test/shed_functional/test_data/blast/blast_datatypes.tar A test/shed_functional/test_data/blast/blastxml_to_top_descr.tar A test/shed_functional/test_data/bwa/bwa_base.tar A test/shed_functional/test_data/bwa/bwa_color.tar A test/shed_functional/test_data/bwa/complex/bwa_base.tar A test/shed_functional/test_data/bwa/complex/readme/tool_dependencies.xml A test/shed_functional/test_data/bwa/complex/tool_dependencies.xml A test/shed_functional/test_data/column_maker/column_maker.tar A test/shed_functional/test_data/convert_chars/convert_chars.tar A test/shed_functional/test_data/emboss/0470_files/emboss_complex_dependency.tar A test/shed_functional/test_data/emboss/0470_files/tool_dependencies.xml A test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml A test/shed_functional/test_data/emboss/emboss.tar A test/shed_functional/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml A test/shed_functional/test_data/filtering/README A test/shed_functional/test_data/filtering/filtering_0000.txt A test/shed_functional/test_data/filtering/filtering_1.1.0.tar A test/shed_functional/test_data/filtering/filtering_2.2.0.tar A test/shed_functional/test_data/filtering/filtering_test_data.tar A test/shed_functional/test_data/filtering/readme.txt A test/shed_functional/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga A test/shed_functional/test_data/freebayes/freebayes.tar A test/shed_functional/test_data/freebayes/freebayes.xml A test/shed_functional/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml A test/shed_functional/test_data/freebayes/sam_fa_indices.loc.sample A test/shed_functional/test_data/freebayes/tool_data_table_conf.xml.sample A test/shed_functional/test_data/freebayes/tool_dependencies.xml A test/shed_functional/test_data/htseq_count/htseq_count.tar A test/shed_functional/test_data/package_matplotlib/package_matplotlib_1_2.tar A test/shed_functional/test_data/package_matplotlib/tool_dependencies.xml A test/shed_functional/test_data/package_numpy/package_numpy_1_7.tar A test/shed_functional/test_data/proteomics_datatypes/proteomics_datatypes.tar A test/shed_functional/test_data/readme.txt A test/shed_functional/test_data/repository_capsules/0490_filtering.tar.gz A test/shed_functional/test_data/repository_capsules/0500_emboss_5.tar.gz A test/shed_functional/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz A test/shed_functional/test_data/repository_capsules/0520_filtering.tar.gz R test/tool_shed/__init__.py R test/tool_shed/base/__init__.py R test/tool_shed/base/common.py R test/tool_shed/base/test_db_util.py R test/tool_shed/base/twilltestcase.py R test/tool_shed/functional/__init__.py R test/tool_shed/functional/test_0000_basic_repository_features.py R test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py R test/tool_shed/functional/test_0020_basic_repository_dependencies.py R test/tool_shed/functional/test_0030_repository_dependency_revisions.py R test/tool_shed/functional/test_0040_repository_circular_dependencies.py R test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_0060_workflows.py R test/tool_shed/functional/test_0070_invalid_tool.py R test/tool_shed/functional/test_0080_advanced_circular_dependencies.py R test/tool_shed/functional/test_0090_tool_search.py R test/tool_shed/functional/test_0100_complex_repository_dependencies.py R test/tool_shed/functional/test_0110_invalid_simple_repository_dependencies.py R test/tool_shed/functional/test_0120_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_0130_datatype_converters.py R test/tool_shed/functional/test_0140_tool_help_images.py R test/tool_shed/functional/test_0150_prior_installation_required.py R test/tool_shed/functional/test_0160_circular_prior_installation_required.py R test/tool_shed/functional/test_0170_complex_prior_installation_required.py R test/tool_shed/functional/test_0300_reset_all_metadata.py R test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0400_repository_component_reviews.py R test/tool_shed/functional/test_0410_repository_component_review_access_control.py R test/tool_shed/functional/test_0420_citable_urls_for_repositories.py R test/tool_shed/functional/test_0430_browse_utilities.py R test/tool_shed/functional/test_0440_deleting_dependency_definitions.py R test/tool_shed/functional/test_0450_skip_tool_tests.py R test/tool_shed/functional/test_0460_upload_to_repository.py R test/tool_shed/functional/test_0470_tool_dependency_repository_type.py R test/tool_shed/functional/test_0480_tool_dependency_xml_verification.py R test/tool_shed/functional/test_0490_export_import_repositories.py R test/tool_shed/functional/test_0500_export_repository_simple_dependency.py R test/tool_shed/functional/test_0510_export_import_repository_complex_dependencies.py R test/tool_shed/functional/test_0520_import_export_circular_dependencies.py R test/tool_shed/functional/test_0530_repository_admin_feature.py R test/tool_shed/functional/test_0540_get_all_metadata_from_api.py R test/tool_shed/functional/test_1000_install_basic_repository.py R test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py R test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py R test/tool_shed/functional/test_1060_install_repository_with_workflow.py R test/tool_shed/functional/test_1070_invalid_tool.py R test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py R test/tool_shed/functional/test_1090_repository_dependency_handling.py R test/tool_shed/functional/test_1100_install_updated_repository_dependencies.py R test/tool_shed/functional/test_1110_install_tool_from_tool_search.py R test/tool_shed/functional/test_1120_install_repository_with_complex_dependencies.py R test/tool_shed/functional/test_1130_install_repository_with_invalid_repository_dependency.py R test/tool_shed/functional/test_1140_simple_repository_dependency_multiple_owners.py R test/tool_shed/functional/test_1150_datatype_converters.py R test/tool_shed/functional/test_1160_tool_help_images.py R test/tool_shed/functional/test_1170_prior_installation_required.py R test/tool_shed/functional/test_1180_circular_prior_installation_required.py R test/tool_shed/functional/test_1190_complex_prior_installation_required.py R test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py R test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py R test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py R test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py R test/tool_shed/functional/test_1300_reset_all_metadata.py R test/tool_shed/functional/test_1400_review_migration_stages.py R test/tool_shed/functional/test_1410_update_manager.py R test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py R test/tool_shed/functional/test_1430_repair_installed_repository.py R test/tool_shed/functional/test_1440_missing_env_sh_files.py R test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py R test/tool_shed/functional/test_1460_data_managers.py R test/tool_shed/functional/test_1470_updating_installed_repositories.py R test/tool_shed/functional_tests.py R test/tool_shed/test_data/0460_files/repository_dependencies.xml R test/tool_shed/test_data/0460_files/repository_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/repository_dependencies_in_subfolder.tar R test/tool_shed/test_data/0460_files/tool_dependencies.xml R test/tool_shed/test_data/0460_files/tool_dependencies_in_root.tar R test/tool_shed/test_data/0460_files/tool_dependencies_in_subfolder.tar R test/tool_shed/test_data/0480_files/tool_dependencies.xml R test/tool_shed/test_data/0540_files/column_maker/column_maker.tar R test/tool_shed/test_data/0540_files/column_maker/repository_dependencies.xml R test/tool_shed/test_data/0540_files/convert_chars/convert_chars.tar R test/tool_shed/test_data/0540_files/convert_chars/tool_dependencies.xml R test/tool_shed/test_data/0540_files/package_bwa/tool_dependencies.xml R test/tool_shed/test_data/1420_files/binary_tarballs/atlas.tar R test/tool_shed/test_data/1420_files/binary_tarballs/boost.tar R test/tool_shed/test_data/1420_files/binary_tarballs/bzlib.tar R test/tool_shed/test_data/1420_files/binary_tarballs/lapack.tar R test/tool_shed/test_data/1420_files/binary_tarballs/numpy.tar R test/tool_shed/test_data/1420_files/binary_tarballs/rdkit.tar R test/tool_shed/test_data/1420_files/package_atlas_3_10_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_boost_1_53_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_bzlib_1_0_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_lapack_3_4_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_numpy_1_7_1420/tool_dependencies.xml R test/tool_shed/test_data/1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml R test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml R test/tool_shed/test_data/1440_files/dependency_definition/tool_dependencies.xml R test/tool_shed/test_data/1460_files/data_manager_files/test_data_manager.tar R test/tool_shed/test_data/bed_to_gff_converter/bed_to_gff_converter.tar R test/tool_shed/test_data/bismark/bismark.tar R test/tool_shed/test_data/bismark/bismark_methylation_extractor.xml R test/tool_shed/test_data/blast/blast_datatypes.tar R test/tool_shed/test_data/blast/blastxml_to_top_descr.tar R test/tool_shed/test_data/bwa/bwa_base.tar R test/tool_shed/test_data/bwa/bwa_color.tar R test/tool_shed/test_data/bwa/complex/bwa_base.tar R test/tool_shed/test_data/bwa/complex/readme/tool_dependencies.xml R test/tool_shed/test_data/bwa/complex/tool_dependencies.xml R test/tool_shed/test_data/column_maker/column_maker.tar R test/tool_shed/test_data/convert_chars/convert_chars.tar R test/tool_shed/test_data/emboss/0470_files/emboss_complex_dependency.tar R test/tool_shed/test_data/emboss/0470_files/tool_dependencies.xml R test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml R test/tool_shed/test_data/emboss/emboss.tar R test/tool_shed/test_data/emboss/emboss_5_0_0/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/emboss_5_0_0/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/first_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/emboss/libx11_proto/second_tool_dependency/tool_dependencies.xml R test/tool_shed/test_data/filtering/README R test/tool_shed/test_data/filtering/filtering_0000.txt R test/tool_shed/test_data/filtering/filtering_1.1.0.tar R test/tool_shed/test_data/filtering/filtering_2.2.0.tar R test/tool_shed/test_data/filtering/filtering_test_data.tar R test/tool_shed/test_data/filtering/readme.txt R test/tool_shed/test_data/filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga R test/tool_shed/test_data/freebayes/freebayes.tar R test/tool_shed/test_data/freebayes/freebayes.xml R test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/malformed_tool_dependencies/tool_dependencies.xml R test/tool_shed/test_data/freebayes/sam_fa_indices.loc.sample R test/tool_shed/test_data/freebayes/tool_data_table_conf.xml.sample R test/tool_shed/test_data/freebayes/tool_dependencies.xml R test/tool_shed/test_data/htseq_count/htseq_count.tar R test/tool_shed/test_data/package_matplotlib/package_matplotlib_1_2.tar R test/tool_shed/test_data/package_matplotlib/tool_dependencies.xml R test/tool_shed/test_data/package_numpy/package_numpy_1_7.tar R test/tool_shed/test_data/proteomics_datatypes/proteomics_datatypes.tar R test/tool_shed/test_data/readme.txt R test/tool_shed/test_data/repository_capsules/0490_filtering.tar.gz R test/tool_shed/test_data/repository_capsules/0500_emboss_5.tar.gz R test/tool_shed/test_data/repository_capsules/0510_trans_proteomic_pipeline.tar.gz R test/tool_shed/test_data/repository_capsules/0520_filtering.tar.gz A test/unit/shed_unit/__init__.py A test/unit/shed_unit/test_fabric_util.py A test/unit/shed_unit/test_td_common_util.py A test/unit/shed_unit/test_tool_panel_manager.py R test/unit/tool_shed_unit_tests/__init__.py R test/unit/tool_shed_unit_tests/test_fabric_util.py R test/unit/tool_shed_unit_tests/test_td_common_util.py R test/unit/tool_shed_unit_tests/test_tool_panel_manager.py Log Message: ----------- Merge pull request #2067 from jmchilton/shed_tests Adjust testing directories so no python root is ever "tool_shed". Compare: https://github.com/galaxyproject/galaxy/compare/1c201a863067...e02e97dc798d

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[galaxyproject/galaxy] d62982: Docstring fixes for lib/galaxy/jobs/runners/pulsar...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d629822912d861db60de7e97a8c264442c37c495 https://github.com/galaxyproject/galaxy/commit/d629822912d861db60de7e97a8c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Docstring fixes for lib/galaxy/jobs/runners/pulsar.py. Commit: 32b945f06321538f8aed36d4d542f0395f4cd192 https://github.com/galaxyproject/galaxy/commit/32b945f06321538f8aed36d4d542… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix pulsar import order. Commit: cc17d5304cc9ca9910162f5dd83640d31175bbad https://github.com/galaxyproject/galaxy/commit/cc17d5304cc9ca9910162f5dd836… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Implement a Pulsar embedded job runner. Closes #1378. Commit: 1c201a8630672524ad217959af9a1bdd3a67d16f https://github.com/galaxyproject/galaxy/commit/1c201a8630672524ad217959af9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Merge pull request #2057 from jmchilton/pulsar_overhaul Implement an Embedded Pulsar Job Runner Compare: https://github.com/galaxyproject/galaxy/compare/991d7282c7b0...1c201a863067

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[galaxyproject/galaxy] 51f63a: Replace embedded Pulsar code with dependency.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51f63a7d3e545db1e7c89621418523356fb1bdee https://github.com/galaxyproject/galaxy/commit/51f63a7d3e545db1e7c896214185… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py Log Message: ----------- Replace embedded Pulsar code with dependency. Pulsar's setup.py has been parameterized to allow it build a special wheel that doesn't depend on galaxy-lib (https://github.com/galaxyproject/pulsar/commit/ce9d4f9e80936407fe4f793afa66…) and instead expects it to come from the environment. This special dependency has been published to PyPI here (https://pypi.python.org/pypi/pulsar-galaxy-lib) and added to StarForge here (https://github.com/galaxyproject/starforge/pull/79) These are now available on wheels.galaxyproject.org. In addition to removing the source dirctories - I have removed doc and CI references to these directories. Commit: 07eb322e8c06e91095fe418c0d71bf725b682db5 https://github.com/galaxyproject/galaxy/commit/07eb322e8c06e91095fe418c0d71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix Pulsar effective working directory for #1688. Commit: 991d7282c7b045edc57710f2acddde9f83816e89 https://github.com/galaxyproject/galaxy/commit/991d7282c7b045edc57710f2acdd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M .ci/flake8_wrapper.sh M .ci/py3_sources.txt M doc/source/lib/modules.rst R doc/source/lib/pulsar.client.rst R doc/source/lib/pulsar.client.staging.rst R doc/source/lib/pulsar.client.transport.rst R doc/source/lib/pulsar.rst M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py R lib/pulsar/__init__.py R lib/pulsar/client/__init__.py R lib/pulsar/client/action_mapper.py R lib/pulsar/client/amqp_exchange.py R lib/pulsar/client/amqp_exchange_factory.py R lib/pulsar/client/client.py R lib/pulsar/client/config_util.py R lib/pulsar/client/decorators.py R lib/pulsar/client/destination.py R lib/pulsar/client/interface.py R lib/pulsar/client/job_directory.py R lib/pulsar/client/manager.py R lib/pulsar/client/object_client.py R lib/pulsar/client/path_mapper.py R lib/pulsar/client/setup_handler.py R lib/pulsar/client/staging/__init__.py R lib/pulsar/client/staging/down.py R lib/pulsar/client/staging/up.py R lib/pulsar/client/transport/__init__.py R lib/pulsar/client/transport/curl.py R lib/pulsar/client/transport/poster.py R lib/pulsar/client/transport/requests.py R lib/pulsar/client/transport/ssh.py R lib/pulsar/client/transport/standard.py R lib/pulsar/client/util.py Log Message: ----------- Merge pull request #2052 from jmchilton/pulsar-deps Pulsar-As-A-Dependency Compare: https://github.com/galaxyproject/galaxy/compare/a03e64268a9e...991d7282c7b0

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[galaxyproject/usegalaxy-playbook] ea5155: Update common_roles (didn't I already do this?)
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ea5155cf8f2d043970af4324dafb7c0c5fd37c00 https://github.com/galaxyproject/usegalaxy-playbook/commit/ea5155cf8f2d0439… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M common_roles Log Message: ----------- Update common_roles (didn't I already do this?) Commit: 19e5407e35304b2cd5162dd587612e3eff923f7a https://github.com/galaxyproject/usegalaxy-playbook/commit/19e5407e35304b2c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: R galaxy.yml M galaxy_infrastructure.yml A galaxy_main.yml M galaxy_static.yml A galaxy_test.yml M production/group_vars/galaxyservers.yml M roles/usegalaxy_privileged/tasks/main.yml M roles/usegalaxy_static/tasks/main.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/common/config/reports.ini.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/supervisor/galaxy.j2 M templates/supervisor/galaxy_datamanager.j2 M templates/supervisor/galaxy_impersonate.j2 M templates/supervisor/galaxy_installer.j2 M templates/supervisor/galaxy_reports.j2 Log Message: ----------- Move Test to CVMFS Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/0f19d175ed68...…

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[galaxyproject/usegalaxy-playbook] 0f19d1: Mutable configs on Test
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0f19d175ed688ad92f64f5aaf81045891bf2c8d9 https://github.com/galaxyproject/usegalaxy-playbook/commit/0f19d175ed688ad9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs on Test

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[galaxyproject/infrastructure-playbook] 3cf641: Additional CVMFS improvements
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3cf64197a761322e9cfda55d6dbc386c712c6219 https://github.com/galaxyproject/infrastructure-playbook/commit/3cf64197a76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M galaxyenv/inventory M galaxyenv/playbook.yml M roles/cvmfs/tasks/server.yml M roles/cvmfs/vars/main.yml M taccenv/group_vars/galaxyservers.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Additional CVMFS improvements

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[galaxyproject/galaxy] 71f473: Disable install button if changeset is installed.
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71f473b16593c317d2387c647860b1442eb9ab5a https://github.com/galaxyproject/galaxy/commit/71f473b16593c317d2387c647860… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Disable install button if changeset is installed. Commit: 0651872f6473ec3efc30c924b872c2d4d8796b2c https://github.com/galaxyproject/galaxy/commit/0651872f6473ec3efc30c924b872… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Remove debug logging. Commit: a03e64268a9ef41fc738fb0027203fc9eda13b51 https://github.com/galaxyproject/galaxy/commit/a03e64268a9ef41fc738fb002720… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M templates/admin/tool_shed_repository/preview_repository.mako Log Message: ----------- Merge pull request #2061 from davebx/api_install_performance Disable install button if changeset is installed. Compare: https://github.com/galaxyproject/galaxy/compare/26569c3ec4b6...a03e64268a9e

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[galaxyproject/infrastructure-playbook] b03e49: Additional CVMFS improvements (including configura...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b03e493eac7e5f9051cd9ef04c8cd6c285233b7f https://github.com/galaxyproject/infrastructure-playbook/commit/b03e493eac7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M roles/cvmfs/handlers/main.yml M roles/cvmfs/tasks/client.yml A roles/cvmfs/tasks/localproxy.yml M roles/cvmfs/tasks/main.yml A roles/cvmfs/tasks/server.yml A roles/cvmfs/templates/squid.conf.j2 M roles/cvmfs/vars/main.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Additional CVMFS improvements (including configuration for stratum1)

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[galaxyproject/galaxy] 4b7e86: Clean up docstrings in lib/galaxy/tools/toolbox/pa...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b7e86fa4323426e954270f2eb6d83b13d6c2752 https://github.com/galaxyproject/galaxy/commit/4b7e86fa4323426e954270f2eb6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py Log Message: ----------- Clean up docstrings in lib/galaxy/tools/toolbox/parser.py. Commit: cb5e786aa906e0bfedb3a4bd85716e46c77a4e13 https://github.com/galaxyproject/galaxy/commit/cb5e786aa906e0bfedb3a4bd8571… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Allow tool confs with a tool_path to not be interpreted as shed confs. Commit: 34e3b7f1c2e3797dcb7afac49125b9f33accad8c https://github.com/galaxyproject/galaxy/commit/34e3b7f1c2e3797dcb7afac49125… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Rename shed_conf attribute to is_shed_conf. Per discussion with @nsoranzo. Commit: 26569c3ec4b64a31f4827168cb042572ede28de0 https://github.com/galaxyproject/galaxy/commit/26569c3ec4b64a31f4827168cb04… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/parser.py M test/functional/tools/samples_tool_conf.xml M test/functional/tools/upload_tool_conf.xml Log Message: ----------- Merge pull request #2066 from jmchilton/static_tool_conf Allow tool confs with a tool_path to not be interpreted as shed confs. Compare: https://github.com/galaxyproject/galaxy/compare/18596a2bb47d...26569c3ec4b6

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[galaxyproject/infrastructure-playbook] b17443: Finish splitting the CVMFS tasks into a client inc...
by GitHub 01 Apr '16

01 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b17443d5333b931871ac619a1ed69c4848017566 https://github.com/galaxyproject/infrastructure-playbook/commit/b17443d5333… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-01 (Fri, 01 Apr 2016) Changed paths: M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/main.yml M taccenv/inventory Log Message: ----------- Finish splitting the CVMFS tasks into a client include as I'd started and then forgot

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