Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c216f1077f4f44b459397f085c26a54c2da547b https://github.com/galaxyproject/galaxy/commit/4c216f1077f4f44b459397f085c26... Author: John Chilton jmchilton@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 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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 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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: ----------- 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/df442a06382f23bdf0401bdd632b9... - 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/27f99cdf4014dbf1d70d6cb2a98a9... Author: Dave Bouvier dave@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/c04d200dc77ecc67d85ae1a41f709... Author: John Chilton jmchilton@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/e02e97dc798dcb3c153ae46ece382... Author: John Chilton jmchilton@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