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 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:
-----------
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
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
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)
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