[galaxyproject/galaxy] 3d57c2: Fix I201 errors from flake8-import-order
by GitHub
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3d57c22b6324dda9e3ab6c92a2592dd20374abc6
https://github.com/galaxyproject/galaxy/commit/3d57c22b6324dda9e3ab6c92a2...
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/actions/admin.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/repository_types/unrestricted.py
M lib/tool_shed/util/web_util.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/drmaa_external_runner.py
M test/api/test_datasets.py
M test/api/test_history_contents_provenance.py
M test/unit/test_sockets.py
M tools/data_source/fetch.py
Log Message:
-----------
Fix I201 errors from flake8-import-order
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
Commit: ad0e6a437ed8be4fdb5513574cac2c5f8570122a
https://github.com/galaxyproject/galaxy/commit/ad0e6a437ed8be4fdb5513574c...
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/actions/admin.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/util/cli/job/slurm_torque.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/quota/__init__.py
M lib/galaxy/tools/actions/data_manager.py
M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/aliaspickler.py
M lib/galaxy/util/dbkeys.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/tool_shed/controllers/groups.py
M lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
M lib/galaxy/webapps/tool_shed/util/ratings_util.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/env_file_builder.py
M lib/tool_shed/repository_types/unrestricted.py
M lib/tool_shed/util/web_util.py
M scripts/api/example_watch_folder.py
M scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_from_import_dir.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/request_type_create_from_xml.py
M scripts/api/requests_update_state.py
M scripts/api/sample_dataset_update_status.py
M scripts/api/sample_update_state.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
M scripts/build_toolbox.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/drmaa_external_runner.py
M test/api/test_datasets.py
M test/api/test_history_contents_provenance.py
M test/unit/test_sockets.py
M tools/data_source/fetch.py
Log Message:
-----------
Merge pull request #3215 from nsoranzo/flake8-import-order
Fix I201 errors from flake8-import-order
Compare: https://github.com/galaxyproject/galaxy/compare/fef5523ed443...ad0e6a437ed8
6 years
[galaxyproject/galaxy] bbc403: Add cached dependency manager
by GitHub
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bbc403b2e1411f2a54fe3c28283dbd26dddbc780
https://github.com/galaxyproject/galaxy/commit/bbc403b2e1411f2a54fe3c2828...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Add cached dependency manager
Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement
a mechanism that allows tool dependencies to be cached.
If the `use_cached_dependency_manager` option is set to True in
galaxy.ini, we build a hash of the combination of a tools' requirements,
and store the resulting environment in a directory specified by the
`tool_dependency_cache_dir` option in galaxy.ini.
Commit: 185856f6afd36d627cd722402e687188b400333b
https://github.com/galaxyproject/galaxy/commit/185856f6afd36d627cd722402e...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo)
Commit: 5606d84f22e2bb21966c65ff37fd8c47013961c9
https://github.com/galaxyproject/galaxy/commit/5606d84f22e2bb21966c65ff37...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Rework cached dependencies to be more robust
to updates or changes in depedencies, folder structure and resolver
configuration. Instead of hashing name, type and version of a
dependency, hash the json representation of the dependencies returned by
the dependency resolver, which include the path to the environment and
the depedency type. This is only applied to resolvers whose cacheable
attribute is set to True (conda-only, currently).
Commit: 66af4295cbb669389a68dcc19403798b84d0f2bc
https://github.com/galaxyproject/galaxy/commit/66af4295cbb669389a68dcc194...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Build dependency cache at install time
and only activate cached environments if they exist.
Commit: df93db40b118777cad6887386d7fc03df3acbf92
https://github.com/galaxyproject/galaxy/commit/df93db40b118777cad6887386d...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Only attempt to build cache once per install
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
Commit: 21b859e555e6e199eece79cb1d718e7b17d827a1
https://github.com/galaxyproject/galaxy/commit/21b859e555e6e199eece79cb1d...
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix NameError
Commit: db93fd32859b9b1f326877833cb843edffd48d66
https://github.com/galaxyproject/galaxy/commit/db93fd32859b9b1f326877833c...
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-23 (Wed, 23 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Merge pull request #3106 from mvdbeek/cached_dep_manager
Add cached dependency manager
Compare: https://github.com/galaxyproject/galaxy/compare/097300ea6219...db93fd32859b
6 years