mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-29 02:26:59 +08:00
mvdbeek
55d06e0d5a
The runner was on the ``check_untyped_defs = False`` list, so mypy skipped the bodies of its unannotated methods entirely. That is how the call sites that broke interactive tools in #23203 drifted out of sync with ``InteractiveToolManager.get_entry_point_path()`` unnoticed, even though ``StructuredApp.interactivetool_manager`` is properly annotated. Verified by reverting that fix on a scratch branch: with this flag gone, mypy reports all four call sites, so the same drift cannot recur silently. Removing the flag also requires the parameter validator fixed in the previous commit, which is the only other error it surfaces.
791 lines
25 KiB
INI
791 lines
25 KiB
INI
[mypy]
|
|
enable_error_code = ignore-without-code
|
|
plugins = pydantic.mypy
|
|
show_error_codes = True
|
|
ignore_missing_imports = True
|
|
check_untyped_defs = True
|
|
exclude = (?x)(
|
|
^build/
|
|
| .*test/functional/tools/cwl_tools/
|
|
| .*tool_shed/test/test_data/repos/
|
|
)
|
|
pretty = True
|
|
no_implicit_reexport = True
|
|
no_implicit_optional = True
|
|
strict_equality = True
|
|
warn_redundant_casts = True
|
|
warn_unreachable = True
|
|
warn_unused_ignores = True
|
|
platform = linux
|
|
explicit_package_bases = True
|
|
|
|
# green list - work on growing these please!
|
|
[mypy-galaxy.jobs.job_destination]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.tool_util.toolbox.lineages.interface]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.tools.cache]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.tools.search]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.util.compression_utils]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.util.custom_logging]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.util.unittest_utils]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.util.xml_macros]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
[mypy-galaxy.managers.secured]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = True
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
|
|
# orange list - still need to enable some of the checks
|
|
[mypy-galaxy.tools.wrappers]
|
|
disallow_any_generics = True
|
|
disallow_subclassing_any = True
|
|
disallow_untyped_calls = False
|
|
disallow_untyped_decorators = True
|
|
disallow_untyped_defs = True
|
|
warn_return_any = True
|
|
warn_unreachable = False
|
|
|
|
# red list - work on reducing these please!
|
|
[mypy-galaxy.celery]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.config]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.datatypes.constructive_solid_geometry]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.datatypes.data]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.datatypes.mothur]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.datatypes.phylip]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.datatypes.qiime2]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.managers.jobs]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_shed.metadata.metadata_generator]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_util.cwl.parser]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_util.cwl.cwltool_deps]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_util.data]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_util.toolbox.base]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tool_util.verify.interactor]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tools]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.tools.parameters.basic]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.webapps.galaxy.api.library_datasets]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.webapps.galaxy.services.jobs]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.workflow.run_request]
|
|
warn_unreachable = False
|
|
[mypy-galaxy_test.driver.driver_util]
|
|
warn_unreachable = False
|
|
[mypy-tool_shed.metadata.repository_metadata_manager]
|
|
warn_unreachable = False
|
|
[mypy-galaxy.util.oset]
|
|
# lots of tricky code in here...
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.reports.controllers.*]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.deletable]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.converters.interval_to_bedstrict_converter]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.base.ssh_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.heartbeat]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.stats.aggregate_scores_in_intervals]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.sr_mapping.srma_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.sr_mapping.bfast_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.sr_assembly.velveth_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.sr_assembly.velvetg_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.solid_tools.solid_qual_stats]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.solid_tools.maq_cs_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.phenotype_association.pagetag]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.maf.maf_to_bed]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.trimmer]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.sff_extract]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.lav_to_bed]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.evolution.add_scores]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.data_source.microbial_import_code]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.converters.pileup_to_interval_index_converter]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.converters.bgzip]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.grids.repository_grid_filter_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web_stack.message]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.middleware.translogger]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.middleware.profile]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.middleware.error]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.topsort]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.submodules]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.monitors]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.util.maf_utilities]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.wrapped_json]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.stats.grouping]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.ngs_simulation.ngs_simulation]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.metag_tools.shrimp_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.random_lines_two_pass]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.brew_exts]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.item_attrs]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.base]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.dataset_collections.structure]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.annotatable]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.util.cli]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.util.maf_utilities]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.dataproviders.decorators]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.maf.maf_to_interval]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.maf.maf_stats]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.maf.interval_maf_to_merged_fasta]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.maf.interval2maf]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.yaml_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.rules_dsl]
|
|
check_untyped_defs = False
|
|
[mypy-test.functional.webhooks.phdcomics]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.path]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util]
|
|
check_untyped_defs = False
|
|
no_implicit_reexport = False
|
|
[mypy-galaxy.tools.bundled.maf.vcf_to_maf_customtrack]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.security]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.hgweb_config]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.workflow.resources]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.reports.config]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.base]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.middleware.remoteuser]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.task]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.sanitize_html]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.commands]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.tool_shed.xml_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.sanitize]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.join]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.output_checker]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.verify.test_data]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.toolbox.parser]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.toolbox.filters]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.parser.output_collection_def]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.mulled.get_tests]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.security.object_wrapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.quota]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.custom_types]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.util.gff_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.dataproviders.line]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.dataproviders.external]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.dataproviders.dataset]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.filters.gff.gff_filter_by_feature_count]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.extract.extract_genomic_dna]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.resolvers]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.mulled.mulled_update_singularity_containers]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.mulled.mulled_search]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.util.hg_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.util.cli.shell.rsh]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.display_applications.parameters]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.search.tool_search]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.search.repo_search]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.hg_util]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.repository_types.util]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.managers.repositories]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.managers.groups]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.workflow.trs_proxy]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web_stack.handlers]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.proxy]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.decorators]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.tool_shed.common_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.expressions.evaluation]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.verify]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.toolbox.watcher]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.toolbox.integrated_panel]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.resolvers.resolver_mixins]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.resolvers.modules]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.cwl.representation]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.util.tool_dependency_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.tools.data_table_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.s3_multipart_upload]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.database_utils]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.dataset_collections.matching]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.sniff]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.config.schema]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.auth.providers.ldap_ad]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.auth.util]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.model.migrate.check]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web_stack]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.legacy_framework.grids]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.helpers.grids]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.util.script]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.repositories]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.s3]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.pithos]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.irods]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.azure_blob]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.objectstore.cloud]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.tool_shed_install]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.metadata]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.admin_util]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.repository_types.registry]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.errors]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.validation]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.dataset_matcher]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.verify.script]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.util.repository_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.security]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.search]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.database_heartbeat]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.tool_shed_install.mapping]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.store]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.orm.scripts]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.taggable]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.splitters.multi]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.display_applications.application]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.metadata_util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.error_reports.plugins.base_git]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.mulled.mulled_build]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.model.dataset_collections.registry]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.metadata]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.util.cli.job.lsf]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.authnz.managers]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.repository_util]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.grids.util]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.error_reports.plugins.gitlab]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.error_reports.plugins.github]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.parser.yaml]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.parser.xml]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.views]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.container_classes]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.resolvers.conda]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.rule_helper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.isa]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.binary]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.utility_containers.utility_container_manager]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.dependencies.attribute_handlers]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.parser.cwl]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.triples]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.tabular]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.sequence]
|
|
check_untyped_defs = False
|
|
[mypy-test.manual.workflows_scaling]
|
|
check_untyped_defs = False
|
|
[mypy-test.manual.gen_history_export_test_artifacts]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.dependencies.repository.relation_builder]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.visualization.data_providers.basic]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.proteomics]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.molecules]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.interval]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.genetics]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.model]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.utility_containers]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.datatypes.registry]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.dynamic_options]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.bundled.data_source.upload]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.lint]
|
|
check_untyped_defs = False
|
|
[mypy-test.functional.tools.upload]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.util.shed_index]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.grids.repository_review_grids]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.grids.admin_grids]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.galaxy_install.dependency_display]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.parameters.meta]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.data_manager.manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.container_resolvers.mulled]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.context]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.citations]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.config.script]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.cache]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.deps.containers]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.users]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.managers.ratable]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.actions.upload]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.actions.model_operations]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.job_execution.output_collect]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.actions.library]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_util.cwl.runtime_actions]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.metadata.set_metadata]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.error_reports]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.dynamic_tool_destination]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.state_handler_factory]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.queue_worker]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.mapper]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.handler]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.workflow.scheduling_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.galaxy_install.installed_repository_manager]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.config]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.main]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.web.framework.middleware.sqldebug]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tools.recommendations]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.tool_shed.galaxy_install.install_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.pulsar]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.pbs]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.local]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.godocker]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.drmaa]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.condor]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.cli]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.chronos]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.state_handlers.resubmit]
|
|
check_untyped_defs = False
|
|
[mypy-integration.objectstore_selection_rules.rules]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.base.controller]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.jobs.runners.univa]
|
|
check_untyped_defs = False
|
|
[mypy-integration.resubmission_runners]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.controllers.upload]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.controllers.repository_review]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.api.repository_revisions]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.api.repositories]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.workflow]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.forms]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.data_manager]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.async]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.admin]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.base.webapp]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-starlette_context.*]
|
|
no_implicit_reexport = False
|
|
[mypy-tool_shed.webapp.buildapp]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.reports.buildapp]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.buildapp]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.visualization]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.user]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.page]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.history]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.dataset]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.controllers.admin_toolshed]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.users]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.tool_shed_repositories]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.provenance]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.plugins]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.library_contents]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.jobs]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.item_tags]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.history_contents]
|
|
warn_unreachable = False
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.genomes]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.datasets]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy.webapps.galaxy.api.authenticate]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.webapp.controllers.user]
|
|
check_untyped_defs = False
|
|
[mypy-test.functional.test_toolbox]
|
|
check_untyped_defs = False
|
|
[mypy-tool_shed.test.base.test_db_util]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_save_job_id_on_datasets]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_config_defaults]
|
|
check_untyped_defs = False
|
|
[mypy-test.functional.test_toolbox_pytest]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.selenium.test_histories_published]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.selenium.test_histories_list]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.api.test_history_contents]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.api.test_histories]
|
|
check_untyped_defs = False
|
|
[mypy-galaxy_test.api.test_folder_contents]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_workflow_sync]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_tool_data_delete]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_shed_tool_tests]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_scripts]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_pulsar_embedded_mq]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_local_job_cancellation]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_job_environments]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_handler_assignment_methods]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_default_permissions]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_data_manager_refgenie]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_data_manager]
|
|
check_untyped_defs = False
|
|
[mypy-integration.objectstore.test_swift_objectstore]
|
|
check_untyped_defs = False
|
|
[mypy-integration.objectstore._base]
|
|
check_untyped_defs = False
|
|
[mypy-test.functional.conftest]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_containerized_jobs]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_chained_dynamic_destinations]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_pulsar_embedded_containers]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_kubernetes_runner]
|
|
check_untyped_defs = False
|
|
[mypy-integration.objectstore.test_objectstore_datatype_upload]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_coexecution]
|
|
check_untyped_defs = False
|
|
[mypy-integration.test_interactivetools_api]
|
|
check_untyped_defs = False
|
|
[mypy-functional.*]
|
|
check_untyped_defs = False
|
|
[mypy-manual.*]
|
|
check_untyped_defs = False
|
|
# unit tests with prickly typing issues still that need to be worked through carefully
|
|
[mypy-*.tools.test_tool_dependency_description]
|
|
check_untyped_defs = False
|
|
[mypy-*.tools.test_dataset_matcher]
|
|
check_untyped_defs = False
|
|
[mypy-*.datatypes.test_vcf]
|
|
check_untyped_defs = False
|
|
[mypy-*.datatypes.test_qiime2]
|
|
check_untyped_defs = False
|
|
[mypy-*.test_galaxy_mapping]
|
|
check_untyped_defs = False
|
|
[mypy-*.workflows.workflow_support]
|
|
check_untyped_defs = False
|
|
[mypy-*.workflows.test_modules]
|
|
check_untyped_defs = False
|
|
[mypy-*.managers.test_HDAManager]
|
|
check_untyped_defs = False
|
|
[mypy-*.managers.test_DatasetManager]
|
|
check_untyped_defs = False
|
|
[mypy-*.config.test_path_resolves_to]
|
|
check_untyped_defs = False
|
|
[mypy-*.config.test_config_values]
|
|
check_untyped_defs = False
|
|
[mypy-*.datatypes.test_storm]
|
|
check_untyped_defs = False
|
|
[mypy-*.datatypes.test_bcsl]
|
|
check_untyped_defs = False
|