[wheel]
universal = 1

[flake8]
# These are exceptions allowed by Galaxy style guidelines:
# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
# E128 continuation line under-indented for visual indent
# E402 module level import not at top of file # TODO, we would like to improve this.
# E501 is line length
# W503 is line breaks before binary operators, which has been reversed in PEP 8.
# D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
ignore = B008,E128,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
exclude = lib/galaxy/util/jstree.py
# For flake8-import-order
# https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
import-order-style = smarkets
application-import-names = galaxy,galaxy_test,tool_shed

[mypy]
show_error_codes = True
ignore_missing_imports = True
check_untyped_defs = True
exclude = lib/galaxy/tools/bundled|test/functional
pretty = True

[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.meme.fimo_wrapper]
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.security]
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.util.bool_expressions]
# following bug fixed with https://github.com/python/mypy/pull/10548 will require a mypy rev I think
check_untyped_defs = False
[mypy-galaxy.util.custom_logging]
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.verify.asserts.archive]
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.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column]
check_untyped_defs = False
[mypy-galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column]
check_untyped_defs = False
[mypy-galaxy.model.migrate.versions.0062_user_openid_table]
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.containers.docker_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
[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.webapp.framework.middleware.remoteuser]
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.dbkeys]
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.tools.bundled.data_source.hbvar_filter]
check_untyped_defs = False
[mypy-galaxy.tool_util.provided_metadata]
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.openid.providers]
check_untyped_defs = False
[mypy-galaxy.model.custom_types]
check_untyped_defs = False
[mypy-galaxy.job_metrics.collectl.processes]
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-test.functional.webhooks.tour_generator]
check_untyped_defs = False
[mypy-galaxy.util.compression_utils]
disallow_any_generics = True
disallow_subclassing_any = True
disallow_untyped_calls = False
disallow_untyped_defs = True
disallow_incomplete_defs = True
check_untyped_defs = True
disallow_untyped_decorators = True
no_implicit_optional = True
warn_unused_ignores = True
warn_return_any = True
no_implicit_reexport = True
strict_equality = True
[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.parser.output_objects]
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_util.client.staging]
check_untyped_defs = False
[mypy-galaxy.tool_shed.util.hg_util]
check_untyped_defs = False
[mypy-galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services]
check_untyped_defs = False
[mypy-galaxy.jobs.runners.util.cli.shell.rsh]
check_untyped_defs = False
[mypy-galaxy.job_metrics]
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.properties]
check_untyped_defs = False
[mypy-galaxy.util.permutations]
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.tools.data]
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.selenium.navigates_galaxy]
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.job_metrics.instrumenters.env]
check_untyped_defs = False
[mypy-galaxy.job_metrics.instrumenters.collectl]
check_untyped_defs = False
[mypy-galaxy.job_metrics.instrumenters.cgroup]
check_untyped_defs = False
[mypy-galaxy.datatypes.sniff]
check_untyped_defs = False
[mypy-galaxy.containers]
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.util.pastescript.loadwsgi]
check_untyped_defs = False
[mypy-galaxy.tools.repositories]
check_untyped_defs = False
[mypy-galaxy.tool_util.verify.interactor]
check_untyped_defs = False
[mypy-galaxy.tool_shed.tool_shed_registry]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.migrate.check]
check_untyped_defs = False
[mypy-galaxy.selenium.context]
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.util.pastescript.serve]
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.tools.error_reports.plugins.sentry]
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]
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-galaxy.containers.docker]
check_untyped_defs = False
[mypy-tool_shed.util.metadata_util]
check_untyped_defs = False
[mypy-galaxy.tools.wrappers]
disallow_any_generics = True
disallow_subclassing_any = True
disallow_untyped_calls = False
disallow_untyped_defs = True
disallow_incomplete_defs = True
check_untyped_defs = True
disallow_untyped_decorators = True
no_implicit_optional = True
warn_unused_ignores = True
no_implicit_reexport = True
strict_equality = True
[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.tool_shed_install.migrate.check]
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.containers.docker_swarm]
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.tool_shed.galaxy_install.tools.tool_panel_manager]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler]
check_untyped_defs = False
[mypy-galaxy.model.migrate.check]
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]
check_untyped_defs = False
[mypy-galaxy.tool_util.parser.cwl]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.tools.data_manager]
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]
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]
check_untyped_defs = False
[mypy-galaxy.datatypes.genetics]
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.toolbox.base]
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.managers.base]
check_untyped_defs = False
[mypy-galaxy.config.script]
check_untyped_defs = False
[mypy-galaxy.visualization.plugins.interactive_environments]
check_untyped_defs = False
[mypy-galaxy.tools.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]
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]
check_untyped_defs = False
[mypy-galaxy.jobs]
check_untyped_defs = False
[mypy-galaxy.tool_shed.metadata.metadata_generator]
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-galaxy.app]
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.kubernetes]
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-galaxy.config.config_manage]
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.tool_shed.galaxy_install.tool_migration_manager]
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.controllers.repository]
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]
check_untyped_defs = False
[mypy-galaxy.tool_shed.galaxy_install.migrate.common]
check_untyped_defs = 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]
check_untyped_defs = False
[mypy-galaxy.webapps.galaxy.api.history_contents]
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.functional_tests]
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-tool_shed.test.base.twilltestcase]
check_untyped_defs = False
[mypy-galaxy_test.selenium.test_published_histories_grid]
check_untyped_defs = False
[mypy-galaxy_test.selenium.test_histories_list]
check_untyped_defs = False
[mypy-galaxy_test.selenium.test_custom_builds]
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_workflow_refactoring]
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-tool_shed.test.functional.test_1470_updating_installed_repositories]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1460_data_managers]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1450_installing_datatypes_sniffers]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1440_missing_env_sh_files]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1430_repair_installed_repository]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1410_update_manager]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1300_reset_all_metadata]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1190_complex_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1180_circular_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1170_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1160_tool_help_images]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1150_datatype_converters]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1100_install_updated_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1090_repository_dependency_handling]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1080_advanced_circular_dependency_installation]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1070_invalid_tool]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1050_circular_dependencies_4_levels]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_1000_install_basic_repository]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0550_metadata_updated_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0540_get_all_metadata_from_api]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0530_repository_admin_feature]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0480_tool_dependency_xml_verification]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0470_tool_dependency_repository_type]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0460_upload_to_repository]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0440_deleting_dependency_definitions]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0430_browse_utilities]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0420_citable_urls_for_repositories]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0410_repository_component_review_access_control]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0400_repository_component_reviews]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0310_hg_api_features]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0300_reset_all_metadata]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0170_complex_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0160_circular_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0150_prior_installation_required]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0140_tool_help_images]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0130_datatype_converters]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0100_complex_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0090_tool_search]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0080_advanced_circular_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0070_invalid_tool]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0050_circular_dependencies_4_levels]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0040_repository_circular_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0030_repository_dependency_revisions]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0020_basic_repository_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0010_repository_with_tool_dependencies]
check_untyped_defs = False
[mypy-tool_shed.test.functional.test_0000_basic_repository_features]
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_kubernetes_staging]
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-*.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