mypy-boto3-omics

Type annotations for boto3 Omics 1.43.123 compatible with VSCode, PyCharm, Emacs, Sublime Text, mypy, pyright and other tools.

Generated with mypy-boto3-builder 8.12.0.

More information can be found on boto3-stubs page and in mypy-boto3-omics docs.

See how it helps you find and fix potential bugs:

• mypy-boto3-omics
  • How to install
    • Generate locally (recommended)
    • VSCode extension
    • From PyPI with pip
  • How to uninstall
  • Usage
    • VSCode
    • PyCharm
    • Emacs
    • Sublime Text
    • Other IDEs
    • mypy
    • pyright
    • Pylint compatibility
  • Explicit type annotations
    • Client annotations
    • Paginators annotations
    • Waiters annotations
    • Literals
    • Type definitions
  • How it works
  • What's new
    • Implemented features
    • Latest changes
  • Versioning
  • Thank you
  • Documentation
  • Support and contributing

How to install

Generate locally (recommended)

You can generate type annotations for boto3 package locally with mypy-boto3-builder. Use uv for build isolation.

1. Run mypy-boto3-builder in your package root directory: uvx --with 'boto3==1.43.123' mypy-boto3-builder
2. Select boto3-stubs AWS SDK.
3. Add Omics service.
4. Use provided commands to install generated packages.

VSCode extension

Add AWS Boto3 extension to your VSCode and run AWS boto3: Quick Start command.

Click Modify and select boto3 common and Omics.

From PyPI with pip

Install boto3-stubs for Omics service.

# install with boto3 type annotations
python -m pip install 'boto3-stubs[omics]'

# Lite version does not provide session.client/resource overloads
# it is more RAM-friendly, but requires explicit type annotations
python -m pip install 'boto3-stubs-lite[omics]'

# standalone installation
python -m pip install mypy-boto3-omics

How to uninstall

python -m pip uninstall -y mypy-boto3-omics

Usage

VSCode

• Install Python extension
• Install Pylance extension
• Set Pylance as your Python Language Server
• Install boto3-stubs[omics] in your environment:

python -m pip install 'boto3-stubs[omics]'

Both type checking and code completion should now work. No explicit type annotations required, write your boto3 code as usual.

PyCharm

⚠️ Due to slow PyCharm performance on Literal overloads (issue PY-40997), it is recommended to use boto3-stubs-lite until the issue is resolved.

⚠️ If you experience slow performance and high CPU usage, try to disable PyCharm type checker and use mypy or pyright instead.

⚠️ To continue using PyCharm type checker, you can try to replace boto3-stubs with boto3-stubs-lite:

pip uninstall boto3-stubs
pip install boto3-stubs-lite

Install boto3-stubs[omics] in your environment:

python -m pip install 'boto3-stubs[omics]'

Both type checking and code completion should now work.

Emacs

• Install boto3-stubs with services you use in your environment:

python -m pip install 'boto3-stubs[omics]'

• Install use-package, lsp, company and flycheck packages
• Install lsp-pyright package

(use-package lsp-pyright
  :ensure t
  :hook (python-mode . (lambda ()
                          (require 'lsp-pyright)
                          (lsp)))  ; or lsp-deferred
  :init (when (executable-find "python3")
          (setq lsp-pyright-python-executable-cmd "python3"))
  )

• Make sure emacs uses the environment where you have installed boto3-stubs

Type checking should now work. No explicit type annotations required, write your boto3 code as usual.

Sublime Text

• Install boto3-stubs[omics] with services you use in your environment:

python -m pip install 'boto3-stubs[omics]'

• Install LSP-pyright package

Type checking should now work. No explicit type annotations required, write your boto3 code as usual.

Other IDEs

Not tested, but as long as your IDE supports mypy or pyright, everything should work.

mypy

• Install mypy: python -m pip install mypy
• Install boto3-stubs[omics] in your environment:

python -m pip install 'boto3-stubs[omics]'

Type checking should now work. No explicit type annotations required, write your boto3 code as usual.

pyright

• Install pyright: npm i -g pyright
• Install boto3-stubs[omics] in your environment:

python -m pip install 'boto3-stubs[omics]'

Optionally, you can install boto3-stubs to typings directory.

Type checking should now work. No explicit type annotations required, write your boto3 code as usual.

Pylint compatibility

It is totally safe to use TYPE_CHECKING flag in order to avoid mypy-boto3-omics dependency in production. However, there is an issue in pylint that it complains about undefined variables. To fix it, set all types to object in non-TYPE_CHECKING mode.

from typing import TYPE_CHECKING

if TYPE_CHECKING:
    from mypy_boto3_ec2 import EC2Client, EC2ServiceResource
    from mypy_boto3_ec2.waiters import BundleTaskCompleteWaiter
    from mypy_boto3_ec2.paginators import DescribeVolumesPaginator
else:
    EC2Client = object
    EC2ServiceResource = object
    BundleTaskCompleteWaiter = object
    DescribeVolumesPaginator = object

...

Explicit type annotations

Client annotations

OmicsClient provides annotations for boto3.client("omics").

from boto3.session import Session

from mypy_boto3_omics import OmicsClient

client: OmicsClient = Session().client("omics")

# now client usage is checked by mypy and IDE should provide code completion

Paginators annotations

mypy_boto3_omics.paginator module contains type annotations for all paginators.

from boto3.session import Session

from mypy_boto3_omics import OmicsClient
from mypy_boto3_omics.paginator import (
    ListAnnotationImportJobsPaginator,
    ListAnnotationStoreVersionsPaginator,
    ListAnnotationStoresPaginator,
    ListBatchPaginator,
    ListConfigurationsPaginator,
    ListMultipartReadSetUploadsPaginator,
    ListReadSetActivationJobsPaginator,
    ListReadSetExportJobsPaginator,
    ListReadSetImportJobsPaginator,
    ListReadSetUploadPartsPaginator,
    ListReadSetsPaginator,
    ListReferenceImportJobsPaginator,
    ListReferenceStoresPaginator,
    ListReferencesPaginator,
    ListRunCachesPaginator,
    ListRunGroupsPaginator,
    ListRunTasksPaginator,
    ListRunsInBatchPaginator,
    ListRunsPaginator,
    ListSequenceStoresPaginator,
    ListSharesPaginator,
    ListVariantImportJobsPaginator,
    ListVariantStoresPaginator,
    ListWorkflowVersionsPaginator,
    ListWorkflowsPaginator,
)

client: OmicsClient = Session().client("omics")

# Explicit type annotations are optional here
# Types should be correctly discovered by mypy and IDEs
list_annotation_import_jobs_paginator: ListAnnotationImportJobsPaginator = client.get_paginator(
    "list_annotation_import_jobs"
)
list_annotation_store_versions_paginator: ListAnnotationStoreVersionsPaginator = (
    client.get_paginator("list_annotation_store_versions")
)
list_annotation_stores_paginator: ListAnnotationStoresPaginator = client.get_paginator(
    "list_annotation_stores"
)
list_batch_paginator: ListBatchPaginator = client.get_paginator("list_batch")
list_configurations_paginator: ListConfigurationsPaginator = client.get_paginator(
    "list_configurations"
)
list_multipart_read_set_uploads_paginator: ListMultipartReadSetUploadsPaginator = (
    client.get_paginator("list_multipart_read_set_uploads")
)
list_read_set_activation_jobs_paginator: ListReadSetActivationJobsPaginator = client.get_paginator(
    "list_read_set_activation_jobs"
)
list_read_set_export_jobs_paginator: ListReadSetExportJobsPaginator = client.get_paginator(
    "list_read_set_export_jobs"
)
list_read_set_import_jobs_paginator: ListReadSetImportJobsPaginator = client.get_paginator(
    "list_read_set_import_jobs"
)
list_read_set_upload_parts_paginator: ListReadSetUploadPartsPaginator = client.get_paginator(
    "list_read_set_upload_parts"
)
list_read_sets_paginator: ListReadSetsPaginator = client.get_paginator("list_read_sets")
list_reference_import_jobs_paginator: ListReferenceImportJobsPaginator = client.get_paginator(
    "list_reference_import_jobs"
)
list_reference_stores_paginator: ListReferenceStoresPaginator = client.get_paginator(
    "list_reference_stores"
)
list_references_paginator: ListReferencesPaginator = client.get_paginator("list_references")
list_run_caches_paginator: ListRunCachesPaginator = client.get_paginator("list_run_caches")
list_run_groups_paginator: ListRunGroupsPaginator = client.get_paginator("list_run_groups")
list_run_tasks_paginator: ListRunTasksPaginator = client.get_paginator("list_run_tasks")
list_runs_in_batch_paginator: ListRunsInBatchPaginator = client.get_paginator("list_runs_in_batch")
list_runs_paginator: ListRunsPaginator = client.get_paginator("list_runs")
list_sequence_stores_paginator: ListSequenceStoresPaginator = client.get_paginator(
    "list_sequence_stores"
)
list_shares_paginator: ListSharesPaginator = client.get_paginator("list_shares")
list_variant_import_jobs_paginator: ListVariantImportJobsPaginator = client.get_paginator(
    "list_variant_import_jobs"
)
list_variant_stores_paginator: ListVariantStoresPaginator = client.get_paginator(
    "list_variant_stores"
)
list_workflow_versions_paginator: ListWorkflowVersionsPaginator = client.get_paginator(
    "list_workflow_versions"
)
list_workflows_paginator: ListWorkflowsPaginator = client.get_paginator("list_workflows")

Waiters annotations

mypy_boto3_omics.waiter module contains type annotations for all waiters.

from boto3.session import Session

from mypy_boto3_omics import OmicsClient
from mypy_boto3_omics.waiter import (
    AnnotationImportJobCreatedWaiter,
    AnnotationStoreCreatedWaiter,
    AnnotationStoreDeletedWaiter,
    AnnotationStoreVersionCreatedWaiter,
    AnnotationStoreVersionDeletedWaiter,
    ReadSetActivationJobCompletedWaiter,
    ReadSetExportJobCompletedWaiter,
    ReadSetImportJobCompletedWaiter,
    ReferenceImportJobCompletedWaiter,
    RunCompletedWaiter,
    RunRunningWaiter,
    TaskCompletedWaiter,
    TaskRunningWaiter,
    VariantImportJobCreatedWaiter,
    VariantStoreCreatedWaiter,
    VariantStoreDeletedWaiter,
    WorkflowActiveWaiter,
    WorkflowVersionActiveWaiter,
)

client: OmicsClient = Session().client("omics")

# Explicit type annotations are optional here
# Types should be correctly discovered by mypy and IDEs
annotation_import_job_created_waiter: AnnotationImportJobCreatedWaiter = client.get_waiter(
    "annotation_import_job_created"
)
annotation_store_created_waiter: AnnotationStoreCreatedWaiter = client.get_waiter(
    "annotation_store_created"
)
annotation_store_deleted_waiter: AnnotationStoreDeletedWaiter = client.get_waiter(
    "annotation_store_deleted"
)
annotation_store_version_created_waiter: AnnotationStoreVersionCreatedWaiter = client.get_waiter(
    "annotation_store_version_created"
)
annotation_store_version_deleted_waiter: AnnotationStoreVersionDeletedWaiter = client.get_waiter(
    "annotation_store_version_deleted"
)
read_set_activation_job_completed_waiter: ReadSetActivationJobCompletedWaiter = client.get_waiter(
    "read_set_activation_job_completed"
)
read_set_export_job_completed_waiter: ReadSetExportJobCompletedWaiter = client.get_waiter(
    "read_set_export_job_completed"
)
read_set_import_job_completed_waiter: ReadSetImportJobCompletedWaiter = client.get_waiter(
    "read_set_import_job_completed"
)
reference_import_job_completed_waiter: ReferenceImportJobCompletedWaiter = client.get_waiter(
    "reference_import_job_completed"
)
run_completed_waiter: RunCompletedWaiter = client.get_waiter("run_completed")
run_running_waiter: RunRunningWaiter = client.get_waiter("run_running")
task_completed_waiter: TaskCompletedWaiter = client.get_waiter("task_completed")
task_running_waiter: TaskRunningWaiter = client.get_waiter("task_running")
variant_import_job_created_waiter: VariantImportJobCreatedWaiter = client.get_waiter(
    "variant_import_job_created"
)
variant_store_created_waiter: VariantStoreCreatedWaiter = client.get_waiter("variant_store_created")
variant_store_deleted_waiter: VariantStoreDeletedWaiter = client.get_waiter("variant_store_deleted")
workflow_active_waiter: WorkflowActiveWaiter = client.get_waiter("workflow_active")
workflow_version_active_waiter: WorkflowVersionActiveWaiter = client.get_waiter(
    "workflow_version_active"
)

Literals

mypy_boto3_omics.literals module contains literals extracted from shapes that can be used in user code for type checking.

Full list of Omics Literals can be found in docs.

from mypy_boto3_omics.literals import AcceleratorsType


def check_value(value: AcceleratorsType) -> bool: ...

Type definitions

mypy_boto3_omics.type_defs module contains structures and shapes assembled to typed dictionaries and unions for additional type checking.

Full list of Omics TypeDefs can be found in docs.

# TypedDict usage example
from mypy_boto3_omics.type_defs import AbortMultipartReadSetUploadRequestTypeDef


def get_value() -> AbortMultipartReadSetUploadRequestTypeDef:
    return {
        "sequenceStoreId": ...,
    }

How it works

Fully automated mypy-boto3-builder carefully generates type annotations for each service, patiently waiting for boto3 updates. It delivers drop-in type annotations for you and makes sure that:

• All available boto3 services are covered.
• Each public class and method of every boto3 service gets valid type annotations extracted from botocore schemas.
• Type annotations include up-to-date documentation.
• Link to documentation is provided for every method.
• Code is processed by ruff for readability.

What's new

Implemented features

• Fully type annotated boto3, botocore, aiobotocore and aioboto3 libraries
• mypy, pyright, VSCode, PyCharm, Sublime Text and Emacs compatibility
• Client, ServiceResource, Resource, Waiter Paginator type annotations for each service
• Generated TypeDefs for each service
• Generated Literals for each service
• Auto discovery of types for boto3.client and boto3.resource calls
• Auto discovery of types for session.client and session.resource calls
• Auto discovery of types for client.get_waiter and client.get_paginator calls
• Auto discovery of types for ServiceResource and Resource collections
• Auto discovery of types for aiobotocore.Session.create_client calls

Latest changes

Builder changelog can be found in Releases.

Versioning

mypy-boto3-omics version is the same as related boto3 version and follows Python Packaging version specifiers.

Thank you

• Allie Fitter for boto3-type-annotations, this package is based on top of his work
• black developers for an awesome formatting tool
• Timothy Edmund Crosley for isort and how flexible it is
• mypy developers for doing all dirty work for us
• pyright team for the new era of typed Python

Documentation

All services type annotations can be found in boto3 docs

Support and contributing

This package is auto-generated. Please reports any bugs or request new features in mypy-boto3-builder repository.