dnaerys 0.1.0__tar.gz

dnaerys-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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dnaerys-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: dnaerys
+Version: 0.1.0
+Summary: Python client library for the Dnaerys genome variant store
+Author-email: Dnaerys <info@dnaerys.org>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/dnaerys/dnaerys-python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: grpcio>=1.78.0
+Requires-Dist: protobuf>=6.33.5
+Provides-Extra: pandas
+Requires-Dist: pandas>=2.0; extra == "pandas"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: grpcio-tools>=1.78.0; extra == "dev"
+Requires-Dist: build>=1.0; extra == "dev"
+Requires-Dist: twine>=5.0; extra == "dev"
+Dynamic: license-file
+
+[![PyPI version](https://img.shields.io/pypi/v/dnaerys)](https://pypi.org/project/dnaerys/) [![Python versions](https://img.shields.io/pypi/pyversions/dnaerys)](https://pypi.org/project/dnaerys/) [![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE) [![Documentation](https://readthedocs.org/projects/dnaerys/badge/)](https://dnaerys-python.readthedocs.io)
+
+# Dnaerys Python Client
+
+Python client library for [Dnaerys](https://dnaerys.org/), a high-performance
+distributed genome variant database. Dnaerys stores indexed variant and sample
+data for large cohorts and serves queries with millisecond latency, including
+VEP annotations, allele frequencies, and pathogenicity predictions. This library
+wraps the gRPC API into Pythonic methods with streaming iteration, pagination,
+and frozen dataclass results. It is designed for bioinformaticians and data
+scientists working with cohort-scale genomic data.
+
+**Full documentation:** [dnaerys-python.readthedocs.io](https://dnaerys-python.readthedocs.io)
+
+## Requirements
+
+Python 3.12 or later.
+
+## Installation
+
+```bash
+pip install dnaerys
+pip install dnaerys[pandas]   # for to_dataframe() support
+```
+
+## Quick Start
+
+```python
+from dnaerys import (
+    DnaerysClient, Region, AnnotationFilter, Consequence, Impact,
+)
+
+tp53 = Region("chr17", 7661779, 7687546)
+
+with DnaerysClient("db.dnaerys.org:443") as client:
+    ann = AnnotationFilter(
+        impact=[Impact.HIGH, Impact.MODERATE],
+        consequence=[Consequence.MISSENSE_VARIANT],
+        clin_significance=["PATHOGENIC", "LIKELY_PATHOGENIC"],
+    )
+
+    stream = client.select_variants(
+        region=tp53,
+        annotations=ann,
+        limit=10,
+    )
+
+    for variant in stream:
+        print(variant)
+
+    # Check response metadata
+    print(f"Elapsed: {stream.metadata.elapsed_ms}ms")
+```
+
+## Features
+
+- **Streaming iteration** — variant results arrive as lazy iterators with constant memory usage.
+- **Pagination** — `paginate_*` methods serve fixed-size pages with transparent buffer refills.
+- **Annotation filtering** — filter by VEP annotations, AF, CADD, AlphaMissense, PolyPhen, SIFT, ClinVar significance, and more.
+- **Inheritance queries** — detect de novo, heterozygous dominant, and homozygous recessive variants across trios.
+- **Kinship analysis** — KING-based kinship estimation for cohorts, duos, trios, and external samples.
+- **Frozen dataclasses** — all result types are immutable, slotted, and hashable; safe to cache, copy, and use as dict keys.
+- **Clean exception hierarchy** — gRPC status codes map to specific exception classes with `is_retryable` flags.
+- **pandas integration** — call `to_dataframe()` on any variant stream to get a DataFrame.
+
+## Documentation
+
+Full documentation including API reference, pagination guide, annotation filter
+reference, and connection options is available at
+[dnaerys-python.readthedocs.io](https://dnaerys-python.readthedocs.io). The API reference
+covers all 27 public methods on `DnaerysClient`.
+
+## License
+
+Apache License 2.0 — see [LICENSE](LICENSE) for details.
+
+## Contributing
+
+Contributions are welcome. Please open an issue to discuss proposed changes
+before submitting a pull request. Bug reports and feature requests can be
+filed at [github.com/dnaerys/dnaerys-python/issues](https://github.com/dnaerys/dnaerys-python/issues).

dnaerys-0.1.0/README.md

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+[![PyPI version](https://img.shields.io/pypi/v/dnaerys)](https://pypi.org/project/dnaerys/) [![Python versions](https://img.shields.io/pypi/pyversions/dnaerys)](https://pypi.org/project/dnaerys/) [![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE) [![Documentation](https://readthedocs.org/projects/dnaerys/badge/)](https://dnaerys-python.readthedocs.io)
+
+# Dnaerys Python Client
+
+Python client library for [Dnaerys](https://dnaerys.org/), a high-performance
+distributed genome variant database. Dnaerys stores indexed variant and sample
+data for large cohorts and serves queries with millisecond latency, including
+VEP annotations, allele frequencies, and pathogenicity predictions. This library
+wraps the gRPC API into Pythonic methods with streaming iteration, pagination,
+and frozen dataclass results. It is designed for bioinformaticians and data
+scientists working with cohort-scale genomic data.
+
+**Full documentation:** [dnaerys-python.readthedocs.io](https://dnaerys-python.readthedocs.io)
+
+## Requirements
+
+Python 3.12 or later.
+
+## Installation
+
+```bash
+pip install dnaerys
+pip install dnaerys[pandas]   # for to_dataframe() support
+```
+
+## Quick Start
+
+```python
+from dnaerys import (
+    DnaerysClient, Region, AnnotationFilter, Consequence, Impact,
+)
+
+tp53 = Region("chr17", 7661779, 7687546)
+
+with DnaerysClient("db.dnaerys.org:443") as client:
+    ann = AnnotationFilter(
+        impact=[Impact.HIGH, Impact.MODERATE],
+        consequence=[Consequence.MISSENSE_VARIANT],
+        clin_significance=["PATHOGENIC", "LIKELY_PATHOGENIC"],
+    )
+
+    stream = client.select_variants(
+        region=tp53,
+        annotations=ann,
+        limit=10,
+    )
+
+    for variant in stream:
+        print(variant)
+
+    # Check response metadata
+    print(f"Elapsed: {stream.metadata.elapsed_ms}ms")
+```
+
+## Features
+
+- **Streaming iteration** — variant results arrive as lazy iterators with constant memory usage.
+- **Pagination** — `paginate_*` methods serve fixed-size pages with transparent buffer refills.
+- **Annotation filtering** — filter by VEP annotations, AF, CADD, AlphaMissense, PolyPhen, SIFT, ClinVar significance, and more.
+- **Inheritance queries** — detect de novo, heterozygous dominant, and homozygous recessive variants across trios.
+- **Kinship analysis** — KING-based kinship estimation for cohorts, duos, trios, and external samples.
+- **Frozen dataclasses** — all result types are immutable, slotted, and hashable; safe to cache, copy, and use as dict keys.
+- **Clean exception hierarchy** — gRPC status codes map to specific exception classes with `is_retryable` flags.
+- **pandas integration** — call `to_dataframe()` on any variant stream to get a DataFrame.
+
+## Documentation
+
+Full documentation including API reference, pagination guide, annotation filter
+reference, and connection options is available at
+[dnaerys-python.readthedocs.io](https://dnaerys-python.readthedocs.io). The API reference
+covers all 27 public methods on `DnaerysClient`.
+
+## License
+
+Apache License 2.0 — see [LICENSE](LICENSE) for details.
+
+## Contributing
+
+Contributions are welcome. Please open an issue to discuss proposed changes
+before submitting a pull request. Bug reports and feature requests can be
+filed at [github.com/dnaerys/dnaerys-python/issues](https://github.com/dnaerys/dnaerys-python/issues).

dnaerys-0.1.0/pyproject.toml

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+[project]
+name = "dnaerys"
+version = "0.1.0"
+description = "Python client library for the Dnaerys genome variant store"
+authors = [{name = "Dnaerys", email = "info@dnaerys.org"}]
+readme = "README.md"
+license = "Apache-2.0"
+requires-python = ">=3.12"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "grpcio>=1.78.0",
+    "protobuf>=6.33.5",
+]
+
+[project.urls]
+Homepage = "https://github.com/dnaerys/dnaerys-python"
+
+[project.optional-dependencies]
+pandas = ["pandas>=2.0"]
+dev = [
+    "pytest>=8.0",
+    "grpcio-tools>=1.78.0",
+    "build>=1.0",
+    "twine>=5.0",
+]
+
+[build-system]
+requires = ["setuptools>=68.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = [
+    "e2e: end-to-end tests against a real Dnaerys cluster (deselect with '-m \"not e2e\"')",
+]

dnaerys-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

dnaerys-0.1.0/src/dnaerys/__init__.py

@@ -0,0 +1,137 @@
+"""Dnaerys Python client library for the Dnaerys genomic data service.
+
+This library provides a Pythonic interface to the Dnaerys gRPC service,
+which offers high-performance variant and sample queries over indexed
+genomic datasets.
+
+Proto version: R1.17.8
+"""
+
+from dnaerys._enums import (
+    AlphaMissense,
+    BioType,
+    Chromosome,
+    ClinSignificance,
+    Consequence,
+    FeatureType,
+    Impact,
+    KinshipDegree,
+    PolyPhen,
+    RefAssembly,
+    SIFT,
+    VariantType,
+    resolve_assembly,
+    resolve_chromosome,
+    resolve_enum,
+)
+from dnaerys._exceptions import (
+    DnaerysAuthenticationError,
+    DnaerysConnectionError,
+    DnaerysError,
+    DnaerysIncompleteResultWarning,
+    DnaerysInvalidRequestError,
+    DnaerysNotFoundError,
+    DnaerysResourceExhausted,
+    DnaerysServerError,
+)
+from dnaerys._client import DnaerysClient
+from dnaerys._pagination import Page, PaginatedQuery
+from dnaerys._stream import (
+    VariantStream,
+    VariantWithStatsStream,
+)
+from dnaerys._types import (
+    AnnotationFilter,
+    Bracket,
+    ClusterNodesResult,
+    Cohort,
+    CountResult,
+    DatasetInfo,
+    FstatXResult,
+    HealthResult,
+    KinshipResult,
+    PrsInfo,
+    PrsResult,
+    Region,
+    Relatedness,
+    ResponseMetadata,
+    SampleKinshipResult,
+    SampleRelatedness,
+    SampleScore,
+    SamplesResult,
+    SampleStat,
+    SexMismatchResult,
+    TopChi2Result,
+    TopHweResult,
+    Variant,
+    VariantWithStats,
+)
+
+PROTO_VERSION: str = "R1.17.8"
+"""Protocol buffer schema version that this library targets."""
+
+__all__ = [
+    # Proto version
+    "PROTO_VERSION",
+    # Client
+    "DnaerysClient",
+    # Enums
+    "Chromosome",
+    "RefAssembly",
+    "VariantType",
+    "FeatureType",
+    "BioType",
+    "Consequence",
+    "Impact",
+    "SIFT",
+    "PolyPhen",
+    "ClinSignificance",
+    "AlphaMissense",
+    "KinshipDegree",
+    # Enum resolution
+    "resolve_chromosome",
+    "resolve_enum",
+    "resolve_assembly",
+    # Input types
+    "Region",
+    "Bracket",
+    "AnnotationFilter",
+    # Core result types
+    "Variant",
+    "VariantWithStats",
+    # Stream wrappers
+    "VariantStream",
+    "VariantWithStatsStream",
+    # Pagination
+    "Page",
+    "PaginatedQuery",
+    # Response wrappers
+    "ResponseMetadata",
+    "CountResult",
+    "SamplesResult",
+    "HealthResult",
+    "ClusterNodesResult",
+    "DatasetInfo",
+    "Cohort",
+    "PrsInfo",
+    "PrsResult",
+    "SampleScore",
+    "SexMismatchResult",
+    "SampleStat",
+    "FstatXResult",
+    "KinshipResult",
+    "Relatedness",
+    "SampleKinshipResult",
+    "SampleRelatedness",
+    "TopHweResult",
+    "TopChi2Result",
+    # Exceptions
+    "DnaerysError",
+    "DnaerysConnectionError",
+    "DnaerysAuthenticationError",
+    "DnaerysNotFoundError",
+    "DnaerysInvalidRequestError",
+    "DnaerysServerError",
+    "DnaerysResourceExhausted",
+    "DnaerysIncompleteResultWarning",
+]

dnaerys-0.1.0/src/dnaerys/_channel.py

@@ -0,0 +1,54 @@
+"""Channel creation for gRPC connections to the Dnaerys service."""
+
+from __future__ import annotations
+
+from typing import Any
+
+import grpc
+
+
+def create_channel(
+    target: str,
+    *,
+    tls: bool,
+    credentials: grpc.ChannelCredentials | None,
+    options: dict[str, Any] | None,
+) -> grpc.Channel:
+    """Create a gRPC channel to the Dnaerys service.
+
+    Parameters
+    ----------
+    target : str
+        Server address in ``host:port`` format.
+    tls : bool
+        If ``True``, create a secure channel. If ``False``, insecure.
+    credentials : grpc.ChannelCredentials | None
+        Custom TLS credentials. If ``None`` and *tls* is ``True``,
+        default SSL credentials are used.
+    options : dict[str, Any] | None
+        gRPC channel options as ``{key: value}`` pairs. Converted to
+        a list of ``(key, value)`` tuples for the gRPC channel constructor.
+
+    Returns
+    -------
+    grpc.Channel
+        The created gRPC channel.
+
+    Raises
+    ------
+    ValueError
+        If *credentials* is provided with ``tls=False`` (insecure channels
+        cannot use TLS credentials).
+    """
+    channel_options = list(options.items()) if options else None
+
+    if tls:
+        creds = credentials if credentials is not None else grpc.ssl_channel_credentials()
+        return grpc.secure_channel(target, creds, options=channel_options)
+    else:
+        if credentials is not None:
+            raise ValueError(
+                "credentials cannot be provided when tls=False; "
+                "use tls=True for secure channels"
+            )
+        return grpc.insecure_channel(target, options=channel_options)