Metadata-Version: 2.4
Name: agentic-proteins
Version: 0.3.3
Summary: Deterministic protein design runtime with replayable execution artifacts, CLI automation, and API surfaces for lab-in-the-loop workflows
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Website, https://bijux.io/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/agentic-proteins/
Project-URL: Repository, https://github.com/bijux/bijux-proteomics
Project-URL: Issues, https://github.com/bijux/bijux-proteomics/issues
Project-URL: Changelog, https://github.com/bijux/bijux-proteomics/blob/main/packages/agentic-proteins/CHANGELOG.md
Project-URL: Security, https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md
Author-email: Bijan Mousavi <bijan@bijux.io>
Maintainer-email: Bijan Mousavi <bijan@bijux.io>
License: Apache-2.0
Keywords: bioinformatics,computational-biology,protein-design,protein-structure,reproducibility,runtime
Requires-Python: <4,>=3.11
Requires-Dist: biopython>=1.83
Requires-Dist: boto3>=1.34
Requires-Dist: click>=8.1
Requires-Dist: fastapi>=0.115
Requires-Dist: loguru>=0.7
Requires-Dist: numpy<2.0,>=1.26
Requires-Dist: pydantic>=2.0.2
Requires-Dist: requests>=2.31
Requires-Dist: slowapi>=0.1
Requires-Dist: uvicorn>=0.30
Provides-Extra: api
Requires-Dist: openprotein-python>=0.8.8; extra == 'api'
Provides-Extra: local-esmfold
Requires-Dist: einops>=0.7; extra == 'local-esmfold'
Requires-Dist: tokenizers>=0.14; extra == 'local-esmfold'
Requires-Dist: torch>=2.8; extra == 'local-esmfold'
Requires-Dist: transformers>=4.53.2; extra == 'local-esmfold'
Provides-Extra: local-rosettafold
Requires-Dist: torch>=2.8; extra == 'local-rosettafold'
Provides-Extra: nl
Requires-Dist: langchain-community>=0.2; extra == 'nl'
Requires-Dist: langchain-core>=0.2; extra == 'nl'
Requires-Dist: langchain-huggingface>=0.3.1; extra == 'nl'
Description-Content-Type: text/markdown

# agentic-proteins

[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-3776AB?logo=python&logoColor=white)](https://pypi.org/project/agentic-proteins/)
[![Typing: typed](https://img.shields.io/badge/typing-typed%20(PEP%20561)-0A7BBB)](https://pypi.org/project/agentic-proteins/)
[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-0F766E)](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
[![CI Status](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml/badge.svg)](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml)
[![GitHub Repository](https://img.shields.io/badge/github-bijux%2Fbijux--proteomics-181717?logo=github)](https://github.com/bijux/bijux-proteomics)

## Package Family

[![agentic-proteins](https://img.shields.io/pypi/v/agentic-proteins?label=agentic--proteins&logo=pypi)](https://pypi.org/project/agentic-proteins/)
[![bijux-proteomics-foundation](https://img.shields.io/pypi/v/bijux-proteomics-foundation?label=foundation&logo=pypi)](https://pypi.org/project/bijux-proteomics-foundation/)
[![bijux-proteomics-core](https://img.shields.io/pypi/v/bijux-proteomics-core?label=core&logo=pypi)](https://pypi.org/project/bijux-proteomics-core/)
[![bijux-proteomics-intelligence](https://img.shields.io/pypi/v/bijux-proteomics-intelligence?label=intelligence&logo=pypi)](https://pypi.org/project/bijux-proteomics-intelligence/)
[![bijux-proteomics-knowledge](https://img.shields.io/pypi/v/bijux-proteomics-knowledge?label=knowledge&logo=pypi)](https://pypi.org/project/bijux-proteomics-knowledge/)
[![bijux-proteomics-lab](https://img.shields.io/pypi/v/bijux-proteomics-lab?label=lab&logo=pypi)](https://pypi.org/project/bijux-proteomics-lab/)

[![Agentic docs](https://img.shields.io/badge/docs-agentic--proteins-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/agentic-proteins/)
[![Foundation docs](https://img.shields.io/badge/docs-foundation-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/bijux-proteomics-foundation/)
[![Core docs](https://img.shields.io/badge/docs-core-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/bijux-proteomics-core/)
[![Intelligence docs](https://img.shields.io/badge/docs-intelligence-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/bijux-proteomics-intelligence/)
[![Knowledge docs](https://img.shields.io/badge/docs-knowledge-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/bijux-proteomics-knowledge/)
[![Lab docs](https://img.shields.io/badge/docs-lab-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/bijux-proteomics-lab/)

`agentic-proteins` provides the deterministic execution engine for protein
design workflows, including replayable runtime artifacts, policy-safe runtime
state transitions, CLI automation, and API boundaries.

Use this package when you need production execution behavior, traceable
artifacts for auditability, or runtime integration points for agentic and
lab-in-the-loop protein design systems.

## Why teams pick this package

- reproducible execution with deterministic run state and replay-oriented controls
- inspectable artifacts for scientific review, incident analysis, and compliance
- integration-ready boundaries for CLI usage, API orchestration, and provider wiring
- clear runtime contracts that keep orchestration behavior stable across releases

## Typical use cases

- run deterministic protein design loops in CI, batch systems, or orchestrators
- capture run artifacts as evidence for downstream review and approval workflows
- expose runtime capabilities through CLI or HTTP integration surfaces
- enforce provider capability checks before expensive or irreversible execution

## Installation

```bash
pip install agentic-proteins
```

## Quick start

```bash
agentic-proteins --help
```

Import-driven usage starts from the runtime and design loop modules:

```python
from agentic_proteins.runtime import models as runtime_models
from agentic_proteins.design_loop import orchestrator
```

## Package boundaries

This package owns runtime execution, lifecycle state, run artifacts, and runtime-facing entrypoints.

It does not own cross-package scientific governance:

- domain lifecycle and review-gate semantics live in `bijux-proteomics-core`
- ranking and scenario reasoning live in `bijux-proteomics-intelligence`
- evidence trust and contradiction resolution live in `bijux-proteomics-knowledge`
- lab scheduling and rerun planning live in `bijux-proteomics-lab`

## Source guide

- [`src/agentic_proteins/runtime`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/src/agentic_proteins/runtime) for runtime lifecycle and execution control
- [`src/agentic_proteins/design_loop`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/src/agentic_proteins/design_loop) for design-loop orchestration
- [`src/agentic_proteins/interfaces`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/src/agentic_proteins/interfaces) for CLI surfaces
- [`src/agentic_proteins/api`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/src/agentic_proteins/api) for HTTP-facing boundaries
- [`tests`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/tests) for executable behavior expectations

## Documentation

- [Package guide](https://bijux.io/bijux-proteomics/agentic-proteins/)
- [Ownership boundary](https://bijux.io/bijux-proteomics/agentic-proteins/foundation/ownership-boundary/)
- [Architecture overview](https://bijux.io/bijux-proteomics/agentic-proteins/architecture/)
- [Interface contracts](https://bijux.io/bijux-proteomics/agentic-proteins/interfaces/)
- [Release and versioning](https://bijux.io/bijux-proteomics/agentic-proteins/operations/release-and-versioning/)
# Changelog

All notable changes for `agentic-proteins` are recorded here.

## 0.3.2 - 2026-04-10

### Changed

- Release history now records the synchronized `v0.3.2` proteomics publication
  line used by the shared tag-driven release workflow.

## 0.3.1 - 2026-04-06

### Added

- Package family PyPI and docs badges were added to README and maintainer
  package notes for cross-package discoverability.

### Changed

- README content was rewritten with clearer package value proposition, usage
  scenarios, installation, quick-start guidance, and boundary definitions.
- Package description text was enhanced for stronger PyPI search relevance and
  package discovery.

## 0.3.0 - 2026-04-06

### Added

- Package-local release manifest and maintainer-facing package docs:
  `README.md`, `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`,
  `docs/CONTRACTS.md`, and `docs/maintainer/pypi.md`.
- Package-local changelog publishing path wired in package and root metadata.

### Changed

- Package URLs now consistently reference `bijux.io/bijux-proteomics` and
  `github.com/bijux/bijux-proteomics`.

### Fixed

- Test path resolution now uses explicit monorepo-root detection so e2e,
  regression, and governance tests stay stable with nested package manifests.

## 0.2.3 - 2026-01-16

### Added

- Expanded provider test coverage for ColabFold, OpenProtein, and local
  ESMFold utilities.
- Runtime capability validation tests and candidate filter unit coverage.
- Stability marking test for module annotations.

### Changed

- Hardened local ESMFold utility tests to exercise error and success branches.

### Fixed

- Reliability checks and helper tests to keep coverage and gating stable.

## 0.2.2 - 2026-01-16

### Added

- Release alignment for docs, gates, and CI structure.

### Changed

- Consistent documentation build and validation wiring.

### Fixed

- Minor release hygiene issues discovered in CI.

## 0.2.1 - 2026-01-16

### Added

- Expanded unit and integration coverage with new invariants, API, and docs
  gates.
- Additional tests for provider isolation, reproducibility, and abuse-case
  blocking.
- Fancy PyPI readme fragments for README + changelog publishing.

### Changed

- Refactored `tests/unit` into a structured layout for clearer ownership.

### Fixed

- Coverage floors and CI gates stabilized around new test layout.

## 0.2.0 - 2026-01-16

### Added

- Architecture invariants, threat model skeleton, and design debt ledger.
- Reproducible runs via `agentic-proteins reproduce <run_id>` with hash
  checks.
- Determinism tests, artifact immutability tests, and invariant regression
  coverage.
- Provider isolation checks and chaos failure test for mid-run provider loss.
- Benchmark regression gate and per-module coverage floors in CI.
- Documentation system contracts, lint gates, and CLI surface audit coverage.
- API error taxonomy enforcement, correlation ID logging test, and OpenAPI
  drift guard.
- Dependency allowlist enforcement for SBOM changes.

## 0.1.0 - 2026-01-14

### Added

- Deterministic, artifact-first execution engine with explicit run directories
  and state snapshots.
- Agent-based architecture covering planning, analysis, execution,
  verification, and reporting.
- End-to-end design loop with failure handling, stagnation detection, and
  human-in-the-loop gating.
- CLI for running, resuming, inspecting, comparing, and exporting protein
  design runs.
- Local and remote provider abstractions with explicit capability and
  requirement checks.
- Structured reporting system with machine-readable artifacts and
  human-readable summaries.
- Integrated evaluation pipeline supporting structure-based metrics and
  ground-truth comparison.
- Reproducibility controls, observability hooks, and execution telemetry.
- Example datasets and reference runs for local experimentation and validation.
- Comprehensive test suite covering unit, integration, regression, and
  execution boundaries.
