Metadata-Version: 2.4
Name: agentic-proteins
Version: 0.3.0
Summary: Deterministic, artifact-first protein design runtime and CLI
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Website, https://bijux.io/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/
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: >=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
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)
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`agentic-proteins` is the deterministic runtime package in the proteomics
workspace. It owns execution flow, runtime artifacts, and replay-oriented
guardrails for protein design workflows.

If you need execution behavior, runtime state transitions, or inspectable run
artifacts, start with this package.

## What this package owns

- deterministic design-loop execution and runtime lifecycle state
- run artifacts, report generation, and replay-safe execution records
- package-local CLI and API entry boundaries
- provider contracts and runtime capability checks

## What this package does not own

- protein program-stage governance and review gate domain contracts
- candidate ranking policy and scenario recommendation behavior
- evidence trust, contradiction policies, and claim-lineage semantics
- lab planning, scheduling, and rerun strategy outputs

## Source map

- [`src/agentic_proteins/runtime`](https://github.com/bijux/bijux-proteomics/tree/main/packages/agentic-proteins/src/agentic_proteins/runtime) for runtime execution control and lifecycle behavior
- [`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 package expectations

## Read this next

- [Architecture](https://github.com/bijux/bijux-proteomics/blob/main/packages/agentic-proteins/docs/ARCHITECTURE.md)
- [Boundaries](https://github.com/bijux/bijux-proteomics/blob/main/packages/agentic-proteins/docs/BOUNDARIES.md)
- [Contracts](https://github.com/bijux/bijux-proteomics/blob/main/packages/agentic-proteins/docs/CONTRACTS.md)
- [PyPI maintainer notes](https://github.com/bijux/bijux-proteomics/blob/main/packages/agentic-proteins/docs/maintainer/pypi.md)

## Primary entrypoint

- console script: `agentic-proteins`
# Changelog

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

## 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.
