Metadata-Version: 2.4
Name: agentic-proteins
Version: 0.3.8
Summary: Legacy compatibility bridge for historical runtime entrypoints, imports, and migration-safe CLI continuity.
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Website, https://bijux.io/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/02-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
License-File: LICENSE
License-File: NOTICE
Keywords: compatibility,forwarding,migration,proteomics,runtime
Requires-Python: <4,>=3.11
Requires-Dist: bijux-proteomics-core<0.4.0,>=0.3.8
Requires-Dist: bijux-proteomics-runtime<0.4.0,>=0.3.8
Provides-Extra: api
Requires-Dist: bijux-proteomics-runtime[api]<0.4.0,>=0.3.8; extra == 'api'
Provides-Extra: local-esmfold
Requires-Dist: bijux-proteomics-runtime[local-esmfold]<0.4.0,>=0.3.8; extra == 'local-esmfold'
Provides-Extra: local-rosettafold
Requires-Dist: bijux-proteomics-runtime[local-rosettafold]<0.4.0,>=0.3.8; extra == 'local-rosettafold'
Provides-Extra: nl
Requires-Dist: bijux-proteomics-runtime[nl]<0.4.0,>=0.3.8; extra == 'nl'
Provides-Extra: test
Requires-Dist: httpx<1.0,>=0.28.1; extra == 'test'
Requires-Dist: pytest-asyncio<2.0,>=1.4.0; extra == 'test'
Requires-Dist: pytest-timeout<3.0,>=2.4.0; extra == 'test'
Requires-Dist: pytest<10.0,>=9.1.1; extra == 'test'
Description-Content-Type: text/markdown

# agentic-proteins

<!-- bijux-proteomics-badges:generated:start -->
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[![agentic-proteins docs](https://img.shields.io/badge/docs-agentic--proteins-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
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<!-- bijux-proteomics-badges:generated:end -->

`agentic-proteins` is a legacy compatibility bridge for runtime entrypoints and imports.

Canonical runtime ownership is `bijux-proteomics-runtime`.

This package owns one thing: legacy compatibility routing for historical CLI,
HTTP, agent, execution, provider, state, and tool entrypoints while all real
behavior stays in canonical packages.

## At a glance

- Use `agentic-proteins` only when an existing integration still depends on
  the legacy command, import root, or bridge submodule tree.
- Start new execution work from the
  [canonical runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
  and treat this package as a migration bridge, not as a second runtime owner.
- Route runtime behavior to `bijux-proteomics-runtime`, lower scientific
  behavior to the canonical `bijux-proteomics-*` packages, and keep this layer
  forwarding-only.

## Compatibility contract

- mirrors the canonical runtime root exports at `agentic_proteins`
- forwards surviving bridge families to `bijux-proteomics-runtime`
- forwards structure-report and lower scientific surfaces to canonical packages
- keeps the historical submodule tree explicit so legacy imports stay
  inspectable
- exists to preserve migration safety for existing integrations

## 0.3.8 Release Highlights

- The package now states its forwarding-only contract directly instead of
  sounding like a second runtime owner.
- Direct dependencies and optional extras are narrowed to the canonical
  `bijux-proteomics-core` and `bijux-proteomics-runtime` packages.
- Legacy CLI and import continuity remain documented, but new integrations are
  pointed at the canonical runtime package first.

## Installation

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

## Quick start

For new workflow execution, start from the canonical runtime CLI:

```bash
bijux-proteomics-runtime --help
```

Use the compatibility CLI only when an existing integration still depends on
the legacy command:

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

Prefer canonical imports for new integrations:

```python
from bijux_proteomics_runtime.api.cli import cli
```

Legacy imports continue to work via forwarding:

```python
from agentic_proteins import cli
from agentic_proteins.interfaces.cli import cli
```

## Public APIs

New integrations should prefer canonical runtime imports, but the compatibility
surface remains executable:

```python
from agentic_proteins import cli as legacy_cli
from bijux_proteomics_runtime import cli as canonical_cli

assert legacy_cli is canonical_cli
```

## Package identity

- Distribution name: `agentic-proteins`
- Import root: `agentic_proteins`
- Legacy compatibility CLI command: `agentic-proteins`
- Canonical replacement package: `bijux-proteomics-runtime`

## Package boundaries

- this package owns compatibility routing only
- the root import `agentic_proteins` mirrors canonical runtime root exports
- this package keeps the durable bridge tree under `interfaces/`, `agents/`,
  `orchestration/`, `providers/`, `state/`, and `tools/`
- historical `execution/`, `agents/execution/`, and
  `providers/experimental/` paths remain only as legacy aliases
- canonical runtime behavior belongs in `bijux-proteomics-runtime`
- canonical domain behavior belongs in the lower `bijux-proteomics-*` packages
- new features should land in canonical packages before compat forwarding expands

## What this package must not do

- introduce package-local runtime semantics
- fork canonical provider or workflow behavior
- become a second owner for scientific or execution logic

## Contract checkpoints

- legacy imports must forward without redefining canonical behavior
- compat docs must name the canonical owner for the surface they describe
- compat modules must stay forwarding-only unless migration policy explicitly says otherwise
- new integrations should start from canonical packages even while compat remains available

## Choose this package when

- you must preserve legacy imports or CLI entrypoints during migration
- the change is forwarding-only and names a canonical owner clearly
- integration continuity matters more than adding fresh behavior

## Route elsewhere when

- the change defines runtime orchestration, provider behavior, or domain
  semantics
- the helper mainly serves new integrations rather than compatibility
- the module would stop being forwarding-only

## Verification route

- check compat `tests` for forwarding and migration proof before treating a new
  legacy surface as safe
- review `docs/BOUNDARIES.md`, `docs/CONTRACTS.md`, and `docs/ARCHITECTURE.md`
  when a change claims to remain forwarding-only
- use `README.md`, `CHANGELOG.md`, and package `docs/*.md` when the change
  affects package publication, metadata, or release-readiness expectations

## Review questions

- does the change preserve legacy continuity for a surface that already has a
  clear canonical owner
- would the implementation still live entirely in canonical packages if the
  compat layer disappeared
- can the change be justified as forwarding-only without adding fresh runtime or
  domain behavior

## Escalation route

- route the change to the canonical owner when the proposal introduces any new
  runtime orchestration or domain semantics
- stop and review `docs/BOUNDARIES.md` and `docs/ARCHITECTURE.md` when the
  compat layer would need behavior beyond import forwarding or stable aliases
- escalate before release when adopting the change would require documenting
  compat-only exceptions instead of the canonical package surface

## Consumer impact signals

- expect review against the canonical owner when compat exports or forwarding
  targets change because consumers rely on stable migration continuity
- treat changes that alter forwarding behavior or canonical mapping as
  high-impact even when public import names stay stable
- expect a lower release burden when the change only tightens documentation or
  internal compat wiring without changing forwarding behavior

## Explicit non-goals

- this package does not own canonical runtime orchestration or lower-package
  domain semantics
- this package does not add fresh product behavior for new integrations
- this package does not replace repository governance or release policy owned by
  the maintainer package

## Documentation

- [Product overview](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-overview/)
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
- [Execution overview](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/execution-overview/)
- [Canonical runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
- [Compatibility package docs](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
- [Changelog](CHANGELOG.md)
# Changelog

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

## Unreleased

## 0.3.8 - 2026-07-01

### Changed

- Reframed the package around the real compatibility-bridge contract instead
  of the retired full-runtime description, with docs and metadata that point
  readers back to canonical runtime ownership.
- Narrowed direct dependencies to the only owners the bridge should forward
  into: `bijux-proteomics-runtime` and `bijux-proteomics-core`.
- Kept legacy CLI and import continuity explicit while preserving
  forwarding-only package ownership and migration-ledger visibility.
- Aligned fallback version and optional dependency floors with the `0.3.8`
  release line.

### Fixed

- Restored clean-checkout compatibility imports, lazy forwarding behavior,
  package contract checks, and isolated local-model test surfaces so the bridge
  behaves like a compatibility shim instead of a second runtime owner.

## 0.3.7 - 2026-04-21

### Changed

- Updated package README links to readable markdown hyperlink text and aligned handbook navigation references with canonical proteomics docs routes.

## 0.3.6 - 2026-04-20

### Changed

- Prepared the `v0.3.6` release line by aligning fallback versions and inter-package dependency floors across the repository.
- Synchronized release automation and governance with the `bijux-std v0.1.3` shared standards baseline.

### Fixed

- `release-pypi.yml` now uses parse-safe publication gating for token/bootstrap checks.
- Protected workflow policy checks now accept shared-manifest-driven standards updates through approved control paths.

## 0.3.5 - 2026-04-19

### Changed

- Maintainer release documentation now references the split repository release
  workflows (`release-artifacts.yml`, `release-pypi.yml`, `release-ghcr.yml`,
  `release-github.yml`) instead of legacy publish workflow names.
- README docs badges and package metadata documentation links now point to the
  numbered handbook route `02-agentic-proteins` for stable docs navigation.

## 0.3.4 - 2026-04-11

### Changed

- Release history now records the synchronized `v0.3.4` proteomics publication
  line used by the shared tag-driven release workflow.

## 0.3.3 - 2026-04-10

### Changed

- Release history now records the synchronized `v0.3.3` proteomics publication
  line used by the shared tag-driven release workflow.

## 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.
