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Rename public GitHub site slug
Flip canonical repo URL from BioSymphony/biosymphony-ferm-doe to BioSymphony/bioprocess-doe across README badge and clone, pyproject project URLs, CITATION, schema $id fields, tool registry, agent harness clone, and RO-Crate retrofit IDs. Python dist name, import name, CLI entry point, and skill folder are unchanged.
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‎CITATION.cff‎

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- ai-agents
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- agentic-ai
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license: MIT
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repository-code: "https://github.com/BioSymphony/biosymphony-ferm-doe"
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repository-code: "https://github.com/BioSymphony/bioprocess-doe"

‎README.md‎

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![BioSymphony Ferm DoE banner](assets/images/biosymphony-ferm-doe-banner.png)
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[![CI](https://github.com/BioSymphony/biosymphony-ferm-doe/actions/workflows/ci.yml/badge.svg)](https://github.com/BioSymphony/biosymphony-ferm-doe/actions/workflows/ci.yml)
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[![CI](https://github.com/BioSymphony/bioprocess-doe/actions/workflows/ci.yml/badge.svg)](https://github.com/BioSymphony/bioprocess-doe/actions/workflows/ci.yml)
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
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[![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/downloads/)
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[![Status: pre-alpha](https://img.shields.io/badge/status-pre--alpha-orange.svg)](#status)
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## Install
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```bash
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git clone https://github.com/BioSymphony/biosymphony-ferm-doe.git
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cd biosymphony-ferm-doe
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git clone https://github.com/BioSymphony/bioprocess-doe.git
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cd bioprocess-doe
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python3 -m venv .venv && source .venv/bin/activate
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python -m pip install -e .
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```

‎docs/AGENT_HARNESSES.md‎

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```bash
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# 1. fresh checkout
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git clone https://github.com/BioSymphony/biosymphony-ferm-doe.git
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cd biosymphony-ferm-doe
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git clone https://github.com/BioSymphony/bioprocess-doe.git
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cd bioprocess-doe
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# 2. validate your harness can call the CLI and parse the output
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PYTHONPATH=src python3 -m biosymphony_ferm_doe.cli validate examples/demo-warnings-walkthrough-public --summary

‎docs/schemas/smoke-artifact-contract.json‎

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://raw.githubusercontent.com/BioSymphony/biosymphony-ferm-doe/main/docs/schemas/smoke-artifact-contract.json",
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"$id": "https://raw.githubusercontent.com/BioSymphony/bioprocess-doe/main/docs/schemas/smoke-artifact-contract.json",
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"title": "Backend smoke-test artifact contract",
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"description": "Required artifacts every backend smoke run must produce so it can be compared against the adaptive-backend evaluation surface (see docs/BIOMANUFACTURING_ADAPTIVE_BACKENDS.md and docs/adaptive-backend-evaluation.json). A backend earns promotion only when every artifact in `required` is present and well-formed.",
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"contract_version": "1.0.0",

‎docs/tool-registry.json‎

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"pyproject_extra": "",
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"license": "MIT",
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"links": {
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"source": "https://github.com/BioSymphony/biosymphony-ferm-doe",
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"source": "https://github.com/BioSymphony/bioprocess-doe",
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"mcp_server": "https://pubmed.ncbi.nlm.nih.gov/"
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},
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"docs_in_repo": [

‎pyproject.toml‎

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]
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[project.urls]
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Homepage = "https://github.com/BioSymphony/biosymphony-ferm-doe"
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Repository = "https://github.com/BioSymphony/biosymphony-ferm-doe"
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Issues = "https://github.com/BioSymphony/biosymphony-ferm-doe/issues"
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Documentation = "https://github.com/BioSymphony/biosymphony-ferm-doe#documentation"
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Changelog = "https://github.com/BioSymphony/biosymphony-ferm-doe/blob/main/CHANGELOG.md"
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Schema = "https://github.com/BioSymphony/biosymphony-ferm-doe/blob/main/schemas/campaign_manifest.schema.json"
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Homepage = "https://github.com/BioSymphony/bioprocess-doe"
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Repository = "https://github.com/BioSymphony/bioprocess-doe"
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Issues = "https://github.com/BioSymphony/bioprocess-doe/issues"
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Documentation = "https://github.com/BioSymphony/bioprocess-doe#documentation"
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Changelog = "https://github.com/BioSymphony/bioprocess-doe/blob/main/CHANGELOG.md"
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Schema = "https://github.com/BioSymphony/bioprocess-doe/blob/main/schemas/campaign_manifest.schema.json"
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[project.scripts]
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ferm-doe = "biosymphony_ferm_doe.cli:main"

‎schemas/campaign_manifest.schema.json‎

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://raw.githubusercontent.com/BioSymphony/biosymphony-ferm-doe/main/schemas/campaign_manifest.schema.json",
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"$id": "https://raw.githubusercontent.com/BioSymphony/bioprocess-doe/main/schemas/campaign_manifest.schema.json",
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"title": "BioSymphony Ferm DoE Campaign Manifest",
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"description": "Flexible manifest for fermentation and upstream bioprocess pre-experiment DoE planning. Optional slots are intentional: long-running agents fill them as the campaign matures. Validators on this manifest emit guidance, not rejection, except when the manifest is structurally incoherent.",
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"type": "object",

‎schemas/task_request.schema.json‎

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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"$id": "https://raw.githubusercontent.com/BioSymphony/biosymphony-ferm-doe/main/schemas/task_request.schema.json",
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"$id": "https://raw.githubusercontent.com/BioSymphony/bioprocess-doe/main/schemas/task_request.schema.json",
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"title": "BioSymphony Ferm DoE Task Request",
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"description": "Public-safe dispatch contract for one bounded Ferm DoE planning task. This schema intentionally avoids private tracker ids, provider mutation fields, private paths, credentials, and private artifacts.",
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"type": "object",

‎skills/biosymphony-ferm-doe/scripts/rocrate_retrofit.py‎

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# SoftwareApplication entities
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biosymphony_app = {
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"@id": "https://github.com/BioSymphony/biosymphony-ferm-doe",
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"@id": "https://github.com/BioSymphony/bioprocess-doe",
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"@type": "SoftwareApplication",
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"name": "biosymphony-ferm-doe",
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"description": (
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"BioSymphony fermentation DoE engine: constraint-aware experimental "
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"design, BoFire adapter, dossier compiler, and provenance toolchain."
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),
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"softwareVersion": "0.1.0",
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"url": "https://github.com/BioSymphony/biosymphony-ferm-doe",
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"url": "https://github.com/BioSymphony/bioprocess-doe",
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"programmingLanguage": {"@id": "https://www.python.org/"},
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}
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"endTime": now,
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"actionStatus": {"@id": "http://schema.org/CompletedActionStatus"},
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"instrument": [
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{"@id": "https://github.com/BioSymphony/biosymphony-ferm-doe"},
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{"@id": "https://github.com/BioSymphony/bioprocess-doe"},
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{"@id": "https://github.com/experimental-design/bofire"},
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],
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"object": [
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"endTime": now,
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"actionStatus": {"@id": "http://schema.org/CompletedActionStatus"},
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"instrument": [
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{"@id": "https://github.com/BioSymphony/biosymphony-ferm-doe"},
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{"@id": "https://github.com/BioSymphony/bioprocess-doe"},
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{"@id": "https://github.com/experimental-design/bofire"},
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],
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"object": [
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"endTime": now,
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"actionStatus": {"@id": "http://schema.org/CompletedActionStatus"},
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"instrument": [
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{"@id": "https://github.com/BioSymphony/biosymphony-ferm-doe"},
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{"@id": "https://github.com/BioSymphony/bioprocess-doe"},
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{"@id": "https://github.com/experimental-design/bofire"},
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],
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"object": [
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"startTime": now,
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"endTime": now,
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"actionStatus": {"@id": "http://schema.org/CompletedActionStatus"},
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"instrument": [{"@id": "https://github.com/BioSymphony/biosymphony-ferm-doe"}],
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"instrument": [{"@id": "https://github.com/BioSymphony/bioprocess-doe"}],
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"object": [
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{"@id": "expected/bofire_strategy_report.json"},
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{"@id": "expected/bofire_phase2_report.json"},

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