opendde-harness 0.0.1__tar.gz

opendde_harness-0.0.1/.gitignore

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+.worktrees/
+.assets
+.env
+node_modules/
+ui-tui/node_modules
+docs/bin/
+scripts/bin/
+external/
+deploy/protein_design/weights/
+# Generated architecture/diagram SVGs at repo root (not source)
+/*.svg
+
+# Engineering working notes — plan + process records, never committed
+revice_notes/
+*.pyc
+dist/
+build/
+*.egg-info/
+*.egg
+*.pyc
+*.pyo
+*.pyd
+*.pyw
+*.pyz
+*.pywz
+*.pyzz
+.venv/
+venv/
+__pycache__/
+poetry.lock
+.pytest_cache/
+.coverage
+.coverage.*
+coverage.xml
+htmlcov/
+botpy.log
+nano.*.save
+swebench_jobs/
+*.env
+!docker/versions.env
+key.env
+sty_readme.md
+CLAUDE.local.md
+logs/
+.DS_Store
+.claude/
+tmp.sh
+.work_context/
+# Runtime-discipline shadow checkpoint repo (Bug2) — never commit snapshots
+.opendde_harness/
+
+# SkillForge dense retrieval cache (auto-built per-deployment, never tracked)
+.skill_index/
+.cache/skill_index/
+.ruff_cache/

opendde_harness-0.0.1/CHANGELOG.md

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+# Changelog
+
+User-facing changes to OpenDDE Harness are documented here.
+
+## [Unreleased]
+
+No changes yet.
+
+## [0.0.1] - 2026-09-09
+
+**Introducing OpenDDE Harness - our first public preview!**
+
+We're excited to share OpenDDE Harness, an open-source tool for agentic antibody
+design. It brings LLM-guided sequence design and OpenDDE structure prediction into
+one workflow, from preparing a target to reviewing candidate sequences and structures.
+
+Describe your design task in natural language, review the plan, and follow the
+results as the agent proposes, evaluates, and refines candidates. This first release
+supports VHH, scFv, and paired VH/VL binders while preserving configured fixed residues.
+A terminal UI guides setup and design, and a tracing dashboard lets you inspect
+candidate structures, scores, and progress across iterations.
+
+Alongside this release, we're sharing a
+[technical report](https://github.com/aurekaresearch/OpenDDE-Harness/blob/v0.0.1/docs/assets/OpenDDE_harness_tech_report.pdf)
+and [design examples](https://github.com/aurekaresearch/OpenDDE-Harness/tree/v0.0.1/docs/examples)
+to introduce the approach and help you get started. Install from PyPI or source
+using the [installation guide](https://github.com/aurekaresearch/OpenDDE-Harness/blob/v0.0.1/README.md#installation),
+then follow the [onboarding guide](https://github.com/aurekaresearch/OpenDDE-Harness/blob/v0.0.1/docs/onboarding.md)
+to connect your LLM provider and compute service.
+
+This is an early preview, and you may encounter bugs. Please
+[open an issue](https://github.com/aurekaresearch/OpenDDE-Harness/issues) with your
+feedback, reproduction steps, and `ddeharness doctor --json` output when relevant.
+Thank you for trying OpenDDE Harness and helping us make it better!
+
+[Unreleased]: https://github.com/aurekaresearch/OpenDDE-Harness/compare/v0.0.1...HEAD
+[0.0.1]: https://github.com/aurekaresearch/OpenDDE-Harness/releases/tag/v0.0.1

opendde_harness-0.0.1/LICENSE

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opendde_harness-0.0.1/LICENSES/MIT-hermes-agent.txt

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+MIT License
+
+Copyright (c) 2025 Nous Research
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

opendde_harness-0.0.1/LICENSES/MIT-ink.txt

@@ -0,0 +1,10 @@
+MIT License
+
+Copyright (c) Vadym Demedes <vadimdemedes@hey.com> (https://github.com/vadimdemedes)
+Copyright (c) Sindre Sorhus <sindresorhus@gmail.com> (https://sindresorhus.com)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

opendde_harness-0.0.1/LICENSES/MIT-nanobot.txt

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+MIT License
+
+Copyright (c) 2025-present Xubin Ren and the nanobot contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

opendde_harness-0.0.1/LICENSES/README.md

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+# Third-Party License Notices
+
+This directory keeps license texts for upstream projects and libraries whose
+notices OpenDDE Harness preserves.
+
+OpenDDE Harness itself is licensed under Apache-2.0. Some imported code, references, and
+design influences originated from MIT-licensed projects; those notices remain
+here so downstream users can audit attribution without searching through the
+history.
+
+## Files
+
+- `MIT-hermes-agent.txt` - Hermes Agent license notice.
+- `MIT-ink.txt` - Ink license notice.
+- `MIT-nanobot.txt` - Nanobot license notice.

opendde_harness-0.0.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: opendde-harness
+Version: 0.0.1
+Summary: OpenDDE Harness - antibody design harness: agent runtime, protein-design plugin, and compute service
+Author: OpenDDE
+License-Expression: Apache-2.0
+License-File: LICENSE
+License-File: LICENSES/MIT-hermes-agent.txt
+License-File: LICENSES/MIT-ink.txt
+License-File: LICENSES/MIT-nanobot.txt
+Keywords: agent,antibody-design,bioinformatics,cli,protein-design
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Requires-Dist: everos[multimodal]==1.2.2
+Requires-Dist: httpx<1.0.0,>=0.28.0
+Requires-Dist: json-repair>=0.30.0
+Requires-Dist: litellm<2.0.0,>=1.82.1
+Requires-Dist: loguru<1.0.0,>=0.7.3
+Requires-Dist: mcp>=1.27.0
+Requires-Dist: numpy<3.0,>=2.0
+Requires-Dist: orjson<4.0,>=3.11.6
+Requires-Dist: pillow>=10.0.0
+Requires-Dist: portalocker>=3.2.0
+Requires-Dist: prompt-toolkit>=3.0.0
+Requires-Dist: pydantic-settings<3.0.0,>=2.14.2
+Requires-Dist: pydantic<3.0.0,>=2.12.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: questionary<3.0.0,>=2.0.0
+Requires-Dist: rich<15.0.0,>=14.0.0
+Requires-Dist: tiktoken<1.0.0,>=0.7.0
+Requires-Dist: tomli-w>=1.2.0
+Requires-Dist: typer<1.0.0,>=0.20.0
+Requires-Dist: watchfiles<2.0,>=0.21
+Provides-Extra: dev
+Requires-Dist: pytest-asyncio>=0.23.0; extra == 'dev'
+Requires-Dist: pytest<10.0,>=8.0; extra == 'dev'
+Requires-Dist: ruff>=0.6.0; extra == 'dev'
+Provides-Extra: protein-design
+Requires-Dist: biotite<2.0,>=1.2; extra == 'protein-design'
+Requires-Dist: fastapi<1.0,>=0.116; extra == 'protein-design'
+Requires-Dist: gradio-client>=0.10.0; extra == 'protein-design'
+Requires-Dist: scipy>=1.10.0; extra == 'protein-design'
+Requires-Dist: torch<2.8.0,>=2.3.0; extra == 'protein-design'
+Requires-Dist: transformers>=4.30.0; extra == 'protein-design'
+Requires-Dist: uvicorn<1.0,>=0.35; extra == 'protein-design'
+Description-Content-Type: text/markdown
+
+# OpenDDE Harness
+
+
+[![Python](https://img.shields.io/badge/python-3.12%2B-blue)](pyproject.toml)
+[![License](https://img.shields.io/badge/license-Apache--2.0-green)](LICENSE)
+![Status](https://img.shields.io/badge/status-preview-orange)
+[![PyPI](https://img.shields.io/pypi/v/opendde-harness.svg?cacheSeconds=300)](https://pypi.org/project/opendde-harness/)
+
+
+![tui](docs/assets/tui.png)
+
+Harness for agentic antibody design: prepare targets, optimize CDR sequences, predict structures with OpenDDE, and inspect results. Supports VHH, scFv and paired VH/VL binders while preserving configured fixed residues.
+
+- Guided setup and reviewed design plans in natural language.
+- Generate antibody sequences through LLM reasoning and structural verification.
+- Agentic evolutional discovery for antibody design.
+
+> [!NOTE]
+> OpenDDE Harness is an early preview, and you may encounter bugs. If something
+> goes wrong, please [open an issue](https://github.com/aurekaresearch/OpenDDE-Harness/issues)
+> with steps to reproduce it and your `ddeharness doctor --json` output.
+> Your feedback helps us fix problems and improve the tool together.
+
+
+## News
+
+- **2026-09-09: Introducing OpenDDE Harness (preview) for agentic antibody design! Read the [technical report](docs/assets/OpenDDE_harness_tech_report.pdf).**
+    - Design VHH, scFv, and paired VH/VL binders with LLM-guided sequence optimization and OpenDDE structure prediction.
+    - Get started with the [installation guide](docs/installation.md), [onboarding](docs/onboarding.md), and [design examples](docs/examples/).
+    - Inspect candidate sequences, structures, and design progress in the [tracing dashboard](docs/tracing-board.md).
+
+See the [changelog](CHANGELOG.md) for release details.
+
+## Installation
+
+Use a Linux or macOS client with Python 3.12 or newer. Native Windows is not
+currently supported. Use
+[`uv`](https://docs.astral.sh/uv/getting-started/installation/) to install the
+`opendde-harness` package and its `ddeharness` command in an isolated environment.
+Choose one of the following methods; no environment activation is needed.
+
+### Install from PyPI
+
+```bash
+uv tool install --python 3.12 opendde-harness
+```
+
+The release wheel includes the built terminal UI.
+
+To update a PyPI installation, close the TUI and run:
+
+```bash
+uv tool upgrade opendde-harness
+```
+
+### Install from source
+
+Install Git, uv, and Node.js 22 or newer with npm, then run:
+
+```bash
+git clone https://github.com/aurekaresearch/OpenDDE-Harness.git
+cd OpenDDE-Harness
+uv tool install --python 3.12 .
+```
+
+The package build compiles and includes the terminal UI automatically. To update,
+close the TUI, preserve any local edits, and run from the checkout:
+
+```bash
+git pull --ff-only
+uv tool install --python 3.12 --reinstall .
+```
+
+### After installation
+
+After either installation, verify the client:
+
+```bash
+ddeharness --version
+ddeharness --help
+ddeharness tui --check
+```
+
+If the command is not found, run `uv tool update-shell` and open a new terminal.
+Updates preserve configuration, results, and model data. Running compute
+containers keep their current code until they exit; later starts use the updated
+code. See the [installation guide](docs/installation.md) for runtime overrides,
+compute environments, and model download options.
+
+### Uninstall
+
+Close the TUI and remove the client with:
+
+```bash
+uv tool uninstall opendde-harness
+```
+
+Configuration, results, model data, and compute services are retained.
+
+## Quick Start
+
+### 1. Configure the client and compute
+
+```bash
+ddeharness onboard
+```
+
+Follow the wizard to configure your LLM provider, optional memory, and a local
+Docker environment or existing Linux compute service. Choose API or local OpenDDE
+folding; both use the Harness compute service.
+
+Local compute requires Linux x86-64 and Docker; CUDA also requires NVIDIA drivers
+and NVIDIA Container Toolkit. See [onboarding](docs/onboarding.md) for setup and
+model preparation details.
+
+After setup, check your configuration, memory service, and compute readiness:
+
+```bash
+ddeharness doctor
+```
+
+Use `ddeharness doctor --probe` to send a test message to your LLM, or
+`ddeharness doctor --compute-only` to check just the compute service. When
+reporting a problem, include `ddeharness doctor --json` output and your command
+or design request. See [troubleshooting](docs/troubleshooting.md) for common issues.
+
+### 2. Start a design
+
+Launch the terminal UI:
+
+```bash
+ddeharness
+```
+
+Then describe your task:
+
+> Design a VHH against human CRLF2. Verify the target and epitope, keep the framework fixed, and design CDRs. Show the plan and start only after I confirm.
+
+CLI-based design workflows are also supported. See the [CLI usage guide](docs/cli.md).
+
+### 3. Inspect results
+
+```bash
+ddeharness tracing
+```
+
+Open the printed URL and select **Protein design** to inspect sequences, structures, metrics and agent activity.
+
+![Candidate sequences, structures and linked metrics](docs/assets/tracing_board_1.png)
+
+![Design progress, agent activity and candidate lineage](docs/assets/tracing_board_2.png)
+
+Started design tasks run in background processes and continue after the TUI
+closes while the client host remains running. Task state and worker logs default
+to `~/.opendde_harness/protein_design/<task_id>/`; set
+`OPENDDE_HARNESS_PROTEIN_DESIGN_ROOT` to change the task root. With remote compute,
+original structure files are stored on the compute host, and the dashboard uses
+structures captured in the client's tracing data. See the [dashboard guide](docs/tracing-board.md).
+
+## Development & License
+
+See the [repository rules](AGENTS.md) and [compute image build instructions](docker/README.md). Ordinary users consume a prebuilt image; Dockerfiles remain available for publishers and customization. Licensed under [Apache-2.0](LICENSE); see [third-party notices](LICENSES/README.md). TUI and memory foundations are adapted from Raven, and long-term memory is served by EverOS. Models may have separate terms. Computational results require experimental validation. Model calls and compute may incur costs.
+
+## Citation and Acknowledgements
+
+If you use OpenDDE Harness in your work, please cite this software and the technical report linked above. When using OpenDDE for structure prediction, also cite the [OpenDDE technical report](https://arxiv.org/abs/2607.03787) and follow its citation and acknowledgement guidance. Cite the original methods for other models and tools used in your experiments, including SolubleMPNN and ESM2 when applicable.
+
+We acknowledge Raven, EverOS, and the upstream projects listed in the [third-party notices](LICENSES/README.md). Their software and model licenses continue to apply.
+
+## Partnership and Collaboration
+
+![Collaboration](docs/assets/hiring.png)