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48 changes: 48 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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name: Bug report
description: Report a reproducible DiffBio bug
title: "[Bug]: "
labels: ["bug"]
body:
- type: textarea
id: summary
attributes:
label: Summary
description: What went wrong?
validations:
required: true
- type: textarea
id: reproduce
attributes:
label: Minimal reproduction
description: Include code, commands, and any input data shape assumptions.
render: python
validations:
required: true
- type: textarea
id: expected
attributes:
label: Expected behavior
validations:
required: true
- type: textarea
id: actual
attributes:
label: Actual behavior
render: text
validations:
required: true
- type: input
id: diffbio-version
attributes:
label: DiffBio version or commit
placeholder: "0.1.0 or git SHA"
validations:
required: true
- type: textarea
id: environment
attributes:
label: Environment
description: Include OS, Python, JAX, jaxlib, accelerator, and installed extras.
render: text
validations:
required: true
1 change: 1 addition & 0 deletions .github/ISSUE_TEMPLATE/config.yml
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blank_issues_enabled: true
33 changes: 33 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.yml
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name: Feature request
description: Propose a new DiffBio capability
title: "[Feature]: "
labels: ["enhancement"]
body:
- type: textarea
id: problem
attributes:
label: Problem
description: What user need or workflow gap should this solve?
validations:
required: true
- type: textarea
id: proposal
attributes:
label: Proposed API or behavior
description: Include example code or CLI usage if possible.
render: python
validations:
required: true
- type: textarea
id: alternatives
attributes:
label: Alternatives considered
validations:
required: false
- type: textarea
id: validation
attributes:
label: Validation plan
description: What tests, docs, or examples would prove this works?
validations:
required: false
25 changes: 25 additions & 0 deletions SECURITY.md
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# Security Policy

## Supported Versions

DiffBio is a research preview. Security fixes target the latest released version
and the current `main` branch.

## Reporting a Vulnerability

Please report suspected vulnerabilities privately by emailing
security@avitai.bio.

Include:

- Affected DiffBio version or commit.
- Environment details, including Python, JAX, and operating system versions.
- A minimal reproduction or proof of impact.
- Any known mitigations.

We will acknowledge reports as soon as practical, investigate privately, and
coordinate disclosure once a fix or mitigation is available.

## Scope

Security-sensitive areas include sequence, variant and molecular file parsing, dataset and reference-genome loading, checkpoint loading, file-system storage, CI release automation, and any code path that processes untrusted biological input data.
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