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Merge remote-tracking branch 'origin/main' into experiment/dimereaction
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‎.github/CODEOWNERS‎

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# CODEOWNERS determines automatically requested reviewers for PRs touching these paths.
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# Syntax: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
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# Core library code
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src/chemtorch/ @heid-lab/chemtorch-maintainers
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# Configuration schemas and experiment presets
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conf/ @heid-lab/chemtorch-maintainers
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# Documentation
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docs/source/ @heid-lab/chemtorch-maintainers
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# CI workflows
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.github/workflows/ @heid-lab/chemtorch-maintainers
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# Release management files
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CHANGELOG.md @heid-lab/chemtorch-maintainers
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.github/release-drafter.yml @heid-lab/chemtorch-maintainers
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# Package metadata
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pyproject.toml @heid-lab/chemtorch-maintainers

‎.github/ISSUE_TEMPLATE/bug_report.yaml‎

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name: Bug report
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description: Report a reproducible bug or regression in ChemTorch.
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labels:
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- bug
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- needs-triage
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body:
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- type: markdown
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attributes:
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value: |
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## Thanks for helping us improve ChemTorch!
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Please provide as much detail as possible so we can reproduce and fix the issue quickly.
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- type: input
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id: summary
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attributes:
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label: Summary
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description: What went wrong?
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placeholder: Short, descriptive title of the problem.
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: What happened?
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description: Describe the behavior you observed. Include any error messages or stack traces (use fenced code blocks for logs).
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validations:
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required: true
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- type: textarea
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id: expected
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attributes:
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label: What did you expect to happen?
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description: Describe the behavior you expected instead.
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validations:
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required: true
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- type: textarea
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id: reproduction
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attributes:
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label: How can we reproduce it?
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description: |
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Provide a minimal reproduction: CLI command(s), configuration overrides, dataset(s), and any code snippets required.
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Feel free to link to a GitHub gist or attach a `yaml` file when helpful.
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placeholder: |
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```bash
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chemtorch +experiment=graph ...
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```
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validations:
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required: true
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- type: dropdown
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id: install
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attributes:
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label: Installation method
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options:
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- uv sync
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- conda / mamba
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- other (explain below)
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: ChemTorch version / commit SHA
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description: Run `chemtorch --version` or `git rev-parse HEAD`.
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validations:
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required: true
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- type: input
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id: python
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attributes:
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label: Python version
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placeholder: e.g. 3.10.15
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validations:
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required: true
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- type: input
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id: os
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attributes:
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label: Operating system
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placeholder: e.g. Ubuntu 22.04, macOS 14.3, Windows 11
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validations:
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required: true
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- type: input
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id: hardware
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attributes:
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label: Hardware / accelerator
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placeholder: e.g. CPU only, NVIDIA RTX 4090 (CUDA 12.1)
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- type: textarea
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id: integrations
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attributes:
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label: Relevant integrations
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description: Mention frameworks or services involved (Hydra, PyTorch Lightning, Weights & Biases, custom datasets, etc.).
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- type: checkboxes
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id: confirmations
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attributes:
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label: Checklist
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options:
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- label: I have searched existing [issues](https://github.com/heid-lab/chemtorch/issues?q=is%3Aissue) and discussions.
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required: true
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- label: I can reproduce this issue consistently on the latest `main` commit.
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required: false
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- label: I am willing to submit a pull request to help fix this.
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required: false

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: false
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contact_links:
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- name: ChemTorch Documentation
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url: https://heid-lab.github.io/chemtorch
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about: Browse the guides and API reference for tutorials and troubleshooting.
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- name: ChemTorch White Paper (ChemRxiv)
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url: https://chemrxiv.org/engage/chemrxiv/article-details/690357d9a482cba122e366b6
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about: Read the research paper for methodology details and benchmark results.

‎.github/ISSUE_TEMPLATE/documentation.yaml‎

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name: Documentation improvement
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description: Help us improve tutorials, guides, and reference material.
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labels:
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- documentation
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- needs-triage
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body:
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- type: markdown
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attributes:
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value: |
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## Documentation feedback
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Let us know what is missing or confusing in the docs or README.
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- type: input
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id: summary
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attributes:
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label: Summary
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placeholder: e.g. "Quick Start sample command fails on macOS".
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validations:
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required: true
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- type: textarea
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id: section
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attributes:
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label: Affected page or section
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description: Provide a URL or path (e.g. `docs/source/getting_started/quick_start.rst`).
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validations:
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required: true
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- type: textarea
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id: details
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attributes:
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label: What needs to change?
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description: Describe the correction, addition, or clarification that would help future users.
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validations:
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required: true
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- type: textarea
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id: context
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attributes:
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label: Additional context
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description: Screenshots, logs, or references to other docs are helpful.
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- type: checkboxes
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id: contribution
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attributes:
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label: Can you help us update the docs?
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options:
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- label: I will open a pull request with the proposed changes.
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- label: I can review updated documentation.
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- label: I am only reporting the issue.

‎.github/ISSUE_TEMPLATE/feature_request.yaml‎

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name: Feature request
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description: Suggest a new capability, component, or workflow improvement.
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labels:
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- enhancement
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- needs-triage
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body:
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- type: markdown
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attributes:
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value: |
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## Shape the ChemTorch roadmap
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Tell us what you would like to build or see us support.
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- type: input
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id: summary
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attributes:
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label: Summary
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description: What is the high-level idea?
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placeholder: e.g. "Add a pretrained reaction classification model".
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validations:
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required: true
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- type: textarea
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id: problem
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attributes:
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label: What problem does this solve?
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description: Explain the research or workflow gap the feature addresses.
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validations:
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required: true
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- type: textarea
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id: proposal
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attributes:
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label: Proposed solution
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description: Outline how you imagine this feature working. Include CLI commands, configuration options, or API sketches if relevant.
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validations:
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required: true
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- type: textarea
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id: alternatives
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attributes:
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label: Alternatives considered
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description: Have you tried anything else? Why is it insufficient?
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- type: textarea
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id: data
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attributes:
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label: Related datasets or benchmarks
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description: Link to datasets, reaction families, or evaluation protocols this feature should support.
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- type: textarea
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id: references
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attributes:
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label: References & supporting material
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description: Link to papers, blog posts, or code that inform this request.
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- type: checkboxes
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id: involvement
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attributes:
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label: How can you help?
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options:
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- label: I am willing to contribute implementation work (code, configs, or docs).
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- label: I can help validate the feature on my data / benchmarks.
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- label: I am only proposing the idea.

‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "monthly" # Keep actions noise low; Renovate will manage Python deps biweekly
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target-branch: "main"
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labels:
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- "dependencies"
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- "ci"
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open-pull-requests-limit: 5
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reviewers:
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- "heid-lab/chemtorch-maintainers"
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# Note:
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# - We use Renovate (see .github/renovate.json5) for Python/uv dependency updates on a biweekly cadence.
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# - Dependabot remains enabled for GitHub Actions only. Security alerts for Python are still surfaced via GitHub Advisories.

‎.github/pull_request_template.md‎

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# Summary
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What *problem* does this PR solve, and what is the *user-visible outcome*?
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Fixes #<issue-number> (optional)
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## Type of change
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- [ ] Feature
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- [ ] Bug fix
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- [ ] Documentation
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- [ ] Refactor / Maintenance
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- [ ] CI / Build
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- [ ] Tests
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- [ ] Other: ___
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## Changes
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- Bullet the key changes (1–5 bullets)
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- Keep it concise but specificg
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## Breaking changes
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- [ ] None
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- [ ] Yes (describe impact and migration notes):
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## How I tested this
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- [ ] Unit tests pass
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- [ ] Integration / e2e checks
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- [ ] Docs build locally
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- [ ] Manual verification (brief steps):
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## Checklist
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Before PR:
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- [ ] Branch name follows policy (feature/bugfix/hotfix/docs/chore/ci/tests/perf/build)
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- [ ] Ran test locally and ALL tests pass
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- [ ] Updated or added tests covering new behavior (if applicable)
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- [ ] Updated configuration defaults (if applicable).
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PR:
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- [ ] This pull request has a clear but concise title (prefixed with a [git commit emoji](https://gist.github.com/parmentf/035de27d6ed1dce0b36a), use`:emoji_name:` to select an emoji)
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- [ ] Relevant labels added
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- [ ] If this PR introduces breaking changes it is labelled with `breaking-change` and provides a migration guide
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## Reviewer notes (optional)
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Anything that would help reviewers focus (areas of risk, follow-ups, docs to check).

‎.github/renovate.json5‎

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{
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// Renovate configuration for uv-managed Python project.
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"$schema": "https://docs.renovatebot.com/renovate-schema.json",
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"extends": [
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"config:base",
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":semanticCommits",
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":disableRateLimiting"
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],
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"timezone": "UTC",
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// Biweekly schedule: runs early Monday every 2 weeks.
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"schedule": ["before 06:00 on Monday every 2 weeks"],
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"labels": ["dependencies"],
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"prConcurrentLimit": 10,
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"branchConcurrentLimit": 10,
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"platformAutomerge": false,
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"dependencyDashboard": true,
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// Managers: Python (pyproject) and GitHub Actions. uv.lock is regenerated via post-upgrade task below.
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"enabledManagers": ["pip", "github-actions"],
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"pip": {
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// Keep broader constraints when appropriate and rely on uv.lock for exact reproducibility.
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"rangeStrategy": "auto"
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},
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// After updating pyproject, refresh uv.lock so PRs are self-contained.
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"postUpgradeTasks": {
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"commands": ["uv lock"],
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"fileFilters": ["pyproject.toml", "uv.lock"],
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"executionMode": "update"
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},
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"packageRules": [
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{
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"matchPackageNames": ["numpy"],
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"separateMinorPatch": true,
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"stabilityDays": 3,
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"labels": ["dependencies", "numpy"],
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"automerge": false
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},
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{
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"matchPackageNames": ["torch"],
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"separateMinorPatch": true,
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"stabilityDays": 7,
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"labels": ["dependencies", "requires-wheels-check"],
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"automerge": false
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},
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{
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"matchPackagePatterns": ["^sphinx", "myst-parser", "pydata-sphinx-theme", "sphinx-.*"],
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"groupName": "docs-stack",
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"labels": ["dependencies", "docs"],
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"stabilityDays": 3,
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"automerge": false
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},
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{
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"matchPackagePatterns": ["^sphinx", "myst-parser", "pydata-sphinx-theme", "sphinx-.*"],
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"matchUpdateTypes": ["patch"],
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"automerge": true
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},
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{
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"matchPackagePatterns": ["^pytest", "coverage", "pytest-.*"],
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"groupName": "test-stack",
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"labels": ["dependencies", "tests"],
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"stabilityDays": 3,
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"automerge": false
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},
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{
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"matchPackagePatterns": ["^pytest", "coverage", "pytest-.*"],
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"matchUpdateTypes": ["patch"],
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"automerge": true
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},
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{
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"matchPackagePatterns": ["^lightning$", "pytorch-lightning"],
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"groupName": "lightning-stack",
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"labels": ["dependencies"],
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"automerge": false
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},
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{
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"matchManagers": ["github-actions"],
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"groupName": "github-actions",
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"labels": ["dependencies", "ci"],
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"schedule": ["before 06:00 on Monday every 4 weeks"],
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"automerge": false
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}
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],
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// Reviewer assignment
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"reviewers": ["heid-lab/chemtorch-maintainers"],
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"assignees": ["heid-lab/chemtorch-maintainers"],
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// Commit message convention (+emoji). Defaults to upgrade arrow; special cases below.
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"commitMessagePrefix": ":arrow_up: deps:",
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"commitMessageAction": "update",
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"commitMessageTopic": "{{depName}}",
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// PR body template (short; release notes are appended automatically)
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"prBodyTemplate": "This PR updates dependencies managed by Renovate.\n\n- Group: {{groupName}}\n- Package: {{depName}}\n- From: {{currentVersion}} -> To: {{newVersion}}\n\nChecklist:\n- [ ] uv lock regenerated (CI or manual)\n- [ ] Tests & docs build pass\n- [ ] (If lightning/torch) Verify PyTorch Geometric extension compatibility.\n\n---\n",
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}

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