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Add initial project setup and configuration files
- Created .gitignore_updated to exclude unnecessary files from version control. - Added VSCode configuration files for debugging and settings. - Included a tasks.json file for creating a Python virtual environment. - Developed a comprehensive CONTRIBUTING.md to guide new contributors. - Established a data directory with example datasets and simulation presets. - Implemented simulation presets in TOML format for various nanoparticle systems. - Created benchmark and setup scripts for performance testing and environment setup.
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‎.copilot/config.py‎

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"""
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Configuration for GitHub Copilot in NanoSimLab.
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This module contains settings and preferences for GitHub Copilot
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to provide better assistance for scientific computing and nanorobotics code.
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"""
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# Copilot context and preferences for NanoSimLab project
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COPILOT_CONTEXT = {
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"project_type": "scientific_computing",
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"domain": "nanorobotics",
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"primary_language": "python",
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"frameworks": [
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"numpy",
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"scipy",
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"matplotlib",
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"pytest",
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"click"
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],
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"scientific_libraries": [
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"mdanalysis",
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"ase",
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"hoomd",
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"openmm",
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"pymatgen"
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],
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"coding_style": {
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"naming_convention": "snake_case",
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"line_length": 100,
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"type_hints": True,
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"docstring_style": "google"
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},
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"preferred_patterns": [
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"numpy array operations",
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"scientific computing best practices",
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"brownian dynamics algorithms",
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"molecular simulation techniques",
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"statistical analysis methods"
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]
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}

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug Report
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description: File a bug report to help us improve NanoSimLab
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title: "[Bug]: "
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labels: ["bug", "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 taking the time to fill out this bug report! Please provide as much detail as possible.
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- type: input
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id: version
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attributes:
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label: NanoSimLab Version
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description: What version of NanoSimLab are you running?
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placeholder: e.g., 0.1.0
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validations:
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required: true
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- type: input
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id: python-version
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attributes:
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label: Python Version
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description: What version of Python are you using?
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placeholder: e.g., 3.11.0
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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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description: What operating system are you using?
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placeholder: e.g., Ubuntu 22.04, macOS 13.0, Windows 11
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validations:
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required: true
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- type: textarea
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id: bug-description
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attributes:
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label: Bug Description
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description: A clear and concise description of what the bug is.
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placeholder: Describe what happened and what you expected to happen.
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validations:
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required: true
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- type: textarea
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id: reproduce-steps
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attributes:
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label: Steps to Reproduce
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description: Please provide step-by-step instructions to reproduce the issue.
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placeholder: |
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1. Import nanosimlab
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2. Create simulation with parameters...
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3. Run simulation...
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4. See error
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validations:
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required: true
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- type: textarea
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id: minimal-example
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attributes:
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label: Minimal Code Example
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description: If possible, provide a minimal code example that reproduces the issue.
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render: python
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placeholder: |
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import nanosimlab
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# Your minimal example here
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- type: textarea
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id: error-output
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attributes:
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label: Error Output
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description: If there's an error message, please include the full traceback.
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render: text
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placeholder: Paste the full error message and traceback here.
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- type: textarea
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id: expected-behavior
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attributes:
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label: Expected Behavior
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description: What did you expect to happen?
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placeholder: Describe the expected behavior.
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- type: textarea
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id: additional-context
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attributes:
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label: Additional Context
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description: Add any other context about the problem here.
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placeholder: Any additional information that might be relevant.
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- type: checkboxes
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id: checklist
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attributes:
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label: Checklist
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description: Please confirm the following before submitting.
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options:
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- label: I have searched existing issues to ensure this is not a duplicate.
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required: true
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- label: I have provided all the requested information above.
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required: true
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- label: I am using a supported version of Python (3.10+).
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required: true

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: Feature Request
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description: Suggest a new feature or enhancement for NanoSimLab
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title: "[Feature]: "
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labels: ["enhancement", "feature-request"]
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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 suggesting a new feature! Please provide as much detail as possible about your idea.
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- type: textarea
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id: feature-description
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attributes:
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label: Feature Description
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description: A clear and concise description of the feature you'd like to see.
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placeholder: Describe the feature you want to be added.
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validations:
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required: true
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- type: textarea
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id: motivation
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attributes:
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label: Motivation
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description: Why is this feature needed? What problem does it solve?
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placeholder: Explain the motivation behind this feature request.
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validations:
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required: true
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- type: textarea
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id: use-case
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attributes:
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label: Use Case
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description: Describe how you would use this feature.
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placeholder: Provide a concrete example of how this feature would be used.
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- type: textarea
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id: proposed-solution
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attributes:
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label: Proposed Solution
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description: How do you think this feature should be implemented?
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placeholder: Describe your proposed solution or implementation approach.
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- type: textarea
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id: alternatives
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attributes:
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label: Alternative Solutions
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description: Are there any alternative solutions or workarounds you've considered?
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placeholder: Describe any alternative approaches you've thought about.
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- type: textarea
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id: example-code
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attributes:
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label: Example Code
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description: If applicable, provide an example of how the feature might be used.
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render: python
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placeholder: |
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# Example usage of the proposed feature
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import nanosimlab
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# Your example here
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- type: dropdown
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id: priority
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attributes:
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label: Priority
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description: How important is this feature to you?
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options:
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- Low - Nice to have
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- Medium - Would be helpful
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- High - Important for my work
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- Critical - Blocking my progress
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validations:
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required: true
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- type: dropdown
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id: complexity
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attributes:
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label: Estimated Complexity
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description: How complex do you think this feature is to implement?
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options:
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- Low - Small change or addition
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- Medium - Moderate implementation effort
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- High - Significant development required
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- Unknown - Not sure about complexity
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- type: checkboxes
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id: contribution
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attributes:
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label: Contribution
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description: Are you willing to help implement this feature?
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options:
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- label: I'm willing to submit a pull request for this feature.
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- label: I can help with testing this feature.
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- label: I can help with documentation for this feature.
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- type: textarea
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id: additional-context
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attributes:
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label: Additional Context
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description: Add any other context, screenshots, or examples about the feature request.
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placeholder: Any additional information that might be relevant.

‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [main, develop]
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pull_request:
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branches: [main]
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Cache pip dependencies
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -e ".[dev,analysis]"
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- name: Lint with flake8
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run: |
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flake8 src/nanosimlab tests/ --count --select=E9,F63,F7,F82 --show-source --statistics
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flake8 src/nanosimlab tests/ --count --exit-zero --max-complexity=10 --max-line-length=100 --statistics
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- name: Type check with mypy
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run: |
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mypy src/nanosimlab
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- name: Format check with black
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run: |
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black --check --diff src/nanosimlab tests/
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- name: Import sort check with isort
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run: |
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isort --check-only --diff src/nanosimlab tests/
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- name: Test with pytest
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run: |
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pytest tests/ -v --cov=nanosimlab --cov-report=xml --cov-report=term
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- name: Upload coverage to Codecov
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if: matrix.python-version == '3.11'
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uses: codecov/codecov-action@v3
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with:
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file: ./coverage.xml
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flags: unittests
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name: codecov-umbrella
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build:
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needs: test
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runs-on: ubuntu-latest
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if: github.event_name == 'push' && github.ref == 'refs/heads/main'
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build twine
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- name: Build package
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run: python -m build
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- name: Check package
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run: twine check dist/*
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- name: Upload build artifacts
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uses: actions/upload-artifact@v3
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with:
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name: dist
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path: dist/

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