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Add GitHub project: CI workflow, issue templates, PR template, Discussions
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‎.github/ISSUE_TEMPLATE/biology_validation.yml‎

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name: Biology / GRN Validation
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description: Report a new measurement of R on a biological network database
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labels: ["biology", "validation"]
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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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Help validate whether the numerical overlap R_∞(SU3) ≈ R(E. coli)
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is robust across other gene regulatory network (GRN) databases.
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- type: input
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id: database
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attributes:
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label: Database / dataset
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placeholder: "e.g. YEASTRACT (S. cerevisiae), STRING v12, ARACNE-AP"
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validations:
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required: true
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- type: input
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id: R_value
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attributes:
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label: Measured R (MIXED fraction)
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placeholder: "e.g. 0.341 ± 0.012 (n=847 regulators, high-confidence only)"
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validations:
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required: true
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- type: textarea
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id: method
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attributes:
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label: Measurement method
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description: How was the sign matrix computed? Which interaction types were included?
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placeholder: |
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Used activation/repression edges only (no unknown).
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BFS shortest-path holonomy with root = node of highest out-degree.
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500 bootstrap resamples for error estimate.
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validations:
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required: true
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- type: textarea
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id: notes
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attributes:
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label: Additional notes / attached files
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validations:
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required: false

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug Report — Simulation / Code
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description: Something crashes or produces wrong physics output
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labels: ["bug"]
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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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Please fill in as much detail as possible.
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Attach the full traceback and the JSON output file if available.
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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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placeholder: "e.g. 3.11.8"
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validations:
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required: true
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- type: input
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id: numpy_scipy
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attributes:
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label: numpy / scipy versions
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placeholder: "e.g. numpy 2.4.2 scipy 1.17.1"
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validations:
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required: true
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- type: dropdown
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id: module
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attributes:
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label: Affected module
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options:
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- su2.py
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- su3.py
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- u1.py
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- lattice.py
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- fields.py
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- action.py
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- observables.py
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- updates.py
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- simulation.py
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- su2_l10_colab.py
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- sm_* modules
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- Other
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validations:
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required: true
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- type: textarea
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id: reproduce
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attributes:
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label: Minimal reproduction
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description: Exact command or code snippet that triggers the bug
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placeholder: "python simulation/su2_l10_colab.py — crash at sweep 142"
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validations:
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required: true
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- type: textarea
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id: traceback
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attributes:
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label: Full traceback or wrong output
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render: shell
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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: Expected behaviour
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validations:
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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: Questions & Discussion
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url: https://github.com/boonsup/hgst-e7/discussions
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about: General questions about the physics, code, or paper
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- name: Zenodo record (data & paper DOI)
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url: https://doi.org/10.5281/zenodo.18873889
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about: Cite the software or access archived data releases

‎.github/ISSUE_TEMPLATE/simulation_run.yml‎

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name: Simulation Run Request
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description: Propose a new lattice run (new L, gauge group, beta, kappa, or 3D)
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labels: ["simulation", "enhancement"]
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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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Use this template to propose a new production simulation that would
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extend the FSS analysis or test a new gauge configuration.
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- type: dropdown
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id: gauge
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attributes:
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label: Gauge group
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options:
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- SU(2)
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- SU(3)
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- U(1)
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- SM (SU3×SU2×U1)
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- SU(N) large-N
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- Other / new
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validations:
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required: true
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- type: input
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id: params
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attributes:
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label: Proposed parameters
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placeholder: "L=12, beta=4.0, kappa=0.3, N_therm=4000, N_meas=500"
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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: Scientific motivation
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description: What physics question does this run answer?
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placeholder: |
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SU(3) L=10 would reduce sigma_syst on R_inf(SU3) from ±0.0195
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to ±0.005, making the SU2/SU3 thermodynamic ordering definitive.
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validations:
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required: true
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- type: textarea
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id: resources
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attributes:
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label: Available compute
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placeholder: "Colab T4 GPU, ~2 hours; or local 8-core CPU, ~6 hours"
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validations:
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required: false
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- type: checkboxes
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id: checklist
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attributes:
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label: I commit to
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options:
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- label: Running the simulation and uploading the JSON result file
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- label: Opening a follow-up PR with data + updated FSS fit

‎.github/PULL_REQUEST_TEMPLATE.md‎

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## Summary
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<!-- One sentence: what does this PR add or fix? -->
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## Type of change
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- [ ] Bug fix (simulation produces wrong result or crashes)
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- [ ] New simulation data (new JSON result file + FSS update)
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- [ ] New feature (new gauge group, new observable, 3D extension, GPU port)
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- [ ] Code quality (refactor, tests, docs)
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- [ ] Paper / LaTeX update
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## Physics checklist (for simulation changes)
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- [ ] Run parameters (L, beta, kappa, seed, N_therm, N_meas) stated in JSON metadata
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- [ ] Output JSON file added to `data/`
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- [ ] Autocorrelation (τ_int via Madras-Sokal) reported
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- [ ] FSS fit updated if a new L point was added
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- [ ] No hard-coded absolute paths
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## Code checklist
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- [ ] `pip install -r requirements.txt && python simulation/su2_l10_colab.py` still runs
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- [ ] New functions have a docstring stating the physics formula implemented
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- [ ] No secrets or `.env` values committed
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## Related issues
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Closes #

‎.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]
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pull_request:
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branches: [main]
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jobs:
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smoke-test:
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name: Python ${{ matrix.python-version }} smoke 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", "3.12"]
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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: Install dependencies
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run: pip install -r requirements.txt
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- name: Syntax check — all simulation modules
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run: |
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python -m py_compile simulation/su2.py
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python -m py_compile simulation/su3.py
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python -m py_compile simulation/u1.py
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python -m py_compile simulation/lattice.py
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python -m py_compile simulation/fields.py
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python -m py_compile simulation/action.py
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python -m py_compile simulation/observables.py
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python -m py_compile simulation/updates.py
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python -m py_compile simulation/simulation.py
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python -m py_compile simulation/su2_l10_colab.py
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- name: Smoke test — su2_l10_colab.py (L=4, 2 sweeps)
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run: |
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python - << 'EOF'
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import ast, sys
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with open("simulation/su2_l10_colab.py", encoding="utf-8") as f:
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src = f.read()
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ast.parse(src)
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# Patch to tiny run
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src = src.replace("L = 10", "L = 4")
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src = src.replace("N_THERM = 4000", "N_THERM = 2")
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src = src.replace("N_MEAS = 500", "N_MEAS = 2")
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src = src.replace("N_SKIP = 5", "N_SKIP = 1")
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exec(src, {"__name__": "__main__"})
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import json
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with open("su2_l10_summary.json") as f:
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r = json.load(f)
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assert r["stub_mode"] == False, "stub_mode must be False"
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assert 0.0 < r["R_mean"] < 1.0, f"R_mean out of range: {r['R_mean']}"
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print(f"PASS R_mean={r['R_mean']:.4f} tau_int={r['tau_int']}")
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EOF
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- name: Verify data files are valid JSON
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run: |
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python -c "
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import json, pathlib, sys
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errors = []
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for f in pathlib.Path('data').glob('*.json'):
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try:
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json.loads(f.read_text(encoding='utf-8'))
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except Exception as e:
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errors.append(f'{f}: {e}')
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if errors:
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print('\\n'.join(errors)); sys.exit(1)
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print(f'All {len(list(pathlib.Path(\"data\").glob(\"*.json\")))} JSON files valid')
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"

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