Boltz web runner

.github/workflows/undefined_names.yml

@@ -1,6 +1,15 @@
 name: undefined_names
 on: [pull_request, push]
 jobs:
+  boltz_trace_format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - run: python scripts/boltz/check_trace_format_fixtures.py
+      - run: python -m unittest tests.test_boltz_trace_validate -v
   undefined_names:
     runs-on: ubuntu-latest
     steps:

.gitignore

@@ -1,6 +1,8 @@
 .vscode/
 .idea/
+.DS_Store
 __pycache__/
+test_output/
 *.egg-info
 build
 dist
@@ -14,7 +16,33 @@ cutlass/
 *.pdb
 *.json
 *.pkl
+*.pt
 *.fasta
 *.sto
 *.a3m
 *.hhr
+
+# Boltz tracing
+slurm-*.out
+slurm-*.err
+logs/
+outputs/boltz_runs/
+outputs/boltz_runs/**
+.cache/
+.cache/**
+**/__pycache__/
+**/*.pyc
+
+# Allow small Boltz example inputs to be tracked
+!scripts/boltz/inputs/
+!scripts/boltz/inputs/*.fasta
+!scripts/boltz/inputs/*.yaml
+!scripts/boltz/boltz_pip_extras.txt
+!scripts/boltz/boltz_constraints.txt
+# Reference trace text fixtures (Issue #42; format-only CI)
+!scripts/boltz/fixtures/
+!scripts/boltz/fixtures/*.txt
+
+# Issue #42 submission evidence
+!submission/issue42-demonstration-evidence/screenshots/
+!submission/issue42-demonstration-evidence/screenshots/*.png

README.md

@@ -7,7 +7,9 @@ This repository has two main components:
 
 ---
 
-Link to Openfold implimentation - [README_vizfold_openfold.md](https://github.com/vizfold/vizfold-foundation/blob/main/README_vizfold_openfold.md)
+Link to Openfold implementation - [README_vizfold_openfold.md](https://github.com/vizfold/vizfold-foundation/blob/main/README_vizfold_openfold.md)
+
+**Boltz-2 inference and VizFold-format traces** (Slurm runner, validation, proxy vs true attention): see [docs/source/Boltz_Inference.md](docs/source/Boltz_Inference.md) and `scripts/boltz/`. Reviewer reproducibility steps and demonstration screenshots: [submission/issue42-demonstration-evidence/REPRODUCIBILITY.md](submission/issue42-demonstration-evidence/REPRODUCIBILITY.md).
 
 ---