feat: decouple throat sizing, LEM prescreening, band-stitch fix

CLAUDE.md

@@ -0,0 +1,79 @@
+# Horn Simulation Pipeline
+
+Nextflow-orchestrated FEM acoustic horn simulation with Docker-containerised packages.
+
+## Quick reference
+
+```bash
+just                  # list all commands
+just build            # build all Docker images (horn-solver, horn-geometry, horn-analysis)
+just test-local       # run tests locally (horn-core, horn-geometry, horn-analysis)
+just test             # run tests in Docker
+just run              # single mode pipeline (default params)
+just run-auto         # auto mode (all 7 profiles, driver ranking)
+just run-fullauto     # fullauto mode (derives geometry from frequency band)
+just clean            # remove Docker images + Nextflow work dirs
+```
+
+## Running the pipeline
+
+Always use `-profile docker` (the justfile does this automatically). The solver requires `dolfinx` which only exists in the Docker container.
+
+```bash
+# Single mode
+just run --profile conical --throat_radius 0.025 --mouth_radius 0.15 --length 0.3
+
+# Auto mode (mid-horn example)
+just run-auto --target_f_low 250 --target_f_high 6500 --throat_radius 0.025 --mouth_radius 0.2 --length 0.3
+
+# Fullauto mode (geometry derived from frequency band)
+just run-fullauto --target_f_low 500 --target_f_high 4000
+
+# Resume a failed/interrupted run
+just run -resume
+```
+
+## Project structure
+
+```
+main.nf                          # Nextflow pipeline (single/auto/fullauto workflows)
+nextflow.config                  # Docker container mappings per process
+justfile                         # Build, test, run commands
+packages/
+  horn-core/                     # Shared data structures, enums, candidate generation (pure Python, no Docker)
+  horn-geometry/                 # STEP file generation via gmsh (Docker: horn-geometry)
+  horn-solver/                   # FEM solver via dolfinx (Docker: horn-solver)
+  horn-analysis/                 # Plots, reports, scoring, rendering (Docker: horn-analysis)
+```
+
+## Horn profiles
+
+7 flare profiles: `conical`, `exponential`, `hyperbolic`, `tractrix`, `os`, `lecleach`, `cd`
+
+## Testing
+
+```bash
+# Local (fast, no Docker needed — covers horn-core, horn-geometry, horn-analysis)
+just test-local
+
+# Single package in Docker
+just test-package horn-solver
+
+# All packages in Docker
+just test
+```
+
+horn-geometry tests need `gmsh` (installed locally). horn-solver tests need `dolfinx` (Docker only).
+
+## Docker images
+
+Build from repo root (context is `.`):
+```bash
+docker build -t horn-geometry:latest --target production -f ./packages/horn-geometry/Dockerfile .
+```
+
+Note: `gmsh` wheels don't have native `aarch64` Linux builds. On Apple Silicon, build with `--platform linux/amd64`.
+
+## Java for Nextflow
+
+Nextflow requires Java 8-22. If the system Java is too new, source `~/.zshrc` which sets the correct `JAVA_CMD`.

justfile

@@ -1,4 +1,5 @@
-packages := "horn-solver horn-geometry horn-analysis"
+docker_packages := "horn-solver horn-geometry horn-analysis"
+local_packages := "horn-core horn-geometry horn-analysis"
 
 # Display help
 default:
@@ -8,30 +9,51 @@ default:
 build:
     #!/usr/bin/env bash
     set -euo pipefail
-    for pkg in {{packages}}; do
-        docker build -t "$pkg:latest" --target production -f "./packages/$pkg/Dockerfile" .
+    for pkg in {{docker_packages}}; do
+        docker build --platform linux/amd64 -t "$pkg:latest" --target production -f "./packages/$pkg/Dockerfile" .
     done
 
-# Run all package tests (build then test)
+# Run all package tests in Docker (build then test)
 test:
     #!/usr/bin/env bash
     set -euo pipefail
-    for pkg in {{packages}}; do
-        docker build -t "$pkg:test" --target test -f "./packages/$pkg/Dockerfile" .
+    for pkg in {{docker_packages}}; do
+        docker build --platform linux/amd64 -t "$pkg:test" --target test -f "./packages/$pkg/Dockerfile" .
     done
-    for pkg in {{packages}}; do
+    for pkg in {{docker_packages}}; do
         echo "Running tests for $pkg..."
         docker run --rm "$pkg:test" pytest "/app/packages/$pkg/tests"
     done
 
-# Build and test a single package: just test-package horn-solver
+# Build and test a single package in Docker: just test-package horn-solver
 test-package pkg:
-    docker build -t "{{pkg}}:test" --target test -f "./packages/{{pkg}}/Dockerfile" .
-    docker run --rm "{{pkg}}:test" pytest "/app/packages/{{pkg}}/tests" -v
+    docker build --platform linux/amd64 -t "{{pkg}}:test" --target test -f "./packages/{{pkg}}/Dockerfile" .
+    docker run --platform linux/amd64 --rm "{{pkg}}:test" pytest "/app/packages/{{pkg}}/tests" -v
 
-# Run the Nextflow pipeline
-run:
-    nextflow run main.nf -profile docker
+# Run tests locally (no Docker — works for horn-core, horn-geometry, horn-analysis)
+test-local:
+    #!/usr/bin/env bash
+    set -euo pipefail
+    echo "Running horn-core tests..."
+    python -m pytest packages/horn-core/tests/ -v
+    echo "Running horn-analysis tests..."
+    python -m pytest packages/horn-analysis/tests/ -v
+    echo "Running horn-geometry tests..."
+    cd packages/horn-geometry && python -m pytest tests/ -v
+
+# Run the Nextflow pipeline (single mode, default params)
+run *ARGS:
+    nextflow run main.nf -profile docker {{ARGS}}
+
+# Run auto mode (unified optimizer): just run-auto --target_f_low 250 --target_f_high 6500
+# Fixed geometry: --mouth_radius 0.15 --length 0.3 (only varies profile)
+# Free geometry: omit mouth_radius/length to derive from frequency band
+run-auto *ARGS:
+    nextflow run main.nf -profile docker --mode auto {{ARGS}}
+
+# Alias for auto mode with all geometry derived (backward compat)
+run-fullauto *ARGS:
+    nextflow run main.nf -profile docker --mode auto {{ARGS}}
 
 # Run Nextflow tests
 test-nextflow:
@@ -42,7 +64,7 @@ clean:
     #!/usr/bin/env bash
     set -euo pipefail
     echo "Cleaning up Docker images..."
-    for pkg in {{packages}}; do
+    for pkg in {{docker_packages}}; do
         docker rmi -f "$pkg:latest" "$pkg:test" || true
     done
     echo "Cleaning up Nextflow files..."