Remove legacy runtime hooks from renunney Track 1 stack

Makefile

@@ -1,6 +1,5 @@
 PYTHON := python3
 REPO_ROOT := $(abspath .)
-LEGACY_ROOT := $(REPO_ROOT)/../collaborations/to_ptbc/evc/cost_of_substitution
 ORCH := $(REPO_ROOT)/scripts/run_orchestration.py
 TRACK1 := $(REPO_ROOT)/scripts/run_track1.py
 
@@ -22,7 +21,7 @@ FIG1_M100 := $(REPO_ROOT)/config/track1_figure1_paper_M_10_0.json
 help:
 	@echo "Targets:"
 	@echo "  init                Create run directories and initialize the SQLite registry"
-	@echo "  doctor              Show key paths and verify local orchestration and legacy backend paths"
+	@echo "  doctor              Show key paths and verify local orchestration and Track 1 paths"
 	@echo "  list-jobs           List jobs in the local registry"
 	@echo "  track1-sim-smoke    Run one local Track 1 simulation through renunney runner"
 	@echo "  run-one             Claim and run one queued job"
@@ -44,7 +43,6 @@ init:
 
 doctor:
 	@echo "REPO_ROOT=$(REPO_ROOT)"
-	@echo "LEGACY_ROOT=$(LEGACY_ROOT)"
 	@echo "ORCH=$(ORCH)"
 	@echo "TRACK1=$(TRACK1)"
 	@echo "DB=$(DB)"
@@ -53,7 +51,6 @@ doctor:
 	@echo "MPLCONFIGDIR=$(MPLCONFIGDIR)"
 	test -f $(ORCH)
 	test -f $(TRACK1)
-	test -d $(LEGACY_ROOT)/python
 
 list-jobs:
 	$(PYTHON) $(ORCH) list --db $(DB)

README.md

@@ -8,12 +8,12 @@ Clean working repository for:
 
 ## Current Scope
 
-This repository is the clean operational wrapper around the current work in:
+This repository was bootstrapped from earlier work in:
 
 - [`../collaborations/to_ptbc/evc/cost_of_substitution`](/mnt/CIFS/pengolodh/Docs/Projects/collaborations/to_ptbc/evc/cost_of_substitution)
 
-The Track 1 simulation backend still lives there. The orchestration control
+That earlier tree remains useful as provenance and historical context. The
-plane and the Track 1 runner/API boundary are now local to `renunney`.
+Track 1 runtime and orchestration stack now live in `renunney`.
 
 `renunney` provides:
 
@@ -97,5 +97,5 @@ The current state is split:
 - Track 1 dataset generator: local to `renunney`
 - Track 1 fit layer: local to `renunney`
 
-This repo is now the clean operational entry point while the simulation code is
+This repo is now the clean operational entry point for the Track 1 runtime and
-migrated in later stages.
+its orchestration stack.

src/renunney/orchestration.py

@@ -17,12 +17,8 @@ from hashlib import sha256
 from pathlib import Path
 from typing import Any, Optional
 
-from .legacy import ensure_legacy_python_path
+from .track1_analysis import LocusThresholdRow, fit_linear_cost_by_loci
-
+from .track1_api import config_from_mapping, run_config, save_payload
-ensure_legacy_python_path()
-
-from track1_analysis import LocusThresholdRow, fit_linear_cost_by_loci
-from track1_api import config_from_mapping, run_config, save_payload
 
 
 def utc_now_iso() -> str:
@@ -43,7 +39,7 @@ def default_worker_host() -> str:
 
 def code_identity(cwd: str | Path | None = None) -> dict[str, Any]:
     identity: dict[str, Any] = {
-        "runner": "renunney orchestration + legacy Track 1 backend",
+        "runner": "renunney orchestration + local Track 1 backend",
         "python_version": platform.python_version(),
         "git_commit": None,
     }
@@ -280,7 +276,7 @@ def expand_track1_figure1_manifest(
         manifests.append(
             {
                 "job_id": job_id,
-                "project": "cost_of_substitution",
+                "project": "renunney",
                 "track": "track1",
                 "job_kind": "track1_locus_threshold",
                 "priority": int(priority),

src/renunney/track1_analysis.py

@@ -2,9 +2,6 @@
 track1_analysis.py
 
 Local Track 1 analysis helpers for renunney.
-
-This stage keeps the simulation kernel in the legacy tree while moving the
-analysis/reporting boundary inward.
 """
 
 from __future__ import annotations

src/renunney/track1_api.py

@@ -2,9 +2,6 @@
 track1_api.py
 
 Local Track 1 API boundary for renunney.
-
-This stage keeps the simulation backend in the legacy tree while moving the
-public config/runner contract into the clean repo.
 """
 
 from __future__ import annotations
@@ -14,7 +11,6 @@ from dataclasses import asdict, dataclass
 from pathlib import Path
 from typing import Any, Optional
 
-from .legacy import ensure_legacy_python_path
 from .track1_analysis import summarize_tracking, sweep_number_of_loci
 from .track1_dataset import generate_extinction_dataset
 from .track1_fit import class_balance, fit_payload_from_jsonl, load_jsonl
@@ -22,8 +18,6 @@ from .track1_reference import Track1Parameters, simulate_run
 from .track1_report import generate_report_bundle
 from .track1_threshold import evaluate_threshold_candidate, search_threshold_over_candidates
 
-ensure_legacy_python_path()
-
 
 @dataclass(frozen=True, init=False)
 class Track1RunConfig:

src/renunney/track1_threshold.py

@@ -2,9 +2,6 @@
 track1_threshold.py
 
 Local Track 1 threshold-search layer for renunney.
-
-This stage keeps the simulation kernel in the legacy tree while moving the
-historical threshold heuristic inward.
 """
 
 from __future__ import annotations

tests/test_orchestration.py

@@ -0,0 +1,296 @@
+import json
+import sys
+from pathlib import Path
+
+ROOT = Path(__file__).resolve().parents[1]
+SRC_DIR = ROOT / "src"
+if str(SRC_DIR) not in sys.path:
+    sys.path.insert(0, str(SRC_DIR))
+
+import renunney.orchestration as orch
+
+
+def test_registry_submit_claim_and_complete(tmp_path: Path):
+    db_path = tmp_path / "jobs.sqlite"
+    orch.initialize_registry(db_path)
+    manifest = {
+        "job_id": "job-1",
+        "project": "renunney",
+        "track": "track1",
+        "job_kind": "track1_locus_threshold",
+        "priority": 5,
+        "created_at": "2026-04-10T00:00:00Z",
+        "created_by": "test",
+        "worker_backend": "python-track1",
+        "config": {
+            "mode": "search",
+            "K": 500,
+            "N0": 500,
+            "n": 1,
+            "u": 0.001,
+            "R": 10.0,
+            "T": 10,
+            "epochs": 1,
+            "runs": 1,
+            "seed": 1,
+            "t_values": [5, 10],
+        },
+        "resources": {"cpu_cores": 1},
+        "result_paths": {"payload_json": "payloads/job-1.json"},
+        "retry": {"max_attempts": 2, "idempotent": True},
+        "notes": "",
+    }
+    orch.submit_job_manifest(db_path, manifest)
+    claimed = orch.claim_next_job(db_path, worker_backend="python-track1", worker_host="worker-a")
+    assert claimed is not None
+    assert claimed.job_id == "job-1"
+    result = {
+        "job_id": "job-1",
+        "status": "succeeded",
+        "worker_backend": "python-track1",
+        "worker_host": "worker-a",
+        "started_at": "2026-04-10T00:00:10Z",
+        "finished_at": "2026-04-10T00:00:20Z",
+        "wall_seconds": 10.0,
+        "exit_code": 0,
+        "config_hash": orch.hash_config(manifest["config"]),
+        "code_identity": {"git_commit": None},
+        "artifacts": {},
+        "summary": {"threshold_T": 10.0},
+        "error": None,
+    }
+    orch.complete_job(db_path, result)
+    jobs = orch.list_jobs(db_path)
+    assert jobs[0]["status"] == "succeeded"
+
+
+def test_run_one_job_executes_python_track1_backend(tmp_path: Path):
+    db_path = tmp_path / "jobs.sqlite"
+    result_root = tmp_path / "results"
+    scratch_root = tmp_path / "scratch"
+    orch.initialize_registry(db_path)
+    manifest = {
+        "job_id": "job-sim-1",
+        "project": "renunney",
+        "track": "track1",
+        "job_kind": "track1_simulate",
+        "priority": 1,
+        "created_at": "2026-04-10T00:00:00Z",
+        "created_by": "test",
+        "worker_backend": "python-track1",
+        "config": {
+            "mode": "simulate",
+            "K": 500,
+            "N0": 500,
+            "n": 1,
+            "u": 0.001,
+            "R": 10.0,
+            "T": 10,
+            "epochs": 1,
+            "seed": 1,
+        },
+        "resources": {"cpu_cores": 1},
+        "result_paths": {
+            "payload_json": "payloads/job-sim-1.json",
+            "log_txt": "logs/job-sim-1.log",
+        },
+        "retry": {"max_attempts": 1, "idempotent": True},
+        "notes": "",
+    }
+    orch.submit_job_manifest(db_path, manifest)
+    result = orch.run_one_job(
+        db_path=db_path,
+        result_root=result_root,
+        worker_backend="python-track1",
+        worker_host="worker-a",
+        scratch_root=scratch_root,
+        cwd=ROOT,
+    )
+    assert result is not None
+    assert result["status"] == "succeeded"
+    payload_path = result_root / "payloads" / "job-sim-1.json"
+    assert payload_path.exists()
+    payload = json.loads(payload_path.read_text(encoding="utf-8"))
+    assert payload["mode"] == "simulate"
+    jobs = orch.list_jobs(db_path)
+    assert jobs[0]["status"] == "succeeded"
+
+
+def test_collate_track1_figure1_groups_rows_and_fits(tmp_path: Path):
+    db_path = tmp_path / "jobs.sqlite"
+    orch.initialize_registry(db_path)
+    for n_value, threshold in [(1, 50.0), (2, 75.0), (3, 100.0)]:
+        manifest = {
+            "job_id": f"job-m1-n{n_value}",
+            "project": "renunney",
+            "track": "track1",
+            "job_kind": "track1_locus_threshold",
+            "priority": 1,
+            "created_at": "2026-04-10T00:00:00Z",
+            "created_by": "test",
+            "worker_backend": "python-track1",
+            "config": {
+                "mode": "search",
+                "K": 5000,
+                "N0": 5000,
+                "n": n_value,
+                "u": 0.0001,
+            },
+            "resources": {"cpu_cores": 1},
+            "result_paths": {"payload_json": f"payloads/job-m1-n{n_value}.json"},
+            "retry": {"max_attempts": 1, "idempotent": True},
+            "notes": "",
+        }
+        orch.submit_job_manifest(db_path, manifest)
+        result = {
+            "job_id": manifest["job_id"],
+            "status": "succeeded",
+            "worker_backend": "python-track1",
+            "worker_host": "worker-a",
+            "started_at": "2026-04-10T00:00:10Z",
+            "finished_at": "2026-04-10T00:00:20Z",
+            "wall_seconds": 10.0,
+            "exit_code": 0,
+            "config_hash": orch.hash_config(manifest["config"]),
+            "code_identity": {"git_commit": None},
+            "artifacts": {},
+            "summary": {
+                "mode": "search",
+                "M": 1.0,
+                "u": 0.0001,
+                "n": n_value,
+                "accepted": True,
+                "threshold_T": threshold,
+                "baseline_extinctions": 0,
+                "check_1_02_extinctions": 0,
+                "check_1_05_extinctions": 0,
+                "check_1_10_extinctions": 0,
+            },
+            "error": None,
+        }
+        orch.complete_job(db_path, result)
+
+    payload = orch.collate_track1_figure1(db_path)
+    assert payload["treatment_count"] == 1
+    treatment = payload["treatments"][0]
+    assert treatment["M"] == 1.0
+    assert [row["n"] for row in treatment["rows"]] == [1, 2, 3]
+    assert treatment["fit"] is not None
+    assert treatment["fit"]["points_used"] == 3
+
+
+def test_expand_track1_figure1_manifest_splits_by_locus():
+    config = {
+        "mode": "loci_regression",
+        "K": 5000,
+        "N0": 5000,
+        "n": 1,
+        "u": 0.0001,
+        "R": 10.0,
+        "T": 500,
+        "epochs": 8,
+        "p": 0.5,
+        "runs": 20,
+        "jobs": 8,
+        "t_values": [1, 2, 4, 6],
+        "loci_values": [1, 3, 5],
+        "seed": 10,
+    }
+    manifests = orch.expand_track1_figure1_manifest(
+        base_job_id_prefix="fig1-m10",
+        config=config,
+        priority=7,
+        created_by="test",
+    )
+    assert [manifest["job_id"] for manifest in manifests] == [
+        "fig1-m10-n1",
+        "fig1-m10-n3",
+        "fig1-m10-n5",
+    ]
+    assert all(manifest["job_kind"] == "track1_locus_threshold" for manifest in manifests)
+    assert all(manifest["config"]["mode"] == "search" for manifest in manifests)
+    assert [manifest["config"]["n"] for manifest in manifests] == [1, 3, 5]
+    assert all("loci_values" not in manifest["config"] for manifest in manifests)
+    assert all(manifest["project"] == "renunney" for manifest in manifests)
+
+
+def test_submit_track1_figure1_jobs_registers_expanded_jobs(tmp_path: Path):
+    db_path = tmp_path / "jobs.sqlite"
+    orch.initialize_registry(db_path)
+    config = {
+        "mode": "loci_regression",
+        "K": 5000,
+        "N0": 5000,
+        "n": 1,
+        "u": 0.0001,
+        "R": 10.0,
+        "T": 500,
+        "epochs": 8,
+        "p": 0.5,
+        "runs": 20,
+        "jobs": 8,
+        "t_values": [1, 2, 4],
+        "loci_values": [2, 4],
+        "seed": 10,
+    }
+    job_ids = orch.submit_track1_figure1_jobs(
+        db_path=db_path,
+        base_job_id_prefix="fig1-m10",
+        config=config,
+    )
+    assert job_ids == ["fig1-m10-n2", "fig1-m10-n4"]
+    jobs = orch.list_jobs(db_path)
+    assert len(jobs) == 2
+    assert {job["job_id"] for job in jobs} == set(job_ids)
+
+
+def test_run_worker_loop_processes_until_queue_empty(tmp_path: Path):
+    db_path = tmp_path / "jobs.sqlite"
+    result_root = tmp_path / "results"
+    scratch_root = tmp_path / "scratch"
+    orch.initialize_registry(db_path)
+    for idx in range(2):
+        manifest = {
+            "job_id": f"job-sim-{idx}",
+            "project": "renunney",
+            "track": "track1",
+            "job_kind": "track1_simulate",
+            "priority": 1,
+            "created_at": "2026-04-10T00:00:00Z",
+            "created_by": "test",
+            "worker_backend": "python-track1",
+            "config": {
+                "mode": "simulate",
+                "K": 500,
+                "N0": 500,
+                "n": 1,
+                "u": 0.001,
+                "R": 10.0,
+                "T": 10,
+                "epochs": 1,
+                "seed": idx + 1,
+            },
+            "resources": {"cpu_cores": 1},
+            "result_paths": {
+                "payload_json": f"payloads/job-sim-{idx}.json",
+                "log_txt": f"logs/job-sim-{idx}.log",
+            },
+            "retry": {"max_attempts": 1, "idempotent": True},
+            "notes": "",
+        }
+        orch.submit_job_manifest(db_path, manifest)
+
+    payload = orch.run_worker_loop(
+        db_path=db_path,
+        result_root=result_root,
+        worker_backend="python-track1",
+        worker_host="worker-a",
+        scratch_root=scratch_root,
+        cwd=ROOT,
+    )
+    assert payload["attempted_jobs"] == 2
+    assert payload["succeeded_jobs"] == 2
+    assert payload["failed_jobs"] == 0
+    assert payload["stopped_because"] == "queue_empty"
+    jobs = orch.list_jobs(db_path)
+    assert all(job["status"] == "succeeded" for job in jobs)