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Remove legacy runtime hooks from renunney Track 1 stack

This commit is contained in:
Codex 2026-04-11 07:01:58 -04:00
parent 7d8a0e622a
commit 15f6a6ac4a
7 changed files with 306 additions and 29 deletions
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5
Makefile
View File

@ -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)

10
README.md
View File

@ -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
plane and the Track 1 runner/API boundary are now local to `renunney`.
That earlier tree remains useful as provenance and historical context. The
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
migrated in later stages.
This repo is now the clean operational entry point for the Track 1 runtime and
its orchestration stack.

12
src/renunney/orchestration.py
View File

@ -17,12 +17,8 @@ from hashlib import sha256
from pathlib import Path
from typing import Any, Optional
from .legacy import ensure_legacy_python_path
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
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),

3
src/renunney/track1_analysis.py
View File

@ -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

6
src/renunney/track1_api.py
View File

@ -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:

3
src/renunney/track1_threshold.py
View File

@ -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

296
tests/test_orchestration.py Normal file
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@ -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)