Migrate Track 1 runner and API boundary into renunney
This commit is contained in:
Codex
parent
a880d9b99d
commit
a6d1326165
9
Makefile
9
Makefile
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@ -2,6 +2,7 @@ PYTHON := python3
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REPO_ROOT := $(abspath .)
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LEGACY_ROOT := $(REPO_ROOT)/../collaborations/to_ptbc/evc/cost_of_substitution
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ORCH := $(REPO_ROOT)/scripts/run_orchestration.py
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TRACK1 := $(REPO_ROOT)/scripts/run_track1.py
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DB := $(REPO_ROOT)/runs/state/cos-orch.sqlite
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RESULT_ROOT := $(REPO_ROOT)/runs/results
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@ -13,7 +14,7 @@ FIG1_M05 := $(REPO_ROOT)/config/track1_figure1_paper_M_0_5.json
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FIG1_M10 := $(REPO_ROOT)/config/track1_figure1_paper_M_1_0.json
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FIG1_M100 := $(REPO_ROOT)/config/track1_figure1_paper_M_10_0.json
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.PHONY: help init doctor list-jobs run-one run-loop run-loop-one collate-figure1 \
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.PHONY: help init doctor list-jobs run-one run-loop run-loop-one collate-figure1 track1-sim-smoke \
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submit-figure1-m005 submit-figure1-m025 submit-figure1-m05 submit-figure1-m10 submit-figure1-m100 \
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submit-all-figure1 status results-tree
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@ -22,6 +23,7 @@ help:
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@echo " init Create run directories and initialize the SQLite registry"
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@echo " doctor Show key paths and verify local orchestration and legacy backend paths"
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@echo " list-jobs List jobs in the local registry"
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@echo " track1-sim-smoke Run one local Track 1 simulation through renunney runner"
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@echo " run-one Claim and run one queued job"
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@echo " run-loop Run worker loop until queue empty"
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@echo " run-loop-one Run exactly one queued job through the worker loop"
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@ -43,15 +45,20 @@ doctor:
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@echo "REPO_ROOT=$(REPO_ROOT)"
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@echo "LEGACY_ROOT=$(LEGACY_ROOT)"
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@echo "ORCH=$(ORCH)"
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@echo "TRACK1=$(TRACK1)"
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@echo "DB=$(DB)"
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@echo "RESULT_ROOT=$(RESULT_ROOT)"
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@echo "SCRATCH_ROOT=$(SCRATCH_ROOT)"
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test -f $(ORCH)
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test -f $(TRACK1)
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test -d $(LEGACY_ROOT)/python
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list-jobs:
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$(PYTHON) $(ORCH) list --db $(DB)
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track1-sim-smoke:
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$(PYTHON) $(TRACK1) --mode simulate --K 5000 --N0 50 --n 1 --u 5e-6 --R 10 --T 40 --epochs 8 --seed 1
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run-one:
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$(PYTHON) $(ORCH) run-one --db $(DB) --result-root $(RESULT_ROOT) --scratch-root $(SCRATCH_ROOT)
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16
README.md
16
README.md
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@ -13,7 +13,7 @@ This repository is the clean operational wrapper around the current work in:
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- [`../collaborations/to_ptbc/evc/cost_of_substitution`](/mnt/CIFS/pengolodh/Docs/Projects/collaborations/to_ptbc/evc/cost_of_substitution)
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The Track 1 simulation backend still lives there. The orchestration control
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plane is now local to `renunney`.
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plane and the Track 1 runner/API boundary are now local to `renunney`.
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`renunney` provides:
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@ -21,6 +21,7 @@ plane is now local to `renunney`.
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- a stable working directory layout,
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- a local orchestration CLI and library,
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- local paper-scale Figure 1 submission configs,
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- a local Track 1 runner and config/API layer,
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- a Makefile for common tasks,
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- migration notes for pulling code into this repo in stages.
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@ -38,6 +39,10 @@ plane is now local to `renunney`.
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- local worker scratch and cache files
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- `src/renunney/`
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- future in-repo Python package and migration target
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- `scripts/`
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- local CLI entrypoints
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- `tests/`
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- local verification for migrated boundaries
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## Start
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@ -53,6 +58,12 @@ Submit a paper-scale Figure 1 treatment:
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make submit-figure1-m10
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```
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Run one local Track 1 simulation through the migrated runner/API boundary:
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```bash
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make track1-sim-smoke
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```
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Run one worker loop locally:
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```bash
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@ -70,8 +81,9 @@ make collate-figure1
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The current state is split:
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- orchestration control plane: local to `renunney`
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- Track 1 runner and config/API layer: local to `renunney`
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- Track 1 simulation backend: still in the older `cost_of_substitution`
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directory
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directory and imported through the local compatibility layer
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This repo is now the clean operational entry point while the simulation code is
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migrated in later stages.
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@ -24,15 +24,20 @@ Operational code still lives in:
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- `src/renunney/orchestration.py`
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- `scripts/run_orchestration.py`
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2. Paper-scale Figure 1 submission configs have been copied locally into `config/`.
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3. Keep the Track 1 simulation backend in the legacy path until real multi-host runs are stable.
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4. Migrate Track 1 runner and API next:
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- `python/run_track1.py`
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- `python/track1_api.py`
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3. Track 1 runner and API boundary have been migrated locally:
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- `scripts/run_track1.py`
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- `src/renunney/track1_api.py`
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4. Keep the Track 1 simulation backend in the legacy path until real multi-host runs are stable.
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5. Migrate the Track 1 simulation core after the runner path is stable:
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- `python/track1_reference.py`
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- `python/track1_threshold.py`
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- `python/track1_analysis.py`
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6. Migrate docs and example configs last, after path references are updated.
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6. Migrate report, dataset, fit, and orchestration-adjacent Track 1 modules after the kernel boundary is stable:
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- `python/track1_report.py`
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- `python/track1_dataset.py`
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- `python/track1_fit.py`
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- `python/track1_extinction.py`
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7. Migrate docs and example configs last, after path references are updated.
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## Constraint
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@ -14,6 +14,12 @@ Check paths:
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make doctor
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```
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Run one local Track 1 simulation through the in-repo runner:
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```bash
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make track1-sim-smoke
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```
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Submit a Figure 1 treatment:
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```bash
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@ -41,6 +47,7 @@ make status
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## Current Assumption
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The Makefile now drives the local orchestration code in `renunney`, while the
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simulation backend is still imported from the legacy `cost_of_substitution`
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directory. The paper-scale Figure 1 configs used for submission are now local
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to `renunney/config`.
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Track 1 runner/API boundary is also local to `renunney`. The simulation kernel
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is still imported from the legacy `cost_of_substitution` directory through the
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compatibility layer in `src/renunney/legacy.py`. The paper-scale Figure 1
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configs used for submission are now local to `renunney/config`.
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@ -0,0 +1,105 @@
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"""
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run_track1.py
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Local Track 1 runner entrypoint for renunney.
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"""
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from __future__ import annotations
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import argparse
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from pathlib import Path
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import sys
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REPO_ROOT = Path(__file__).resolve().parents[1]
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SRC_DIR = REPO_ROOT / "src"
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if str(SRC_DIR) not in sys.path:
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sys.path.insert(0, str(SRC_DIR))
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from renunney.track1_api import Track1RunConfig, load_config, run_config, save_payload
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def build_parser() -> argparse.ArgumentParser:
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parser = argparse.ArgumentParser(description="Run Track 1 cost-of-substitution experiments.")
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parser.add_argument("--mode", choices=["simulate", "report", "threshold", "search", "loci_regression", "extinction_dataset", "extinction_fit"], default="simulate")
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parser.add_argument("--config", type=str, default=None)
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parser.add_argument("--K", type=int, default=5000)
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parser.add_argument("--N0", type=int, default=500)
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parser.add_argument("--n", type=int, default=1)
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parser.add_argument("--u", type=float, default=5.0e-6)
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parser.add_argument("--M", type=float, default=None)
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parser.add_argument("--R", type=float, default=10.0)
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parser.add_argument("--T", type=int, default=300)
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parser.add_argument("--epochs", type=int, default=8)
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parser.add_argument("--p", type=float, default=0.5)
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parser.add_argument("--a-max", dest="a_max", type=int, default=None)
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parser.add_argument("--seed", type=int, default=0)
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parser.add_argument("--runs", type=int, default=20)
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parser.add_argument("--t-start", type=int, default=50)
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parser.add_argument("--t-stop", type=int, default=500)
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parser.add_argument("--t-step", type=int, default=10)
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parser.add_argument("--t-values", type=str, default=None)
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parser.add_argument("--loci-values", type=str, default=None)
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parser.add_argument("--cache-path", type=str, default=None)
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parser.add_argument("--jobs", type=int, default=1)
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parser.add_argument("--report-dir", type=str, default=None)
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parser.add_argument("--dataset-dir", type=str, default=None)
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parser.add_argument("--run-rows-path", type=str, default=None)
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parser.add_argument("--output", type=str, default=None)
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return parser
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def config_from_args(args: argparse.Namespace) -> Track1RunConfig:
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loci_values = None
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if args.loci_values:
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loci_values = [int(part.strip()) for part in args.loci_values.split(",") if part.strip()]
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t_values = None
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if args.t_values:
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t_values = [float(part.strip()) for part in args.t_values.split(",") if part.strip()]
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return Track1RunConfig(
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mode=args.mode,
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K=args.K,
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N0=args.N0,
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n=args.n,
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u=args.u if args.M is None else None,
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M=args.M,
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R=args.R,
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T=args.T,
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epochs=args.epochs,
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p=args.p,
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a_max=args.a_max,
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seed=args.seed,
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runs=args.runs,
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t_start=args.t_start,
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t_stop=args.t_stop,
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t_step=args.t_step,
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t_values=t_values,
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loci_values=loci_values,
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cache_path=args.cache_path,
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jobs=args.jobs,
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report_dir=args.report_dir,
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dataset_dir=args.dataset_dir,
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run_rows_path=args.run_rows_path,
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)
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def main() -> int:
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parser = build_parser()
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args = parser.parse_args()
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if args.config:
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config = load_config(args.config)
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else:
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config = config_from_args(args)
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payload = run_config(config)
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import json
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rendered = json.dumps(payload, indent=2, sort_keys=True)
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if args.output:
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save_payload(payload, Path(args.output))
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print(rendered)
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return 0
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if __name__ == "__main__":
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raise SystemExit(main())
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@ -18,6 +18,7 @@ from .orchestration import (
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submit_job_manifest,
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submit_track1_figure1_jobs,
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)
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from .track1_api import Track1RunConfig, config_from_mapping, load_config, run_config, save_payload
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__all__ = [
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"ClaimedJob",
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@ -39,4 +40,9 @@ __all__ = [
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"run_worker_loop",
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"submit_job_manifest",
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"submit_track1_figure1_jobs",
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"Track1RunConfig",
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"config_from_mapping",
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"load_config",
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"run_config",
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"save_payload",
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]
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@ -0,0 +1,289 @@
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"""
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track1_api.py
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Local Track 1 API boundary for renunney.
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This stage keeps the simulation backend in the legacy tree while moving the
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public config/runner contract into the clean repo.
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"""
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from __future__ import annotations
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import json
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from dataclasses import asdict, dataclass
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from pathlib import Path
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from typing import Any, Optional
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from .legacy import ensure_legacy_python_path
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ensure_legacy_python_path()
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from track1_analysis import summarize_tracking, sweep_number_of_loci
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from track1_dataset import generate_extinction_dataset
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from track1_fit import class_balance, fit_payload_from_jsonl, load_jsonl
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from track1_reference import Track1Parameters, simulate_run
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from track1_report import generate_report_bundle
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from track1_threshold import evaluate_threshold_candidate, search_threshold_over_candidates
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@dataclass(frozen=True, init=False)
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class Track1RunConfig:
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mode: str = "simulate"
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K: int = 5000
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N0: int = 500
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n: int = 1
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u: float = 5.0e-6
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R: float = 10.0
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T: int = 300
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epochs: int = 8
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p: float = 0.5
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a_max: Optional[int] = None
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seed: int = 0
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runs: int = 20
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t_start: int = 50
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t_stop: int = 500
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t_step: int = 10
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t_values: Optional[list[float]] = None
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loci_values: Optional[list[int]] = None
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cache_path: Optional[str] = None
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jobs: int = 1
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report_dir: Optional[str] = None
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dataset_dir: Optional[str] = None
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run_rows_path: Optional[str] = None
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grid: Optional[dict[str, list[Any]]] = None
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def __init__(
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self,
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mode: str = "simulate",
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K: int = 5000,
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N0: int = 500,
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n: int = 1,
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u: float | None = 5.0e-6,
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R: float = 10.0,
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T: int = 300,
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epochs: int = 8,
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p: float = 0.5,
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a_max: Optional[int] = None,
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seed: int = 0,
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runs: int = 20,
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t_start: int = 50,
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t_stop: int = 500,
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t_step: int = 10,
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t_values: Optional[list[float]] = None,
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loci_values: Optional[list[int]] = None,
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cache_path: Optional[str] = None,
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jobs: int = 1,
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report_dir: Optional[str] = None,
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dataset_dir: Optional[str] = None,
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run_rows_path: Optional[str] = None,
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grid: Optional[dict[str, list[Any]]] = None,
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M: float | None = None,
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) -> None:
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if u is None:
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if M is None:
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raise ValueError("Track1RunConfig requires u, or convenience M to derive u.")
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u = float(M / (2.0 * K))
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object.__setattr__(self, "mode", mode)
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object.__setattr__(self, "K", int(K))
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object.__setattr__(self, "N0", int(N0))
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object.__setattr__(self, "n", int(n))
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object.__setattr__(self, "u", float(u))
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object.__setattr__(self, "R", float(R))
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object.__setattr__(self, "T", int(T))
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object.__setattr__(self, "epochs", int(epochs))
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object.__setattr__(self, "p", float(p))
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object.__setattr__(self, "a_max", a_max)
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object.__setattr__(self, "seed", int(seed))
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object.__setattr__(self, "runs", int(runs))
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object.__setattr__(self, "t_start", int(t_start))
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object.__setattr__(self, "t_stop", int(t_stop))
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object.__setattr__(self, "t_step", int(t_step))
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object.__setattr__(self, "t_values", t_values)
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object.__setattr__(self, "loci_values", loci_values)
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object.__setattr__(self, "cache_path", cache_path)
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object.__setattr__(self, "jobs", int(jobs))
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object.__setattr__(self, "report_dir", report_dir)
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object.__setattr__(self, "dataset_dir", dataset_dir)
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object.__setattr__(self, "run_rows_path", run_rows_path)
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object.__setattr__(self, "grid", grid)
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@property
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def M(self) -> float:
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return float(2.0 * self.K * self.u)
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def to_parameters(self) -> Track1Parameters:
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return Track1Parameters(
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K=self.K,
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N0=self.N0,
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n=self.n,
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u=self.u,
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R=self.R,
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T=self.T,
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epochs=self.epochs,
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p=self.p,
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a_max=self.a_max,
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)
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def parameter_payload(params: Track1Parameters) -> dict[str, Any]:
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payload = asdict(params)
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payload["M"] = params.M
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return payload
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def config_from_mapping(mapping: dict[str, Any]) -> Track1RunConfig:
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allowed = set(Track1RunConfig.__dataclass_fields__.keys())
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filtered = {key: value for key, value in mapping.items() if key in allowed}
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if "M" in mapping and "u" not in filtered:
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filtered["M"] = mapping["M"]
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return Track1RunConfig(**filtered)
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def load_config(path: str | Path) -> Track1RunConfig:
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raw = json.loads(Path(path).read_text(encoding="utf-8"))
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return config_from_mapping(raw)
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def save_payload(payload: dict[str, Any], path: str | Path) -> None:
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out = Path(path)
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out.parent.mkdir(parents=True, exist_ok=True)
|
||||
out.write_text(json.dumps(payload, indent=2, sort_keys=True) + "\n", encoding="utf-8")
|
||||
|
||||
|
||||
def run_config(config: Track1RunConfig) -> dict[str, Any]:
|
||||
params = config.to_parameters()
|
||||
candidate_values = (
|
||||
[float(value) for value in config.t_values]
|
||||
if config.t_values is not None
|
||||
else list(range(config.t_start, config.t_stop + 1, config.t_step))
|
||||
)
|
||||
|
||||
if config.mode == "simulate":
|
||||
summaries = simulate_run(params, seed=config.seed)
|
||||
return {
|
||||
"mode": "simulate",
|
||||
"parameters": parameter_payload(params),
|
||||
"generations_recorded": len(summaries),
|
||||
"extinct": bool(summaries[-1].extinct) if summaries else True,
|
||||
"tracking_summary": asdict(summarize_tracking(summaries)),
|
||||
"final_summary": asdict(summaries[-1]) if summaries else None,
|
||||
}
|
||||
|
||||
if config.mode == "report":
|
||||
report_dir = config.report_dir or "/tmp/track1-report"
|
||||
return generate_report_bundle(
|
||||
params=params,
|
||||
runs=config.runs,
|
||||
seed_start=config.seed,
|
||||
report_dir=report_dir,
|
||||
)
|
||||
|
||||
if config.mode == "extinction_dataset":
|
||||
dataset_dir = config.dataset_dir or "/tmp/track1-extinction-dataset"
|
||||
metadata = generate_extinction_dataset(
|
||||
params=params,
|
||||
runs=config.runs,
|
||||
seed_start=config.seed,
|
||||
dataset_dir=dataset_dir,
|
||||
grid=config.grid,
|
||||
)
|
||||
return {
|
||||
"mode": "extinction_dataset",
|
||||
"parameters": parameter_payload(params),
|
||||
**metadata,
|
||||
}
|
||||
|
||||
if config.mode == "extinction_fit":
|
||||
run_rows_path = config.run_rows_path
|
||||
if run_rows_path is None:
|
||||
dataset_dir = config.dataset_dir or "/tmp/track1-extinction-dataset"
|
||||
run_rows_path = str(Path(dataset_dir) / "run_rows.jsonl")
|
||||
try:
|
||||
payload = fit_payload_from_jsonl(run_rows_path)
|
||||
fit_status = "ok"
|
||||
fit_error = None
|
||||
except ValueError as exc:
|
||||
rows = load_jsonl(run_rows_path)
|
||||
payload = {
|
||||
"run_rows_path": str(Path(run_rows_path)),
|
||||
"model": None,
|
||||
"summary": asdict(class_balance(rows)),
|
||||
}
|
||||
fit_status = "insufficient_outcome_variation"
|
||||
fit_error = str(exc)
|
||||
return {
|
||||
"mode": "extinction_fit",
|
||||
"parameters": parameter_payload(params),
|
||||
"fit_status": fit_status,
|
||||
"fit_error": fit_error,
|
||||
**payload,
|
||||
}
|
||||
|
||||
if config.mode == "threshold":
|
||||
result = evaluate_threshold_candidate(
|
||||
params=params,
|
||||
T_value=float(config.T),
|
||||
runs=config.runs,
|
||||
seed_start=config.seed,
|
||||
cache_path=config.cache_path,
|
||||
jobs=config.jobs,
|
||||
)
|
||||
return {
|
||||
"mode": "threshold",
|
||||
"parameters": parameter_payload(params),
|
||||
"result": {
|
||||
"threshold_T": result.threshold_T,
|
||||
"baseline_check": asdict(result.baseline_check),
|
||||
"check_1_02": asdict(result.check_1_02),
|
||||
"check_1_05": asdict(result.check_1_05),
|
||||
"check_1_10": asdict(result.check_1_10),
|
||||
"retest_check": asdict(result.retest_check) if result.retest_check else None,
|
||||
},
|
||||
}
|
||||
|
||||
if config.mode == "search":
|
||||
result = search_threshold_over_candidates(
|
||||
params=params,
|
||||
candidate_T_values=candidate_values,
|
||||
runs=config.runs,
|
||||
seed_start=config.seed,
|
||||
cache_path=config.cache_path,
|
||||
jobs=config.jobs,
|
||||
)
|
||||
return {
|
||||
"mode": "search",
|
||||
"parameters": parameter_payload(params),
|
||||
"candidates": candidate_values,
|
||||
"result": None
|
||||
if result is None
|
||||
else {
|
||||
"threshold_T": result.threshold_T,
|
||||
"baseline_check": asdict(result.baseline_check),
|
||||
"check_1_02": asdict(result.check_1_02),
|
||||
"check_1_05": asdict(result.check_1_05),
|
||||
"check_1_10": asdict(result.check_1_10),
|
||||
"retest_check": asdict(result.retest_check) if result.retest_check else None,
|
||||
},
|
||||
}
|
||||
|
||||
if config.mode == "loci_regression":
|
||||
loci_values = config.loci_values if config.loci_values is not None else [1, 2, 3, 4, 5, 6, 7]
|
||||
sweep = sweep_number_of_loci(
|
||||
params=params,
|
||||
loci_values=loci_values,
|
||||
candidate_T_values=candidate_values,
|
||||
runs=config.runs,
|
||||
seed_start=config.seed,
|
||||
cache_path=config.cache_path,
|
||||
jobs=config.jobs,
|
||||
)
|
||||
return {
|
||||
"mode": "loci_regression",
|
||||
"parameters": parameter_payload(params),
|
||||
"loci_values": loci_values,
|
||||
"candidates": candidate_values,
|
||||
"rows": [asdict(row) for row in sweep.rows],
|
||||
"fit": None if sweep.fit is None else asdict(sweep.fit),
|
||||
}
|
||||
|
||||
raise ValueError(f"Unsupported Track 1 mode: {config.mode}")
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
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))
|
||||
|
||||
from renunney import track1_api as api
|
||||
|
||||
|
||||
def test_run_config_simulate_mode_returns_contract():
|
||||
config = api.Track1RunConfig(mode="simulate", K=5000, N0=20, n=1, u=5e-6, R=10.0, T=20, seed=1)
|
||||
payload = api.run_config(config)
|
||||
assert payload["mode"] == "simulate"
|
||||
assert payload["parameters"]["u"] == 5e-6
|
||||
assert payload["parameters"]["M"] == 0.05
|
||||
assert "final_summary" in payload
|
||||
assert "tracking_summary" in payload
|
||||
|
||||
|
||||
def test_config_roundtrip_from_mapping_and_file(tmp_path: Path):
|
||||
raw = {
|
||||
"mode": "search",
|
||||
"K": 5000,
|
||||
"N0": 20,
|
||||
"n": 1,
|
||||
"u": 5e-6,
|
||||
"R": 10.0,
|
||||
"T": 20,
|
||||
"runs": 1,
|
||||
"jobs": 1,
|
||||
"t_values": [5, 10],
|
||||
}
|
||||
cfg = api.config_from_mapping(raw)
|
||||
path = tmp_path / "track1.json"
|
||||
path.write_text(json.dumps(raw), encoding="utf-8")
|
||||
loaded = api.load_config(path)
|
||||
assert loaded == cfg
|
||||
Loading…
Reference in New Issue