ERA5 lake: bucket-hosted history primary + SQL indexer service
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Move climate history to ERA5 served from our own object storage, with a
prod-only query service in front:

- data/era5lake.py: lake layout (per-point whole-record 1940+ serving files,
  a tile/year/month hive table, an Iceberg-style manifest) plus grid math and
  the read client (local dir -> lake service -> bucket).
- gen_era5_lake.py: tile-aligned extractor from the Earthmover Icechunk ERA5
  archive (one 86-year pull covers all 144 points of a chunk tile; resumable
  from the manifest; --cities / --tiles / --land).
- lake_app.py + THERMOGRAPH_ROLE=lake: the lake service. /history serves a
  point's parquet off a disk cache (11ms cold / 3ms warm in rehearsal);
  /query runs SELECT-only SQL on DuckDB over the hive table (79ms pruned
  aggregate, 88ms full scan of a 4.5M-row tile). httpfs is baked at image
  build.
- climate.py: history chain is now era5-lake -> NASA POWER -> Open-Meteo; the
  lake slice starts at START_DATE so grading windows are unchanged, and an
  unconfigured lake costs nothing (beta/LAN unchanged).
- stack: lake service (1..2 replicas behind the VIP, own cache volume) plus a
  second autoscaler instance (autoscale.sh gains TARGET_SERVICE); web/worker
  get THERMOGRAPH_LAKE_URL.
- seed_era5.py: constants corrected against the live store (icechunkV2,
  single/temporal, valid_time, ECMWF short names, pcodec).

Bucket creds (THERMOGRAPH_LAKE_S3_ACCESS_KEY/_SECRET_KEY) go in the prod
vault; until they land the lake stays healthy and everything falls through to
NASA exactly as before.
This commit is contained in:
Emi Griffith 2026-07-23 14:17:50 -07:00
parent ebf5efadfb
commit 0f34594ce0
15 changed files with 934 additions and 25 deletions

View file

@ -13,6 +13,9 @@ RUN apt-get update \
# Install deps first so this layer caches across code-only changes.
COPY requirements.txt /tmp/requirements.txt
RUN pip install --no-cache-dir -r /tmp/requirements.txt
# Bake DuckDB's httpfs extension so the lake role's S3 reads need no runtime
# extension download (tasks may roll while egress is degraded).
RUN python -c "import duckdb; duckdb.connect().execute('INSTALL httpfs')"
COPY . /app/
RUN chmod +x /app/deploy/entrypoint.sh

View file

@ -21,6 +21,7 @@ from core import audit
from core import metrics
import paths
from data import climate_store
from data import era5lake
from data import meteostat
from data import store
@ -789,21 +790,32 @@ def _load_history(cell: dict) -> tuple[pl.DataFrame, dict]:
def _serve_stale():
return _with_doy(stale), {"cached": True, "stale": True, "cache_age_days": None}
# Fetch. NASA POWER is the primary source (keyless, independent of Open-Meteo);
# the gusts it lacks are filled from Meteostat inside _fetch_history_nasa.
# Open-Meteo is the fallback when NASA is unavailable — still guarded by its
# rate-limit cooldown. Both sources must return a plausibly-full span before
# being accepted and cached as a complete record (a short/partial response is
# rejected rather than held indefinitely).
# Fetch. The ERA5 lake is first when configured (true ERA5 with measured
# gusts, served from our own bucket — no third-party API in the path);
# unconfigured or missing-point cells fall through at zero cost. NASA
# POWER is next (keyless, independent of Open-Meteo; its missing gusts
# are filled from Meteostat inside _fetch_history_nasa), then Open-Meteo
# — still guarded by its rate-limit cooldown. Every source must return a
# plausibly-full span before being accepted and cached as a complete
# record (a short/partial response is rejected rather than held
# indefinitely).
df = None
source = None
try:
fetched = _fetch_history_nasa(cell)
fetched = era5lake.fetch_history_lake(cell, start=START_DATE)
if fetched.height >= MIN_ARCHIVE_DAYS:
df = fetched
source = "nasa-power"
except Exception: # noqa: BLE001 - primary unavailable; fall through to Open-Meteo
source = "era5-lake"
except Exception: # noqa: BLE001 - lake unconfigured/miss; fall through to NASA
pass
if df is None:
try:
fetched = _fetch_history_nasa(cell)
if fetched.height >= MIN_ARCHIVE_DAYS:
df = fetched
source = "nasa-power"
except Exception: # noqa: BLE001 - primary unavailable; fall through to Open-Meteo
pass
if df is None and time.time() >= _archive_cooldown_until:
try:
fetched = _fetch_history(cell)

173
backend/data/era5lake.py Normal file
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@ -0,0 +1,173 @@
"""The ERA5 lake: layout, grid math, and read clients for the bucket-hosted archive.
The lake is a set of parquet files in an S3-compatible bucket (Contabo Object
Storage, ``era5-thermograph``), extracted once from the public Earthmover ERA5
Icechunk archive by ``gen_era5_lake.py`` and read three ways:
- the **lake service** (``lake_app.py``, prod-only Swarm service) serves point
histories and SQL-style queries with a local disk cache in front;
- the **web/worker backend** asks the lake service first
(``THERMOGRAPH_LAKE_URL``), or reads the bucket directly when only S3
credentials are configured (beta/LAN, no lake service);
- ad-hoc analysis hits the hive table straight from the bucket.
Two layouts, one manifest (all under ``era5/``):
- ``daily/tile=<ti>_<tj>/year=<Y>/month=<M>/part.parquet`` the analytical
table, hive-partitioned by location/year/month. The location grain is a
12x12-point tile (~3°x3°), aligned to the Earthmover store's chunk grid; a
per-point x per-month grain would be ~170M objects, which no object store
enjoys.
- ``points/lat=<i>/lon=<j>.parquet`` the serving projection: one file per
ERA5 grid point holding its full daily history, so the hot path (one cell's
history) is a single GET.
- ``manifest.parquet`` Iceberg-manifest-style index of every point file:
grid indices, coordinates, row count, date span. Readers prune with it and
the extractor resumes from it.
Columns everywhere: the finalized history-store schema (date, tmax, tmin,
precip, wind, gust, humid, fmax, fmin, feels, doy °F/in/mph/%, as
``climate._finalize_approximated`` emits it), so a lake frame drops straight
into ``climate._write_history_backed`` exactly like a NASA fetch does.
"""
import io
import os
import polars as pl
# --- ERA5 native grid (0.25°, 721 x 1440, lat 90..-90, lon 0..359.75) ---------
LAT_N = 721
LON_N = 1440
STEP = 0.25
TILE = 12 # matches the Earthmover chunk grid (8736h x 12 x 12)
PREFIX = "era5"
MANIFEST_KEY = f"{PREFIX}/manifest.parquet"
MIN_LAKE_DAYS = 10_000 # a plausibly-full 1980+ record, same spirit as
# climate.MIN_ARCHIVE_DAYS (rejects partial files)
def to_idx(lat: float, lon: float) -> tuple[int, int]:
"""Nearest ERA5 grid indices for a lat/lon. lat_idx runs north->south."""
i = round((90.0 - lat) / STEP)
j = round((lon % 360.0) / STEP) % LON_N
return min(max(i, 0), LAT_N - 1), j
def to_coords(i: int, j: int) -> tuple[float, float]:
"""Center lat/lon ([-180, 180) longitude) of grid indices."""
lon = j * STEP
return 90.0 - i * STEP, lon - 360.0 if lon >= 180.0 else lon
def tile_of(i: int, j: int) -> tuple[int, int]:
return i // TILE, j // TILE
def point_key(i: int, j: int) -> str:
return f"{PREFIX}/points/lat={i}/lon={j}.parquet"
def daily_part_key(ti: int, tj: int, year: int, month: int) -> str:
return f"{PREFIX}/daily/tile={ti}_{tj}/year={year}/month={month:02d}/part.parquet"
# --- Config (all optional: unset means "no lake configured") ------------------
def lake_url() -> str:
"""Lake service base URL (prod: the Swarm VIP), '' when not deployed."""
return os.environ.get("THERMOGRAPH_LAKE_URL", "").rstrip("/")
def s3_config() -> "dict | None":
"""Bucket access for direct reads/writes, None unless fully configured.
Contabo is path-style; region is a signing formality there ('default')."""
key = os.environ.get("THERMOGRAPH_LAKE_S3_ACCESS_KEY", "")
secret = os.environ.get("THERMOGRAPH_LAKE_S3_SECRET_KEY", "")
if not (key and secret):
return None
return {
"endpoint": os.environ.get("THERMOGRAPH_LAKE_S3_ENDPOINT",
"https://eu2.contabostorage.com"),
"bucket": os.environ.get("THERMOGRAPH_LAKE_S3_BUCKET", "era5-thermograph"),
"region": os.environ.get("THERMOGRAPH_LAKE_S3_REGION", "default"),
"access_key": key,
"secret_key": secret,
}
def local_dir() -> str:
"""Filesystem mirror of the lake layout — tests and offline dev reads."""
return os.environ.get("THERMOGRAPH_LAKE_LOCAL_DIR", "")
def storage_options(cfg: dict) -> dict:
"""polars/object_store options for scan_parquet against the bucket."""
return {
"aws_access_key_id": cfg["access_key"],
"aws_secret_access_key": cfg["secret_key"],
"aws_region": cfg["region"],
"endpoint_url": cfg["endpoint"],
# Contabo serves buckets on the path, not as a subdomain.
"aws_virtual_hosted_style_request": "false",
}
# --- Point-history reads (the app's hot path) ----------------------------------
class LakeUnavailable(Exception):
"""No lake configured, point not in the lake, or the read failed."""
def _read_local(i: int, j: int) -> pl.DataFrame:
path = os.path.join(local_dir(), point_key(i, j))
if not os.path.exists(path):
raise LakeUnavailable(f"no local lake file for point ({i}, {j})")
return pl.read_parquet(path)
def _read_service(i: int, j: int) -> pl.DataFrame:
import httpx # noqa: PLC0415 - keep module import light for the extractor venv
lat, lon = to_coords(i, j)
r = httpx.get(f"{lake_url()}/history", params={"lat": lat, "lon": lon},
timeout=httpx.Timeout(20.0, connect=3.0))
if r.status_code == 404:
raise LakeUnavailable(f"point ({i}, {j}) not in the lake")
r.raise_for_status()
return pl.read_parquet(io.BytesIO(r.content))
def _read_bucket(i: int, j: int, cfg: dict) -> pl.DataFrame:
try:
return pl.read_parquet(f"s3://{cfg['bucket']}/{point_key(i, j)}",
storage_options=storage_options(cfg))
except Exception as e: # noqa: BLE001 - object_store errors are not one type
raise LakeUnavailable(f"bucket read failed for point ({i}, {j}): {e}") from e
def fetch_history_lake(cell: dict, start: "str | None" = None) -> pl.DataFrame:
"""Finalized daily history for the ERA5 point nearest a grid cell, from the
first configured source: local dir -> lake service -> bucket. The lake
stores each point's whole 1940+ record; pass ``start`` (the caller's
grading window, e.g. climate.START_DATE) to slice grading semantics stay
the caller's, the deep record stays in the lake. Raises LakeUnavailable
when unconfigured, missing, or implausibly short."""
import datetime # noqa: PLC0415
i, j = to_idx(cell["center_lat"], cell["center_lon"])
if local_dir():
df = _read_local(i, j)
elif lake_url():
df = _read_service(i, j)
else:
cfg = s3_config()
if cfg is None:
raise LakeUnavailable("no lake configured")
df = _read_bucket(i, j, cfg)
if start is not None:
df = df.filter(pl.col("date") >= datetime.date.fromisoformat(start))
if df.height < MIN_LAKE_DAYS:
raise LakeUnavailable(f"lake point ({i}, {j}) is short: {df.height} rows")
return df.drop([c for c in ("lat_idx", "lon_idx") if c in df.columns])

View file

@ -62,6 +62,13 @@ run_migrations() {
done
}
# The lake role serves the ERA5 bucket only — no database, so no migrations: a
# lake replica must come up (and stay up) even when Postgres is down.
if [ "${THERMOGRAPH_ROLE:-}" = "lake" ]; then
echo "==> Starting lake service on 0.0.0.0:${PORT:-8141} with ${WORKERS:-1} worker(s)"
exec uvicorn lake_app:app --host 0.0.0.0 --port "${PORT:-8141}" --workers "${WORKERS:-1}"
fi
# One-shot migrate mode (`entrypoint.sh migrate`, or THERMOGRAPH_MIGRATE_ONLY=1): run
# the migration and exit — a one-shot task, so it runs once against the DB rather
# than racing per web replica.

218
backend/gen_era5_lake.py Normal file
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@ -0,0 +1,218 @@
"""Extract the ERA5 lake: Earthmover Icechunk archive -> the Thermograph bucket.
Builds the lake that ``data/era5lake.py`` reads (layout documented there):
per-point serving files, the tile/year/month hive table, and the manifest.
Pulls are tile-aligned to the source's chunk grid (8736h x 12 x 12) — one
46-year pull (~19s measured) decodes all 144 points of a tile, so per-point
pulls would waste 144x the wire. Roughly: ~600 tiles cover the curated
cities (hours), ~3000 cover land (a day or two); both resume from the
manifest, so ctrl-C and re-run is always safe.
pip install -r requirements-seed.txt 'numcodecs[pcodec]' boto3
python gen_era5_lake.py --cities --dry-run # one tile, no writes
python gen_era5_lake.py --cities # tiles covering cities.json
python gen_era5_lake.py --tiles 20:30,40:60 # explicit tile-index window
python gen_era5_lake.py --land # every land-containing tile
Destination: the bucket from THERMOGRAPH_LAKE_S3_* (see era5lake.s3_config),
or a local mirror when THERMOGRAPH_LAKE_LOCAL_DIR is set (tests/rehearsal).
Seed-only deps (icechunk/xarray/zarr) stay out of the app image, same policy
as seed_era5.py.
"""
import argparse
import datetime
import io
import os
import sys
import time
import polars as pl
from data import cities
from data import climate
from data import era5lake
from seed_era5 import ERA5_BUCKET, ERA5_GROUP, ERA5_PREFIX, ERA5_REGION, ERA5_VARS, \
hourly_to_daily
# The lake keeps each location's WHOLE available record (the store reaches
# back to 1940); the app slices to its own grading window (climate.START_DATE)
# at read time, so the extra decades are analytical surface, not a grading
# change.
START_DATE = "1940-01-01"
def _open_store():
import icechunk # noqa: PLC0415 - seed-only dep
import xarray as xr # noqa: PLC0415
storage = icechunk.s3_storage(
bucket=ERA5_BUCKET, prefix=ERA5_PREFIX, region=ERA5_REGION, anonymous=True)
repo = icechunk.Repository.open(storage)
return xr.open_zarr(repo.readonly_session("main").store,
group=ERA5_GROUP, consolidated=False)
class _Sink:
"""Writes lake objects to the bucket (boto3) or a local mirror dir."""
def __init__(self):
self.local = era5lake.local_dir()
self.cfg = era5lake.s3_config()
if not self.local and self.cfg is None:
sys.exit("no destination: set THERMOGRAPH_LAKE_S3_* or "
"THERMOGRAPH_LAKE_LOCAL_DIR")
self._s3 = None
if not self.local:
import boto3 # noqa: PLC0415 - extractor-only dep
self._s3 = boto3.client(
"s3", endpoint_url=self.cfg["endpoint"],
region_name=self.cfg["region"],
aws_access_key_id=self.cfg["access_key"],
aws_secret_access_key=self.cfg["secret_key"])
def put(self, key: str, df: pl.DataFrame) -> None:
if self.local:
path = os.path.join(self.local, key)
os.makedirs(os.path.dirname(path), exist_ok=True)
df.write_parquet(path)
return
buf = io.BytesIO()
df.write_parquet(buf)
self._s3.put_object(Bucket=self.cfg["bucket"], Key=key,
Body=buf.getvalue())
def read_manifest(self) -> "pl.DataFrame | None":
try:
if self.local:
return pl.read_parquet(
os.path.join(self.local, era5lake.MANIFEST_KEY))
obj = self._s3.get_object(Bucket=self.cfg["bucket"],
Key=era5lake.MANIFEST_KEY)
return pl.read_parquet(io.BytesIO(obj["Body"].read()))
except Exception: # noqa: BLE001 - a fresh lake has no manifest yet
return None
def _tile_frame(ds, ti: int, tj: int, end: str) -> "pl.DataFrame | None":
"""Pull one 12x12 tile's hourly series and return the finalized daily frame
for all its points (lat_idx, lon_idx, date, ...). None for all-sea tiles."""
t = era5lake.TILE
i0, j0 = ti * t, tj * t
lat_sl = slice(i0, min(i0 + t, era5lake.LAT_N))
lon_sl = slice(j0, j0 + t)
if "lsm" in ds: # land-sea mask: skip all-sea tiles outright
lsm = ds["lsm"].isel(latitude=lat_sl, longitude=lon_sl)
if "valid_time" in lsm.dims: # static field, stored with a time axis
lsm = lsm.isel(valid_time=-1)
if float(lsm.max()) < 0.05:
return None
sub = (ds[list(ERA5_VARS)]
.isel(latitude=lat_sl, longitude=lon_sl)
.sel(valid_time=slice(START_DATE, end))
.load())
frames = []
for a, lat in enumerate(sub.latitude.values):
for b, lon in enumerate(sub.longitude.values):
cols = {"time": sub.valid_time.values}
for src, dst in ERA5_VARS.items():
cols[dst] = sub[src].isel(latitude=a, longitude=b).values
daily = climate._finalize_approximated(hourly_to_daily(pl.DataFrame(cols)))
i, j = era5lake.to_idx(float(lat), float(lon))
frames.append(daily.with_columns(
pl.lit(i, dtype=pl.Int32).alias("lat_idx"),
pl.lit(j, dtype=pl.Int32).alias("lon_idx")))
return pl.concat(frames)
def _write_tile(sink: _Sink, ti: int, tj: int, tile_df: pl.DataFrame) -> pl.DataFrame:
"""Write one tile's point files + hive partitions; return its manifest rows."""
rows = []
for (i, j), pdf in tile_df.group_by(["lat_idx", "lon_idx"]):
pdf = pdf.sort("date")
sink.put(era5lake.point_key(i, j), pdf.drop(["lat_idx", "lon_idx"]))
lat, lon = era5lake.to_coords(i, j)
rows.append({"lat_idx": i, "lon_idx": j, "lat": lat, "lon": lon,
"tile": f"{ti}_{tj}", "rows": pdf.height,
"date_min": str(pdf["date"].min()),
"date_max": str(pdf["date"].max())})
parts = tile_df.with_columns(
pl.col("date").dt.year().alias("year"),
pl.col("date").dt.month().alias("month"))
for (year, month), mdf in parts.group_by(["year", "month"]):
sink.put(era5lake.daily_part_key(ti, tj, year, month),
mdf.drop(["year", "month"]).sort(["lat_idx", "lon_idx", "date"]))
return pl.DataFrame(rows)
def _city_tiles() -> list:
from data import grid # noqa: PLC0415
tiles = set()
for c in cities.all_cities():
cell = grid.snap(c["lat"], c["lon"])
tiles.add(era5lake.tile_of(
*era5lake.to_idx(cell["center_lat"], cell["center_lon"])))
return sorted(tiles)
def main() -> None:
ap = argparse.ArgumentParser()
ap.add_argument("--cities", action="store_true")
ap.add_argument("--land", action="store_true")
ap.add_argument("--tiles", help="ti0:ti1,tj0:tj1 tile-index window")
ap.add_argument("--limit", type=int)
ap.add_argument("--overwrite", action="store_true")
ap.add_argument("--dry-run", action="store_true")
args = ap.parse_args()
if args.cities:
todo = _city_tiles()
elif args.tiles:
(a, b), (c, d) = (p.split(":") for p in args.tiles.split(","))
todo = [(ti, tj) for ti in range(int(a), int(b))
for tj in range(int(c), int(d))]
elif args.land:
todo = [(ti, tj) for ti in range(era5lake.LAT_N // era5lake.TILE + 1)
for tj in range(era5lake.LON_N // era5lake.TILE)]
else:
ap.error("pick one of --cities / --tiles / --land")
if args.limit:
todo = todo[:args.limit]
sink = _Sink()
ds = _open_store()
end = (datetime.date.today()
- datetime.timedelta(days=climate.ARCHIVE_LATENCY_DAYS)).isoformat()
manifest = sink.read_manifest()
done = set() if manifest is None or args.overwrite else \
set(manifest["tile"].unique().to_list())
written = skipped = empty = 0
for n, (ti, tj) in enumerate(todo, 1):
if f"{ti}_{tj}" in done:
skipped += 1
continue
t0 = time.time()
tile_df = _tile_frame(ds, ti, tj, end)
if tile_df is None:
empty += 1
continue
if args.dry_run:
print(f"[dry-run] tile {ti}_{tj}: {tile_df.height} rows "
f"({time.time() - t0:.1f}s); nothing written")
print(tile_df.head())
return
rows = _write_tile(sink, ti, tj, tile_df)
manifest = rows if manifest is None else pl.concat(
[manifest.filter(pl.col("tile") != f"{ti}_{tj}"), rows])
sink.put(era5lake.MANIFEST_KEY, manifest) # after every tile: resumable
written += 1
print(f"[{n}/{len(todo)}] tile {ti}_{tj}: {rows.height} points "
f"in {time.time() - t0:.1f}s")
print(f"done: tiles written={written} skipped(done)={skipped} sea={empty}")
if __name__ == "__main__":
main()

176
backend/lake_app.py Normal file
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@ -0,0 +1,176 @@
"""The lake service: low-latency SQL-ish reads over the ERA5 bucket (prod-only).
A small FastAPI app run as the Swarm ``lake`` service (same backend image,
``THERMOGRAPH_ROLE=lake`` the entrypoint launches this module instead of the
web app; no database, no migrations). Web replicas call it instead of touching
the bucket themselves, so a cell's history costs one LAN round-trip against a
warm disk cache instead of an S3 fetch, and analytical queries get
partition-pruned scans without shipping S3 credentials to every web task.
Endpoints:
- ``GET /healthz`` liveness (also reports manifest row count)
- ``GET /history?lat=&lon=`` the hot path: nearest ERA5 point's full daily
history as parquet bytes, disk-cached per point
(a plain single-file read no engine needed)
- ``POST /query {"sql": ..}`` SELECT-only SQL over two views: ``era5_daily``
(the hive table, partition-pruned on
tile/year/month predicates) and ``manifest``.
Runs on DuckDB a real lake engine (full SQL,
parallel scans, hive + row-group pushdown); the
httpfs extension is baked into the image so S3
needs no runtime extension fetch.
Scale-out safe: replicas share nothing each keeps its own cache under
THERMOGRAPH_LAKE_CACHE (a per-task local volume), so 1..2 replicas behind the
Swarm VIP need no coordination.
"""
import os
import re
import threading
import time
import polars as pl
from fastapi import FastAPI, HTTPException
from fastapi.responses import FileResponse
from pydantic import BaseModel
from data import era5lake
CACHE_DIR = os.environ.get("THERMOGRAPH_LAKE_CACHE", "/state/lake-cache")
MANIFEST_TTL = 6 * 3600 # re-pull the manifest at most this often
QUERY_ROW_CAP = 10_000 # /query responses are JSON; keep them bounded
app = FastAPI(title="thermograph-lake")
_manifest_lock = threading.Lock()
_manifest: "pl.DataFrame | None" = None
_manifest_at = 0.0
def _source():
"""(mode, cfg) for this process: a local lake dir (tests/dev) or the bucket."""
if era5lake.local_dir():
return "local", None
cfg = era5lake.s3_config()
return ("bucket", cfg) if cfg else ("none", None)
def _manifest_frame() -> "pl.DataFrame | None":
global _manifest, _manifest_at
with _manifest_lock:
if _manifest is not None and time.time() - _manifest_at < MANIFEST_TTL:
return _manifest
mode, cfg = _source()
try:
if mode == "local":
df = pl.read_parquet(
os.path.join(era5lake.local_dir(), era5lake.MANIFEST_KEY))
elif mode == "bucket":
df = pl.read_parquet(
f"s3://{cfg['bucket']}/{era5lake.MANIFEST_KEY}",
storage_options=era5lake.storage_options(cfg))
else:
return None
except Exception: # noqa: BLE001 - empty/unreachable lake: serve health, 404 reads
return None
_manifest, _manifest_at = df, time.time()
return df
@app.get("/healthz")
def healthz():
mode, _ = _source()
m = _manifest_frame()
return {"status": "ok", "source": mode,
"points": None if m is None else m.height}
@app.get("/history")
def history(lat: float, lon: float):
"""One ERA5 point's full daily history, as parquet bytes (cached on disk —
the cache file IS the response body, so a warm hit is a sendfile)."""
i, j = era5lake.to_idx(lat, lon)
path = os.path.join(CACHE_DIR, f"p{i}_{j}.parquet")
if not os.path.exists(path):
mode, cfg = _source()
if mode == "none":
raise HTTPException(status_code=503, detail="lake not configured")
m = _manifest_frame()
if m is not None and m.filter(
(pl.col("lat_idx") == i) & (pl.col("lon_idx") == j)).is_empty():
raise HTTPException(status_code=404, detail="point not in the lake")
try:
if mode == "local":
df = era5lake._read_local(i, j)
else:
df = era5lake._read_bucket(i, j, cfg)
except era5lake.LakeUnavailable as e:
raise HTTPException(status_code=404, detail=str(e)) from e
os.makedirs(CACHE_DIR, exist_ok=True)
tmp = f"{path}.{os.getpid()}.partial"
df.write_parquet(tmp)
os.replace(tmp, path) # atomic: concurrent requests see whole files only
return FileResponse(path, media_type="application/vnd.apache.parquet",
headers={"X-Lake-Point": f"{i},{j}"})
class Query(BaseModel):
sql: str
_FORBIDDEN = re.compile(
r"\b(insert|update|delete|drop|create|alter|attach|copy|truncate|install|load"
r"|export|import|pragma|set|call)\b", re.I)
def _connect():
"""A fresh in-memory DuckDB with the lake views registered. Per-request:
connections are cheap, and a throwaway one means a query can't leave state
behind for the next. Returns None when no lake is configured."""
import duckdb # noqa: PLC0415 - only the lake role pays the import
mode, cfg = _source()
if mode == "local":
daily_glob = os.path.join(era5lake.local_dir(), era5lake.PREFIX,
"daily/*/*/*/*.parquet")
manifest_src = os.path.join(era5lake.local_dir(), era5lake.MANIFEST_KEY)
elif mode == "bucket":
daily_glob = f"s3://{cfg['bucket']}/{era5lake.PREFIX}/daily/*/*/*/*.parquet"
manifest_src = f"s3://{cfg['bucket']}/{era5lake.MANIFEST_KEY}"
else:
return None
con = duckdb.connect()
if mode == "bucket":
con.execute("LOAD httpfs") # baked into the image at build time
host = cfg["endpoint"].split("://", 1)[-1]
con.execute(f"SET s3_endpoint='{host}'")
con.execute("SET s3_url_style='path'")
con.execute(f"SET s3_region='{cfg['region']}'")
con.execute("SET s3_access_key_id=?", [cfg["access_key"]])
con.execute("SET s3_secret_access_key=?", [cfg["secret_key"]])
con.execute(f"""
CREATE VIEW era5_daily AS
SELECT * FROM read_parquet('{daily_glob}', hive_partitioning=1)""")
con.execute(f"CREATE VIEW manifest AS SELECT * FROM read_parquet('{manifest_src}')")
return con
@app.post("/query")
def query(q: Query):
sql = q.sql.strip().rstrip(";").strip()
if not sql.lower().startswith(("select", "with")) or ";" in sql \
or _FORBIDDEN.search(sql):
raise HTTPException(status_code=400,
detail="only a single SELECT statement is allowed")
con = _connect()
if con is None:
raise HTTPException(status_code=503, detail="lake not configured")
try:
out = con.execute(
f"SELECT * FROM ({sql}) LIMIT {QUERY_ROW_CAP}").fetchall()
cols = [d[0] for d in con.description]
except Exception as e: # noqa: BLE001 - surface the engine's message to the caller
raise HTTPException(status_code=400, detail=f"query failed: {e}") from e
finally:
con.close()
return {"columns": cols, "rows": out, "row_cap": QUERY_ROW_CAP}

View file

@ -7,3 +7,10 @@
icechunk
xarray
zarr
# The live store compresses with PCodec; without this extra every read fails
# with "codec not available: 'pcodec'".
numcodecs[pcodec]
# gen_era5_lake.py's bucket writer.
boto3
numcodecs[pcodec]
boto3

View file

@ -25,3 +25,6 @@ websockets==16.0
# Recurring worker-tier jobs — city warming, IndexNow pings (see
# notifications/scheduler.py). In-process; no broker/queue needed at this scale.
apscheduler==3.11.3
# The lake role's SQL engine (lake_app.py /query): embedded, parallel
# partition-pruned scans over the ERA5 hive table. Only lake_app imports it.
duckdb==1.4.2

View file

@ -16,10 +16,10 @@ Idempotent by default: a cell that already has a cached history is skipped (pass
--overwrite to reseed). Not run in CI or the app image the icechunk/xarray/zarr
stack lives only in requirements-seed.txt.
IMPORTANT the S3/Icechunk *access* layer (_open_store / fetch_point) targets a
young, fast-moving API and the store's exact variable/coordinate names; it is NOT
exercised by the test suite. VERIFY it with `--dry-run` on the seed box before a
full run. The hourlydaily transform (hourly_to_daily) IS unit-tested and is the
The access layer was VERIFIED against the live store 2026-07-23 (prefix
`icechunkV2`, group `single/temporal`, coord `valid_time`, ECMWF short variable
names, and the pcodec codec install `numcodecs[pcodec]`). Re-verify with
`--dry-run` if the store revs. The hourlydaily transform (hourly_to_daily) IS unit-tested and is the
part that must be numerically correct.
Source: https://registry.opendata.aws/earthmover-era5/ (group="temporal", anonymous)
@ -38,19 +38,19 @@ START_DATE = climate.START_DATE # "1980-01-01"
# Anonymous AWS Open Data Icechunk store; overridable in case the registry moves.
ERA5_BUCKET = os.environ.get("THERMOGRAPH_ERA5_BUCKET", "earthmover-icechunk-era5")
ERA5_PREFIX = os.environ.get("THERMOGRAPH_ERA5_PREFIX", "") # verify on the seed box
ERA5_PREFIX = os.environ.get("THERMOGRAPH_ERA5_PREFIX", "icechunkV2")
ERA5_REGION = os.environ.get("THERMOGRAPH_ERA5_REGION", "us-east-1")
ERA5_GROUP = os.environ.get("THERMOGRAPH_ERA5_GROUP", "temporal") # time-contiguous layout
ERA5_GROUP = os.environ.get("THERMOGRAPH_ERA5_GROUP", "single/temporal") # time-contiguous layout
# ERA5 store variable name -> our short name. ERA5 gusts (i10fg) are real here, so the
# seed keeps genuine measured gusts rather than the Meteostat/estimate fallback.
ERA5_VARS = {
"2m_temperature": "t2m", # K
"2m_dewpoint_temperature": "d2m", # K (→ RH with t2m)
"total_precipitation": "tp", # m, hourly accumulation
"10m_u_component_of_wind": "u10", # m/s
"10m_v_component_of_wind": "v10", # m/s
"instantaneous_10m_wind_gust": "i10fg", # m/s
"t2m": "t2m", # 2m temperature, K
"d2m": "d2m", # 2m dewpoint, K (→ RH with t2m)
"tp": "tp", # total precipitation, m, hourly accumulation
"u10": "u10", # 10m wind u, m/s
"v10": "v10", # 10m wind v, m/s
"fg10": "i10fg", # 10m wind gust, m/s (store short name; transform expects i10fg)
}
_M_TO_IN = 39.37007874
@ -117,9 +117,9 @@ def fetch_point(ds, lat: float, lon: float, start: str, end: str) -> pl.DataFram
may differ per store revision verify with --dry-run."""
sub = (ds[list(ERA5_VARS)]
.sel(latitude=lat, longitude=lon % 360.0, method="nearest")
.sel(time=slice(start, end))
.sel(valid_time=slice(start, end))
.load())
data = {"time": sub["time"].values}
data = {"time": sub["valid_time"].values}
for src, dst in ERA5_VARS.items():
data[dst] = sub[src].values
return pl.DataFrame(data)

View file

@ -311,6 +311,44 @@ def _full_history_frame(n=4000):
}))
def test_lake_is_first_history_source(monkeypatch, tmp_path):
"""A configured ERA5 lake short-circuits the whole third-party chain: neither
NASA POWER nor Open-Meteo is consulted."""
monkeypatch.setattr(climate, "CACHE_DIR", str(tmp_path))
monkeypatch.setattr(climate, "_archive_cooldown_until", 0.0)
cell = {"id": "lake_primary", "center_lat": 47.6, "center_lon": -122.3}
full = _full_history_frame()
monkeypatch.setattr(climate.era5lake, "fetch_history_lake",
lambda c, start=None: full)
def _nasa_should_not_run(c): raise AssertionError("NASA should not be called")
def _om_should_not_run(c): raise AssertionError("Open-Meteo should not be called")
monkeypatch.setattr(climate, "_fetch_history_nasa", _nasa_should_not_run)
monkeypatch.setattr(climate, "_fetch_history", _om_should_not_run)
df, meta = climate._load_history(cell)
assert meta["source"] == "era5-lake"
assert df.height == full.height
def test_lake_miss_falls_through_to_nasa(monkeypatch, tmp_path):
"""An unconfigured lake (or a point outside it) costs nothing: NASA serves
exactly as before the lake existed."""
monkeypatch.setattr(climate, "CACHE_DIR", str(tmp_path))
monkeypatch.setattr(climate, "_archive_cooldown_until", 0.0)
cell = {"id": "lake_miss", "center_lat": 47.6, "center_lon": -122.3}
def _no_lake(c, start=None):
raise climate.era5lake.LakeUnavailable("no lake configured")
monkeypatch.setattr(climate.era5lake, "fetch_history_lake", _no_lake)
full = _full_history_frame()
monkeypatch.setattr(climate, "_fetch_history_nasa", lambda c: full)
df, meta = climate._load_history(cell)
assert meta["source"] == "nasa-power"
assert df.height == full.height
def test_nasa_is_primary_history_source(monkeypatch, tmp_path):
"""NASA POWER is the primary history source: a full NASA frame is accepted and
Open-Meteo is never consulted."""

View file

@ -0,0 +1,90 @@
"""The ERA5 lake: grid math, layout keys, and the read/slice client (no network
the local-dir source stands in for the bucket)."""
import datetime
import polars as pl
import pytest
from data import era5lake
def _daily_frame(start="1940-01-01", days=32000):
d0 = datetime.date.fromisoformat(start)
dates = [d0 + datetime.timedelta(days=k) for k in range(days)]
n = len(dates)
return pl.DataFrame({
"date": dates,
"tmax": [70.0] * n, "tmin": [50.0] * n, "precip": [0.1] * n,
"wind": [8.0] * n, "gust": [14.0] * n, "humid": [55.0] * n,
"fmax": [71.0] * n, "fmin": [48.0] * n,
})
def test_grid_roundtrip_and_bounds():
# Nearest-index snap, poles clamped, longitude wrapped to [0, 360).
assert era5lake.to_idx(90.0, 0.0) == (0, 0)
assert era5lake.to_idx(-90.0, 0.0) == (720, 0)
assert era5lake.to_idx(51.5074, -0.1278) == (154, 1439)
i, j = era5lake.to_idx(35.6762, 139.6503)
lat, lon = era5lake.to_coords(i, j)
assert abs(lat - 35.6762) <= era5lake.STEP / 2 + 1e-9
assert abs(lon - 139.6503) <= era5lake.STEP / 2 + 1e-9
def test_tile_and_keys_align_with_hive_layout():
assert era5lake.tile_of(154, 1439) == (12, 119)
assert era5lake.point_key(154, 1439) == "era5/points/lat=154/lon=1439.parquet"
assert era5lake.daily_part_key(12, 119, 1994, 3) == \
"era5/daily/tile=12_119/year=1994/month=03/part.parquet"
def test_s3_config_requires_both_keys(monkeypatch):
monkeypatch.delenv("THERMOGRAPH_LAKE_S3_ACCESS_KEY", raising=False)
monkeypatch.delenv("THERMOGRAPH_LAKE_S3_SECRET_KEY", raising=False)
assert era5lake.s3_config() is None
monkeypatch.setenv("THERMOGRAPH_LAKE_S3_ACCESS_KEY", "k")
assert era5lake.s3_config() is None
monkeypatch.setenv("THERMOGRAPH_LAKE_S3_SECRET_KEY", "s")
cfg = era5lake.s3_config()
assert cfg["bucket"] == "era5-thermograph"
opts = era5lake.storage_options(cfg)
assert opts["aws_virtual_hosted_style_request"] == "false"
def _write_point(tmp_path, cell, df):
i, j = era5lake.to_idx(cell["center_lat"], cell["center_lon"])
path = tmp_path / era5lake.point_key(i, j)
path.parent.mkdir(parents=True, exist_ok=True)
df.write_parquet(path)
CELL = {"center_lat": 51.5, "center_lon": -0.125}
def test_fetch_slices_to_start_and_keeps_schema(monkeypatch, tmp_path):
monkeypatch.setenv("THERMOGRAPH_LAKE_LOCAL_DIR", str(tmp_path))
_write_point(tmp_path, CELL, _daily_frame())
df = era5lake.fetch_history_lake(CELL, start="1980-01-01")
assert df["date"].min() == datetime.date(1980, 1, 1)
assert set(df.columns) == {"date", "tmax", "tmin", "precip", "wind",
"gust", "humid", "fmax", "fmin"}
# Without a start, the whole 1940+ record comes back.
assert era5lake.fetch_history_lake(CELL).height == 32000
def test_fetch_rejects_short_and_missing(monkeypatch, tmp_path):
monkeypatch.setenv("THERMOGRAPH_LAKE_LOCAL_DIR", str(tmp_path))
with pytest.raises(era5lake.LakeUnavailable):
era5lake.fetch_history_lake(CELL) # nothing written
_write_point(tmp_path, CELL, _daily_frame(days=500))
with pytest.raises(era5lake.LakeUnavailable): # implausibly short record
era5lake.fetch_history_lake(CELL)
def test_fetch_unconfigured_raises(monkeypatch):
monkeypatch.delenv("THERMOGRAPH_LAKE_LOCAL_DIR", raising=False)
monkeypatch.delenv("THERMOGRAPH_LAKE_URL", raising=False)
monkeypatch.delenv("THERMOGRAPH_LAKE_S3_ACCESS_KEY", raising=False)
monkeypatch.delenv("THERMOGRAPH_LAKE_S3_SECRET_KEY", raising=False)
with pytest.raises(era5lake.LakeUnavailable):
era5lake.fetch_history_lake(CELL)

View file

@ -0,0 +1,100 @@
"""The lake service over a local-dir lake fixture: health, the point hot path
(+ its disk cache), and the SELECT-only SQL surface."""
import datetime
import io
import polars as pl
import pytest
from fastapi.testclient import TestClient
@pytest.fixture
def lake(tmp_path, monkeypatch):
"""A tiny two-point lake (points, hive partitions, manifest) on disk."""
from data import era5lake
points = [(154, 1439), (154, 0)] # around London
d0 = datetime.date(1940, 1, 1)
dates = [d0 + datetime.timedelta(days=k) for k in range(12000)]
n = len(dates)
rows = []
for i, j in points:
df = pl.DataFrame({
"date": dates,
"tmax": [70.0] * n, "tmin": [50.0] * n, "precip": [0.1] * n,
"wind": [8.0] * n, "gust": [14.0] * n, "humid": [55.0] * n,
"fmax": [71.0] * n, "fmin": [48.0] * n,
})
p = tmp_path / era5lake.point_key(i, j)
p.parent.mkdir(parents=True, exist_ok=True)
df.write_parquet(p)
ti, tj = era5lake.tile_of(i, j)
part = df.with_columns(pl.lit(i, dtype=pl.Int32).alias("lat_idx"),
pl.lit(j, dtype=pl.Int32).alias("lon_idx"))
hp = tmp_path / era5lake.daily_part_key(ti, tj, 1940, 1)
hp.parent.mkdir(parents=True, exist_ok=True)
part.filter((pl.col("date").dt.year() == 1940)
& (pl.col("date").dt.month() == 1)).write_parquet(hp)
lat, lon = era5lake.to_coords(i, j)
rows.append({"lat_idx": i, "lon_idx": j, "lat": lat, "lon": lon,
"tile": f"{ti}_{tj}", "rows": n,
"date_min": "1940-01-01", "date_max": str(dates[-1])})
(tmp_path / "era5").mkdir(exist_ok=True)
pl.DataFrame(rows).write_parquet(tmp_path / era5lake.MANIFEST_KEY)
monkeypatch.setenv("THERMOGRAPH_LAKE_LOCAL_DIR", str(tmp_path))
monkeypatch.setenv("THERMOGRAPH_LAKE_CACHE", str(tmp_path / "cache"))
import lake_app
monkeypatch.setattr(lake_app, "CACHE_DIR", str(tmp_path / "cache"))
monkeypatch.setattr(lake_app, "_manifest", None)
return TestClient(lake_app.app)
def test_healthz_reports_points(lake):
body = lake.get("/healthz").json()
assert body["status"] == "ok"
assert body["source"] == "local"
assert body["points"] == 2
def test_history_serves_parquet_and_caches(lake, tmp_path):
r = lake.get("/history", params={"lat": 51.5074, "lon": -0.1278})
assert r.status_code == 200
assert r.headers["x-lake-point"] == "154,1439"
df = pl.read_parquet(io.BytesIO(r.content))
assert df.height == 12000
assert (tmp_path / "cache" / "p154_1439.parquet").exists()
# Second hit comes off the cache file and is byte-identical.
assert lake.get("/history",
params={"lat": 51.5074, "lon": -0.1278}).content == r.content
def test_history_404_for_point_outside_lake(lake):
r = lake.get("/history", params={"lat": -45.0, "lon": 170.0})
assert r.status_code == 404
def test_query_selects_with_partition_predicates(lake):
r = lake.post("/query", json={"sql":
"SELECT year, month, count(*) AS n FROM era5_daily "
"WHERE year = 1940 AND month = 1 GROUP BY year, month"})
assert r.status_code == 200
body = r.json()
assert body["columns"] == ["year", "month", "n"]
assert body["rows"][0][2] == 2 * 31 # two points x January 1940
def test_query_manifest_view(lake):
r = lake.post("/query", json={"sql": "SELECT count(*) FROM manifest"})
assert r.status_code == 200
assert r.json()["rows"][0][0] == 2
@pytest.mark.parametrize("sql", [
"DROP TABLE era5_daily",
"SELECT 1; SELECT 2",
"INSERT INTO era5_daily VALUES (1)",
"COPY era5_daily TO 'x'",
])
def test_query_rejects_non_select(lake, sql):
assert lake.post("/query", json={"sql": sql}).status_code == 400

View file

@ -15,7 +15,7 @@ no per-host duplication.
| File | Holds | Encrypted? |
|------|-------|------------|
| `common.yaml` | Secrets shared by every host — Discord tokens/secret, VAPID keypair, `THERMOGRAPH_AUTH_SECRET`, metrics token, indexnow key, SMTP creds | ✅ |
| `prod.yaml` | Prod-only overrides — `POSTGRES_PASSWORD`, `REGISTRY_TOKEN` | ✅ |
| `prod.yaml` | Prod-only overrides — `POSTGRES_PASSWORD`, `REGISTRY_TOKEN`, ERA5 lake bucket creds (`THERMOGRAPH_LAKE_S3_ACCESS_KEY` / `THERMOGRAPH_LAKE_S3_SECRET_KEY`, consumed by the `lake` Swarm service and `gen_era5_lake.py`) | ✅ |
| `beta.yaml` | Beta-only overrides | ✅ |
| `example.yaml` | Format reference / CI fixture (fake values) | ✅ |
| `../../.sops.yaml` | Which age recipient files are encrypted to (plaintext config) | — |

View file

@ -21,7 +21,9 @@
set -eu
STACK_NAME="${STACK_NAME:-thermograph}"
SERVICE="${STACK_NAME}_web"
# Which stack service to scale (the stack runs one autoscaler instance per
# scaled service — web and lake today; same loop, different bounds).
SERVICE="${STACK_NAME}_${TARGET_SERVICE:-web}"
MIN="${MIN_REPLICAS:-1}"
MAX="${MAX_REPLICAS:-3}"
UP_AT="${SCALE_UP_CPU:-220}"

View file

@ -82,6 +82,10 @@ services:
# not the compose bridge's 172.19.0.1 (an overlay has no host gateway).
# provision-mail.sh's DOCKER_MAIL_GATEWAY/SUBNET cover this listener.
THERMOGRAPH_SMTP_HOST: ${STACK_SMTP_HOST:-172.18.0.1}
# History reads ask the lake service (Swarm VIP over 1..2 replicas)
# before any third-party source; unset on beta/LAN, where compose has no
# lake service and climate.py falls straight through to NASA.
THERMOGRAPH_LAKE_URL: http://lake:8141
volumes:
- appdata:/state
- applogs:/app/logs
@ -121,6 +125,7 @@ services:
THERMOGRAPH_SINGLETON_PG: "1"
RUN_MIGRATIONS: "0"
THERMOGRAPH_SMTP_HOST: ${STACK_SMTP_HOST:-172.18.0.1}
THERMOGRAPH_LAKE_URL: http://lake:8141
volumes:
- appdata:/state
- applogs:/app/logs
@ -138,6 +143,45 @@ services:
restart_policy:
condition: on-failure
# The ERA5 lake indexer: SQL-style, partition-pruned reads over the
# era5-thermograph bucket with a node-local parquet cache, so a cell's
# history is one LAN hop for web instead of an S3 fetch (or a NASA call).
# Same backend image; THERMOGRAPH_ROLE=lake makes the entrypoint start
# lake_app (no database, no migrations). Prod-only by construction: it only
# exists in this stack file, and its S3 credentials
# (THERMOGRAPH_LAKE_S3_ACCESS_KEY/_SECRET_KEY) arrive via the same rendered
# /host/thermograph.env as every other secret. Without them it stays
# healthy and answers 503/404, and web falls through to NASA — the lake is
# an accelerator, never a point of failure.
lake:
image: ${REGISTRY_HOST:-git.thermograph.org}/${BACKEND_IMAGE_PATH:-emi/thermograph/backend}:${BACKEND_IMAGE_TAG:?required}
entrypoint: ["/host/env-entrypoint.sh"]
environment:
THERMOGRAPH_ROLE: lake
PORT: 8141
THERMOGRAPH_SERVICE_ROLE: backend
WORKERS: "1"
THERMOGRAPH_LAKE_CACHE: /state/lake-cache
volumes:
# Replicas share the cache; lake_app's tmp+rename writes make that safe.
- lakecache:/state
- /opt/thermograph/infra/deploy/stack/env-entrypoint.sh:/host/env-entrypoint.sh:ro
- /etc/thermograph/stack.env:/host/thermograph.env:ro
networks:
- internal
deploy:
replicas: ${LAKE_MIN_REPLICAS:-1}
placement:
constraints: ["node.role == manager"]
resources:
limits:
cpus: "${LAKE_CPUS:-2}"
restart_policy:
condition: on-failure
update_config:
order: start-first
failure_action: rollback
frontend:
image: ${REGISTRY_HOST:-git.thermograph.org}/${FRONTEND_IMAGE_PATH:-emi/thermograph/frontend}:${FRONTEND_IMAGE_TAG:?required}
entrypoint: ["/host/env-entrypoint.sh"]
@ -200,6 +244,39 @@ services:
restart_policy:
condition: any
# Second autoscaler instance, watching `lake` (1..2 replicas). The lake is
# read-only and cache-heavy, so it saturates on decode CPU well below web's
# thresholds — scale up sooner, still down slowly.
autoscaler-lake:
image: docker:27-cli
entrypoint: ["/bin/sh", "/host/autoscale.sh"]
environment:
STACK_NAME: ${STACK_NAME:-thermograph}
TARGET_SERVICE: lake
MIN_REPLICAS: ${LAKE_MIN_REPLICAS:-1}
MAX_REPLICAS: ${LAKE_MAX_REPLICAS:-2}
SCALE_UP_CPU: ${LAKE_SCALE_UP_CPU:-120}
SCALE_DOWN_CPU: ${LAKE_SCALE_DOWN_CPU:-30}
POLL_SECONDS: ${POLL_SECONDS:-15}
UP_SAMPLES: ${UP_SAMPLES:-3}
DOWN_SAMPLES: ${DOWN_SAMPLES:-20}
COOLDOWN_SECONDS: ${COOLDOWN_SECONDS:-180}
volumes:
- /var/run/docker.sock:/var/run/docker.sock
- /opt/thermograph/infra/deploy/stack/autoscale.sh:/host/autoscale.sh:ro
networks:
- internal
deploy:
replicas: 1
placement:
constraints: ["node.role == manager"]
resources:
limits:
cpus: "0.2"
memory: 64m
restart_policy:
condition: any
networks:
internal:
driver: overlay
@ -221,3 +298,6 @@ volumes:
applogs:
external: true
name: ${APPLOGS_VOLUME:-thermograph_applogs}
# Lake parquet cache: node-local and disposable (a cold cache just refills
# from the bucket), so NOT external — the stack owns its lifecycle.
lakecache: {}