pystilt 0.1.0a1__py3-none-any.whl

pystilt-0.1.0a1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: pystilt
+Version: 0.1.0a1
+Summary: A Python implementation of the STILT Lagrangian atmospheric transport model.
+Author-email: James Mineau <jameskmineau@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/jmineau/PYSTILT
+Project-URL: Documentation, https://jmineau.github.io/PYSTILT/
+Project-URL: Repository, https://github.com/jmineau/PYSTILT
+Project-URL: Issues, https://github.com/jmineau/PYSTILT/issues
+Keywords: stilt,hysplit,atmospheric-transport,lagrangian,footprint,meteorology
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: arlmet>=0.1.0a1
+Requires-Dist: fsspec>=2024.2
+Requires-Dist: netcdf4>=1.6.5
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyarrow>=14.0
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pydantic-settings>=2.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: shapely>=2.0
+Requires-Dist: typer>=0.9
+Requires-Dist: typing-extensions>=4.0
+Requires-Dist: xarray>=2023.6
+Provides-Extra: projection
+Requires-Dist: pyproj>=3.5; extra == "projection"
+Provides-Extra: visualization
+Requires-Dist: matplotlib>=3.7; extra == "visualization"
+Provides-Extra: cloud
+Requires-Dist: gcsfs>=2024.2; extra == "cloud"
+Requires-Dist: psycopg[binary]>=3.1; extra == "cloud"
+Requires-Dist: kubernetes>=28.0; extra == "cloud"
+Requires-Dist: s3fs>=2024.2; extra == "cloud"
+Provides-Extra: complete
+Requires-Dist: pystilt[projection]; extra == "complete"
+Requires-Dist: pystilt[visualization]; extra == "complete"
+Requires-Dist: pystilt[cloud]; extra == "complete"
+Dynamic: license-file
+
+# PYSTILT
+
+[![Tests](https://github.com/jmineau/PYSTILT/actions/workflows/tests.yml/badge.svg)](https://github.com/jmineau/PYSTILT/actions/workflows/tests.yml)
+[![Documentation](https://github.com/jmineau/PYSTILT/actions/workflows/docs.yml/badge.svg)](https://github.com/jmineau/PYSTILT/actions/workflows/docs.yml)
+[![Code Quality](https://github.com/jmineau/PYSTILT/actions/workflows/quality.yml/badge.svg)](https://github.com/jmineau/PYSTILT/actions/workflows/quality.yml)
+[![codecov](https://codecov.io/gh/jmineau/PYSTILT/branch/main/graph/badge.svg)](https://codecov.io/gh/jmineau/PYSTILT)
+[![PyPI version](https://badge.fury.io/py/pystilt.svg)](https://badge.fury.io/py/pystilt)
+[![Python Version](https://img.shields.io/pypi/pyversions/pystilt.svg)](https://pypi.org/project/pystilt/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Pyright](https://img.shields.io/badge/pyright-checked-brightgreen.svg)](https://github.com/microsoft/pyright)
+
+PYSTILT is a Python implementation of the [STILT](https://uataq.github.io/stilt/) Lagrangian atmospheric transport model.
+It runs backward trajectories with [HYSPLIT](https://www.ready.noaa.gov/HYSPLIT.php) and computes receptor footprints
+that map where upwind surface fluxes influence a measurement.
+
+The project is in alpha and focused on a unified execution model that works for one-off runs,
+large batch runs, and streaming queue workers.
+
+## Status
+
+PYSTILT is alpha software (v0.1.0a1). No backward compatibility guarantees before v1.0.
+
+The core transport is stable: HYSPLIT execution, trajectory and footprint generation,
+numerical R-STILT parity, and the local and SLURM execution paths are all exercised by the
+test suite. The public API may change while the package settles.
+
+## Choose a workflow
+
+- **One-off transport runs** for local analysis and notebooks:
+  use `Model.run()` or `stilt run`.
+- **Queue-backed batch or service runs** for HPC/cloud execution:
+  use `Model.register_pending()`, `stilt register`, `stilt pull-worker`, and
+  `stilt serve` with a PostgreSQL-backed queue index configured via
+  `PYSTILT_DB_URL`.
+- **Observation-driven workflows** for science-facing code:
+  use `stilt.observations` to turn normalized observations into `Receptor`
+  objects before feeding them into the same runtime.
+
+## Roadmap
+
+PYSTILT draws design and science inspiration from two sister projects:
+[X-STILT](https://github.com/uataq/X-STILT) for column and satellite science workflows, and
+[stiltctl](https://github.com/jmineau/air-tracker-stiltctl) for cloud-native execution
+patterns. The tables below track what has been absorbed and what remains in scope.
+See the full [roadmap](https://jmineau.github.io/PYSTILT/roadmap.html) for more details.
+
+### Execution and orchestration (from stiltctl)
+
+| Feature | Status |
+|---|---|
+| Pull-mode queue workers (`stilt pull-worker`) | Implemented |
+| Long-lived streaming mode (`stilt serve`) | Implemented |
+| PostgreSQL-backed simulation registry | Implemented |
+| Scene-based submission grouping | Implemented |
+| Thin CLI → Model → worker call path | Implemented |
+| Kubernetes worker deployment | Partial |
+| Cloud object store outputs (GCS, S3) | In scope |
+
+### Column and satellite science (from X-STILT)
+
+Full X-STILT feature parity is not a goal. PYSTILT absorbs X-STILT's observation-layer
+design and column-weighting concepts without trying to replicate every script.
+
+| Feature | Status |
+|---|---|
+| `stilt.observations` layer (`Observation`, `Scene`, sensor families) | Implemented |
+| Column receptor support | Implemented |
+| Vertical operator particle transforms (AK / pressure weighting) | Implemented |
+| First-order lifetime decay transform | Implemented |
+| Declarative per-footprint transforms in config | Implemented |
+| Slant-column receptor support | In scope (pending HYSPLIT validation) |
+| Additional transform types | In scope |
+| Specific sensor adapters (OCO-2/3, TROPOMI, TCCON) | Deferred |
+| Inventory coupling and background estimation | Deferred |
+
+## Installation
+
+```bash
+pip install pystilt
+```
+
+For Slurm, Kubernetes, projections, plotting, and cloud object stores:
+
+```bash
+pip install "pystilt[complete]"
+```
+
+## Quickstart: one-off run
+
+Define a receptor, configure meteorology and footprint grid, then run:
+
+```python
+import pandas as pd
+import stilt
+
+receptor = stilt.Receptor(
+    time=pd.Timestamp("2023-07-15 18:00", tz="UTC"),
+    latitude=40.766,
+    longitude=-111.848,
+    altitude=10,
+)
+
+model = stilt.Model(
+    project="./my_project",
+    receptors=[receptor],
+    config=stilt.ModelConfig(
+        n_hours=-24,
+        numpar=100,
+        mets={
+            "hrrr": stilt.MetConfig(
+                directory="/data/hrrr",
+                file_format="hrrr_%Y%m%d.arl",
+                file_tres="1h",
+            )
+        },
+        footprints={
+            "default": stilt.FootprintConfig(
+                grid=stilt.Grid(
+                    xmin=-113.0,
+                    xmax=-110.5,
+                    ymin=40.0,
+                    ymax=42.0,
+                    xres=0.01,
+                    yres=0.01,
+                )
+            )
+        },
+    ),
+)
+
+handle = model.run()
+handle.wait()
+
+sim = list(model.simulations.values())[0]
+traj = sim.trajectories
+foot = sim.get_footprint("default")
+```
+
+## Quickstart: queue/service runtime
+
+```bash
+# Queue workers require a PostgreSQL-backed queue index.
+export PYSTILT_DB_URL=postgresql://user:pass@host:5432/pystilt
+
+# Initialize project files (config.yaml and receptors.csv)
+stilt init ./my_project
+
+# Run with local workers (blocks until complete)
+stilt run ./my_project --backend local --n-workers 8
+
+# Register one grouped scene submission
+stilt register ./my_project --scene-id daily_2026_04_13
+
+# Drain queue from worker processes (batch mode)
+stilt pull-worker ./my_project
+
+# Long-lived queue workers (streaming mode)
+stilt serve ./my_project
+
+# Check project status
+stilt status ./my_project
+```
+
+The same queue model is available in Python:
+
+```python
+import stilt
+from stilt.execution import pull_simulations
+
+model = stilt.Model(project="./my_project")
+model.register_pending(scene_id="daily_2026_04_14")
+pull_simulations(model, follow=False)  # batch mode
+print(model.status(scene_id="daily_2026_04_14"))
+```
+
+In all modes, workers claim simulations from the PostgreSQL-backed index and
+write terminal state directly back to the same registry.
+
+## Quickstart: observation layer
+
+PYSTILT also includes a narrow science-facing layer in `stilt.observations`.
+It is designed to sit above `Receptor`, not replace the transport/runtime core.
+
+```python
+import stilt
+from stilt.observations import PointSensor
+
+sensor = PointSensor(name="tower", supported_species=("co2",))
+observations = [
+    sensor.make_observation(
+        time="2023-01-01 12:00:00",
+        latitude=40.77,
+        longitude=-111.85,
+        altitude=30.0,
+        observation_id="tower-001",
+    )
+]
+
+[scene] = sensor.group_scenes(observations)
+receptors = [sensor.build_receptor(obs) for obs in scene.observations]
+
+model = stilt.Model(project="./my_project")  # existing project config on disk
+model.register_pending(receptors=receptors, scene_id=scene.id)
+```
+
+Direct `Observation(...)` construction is still available when you already
+have a separate product-specific normalization layer. The sensor helper just
+keeps the common path less repetitive.
+
+This layer currently focuses on:
+
+- normalized `Observation` and `Scene` objects
+- geometry/operator metadata
+- generic point/column sensor families
+- observation-to-receptor conversion
+
+See `docs/advanced/observations.rst` for the intended workflow boundary.
+
+## Declarative transforms
+
+Per-footprint transforms can be declared in config instead of embedded as
+ad hoc callbacks.
+
+```yaml
+footprints:
+  column:
+    grid: slv
+    transforms:
+      - kind: vertical_operator
+        mode: ak_pwf
+        levels: [0.0, 1000.0, 2000.0]
+        values: [0.2, 0.5, 0.3]
+        coordinate: xhgt
+      - kind: first_order_lifetime
+        lifetime_hours: 4.0
+        time_column: time
+        time_unit: min
+```
+
+The built-in transform interface is intentionally small:
+
+- vertical operator weighting
+- first-order lifetime decay
+- runtime typed transforms for more advanced Python workflows
+
+## Accessing results
+
+```python
+import pandas as pd
+
+for sim in model.simulations.values():
+    traj = sim.trajectories
+    foot = sim.get_footprint("default")
+
+# Load footprints across all matching simulations
+footprints = model.footprints["default"].load(
+    time_range=("2023-01-01", "2023-01-31")
+)
+
+coords = [(-111.9, 40.7), (-111.8, 40.8)]
+time_bins = pd.interval_range(
+    start=pd.Timestamp("2023-01-01 00:00", tz="UTC"),
+    end=pd.Timestamp("2023-01-02 00:00", tz="UTC"),
+    freq="1h",
+)
+
+for footprint in footprints:
+    hourly = footprint.aggregate(coords=coords, time_bins=time_bins)
+```
+
+If a footprint is tracked as `complete-empty`, no NetCDF file is expected for that footprint.
+The model APIs treat it as a successful terminal outcome while skipping missing file loads.
+
+## R-STILT parity
+
+PYSTILT footprints match the [uataq/stilt](https://github.com/uataq/stilt) R
+implementation on **numerical values** at `rtol=1e-7` per cell, validated by
+end-to-end fidelity scenarios against a **pinned upstream commit**.
+NetCDF output is not byte-compatible with R-STILT;
+it should be read as generic CF-1.8 NetCDF.
+See [STILT-R.md](STILT-R.md) for more details.
+
+## Documentation
+
+Full documentation is available at [https://jmineau.github.io/PYSTILT/](https://jmineau.github.io/PYSTILT/)
+
+## Contributing
+
+Contributions are welcome! Please see [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.
+
+## Author
+
+**James Mineau** - [jmineau](https://github.com/jmineau)

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+stilt/observations/sensors/point.py,sha256=DKLTFI_sKva95OO127vYiY_kiLbEpnITUESxM8nHAqw,1361
+stilt/service/__init__.py,sha256=OQw4Skq1sr9KpQ5RJL9extUD8C12OME_Jl-MymUXI7I,102
+stilt/service/kubernetes.py,sha256=M0E0vsnCWEnZ7FEgMpWWg2l-jCi8ZKn-CR7fkDr8tq8,8719
+stilt/storage/__init__.py,sha256=-uPWYKtNOXzbUQOWNP6mYVvfGiXIURnqECuvF-12qWU,1359
+stilt/storage/files.py,sha256=9LMep_5fDnNdNeYlJ5cQIQNRY4kkKbhvwVVsiU_TCdA,7078
+stilt/storage/layout.py,sha256=uhW4uObzMjWSHC0mjx3Pbeua-Xm76w3uixg164fnBHk,3562
+stilt/storage/project.py,sha256=jQsCtf0gLhIzNLH1iZdLmwiOgrxhBDSDQXMiGImklxI,5421
+stilt/storage/store.py,sha256=TbPvexA6O1xHOHu5swOJkYuhQ6njSVShJK1VQXaZgF4,11839
+pystilt-0.1.0a1.dist-info/METADATA,sha256=AgZP2OuhQclYqNk8l457e1l_do-f_yRlUilqKvta3bI,12151
+pystilt-0.1.0a1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+pystilt-0.1.0a1.dist-info/entry_points.txt,sha256=SZ_xrPLIvshGKAGIWSZOLXSgmTmECa01eT7WQo-1vuQ,40
+pystilt-0.1.0a1.dist-info/top_level.txt,sha256=DygYFBeEKKI0HDXaHdP-sa_XD5qBYsZQyWN71M4kwsI,6
+pystilt-0.1.0a1.dist-info/RECORD,,

pystilt-0.1.0a1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pystilt-0.1.0a1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+stilt = stilt.cli:app

pystilt-0.1.0a1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 James Mineau
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pystilt-0.1.0a1.dist-info/top_level.txt

@@ -0,0 +1 @@
+stilt

stilt/__init__.py

@@ -0,0 +1,64 @@
+"""PYSTILT public package surface."""
+
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as _version
+
+from .config import (
+    Bounds,
+    FootprintConfig,
+    Grid,
+    MetConfig,
+    ModelConfig,
+    RuntimeSettings,
+)
+from .footprint import Footprint
+from .meteorology import MetStream
+from .model import Model
+from .receptors import (
+    ColumnReceptor,
+    LocationID,
+    MultiPointReceptor,
+    PointReceptor,
+    Receptor,
+    ReceptorID,
+    read_receptors,
+)
+from .simulation import SimID, Simulation
+from .trajectory import Trajectories
+from .transforms import ParticleTransform
+
+try:
+    __version__ = _version("pystilt")
+except PackageNotFoundError:
+    __version__ = "0+unknown"
+__author__ = "James Mineau"
+__email__ = "jameskmineau@gmail.com"
+
+__all__ = [
+    # Core
+    "Model",
+    # Configuration
+    "ModelConfig",
+    "FootprintConfig",
+    "Grid",
+    "Bounds",
+    "MetConfig",
+    "RuntimeSettings",
+    # Data objects (returned by Model methods)
+    "Simulation",
+    "SimID",
+    "Footprint",
+    "Trajectories",
+    # Receptors
+    "Receptor",
+    "ColumnReceptor",
+    "LocationID",
+    "MultiPointReceptor",
+    "PointReceptor",
+    "ReceptorID",
+    "read_receptors",
+    # Meteorology
+    "MetStream",
+    # Transforms
+    "ParticleTransform",
+]

stilt/__main__.py

@@ -0,0 +1,12 @@
+"""Module entry point for ``python -m stilt``."""
+
+from stilt.cli import app
+
+
+def main() -> None:
+    """Run the Typer CLI."""
+    app()
+
+
+if __name__ == "__main__":
+    main()