Dev (#1)

* Initial release

.github/workflows/build.yaml

@@ -0,0 +1,26 @@
+name: Build and test
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip" # caching pip dependencies
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Test with pytest
+        run: |
+          pytest

.github/workflows/lint.yaml

@@ -1,4 +1,4 @@
-name: pre-commit
+name: linting
 
 on:
   pull_request:

.gitignore

@@ -159,3 +159,8 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
 .vscode
+
+# Data files
+*.mseed
+
+test/data/

.pre-commit-config.yaml

@@ -9,16 +9,16 @@ repos:
       - id: check-yaml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
         # It is recommended to specify the latest version of Python
         # supported by your project here, or alternatively use
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
-        language_version: python3.9
+        # language_version: python3.9
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: "v0.0.241"
+    rev: "v0.0.275"
     hooks:
       - id: ruff

README.md

@@ -0,0 +1,75 @@
+# Lassie
+
+*The friendly earthquake detector*
+
+![Python 3.10+](https://img.shields.io/badge/python-3.10-blue.svg)
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://pre-commit.com/)
+<!-- [![PyPI](https://img.shields.io/pypi/v/lassie)](https://pypi.org/project/lassie/) -->
+
+Lassie is an earthquake detector based on stacking and migration method. It combines neural network phase picks with an iterative octree localisation approach.
+
+Key features are of the tools are:
+
+* Phase detection using SeisBench
+* Efficient and accurate Octree localisation approach
+* Extraction of event features
+    * Local magnitudes
+    * Ground motion attributes
+* Determination of station corrections
+
+## Installation
+
+```sh
+git clone https://github.com/miili/lassie-v2
+cd lassie-v2
+pip3 install .
+```
+
+## Project Initialisation
+
+Initialize a new project in a fresh directory.
+
+```sh
+lassie new project-dir/
+```
+
+Edit the `search.json`
+
+Start the detection
+
+```sh
+lassie run search.json
+```
+
+## Packaging
+
+The simplest and recommended way of installing from source:
+
+### Development
+
+Local development through pip.
+
+```sh
+cd lightguide
+pip3 install .[dev]
+```
+
+The project utilizes pre-commit for clean commits, install the hooks via:
+
+```sh
+pip install pre-commit
+pre-commit install
+```
+
+## Citation
+
+Please cite lassie as:
+
+> TBD
+
+## License
+
+Contribution and merge requests by the community are welcome!
+
+Lassie-v@ was written by Marius Paul Isken and is licensed under the GNU GENERAL PUBLIC LICENSE v3.

lassie/apps/lassie.py

@@ -1,30 +1,208 @@
+from __future__ import annotations
+
 import argparse
+import asyncio
+import logging
+from datetime import datetime
 from pathlib import Path
 
-from lassie.config import Config
+import nest_asyncio
+from pkg_resources import get_distribution
+
+from lassie.console import console
+from lassie.images import ImageFunctions
+from lassie.images.phase_net import PhaseNet
+from lassie.models import Stations
+from lassie.search import SquirrelSearch
+from lassie.server import WebServer
+from lassie.station_corrections import StationCorrections
+from lassie.tracers import RayTracers
+from lassie.tracers.cake import CakeTracer
+from lassie.utils import ANSI, setup_rich_logging
+
+nest_asyncio.apply()
 
+logger = logging.getLogger(__name__)
 
-def main():
+
+def main() -> None:
     parser = argparse.ArgumentParser(
         prog="lassie",
         description="The friendly earthquake detector - V2",
     )
+    parser.add_argument(
+        "--verbose",
+        "-v",
+        action="count",
+        default=0,
+        help="increase verbosity of the log messages, default level is INFO",
+    )
+    parser.add_argument(
+        "--version",
+        action="version",
+        version=get_distribution("lassie").version,
+        help="show version and exit",
+    )
+
     subparsers = parser.add_subparsers(title="commands", required=True, dest="command")
-    subparsers.add_parser("dump-config", help="Print a new config to terminal.")
 
-    run = subparsers.add_parser("run", help="Start a run.")
+    run = subparsers.add_parser(
+        "run",
+        help="start a new detection run",
+        description="detect, localize and characterize earthquakes in a dataset",
+    )
+    run.add_argument("config", type=Path, help="path to config file")
     run.add_argument(
-        "config",
-        type=Path,
-        help="Path to config file.",
+        "--force",
+        action="store_true",
+        default=False,
+        help="backup old rundir and create a new",
+    )
+
+    continue_run = subparsers.add_parser(
+        "continue",
+        help="continue an aborted run",
+        description="continue a run from an existing rundir",
+    )
+    continue_run.add_argument("rundir", type=Path, help="existing runding to continue")
+
+    features = subparsers.add_parser(
+        "feature-extraction",
+        help="extract features from an existing run",
+        description="modify the search.json for re-evaluation of the event's features",
     )
+    features.add_argument("rundir", type=Path, help="path of existing run")
+
+    station_corrections = subparsers.add_parser(
+        "station-corrections",
+        help="analyse station corrections from existing run",
+        description="analyze and plot station corrections from a finished run",
+    )
+    station_corrections.add_argument(
+        "--plot",
+        action="store_true",
+        default=False,
+        help="plot station correction results and save to rundir",
+    )
+    station_corrections.add_argument("rundir", type=Path, help="path of existing run")
+
+    serve = subparsers.add_parser(
+        "serve",
+        help="serve results from an existing run",
+        description="start a webserver and serve detections and results from a run",
+    )
+    serve.add_argument("rundir", type=Path, help="rundir to serve")
+
+    new = subparsers.add_parser(
+        "new",
+        help="initialize a new project",
+    )
+    new.add_argument("folder", type=Path, help="folder to initialize project in")
+
+    dump_schemas = subparsers.add_parser(
+        "dump-schemas",
+        help="dump models to json-schema (development)",
+    )
+    dump_schemas.add_argument("folder", type=Path, help="folder to dump schemas to")
 
     args = parser.parse_args()
-    if args.command == "dump-config":
-        config = Config.construct()
-        print(config.json(indent=2))
-        return
+    setup_rich_logging(level=logging.INFO - args.verbose * 10)
+
+    if args.command == "new":
+        folder: Path = args.folder
+        if folder.exists():
+            raise FileExistsError(f"Folder {folder} already exists")
+        folder.mkdir()
+
+        pyrocko_stations = folder / "pyrocko-stations.yaml"
+        pyrocko_stations.touch()
+
+        config = SquirrelSearch(
+            ray_tracers=RayTracers(root=[CakeTracer()]),
+            image_functions=ImageFunctions(
+                root=[PhaseNet(phase_map={"P": "cake:P", "S": "cake:S"})]
+            ),
+            stations=Stations(pyrocko_station_yamls=[pyrocko_stations]),
+            waveform_data=[Path("/data/")],
+            time_span=(
+                datetime.fromisoformat("2023-04-11T00:00:00+00:00"),
+                datetime.fromisoformat("2023-04-18T00:00:00+00:00"),
+            ),
+        )
+
+        config_file = folder / "config.json"
+        config_file.write_text(config.model_dump_json(by_alias=False, indent=2))
+        logger.info("initialized new project in folder %s", folder)
+        logger.info(
+            "start detecting with:\n\t%slassie run config.json%s", ANSI.Bold, ANSI.Reset
+        )
+
     elif args.command == "run":
-        ...
-    else:
-        raise ValueError("No command provided")
+        search = SquirrelSearch.from_config(args.config)
+        search.init_rundir(force=args.force)
+
+        webserver = WebServer(search)
+
+        async def _run() -> None:
+            http = asyncio.create_task(webserver.start())
+            await search.scan_squirrel()
+            await http
+
+        asyncio.run(_run())
+
+    elif args.command == "continue":
+        search = SquirrelSearch.load_rundir(args.rundir)
+        if search.progress.time_progress:
+            console.rule(f"Continuing search from {search.progress.time_progress}")
+        else:
+            console.rule("Starting search from scratch")
+
+        webserver = WebServer(search)
+
+        async def _run() -> None:
+            http = asyncio.create_task(webserver.start())
+            await search.scan_squirrel()
+            await http
+
+        asyncio.run(_run())
+
+    elif args.command == "feature-extraction":
+        search = SquirrelSearch.load_rundir(args.rundir)
+
+        async def extract() -> None:
+            for detection in search._detections.detections:
+                await search.add_features(detection)
+
+        asyncio.run(extract())
+
+    elif args.command == "station-corrections":
+        rundir = Path(args.rundir)
+        station_corrections = StationCorrections(rundir=rundir)
+        if args.plot:
+            station_corrections.save_plots(rundir / "station_corrections")
+        station_corrections.save_csv(filename=rundir / "station_corrections_stats.csv")
+
+    elif args.command == "serve":
+        search = SquirrelSearch.load_rundir(args.rundir)
+        webserver = WebServer(search)
+
+        loop = asyncio.get_event_loop()
+        loop.create_task(webserver.start())
+        loop.run_forever()
+
+    elif args.command == "dump-schemas":
+        from lassie.models.detection import EventDetections
+
+        if not args.folder.exists():
+            raise EnvironmentError(f"folder {args.folder} does not exist")
+
+        file = args.folder / "search.schema.json"
+        print(f"writing JSON schemas to {args.folder}")
+        file.write_text(SquirrelSearch.model_json_schema(indent=2))
+
+        file = args.folder / "detections.schema.json"
+        file.write_text(EventDetections.model_json_schema(indent=2))
+
+
+if __name__ == "__main__":
+    main()