Development update

pyrocko · Jul 17, 2024 · e744bab · e744bab
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,15 +2,15 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-added-large-files
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.2
+    rev: v0.5.2
     hooks:
       - id: ruff
       - id: ruff-format

diff --git a/README.md b/README.md
@@ -13,17 +13,24 @@ Qseek is an earthquake detection and localisation framework based on stacking an
 
 Key features are of the earthquake detection and localisation framework are:
 
-* Earthquake phase detection using machine-learning pickers from [SeisBench](https://github.com/seisbench/seisbench)
+* Earthquake phase detection using machine-learning model from [SeisBench](https://github.com/seisbench/seisbench), pre-trained on different data sets.
+  * [PhaseNet (Zhu and Beroza, 2018](https://doi.org/10.1093/gji/ggy423)
+  * [EQTransformer (Mousavi et al., 2020)](https://doi.org/10.1038/s41467-020-17591-w)
+  * [OBSTransformer (Niksejel and Zahng, 2024)](https://doi.org/10.1093/gji/ggae049)
+  * LFEDetect
 * Octree localisation approach for efficient and accurate search
 * Different velocity models:
   * Constant velocity
   * 1D Layered velocity model
   * 3D fast-marching velocity model (NonLinLoc compatible)
 * Extraction of earthquake event features:
-    * Local magnitudes
-    * Ground motion attributes
+  * Moment Magnitudes (MW) based on modelled peak ground motions
+  * Local magnitudes (ML), different models
+  * Ground motion attributes (e.g. PGA, PGV, ...)
 * Automatic extraction of modelled and picked travel times
-* Calculation and application of station corrections / station delay times
+* Station Corrections
+  * station specific corrections (SST)
+  * source specific station corrections (SSST)
 
 Qseek is built on top of [Pyrocko](https://pyrocko.org).
 

diff --git a/docs/components/image_function.md b/docs/components/image_function.md
@@ -2,14 +2,16 @@
 
 For image functions this version of Qseek relies heavily on machine learning pickers delivered by [SeisBench](https://github.com/seisbench/seisbench).
 
-## PhaseNet Image Function
+## SeisBench Image Function
+
+SeisBench offers access to a variety of machine learning phase pickers pre-trained on various data sets.
 
 !!! abstract "Citation PhaseNet"
     *Zhu, Weiqiang, and Gregory C. Beroza. "PhaseNet: A Deep-Neural-Network-Based Seismic Arrival Time Picking Method." arXiv preprint arXiv:1803.03211 (2018).*
 
 ```python exec='on'
 from qseek.utils import generate_docs
-from qseek.images.phase_net import PhaseNet
+from qseek.images.seisbench import SeisBench
 
-print(generate_docs(PhaseNet()))
+print(generate_docs(SeisBench()))
 ```
diff --git a/docs/components/seismic_data.md b/docs/components/seismic_data.md
@@ -10,7 +10,7 @@ To prepare your data for EQ detection and localisation, **organize it in a MiniS
 from qseek.utils import generate_docs
 from qseek.waveforms.squirrel import PyrockoSquirrel
 
-print(generate_docs(PyrockoSquirrel()))
+print(generate_docs(PyrockoSquirrel(persistent="docs")))
 ```
 
 ## Meta Data

diff --git a/docs/index.md b/docs/index.md
@@ -14,14 +14,18 @@ The detector is leveraging [Pyrocko](https://pyrocko.org) and [SeisBench](https:
 ## Features
 
 * [x] Earthquake phase detection using machine-learning pickers from [SeisBench](https://github.com/seisbench/seisbench)
+    * [x] [PhaseNet (Zhu and Beroza, 2018](https://doi.org/10.1093/gji/ggy423)
+    * [x] [EQTransformer (Mousavi et al., 2020)](https://doi.org/10.1038/s41467-020-17591-w)
+    * [x] [OBSTransformer (Niksejel and Zahng, 2024)](https://doi.org/10.1093/gji/ggae049)
+    * [x] LFEDetect
 * [x] Octree localisation approach for efficient and accurate search
 * [x] Different velocity models:
-  * [x] Constant velocity
-  * [x] 1D Layered velocity model
-  * [x] 3D fast-marching velocity model (NonLinLoc compatible)
+    * [x] Constant velocity
+    * [x] 1D Layered velocity model
+    * [x] 3D fast-marching velocity model (NonLinLoc compatible)
 * [x] Extraction of earthquake event features:
-  * [x] Local magnitudes
-  * [x] Ground motion attributes
+    * [x] Local magnitudes
+    * [x] Ground motion attributes
 * [x] Automatic extraction of modelled and picked travel times
 * [x] Calculation and application of station corrections / station delay times
 * [ ] Real-time analytics on streaming data (e.g. SeedLink)

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -77,7 +77,7 @@ nav:
     - Getting Started 🚀: getting_started.md
     - Visualising Detections: visualizing_results.md
     - Benchmark: benchmark.md
-  - Usage:
+  - Configuration:
     - The Search: components/configuration.md
     - Seismic Data: components/seismic_data.md
     - Ray Tracer: components/ray_tracer.md

diff --git a/pyproject.toml b/pyproject.toml
@@ -33,7 +33,7 @@ keywords = [
 ]
 
 dependencies = [
-    "numpy>=1.17.3",
+    "numpy>=1.17.3, <2",
     "scipy>=1.8.0",
     "pyrocko>=2022.06.10",
     "seisbench>=0.5.0",
@@ -45,7 +45,10 @@ dependencies = [
     "rich>=13.4",
     "nest_asyncio>=1.5",
     "pyevtk>=1.6",
+    "psutil>=5.9",
     "aiofiles>=23.0",
+    "typer >=0.12.3",
+    "scikit-fmm >= 2024.05",
 ]
 
 classifiers = [
@@ -62,18 +65,12 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit>=3.4",
-    "black>=23.7",
-    "ruff>=0.1.14",
-    "pytest>=7.4",
-    "pytest-asyncio>=0.21",
-]
+dev = ["pre-commit>=3.4", "ruff>=0.3.0", "pytest>=7.4", "pytest-asyncio>=0.21"]
 
 docs = [
-    "mkdocs-material>=9.5.13",
-    "mkdocstrings[python]>=0.23",
-    "markdown-exec>=1.8.0",
+    "mkdocs-material>=9.5",
+    "mkdocstrings[python]>=0.25",
+    "markdown-exec>=1.9",
 ]
 completion = ["argcomplete>=3.2"]
 
@@ -106,13 +103,27 @@ extend-select = [
     'I',
     'RUF',
     'T20',
+    'D',
 ]
 
-ignore = ["RUF012", "RUF009"]
+ignore = [
+    "RUF012",
+    "RUF009",
+    "D100",
+    "D101",
+    "D102",
+    "D103",
+    "D104",
+    "D105",
+    "D107",
+]
 
 [tool.ruff]
 target-version = 'py311'
 
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
 [tool.pytest.ini_options]
 markers = ["plot: plot figures in tests"]