Merge branch 'main' into jax-sbas

.github/workflows/test-build-push.yml

@@ -40,6 +40,8 @@ jobs:
               threadpoolctl>=3.0
               dask
               rasterio
+              pyaps3>=0.3
+              opera-utils>=0.1.5
         exclude:  # TODO: Remove this once pymp is gone
           - os: macos-latest
             deps:

.pre-commit-config.yaml

@@ -21,25 +21,17 @@ repos:
 
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.8
+    rev: v0.1.9
     hooks:
       - id: ruff
-        args: [--fix, --exit-non-zero-on-fix]
+        args: [--fix, --exit-non-zero-on-fix, --show-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.7.1"
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:
         - types-pkg_resources
         - types-requests
         - "pydantic>=2.4"
-
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: "6.3.0"
-    hooks:
-      - id: pydocstyle
-        # https://github.com/PyCQA/pydocstyle/pull/608#issuecomment-1381168417
-        additional_dependencies: ['.[toml]']
-        exclude: tests

CHANGELOG.md

@@ -1,8 +1,12 @@
-# [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.7.0...main)
+# [Unreleased](https://github.com/isce-framework/dolphin/compare/v0.8.0...main)
+
+# [v0.8.0](https://github.com/isce-framework/dolphin/compare/v0.7.0...v0.8.0)
 
 **Added**
-- Ability to unwrap interferorgams with the [`snaphu-py`](https://github.com/isce-framework/snaphu-py) (not a required dependency)
+- Ability to unwrap interferograms with the [`snaphu-py`](https://github.com/isce-framework/snaphu-py) (not a required dependency)
 - Added ability to make annual ifgs in `Network`
+- Start of tropospheric corection support in `dolphin.atmosphere` using PyAPS and Raider packages
+- Expose the unwrap skipping with `dolphin config --no-unwrap`
 
 **Changed**
 - The output directory for interferograms is now just "interferograms/" instead of "interferograms/stiched"
@@ -11,7 +15,7 @@
 - Switched output filename from `tcorr` to `temporal_coherence` for the temporal coherence of phase linking.
   - Also added the date span to the `temporal_coherence` output name
 - The default extension for conncomps is now `.tif`. Use geotiffs instead of ENVI format for connected components.
-
+- Using ruff instead of pydocstyle due to archived repo
 
 # [v0.7.0](https://github.com/isce-framework/dolphin/compare/v0.6.1...v0.7.0)
 

conda-env.yml

@@ -11,7 +11,7 @@ dependencies:
   - hdf5!=1.12.2 # https://github.com/SciTools/iris/issues/5187 and https://github.com/pydata/xarray/issues/7549
   - numba>=0.54
   - numpy>=1.20
-  - opera-utils>=0.1.1
+  - opera-utils>=0.1.5
   - pydantic>=2.1
   - pymp-pypi>=0.4.5
   - pyproj>=3.3

pyproject.toml

@@ -47,6 +47,14 @@ version_scheme = "no-guess-dev" # Will not guess the next version
 
 [tool.ruff]
 src = ["src"]
+ignore = [
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # Missing docstring in magic method
+  "D203", # 1 blank line required before class docstring
+  "D212", # Multi-line docstring summary should start at the first line
+  "PLR",  # Pylint Refactor
+]
 
 [tool.ruff.lint]
 # Enable the isort rules.
@@ -65,9 +73,10 @@ python_version = "3.10"
 ignore_missing_imports = true
 plugins = ["pydantic.mypy"]
 
+[tool.ruff.per-file-ignores]
+"**/__init__.py" = ["F401"]
+"test/**" = ["D"]
 
-[tool.pydocstyle]
-ignore = "D100,D102,D104,D105,D106,D107,D203,D204,D213,D413"
 
 [tool.pytest.ini_options]
 doctest_optionflags = "NORMALIZE_WHITESPACE NUMBER"

requirements.txt

@@ -2,6 +2,7 @@
 h5py>=3.6
 numba>=0.54
 numpy>=1.20
+opera-utils>=0.1.5
 pydantic>=2.1
 pymp-pypi>=0.4.5
 pyproj>=3.3

src/dolphin/_types.py

@@ -2,8 +2,9 @@
 
 import datetime
 import sys
+from enum import Enum
 from os import PathLike
-from typing import TYPE_CHECKING, Tuple, TypeVar, Union
+from typing import TYPE_CHECKING, NamedTuple, TypeVar, Union
 
 if sys.version_info >= (3, 10):
     from typing import ParamSpec
@@ -24,11 +25,60 @@
 # TypeVar added for generic functions which should return the same type as the input
 PathLikeT = TypeVar("PathLikeT", str, PathLikeStr)
 
-# left, bottom, right, top
-Bbox = Tuple[float, float, float, float]
+
+class Bbox(NamedTuple):
+    """Bounding box named tuple, defining extent in cartesian coordinates.
+
+    Usage:
+
+        Bbox(left, bottom, right, top)
+
+    Attributes
+    ----------
+    left : float
+        Left coordinate (xmin)
+    bottom : float
+        Bottom coordinate (ymin)
+    right : float
+        Right coordinate (xmax)
+    top : float
+        Top coordinate (ymax)
+    """
+
+    left: float
+    bottom: float
+    right: float
+    top: float
+
 
 # Used for callable types
 T = TypeVar("T")
 P = ParamSpec("P")
 
 DateOrDatetime = Union[datetime.datetime, datetime.date]
+
+
+class TropoModel(Enum):
+    """Enumeration representing different tropospheric models."""
+
+    ERA5 = "ERA5"
+    HRES = "HRES"
+    ERAINT = "ERAINT"
+    ERAI = "ERAI"
+    MERRA = "MERRA"
+    NARR = "NARR"
+    HRRR = "HRRR"
+    GMAO = "GMAO"
+
+
+class TropoType(Enum):
+    """Type of tropospheric delay."""
+
+    WET = "wet"
+    """Wet tropospheric delay."""
+    DRY = "dry"
+    """Dry delay (same as hydrostatic, named "dry" in PyAPS)"""
+    HYDROSTATIC = "hydrostatic"
+    """Hydrostatic (same as dry, named differently in raider)"""
+    COMB = "comb"
+    """Combined wet + dry delay."""

src/dolphin/atmosphere/__init__.py

@@ -0,0 +1,3 @@
+"""Atmospheric corrections."""
+
+from .troposphere import *  # noqa