Add missing annotations to make Python 3.9 compatible (#487)

* Add missing annotations to make Python 3.9 compatible

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix conda env

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

conda-env.yml

@@ -2,7 +2,7 @@ name: dolphin-env
 channels:
   - conda-forge
 dependencies:
-  - python>=3.8
+  - python>=3.9
   - pip>=21.3  # https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/#editable-installation
   - git  # for pip install, due to setuptools_scm
   - gdal>=3.3

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "dolphin"
 description = "Workflows for generating surface displacement maps using InSAR"
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",

src/dolphin/_cli_unwrap.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import argparse
 from pathlib import Path
 from typing import TYPE_CHECKING, Any

src/dolphin/_log.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 import logging
 import logging.config

src/dolphin/_overviews.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import argparse
 import logging
 from enum import Enum

src/dolphin/filtering.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import multiprocessing as mp
 from concurrent.futures import ProcessPoolExecutor
 from itertools import repeat

src/dolphin/goldstein.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 from numpy.typing import NDArray
 

src/dolphin/interpolation.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numba

src/dolphin/io/_process.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from concurrent.futures import FIRST_EXCEPTION, Future, ThreadPoolExecutor, wait
 from typing import Protocol, Sequence
 

src/dolphin/phase_link/_compress.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import warnings
 
 import numpy as np

src/dolphin/phase_link/metrics.py

@@ -1,5 +1,7 @@
 """Module for computing quality metrics of estimated solutions."""
 
+from __future__ import annotations
+
 import jax.numpy as jnp
 from jax import Array, jit, vmap
 from jax.typing import ArrayLike

src/dolphin/phase_link/simulate.py

@@ -4,6 +4,8 @@
 full CPU/GPU stack implementations.
 """
 
+from __future__ import annotations
+
 import numpy as np
 import numpy.linalg as la
 import scipy.ndimage as ndi

src/dolphin/similarity.py

@@ -3,6 +3,8 @@
 Uses metric from [@Wang2022AccuratePersistentScatterer] for similarity.
 """
 
+from __future__ import annotations
+
 import logging
 from pathlib import Path
 from typing import Callable, Literal, Sequence

src/dolphin/stack.py

@@ -151,18 +151,18 @@ class CompressedSlcInfo(BaseModel):
         ..., description="Datetime of the last real SLC used in the compression."
     )
 
-    real_slc_file_list: list[Filename] | None = Field(
+    real_slc_file_list: Optional[list[Filename]] = Field(
         None,
         description="List of real SLC filenames in the ministack.",
     )
-    real_slc_dates: list[datetime] | None = Field(
+    real_slc_dates: Optional[list[datetime]] = Field(
         None,
         description=(
             "List of date sequences, one for each SLC in the ministack. "
             "Each item is a list/tuple of datetime.date or datetime.datetime objects."
         ),
     )
-    compressed_slc_file_list: list[Filename] | None = Field(
+    compressed_slc_file_list: Optional[list[Filename]] = Field(
         None,
         description="List of compressed SLC filenames in the ministack.",
     )

src/dolphin/unwrap/_post_process.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 
 import numpy as np

src/dolphin/unwrap/_tophu.py

@@ -189,9 +189,10 @@ def _get_cb_and_nodata(unwrap_method, unwrap_callback, nodata):
         # Fill in the nan pixels with the nearest ambiguities
         from ._post_process import interpolate_masked_gaps
 
-        with rio.open(unw_filename, mode="r+") as u_src, rio.open(
-            igram_rb.filepath
-        ) as i_src:
+        with (
+            rio.open(unw_filename, mode="r+") as u_src,
+            rio.open(igram_rb.filepath) as i_src,
+        ):
             unw = u_src.read(1)
             ifg = i_src.read(1)
             # nodata_mask = i_src.read_masks(1) != 0

src/dolphin/unwrap/_unwrap_3d.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import logging
 import shutil
 import subprocess

src/dolphin/workflows/_cli_run.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import argparse
 from typing import TYPE_CHECKING, Any, Optional, Sequence
 

src/dolphin/workflows/config/_yaml_model.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 import sys
 import textwrap

tests/test_io_readers.py

@@ -40,15 +40,18 @@ def binary_file_list(tmp_path_factory, slc_stack):
     for i, slc in enumerate(slc_stack):
         f = tmp_path / f"test_{i}.bin"
         # Ignore warning
-        with pytest.warns(NotGeoreferencedWarning), rio.open(
-            f,
-            "w",
-            driver="ENVI",
-            width=shape[1],
-            height=shape[0],
-            count=1,
-            dtype=dtype,
-        ) as dst:
+        with (
+            pytest.warns(NotGeoreferencedWarning),
+            rio.open(
+                f,
+                "w",
+                driver="ENVI",
+                width=shape[1],
+                height=shape[0],
+                count=1,
+                dtype=dtype,
+            ) as dst,
+        ):
             dst.write(slc, 1)
         files.append(f)