diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index ac112ee..c650790 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -36,7 +36,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: [3.7, 3.8, 3.9] + python-version: ['3.9', '3.10', '3.11'] steps: - name: Clone repo diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fd21316..405e167 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,21 +1,27 @@ repos: + - repo: https://github.com/asottile/pyupgrade + rev: v3.15.2 + hooks: + - id: pyupgrade + args: [--py39-plus] + - repo: https://github.com/pycqa/isort - rev: 5.10.1 + rev: 5.13.2 hooks: - id: isort - repo: https://github.com/psf/black - rev: 22.10.0 + rev: 24.4.0 hooks: - id: black - repo: https://github.com/pycqa/flake8 - rev: 6.0.0 + rev: 7.0.0 hooks: - id: flake8 - repo: https://github.com/pre-commit/mirrors-mypy - rev: v0.991 + rev: v1.9.0 hooks: - id: mypy args: [--strict, --ignore-missing-imports, --show-error-codes] @@ -23,10 +29,8 @@ repos: exclude: (docs|tests)/ - repo: https://github.com/python-poetry/poetry - rev: 1.2.2 + rev: 1.8.0 hooks: - id: poetry-check - # Commented out due to lock files being generated by different versions of poetry - # Refer python-poetry/poetry#4978. Uncomment once poetry 1.2 is released. - # - id: poetry-lock - # args: [--no-update] + - id: poetry-lock + args: [--no-update] diff --git a/changedet/algos/catalog.py b/changedet/algos/catalog.py index 7960070..f1807d7 100644 --- a/changedet/algos/catalog.py +++ b/changedet/algos/catalog.py @@ -1,11 +1,11 @@ from collections import UserDict -from typing import TYPE_CHECKING, Callable, List, Type +from typing import TYPE_CHECKING, Callable from changedet.algos.base import MetaAlgo # Refer https://github.com/python/typing/issues/60 if TYPE_CHECKING: - _Base = UserDict[str, Type[MetaAlgo]] + _Base = UserDict[str, type[MetaAlgo]] # pragma: no cover else: _Base = UserDict @@ -30,8 +30,8 @@ class AlgoCatalog_(_Base): """ - def register(self, name: str) -> Callable[[Type[MetaAlgo]], Type[MetaAlgo]]: - def inner_wrapper(wrapped_class: Type[MetaAlgo]) -> Type[MetaAlgo]: + def register(self, name: str) -> Callable[[type[MetaAlgo]], type[MetaAlgo]]: + def inner_wrapper(wrapped_class: type[MetaAlgo]) -> type[MetaAlgo]: if name in self.keys(): raise AssertionError(f"Algorithm {name} already exists.") self[name] = wrapped_class @@ -39,7 +39,7 @@ def inner_wrapper(wrapped_class: Type[MetaAlgo]) -> Type[MetaAlgo]: return inner_wrapper - def get(self, name: str) -> Type[MetaAlgo]: # type: ignore[override] + def get(self, name: str) -> type[MetaAlgo]: # type: ignore[override] try: f = self[name] except KeyError as e: @@ -52,7 +52,7 @@ def get(self, name: str) -> Type[MetaAlgo]: # type: ignore[override] f = None return f - def list(self) -> List[str]: + def list(self) -> list[str]: """List all registered algorithms. Returns: diff --git a/changedet/algos/cva.py b/changedet/algos/cva.py index b7bf3bb..60437ce 100644 --- a/changedet/algos/cva.py +++ b/changedet/algos/cva.py @@ -1,4 +1,4 @@ -from typing import Any, Tuple +from typing import Any import numpy as np @@ -8,7 +8,7 @@ def calc_cvs( im1: np.ndarray, im2: np.ndarray, distance: str = "euclidean" -) -> Tuple[np.ndarray, np.ndarray]: +) -> tuple[np.ndarray, np.ndarray]: diffmap = im2 - im1 if distance == "manhattan": # Manhattan distance/L1 norm diff --git a/changedet/pipeline.py b/changedet/pipeline.py index 1cd54a5..21736c7 100644 --- a/changedet/pipeline.py +++ b/changedet/pipeline.py @@ -1,5 +1,5 @@ from pathlib import Path -from typing import Any, Tuple +from typing import Any import numpy as np import rasterio as rio @@ -35,7 +35,7 @@ def __init__(self, algo: str): self.logger = init_logger("changedet") # Image loading and sanity checks should be done here - def read(self, im1: str, im2: str, band: int) -> Tuple[np.ndarray, np.ndarray]: + def read(self, im1: str, im2: str, band: int) -> tuple[np.ndarray, np.ndarray]: """Read and prepare images Args: @@ -75,7 +75,7 @@ def read(self, im1: str, im2: str, band: int) -> Tuple[np.ndarray, np.ndarray]: return arr1, arr2 - def _read(self, im: str, band: int) -> Tuple[np.ndarray, CRS, Profile]: + def _read(self, im: str, band: int) -> tuple[np.ndarray, CRS, Profile]: with rio.open(im) as raster: profile = raster.profile crs = raster.crs diff --git a/changedet/utils.py b/changedet/utils.py index ea52884..d0ef2df 100644 --- a/changedet/utils.py +++ b/changedet/utils.py @@ -1,7 +1,7 @@ import logging import sys from pathlib import Path -from typing import List, Optional, Tuple +from typing import Optional import matplotlib.pyplot as plt import numpy as np @@ -136,7 +136,7 @@ def prepare(self, im1: np.ndarray, im2: np.ndarray, plot: bool = True) -> np.nda return icm @staticmethod - def roots(mean: np.ndarray, var: np.ndarray, pi: np.ndarray) -> Tuple[float, float]: + def roots(mean: np.ndarray, var: np.ndarray, pi: np.ndarray) -> tuple[float, float]: """Compute the threshold between the no-change and change distributions from the mean, variance and mixture weight (pi) of no change, change and ambigous distributions. @@ -183,7 +183,7 @@ def __init__( def init_cluster_params( self, X: np.ndarray - ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: + ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: """Initialse cluster parameters Shape notation: @@ -308,7 +308,7 @@ def e_step( cov: np.ndarray, pi: np.ndarray, sample_inds: ArrayLike, - ) -> Tuple[np.ndarray, np.ndarray]: + ) -> tuple[np.ndarray, np.ndarray]: """Expectation step Shape notation: @@ -344,7 +344,7 @@ def e_step( def m_step( self, X: np.ndarray, resp: np.ndarray - ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: + ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: """Maximisation step Shape notation: @@ -455,7 +455,7 @@ def update(self, X: np.ndarray, weights: Optional[np.ndarray] = None) -> None: def np_weight_stats( x: np.ndarray, ws: Optional[np.ndarray] = None -) -> Tuple[np.ndarray, np.ndarray]: +) -> tuple[np.ndarray, np.ndarray]: """Calculate weighted mean and sample covariance. Args: @@ -481,7 +481,7 @@ def contrast_stretch( *, target_type: str = "uint8", stretch_type: str = "minmax", - percentile: Tuple[int, int] = (2, 98), + percentile: tuple[int, int] = (2, 98), ) -> np.ndarray: """Change image distribution to cover full range of target_type. @@ -518,7 +518,7 @@ def contrast_stretch( def histogram_equalisation( im: np.ndarray, nbr_bins: int = 256 -) -> Tuple[np.ndarray, np.ndarray]: +) -> tuple[np.ndarray, np.ndarray]: # Refer http://www.janeriksolem.net/histogram-equalization-with-python-and.html # get image histogram imhist, bins = np.histogram(im.flatten(), nbr_bins) @@ -560,7 +560,7 @@ def format(self, record: logging.LogRecord) -> str: # Python3 compatibility self._style._fmt = fmt self._fmt = fmt - return super(_ColorFormatter, self).format(record) + return super().format(record) def init_logger(name: str = "logger", output: Optional[str] = None) -> logging.Logger: @@ -597,7 +597,7 @@ def init_logger(name: str = "logger", output: Optional[str] = None) -> logging.L return logger -def histplot(xlist: ArrayLike, xlabel: List[str], bins: Optional[int] = 50) -> Figure: +def histplot(xlist: ArrayLike, xlabel: list[str], bins: Optional[int] = 50) -> Figure: """Plot multiple histograms in the same figure Args: diff --git a/poetry.lock b/poetry.lock index 4e48619..bc4f6ae 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,43 +1,84 @@ +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. + [[package]] name = "affine" -version = "2.3.0" -description = "Matrices describing affine transformation of the plane." -category = "main" +version = "2.4.0" +description = "Matrices describing affine transformation of the plane" optional = false -python-versions = "*" +python-versions = ">=3.7" +files = [ + {file = "affine-2.4.0-py3-none-any.whl", hash = "sha256:8a3df80e2b2378aef598a83c1392efd47967afec4242021a0b06b4c7cbc61a92"}, + {file = "affine-2.4.0.tar.gz", hash = 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