Merge pull request #187 from siapy/fix

chore: [pre-commit.ci] pre-commit autoupdate

Author: janezlapajne

.github/workflows/docs.yml

@@ -18,6 +18,9 @@ jobs:
         uses: actions/checkout@v4
       - name: Setup PDM
         uses: pdm-project/setup-pdm@v4
+        with:
+          python-version: 3.10
+          cache: true
       - name: Install dependencies
         run: pdm install -G docs
       - name: Build MkDocs site

.github/workflows/publish.yml

@@ -36,6 +36,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: pdm-project/setup-pdm@v4
         with:
-          version: "head"
+          python-version: 3.10
+          cache: true
       - name: Publish package distributions to PyPI
         run: pdm publish

.github/workflows/test.yml

@@ -11,13 +11,22 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+      fail-fast: false
+
+    name: Test Python ${{ matrix.python-version }}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
           lfs: true # This option ensures that Git LFS files are checked out
       - name: Setup PDM
         uses: pdm-project/setup-pdm@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: true
       - name: Install dependencies
         run: pdm install
       - name: Lint code
@@ -27,6 +36,8 @@ jobs:
         run: ./scripts/test.sh "Coverage for ${{ github.sha }}"
       - name: Store coverage files
         uses: actions/upload-artifact@v4
+        # Only upload for Python 3.12
+        if: matrix.python-version == '3.12'
         with:
           name: coverage-html
           path: htmlcov

Makefile

@@ -30,6 +30,9 @@ lint: .pdm
 test: .pdm
 	./scripts/test.sh "Develop"
 
+.PHONY: flt ## Run format, lint, and test
+flt: format lint test
+
 .PHONY: codespell  ## Use Codespell to do spellchecking
 codespell: .pre-commit
 	pdm run pre-commit run codespell --all-files
@@ -47,24 +50,7 @@ update-branches:
 
 .PHONY: clean  ## Clear local caches and build artifacts
 clean:
-	rm -rf `find . -name __pycache__`
-	rm -f `find . -type f -name '*.py[co]'`
-	rm -f `find . -type f -name '*~'`
-	rm -f `find . -type f -name '.*~'`
-	rm -rf .pdm-build
-	rm -rf .mypy_cache
-	rm -rf .cache
-	rm -rf .pytest_cache
-	rm -rf .ruff_cache
-	rm -rf htmlcov
-	rm -rf *.egg-info
-	rm -f .coverage
-	rm -f .coverage.*
-	rm -rf build
-	rm -rf dist
-	rm -rf site
-	rm -rf docs/_build
-	rm -rf coverage.xml
+	./scripts/clean.sh
 
 .PHONY: generate-docs  ## Generate the docs
 generate-docs:

docs/examples/src/spectral_imageset_load_01.py

@@ -5,9 +5,7 @@
 
     print("Libraries detected successfully.")
 except ImportError as e:
-    print(
-        f"Error: {e}. Please ensure that the SiaPy library is installed and the environment is activated."
-    )
+    print(f"Error: {e}. Please ensure that the SiaPy library is installed and the environment is activated.")
     exit(1)
 
 # Set the path to the directory containing the data

docs/examples/src/transformations_02.py

@@ -40,9 +40,7 @@
 selected_areas_vnir = pixels_select_lasso(image_vnir)
 
 # Transform the selected areas from the VNIR image to the space of the SWIR image.
-selected_areas_swir = [
-    corregistrator.transform(pixels_vnir, matx) for pixels_vnir in selected_areas_vnir
-]
+selected_areas_swir = [corregistrator.transform(pixels_vnir, matx) for pixels_vnir in selected_areas_vnir]
 
 # Display the selected areas in both images
 display_multiple_images_with_areas(

pdm.lock

@@ -3,7 +3,7 @@ name = "siapy"
 version = "0.5.9"
 description = "A python library for efficient processing of spectral images."
 authors = [{ name = "janezlapajne", email = "janez.lapajne@kis.si" }]
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.13"
 readme = "README.md"
 license = { text = "MIT" }
 
@@ -43,13 +43,7 @@ dependencies = [
 ]
 
 [dependency-groups]
-lint = [
-    "black>=24.4.2",
-    "flake8>=7.0.0",
-    "ruff>=0.4.8",
-    "mypy>=1.10.1",
-    "pandas-stubs>=2.2.2.240603",
-]
+lint = ["ruff>=0.4.8", "mypy>=1.10.1", "pandas-stubs>=2.2.2.240603"]
 dev = ["pre-commit>=3.7.1", "tomli>=2.0.1", "codespell>=2.3.0"]
 test = ["pytest>=8.2.2", "pytest-cov>=5.0.0", "pytest-xdist>=3.6.1"]
 docs = [
@@ -95,14 +89,8 @@ ignore_missing_imports = true
 module = "sklearn.*"
 ignore_missing_imports = true
 
-[tool.flake8]
-ignore = "E302, E305, E203, E501, W503, E501"
-select = "C,E,F,W,B,B950"
-max-line-length = 100
-exclude = [".git", "__pycache__", "__init__.py", ".mypy_cache", ".pytest_cache"]
-per-file-ignores = ["tests/*:F401,F811"]
-
 [tool.ruff]
+line-length = 120
 extend-exclude = []
 exclude = []
 lint.ignore = ["F811"]

pyproject.toml

@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+set -e
+set -x
+
+rm -rf $(find . -name __pycache__)
+rm -f $(find . -type f -name '*.py[co]')
+rm -f $(find . -type f -name '*~')
+rm -f $(find . -type f -name '.*~')
+rm -rf .pdm-build
+rm -rf .mypy_cache
+rm -rf .cache
+rm -rf .pytest_cache
+rm -rf .ruff_cache
+rm -rf htmlcov
+rm -rf *.egg-info
+rm -f .coverage
+rm -f .coverage.*
+rm -rf build
+rm -rf dist
+rm -rf site
+rm -rf docs/_build
+rm -rf coverage.xml

scripts/clean.sh

@@ -51,9 +51,7 @@ def __init__(
         self.input_type: Any = type(input_value)
         self.allowed_types: type | tuple[type, ...] = allowed_types
         self.message: str = message
-        super().__init__(
-            f"{message}: {input_value} (type: {self.input_type}). Allowed types: {allowed_types}"
-        )
+        super().__init__(f"{message}: {input_value} (type: {self.input_type}). Allowed types: {allowed_types}")
 
 
 class ProcessingError(SiapyError):
@@ -78,9 +76,7 @@ class MethodNotImplementedError(SiapyError):
     def __init__(self, class_name: str, method_name: str) -> None:
         self.class_name: str = class_name
         self.method_name: str = method_name
-        super().__init__(
-            f"Method '{method_name}' not implemented in class '{class_name}'"
-        )
+        super().__init__(f"Method '{method_name}' not implemented in class '{class_name}'")
 
 
 class DirectInitializationError(SiapyError):