Feature/convert python environment to uv

.github/workflows/python-CD.yml

@@ -23,18 +23,21 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black flake8
-      - name: Format with Black
+          pip install ruff
+      - name: Lint with ruff
         run: |
-          black --check .
+          ruff check .
+      - name: Format check with ruff
+        run: |
+          ruff format --check .
 
   build:
     needs: format_and_check
     runs-on: ubuntu-22.04
     environment: ${{ github.ref == 'refs/heads/master' && 'production' || 'staging' }}
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v3
@@ -45,20 +48,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Install setuptools
-        run: |
-          pip install setuptools wheel
+          pip install pytest build
       - name: Build Python package
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
       - name: Install Python Package
         run: |
           pip install dist/*.whl
       - name: Test with pytest
         run: |
-          pytest test.py -v
+          pytest tests/ -v
 
   deploy:
     needs: build
@@ -73,14 +72,10 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Install setuptools
-        run: |
-          pip install setuptools wheel
+          pip install pytest build
       - name: re-Build Python package
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
       - name: Install Python Package
         run: |
           pip install dist/*.whl
@@ -108,7 +103,7 @@ jobs:
       - name: Get Package version
         id: get_version
         run: |
-          echo "version=$(python setup.py --version)" >> $GITHUB_ENV
+          echo "version=$(python -c "import re; print(re.search(r'version = \"(.*?)\"', open('pyproject.toml').read()).group(1))")" >> $GITHUB_ENV
       - name: Check if release exists
         id: check_release
         run: |

.github/workflows/python-CI.yml

@@ -22,18 +22,21 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black flake8
-      - name: Format with Black
+          pip install ruff
+      - name: Lint with ruff
         run: |
-          black --check .
+          ruff check .
+      - name: Format check with ruff
+        run: |
+          ruff format --check .
 
   build:
     needs: format_and_check
     runs-on: ubuntu-22.04
     environment: development
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -43,17 +46,13 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      - name: Install setuptools
-        run: |
-          pip install setuptools wheel
+          pip install pytest build
       - name: Build Python package
         run: |
-          python setup.py sdist bdist_wheel
+          python -m build
       - name: Install Python Package
         run: |
           pip install dist/*.whl
       - name: Test with pytest
         run: |
-          pytest test.py -v
+          pytest tests/ -v

.gitignore

@@ -76,7 +76,15 @@ target/
 .ipynb_checkpoints/
 
 # exclude data from source control by default
-/data/processed/
+tests/data/processed/
+tests/data/interim/
+tests/data/external/
+
+# Keep .gitkeep files in data directories
+!tests/data/**/.gitkeep
+
+# Ignore large TIFF files in raw if they are not needed for basic CI
+# tests/data/raw/TIF/*.tif
 
 # Mac OS-specific storage files
 .DS_Store

.pre-commit-config.yaml

@@ -1,8 +1,8 @@
-# Format code with black
+# Format and lint code with ruff
 repos:
-  # Run black
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.7
     hooks:
-      - id: black
-        language_version: python3.10
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format

LICENSE

@@ -1,10 +1,9 @@
 
 The MIT License (MIT)
-Copyright (c) 2025, Caihao Cui
+Copyright (c) 2026, Caihao Cui
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
 
 The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-

Makefile

@@ -1,4 +1,4 @@
-.PHONY: clean data lint requirements  test_environment help
+.PHONY: clean lint requirements rebuild upload gh-pages test help
 
 #################################################################################
 # GLOBALS                                                                       #
@@ -21,13 +21,8 @@ endif
 #################################################################################
 
 ## Install Python Dependencies
-requirements: test_environment
-	$(PYTHON_INTERPRETER) -m pip install -U pip setuptools wheel
-	$(PYTHON_INTERPRETER) -m pip install -r requirements.txt
-
-## Make Dataset
-data: requirements
-	$(PYTHON_INTERPRETER) src/data/make_dataset.py data/raw data/processed
+requirements:
+	uv sync
 
 ## Delete all compiled Python files
 clean:
@@ -37,27 +32,25 @@ clean:
 ## Rebuilt the wheel and upload to PyPI
 rebuild:
 	rm -rf build dist
-	$(PYTHON_INTERPRETER) setup.py sdist bdist_wheel
+	uv build
 	twine upload dist/*
 ## Upload to PyPI
 upload:
-	$(PYTHON_INTERPRETER) setup.py sdist bdist_wheel
+	uv build
 	twine upload dist/*
 
 ## Update Github Pages
 gh-pages:
-	$(PYTHON_INTERPRETER) -m pip install -q mkdocs mkdocs-material
-	mkdocs gh-deploy
+	mkdocs gh-deploy --force
 
+## Run tests
+test:
+	pytest tests/ -v
 
-# ## Lint using flake8
+## Lint and format using ruff
 lint:
-	black src
-
-
-## Test python environment is setup correctly
-test_environment:
-	$(PYTHON_INTERPRETER) test_environment.py
+	ruff check . --fix
+	ruff format .
 
 #################################################################################
 # PROJECT RULES                                                                 #