Use uv for testing

.github/workflows/Conda-app.yml

@@ -1,10 +1,10 @@
-name: Conda package
+name: Continuous integration tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
   ci:
@@ -35,39 +35,43 @@ jobs:
       - name: Install opencv dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y libgl1 and libglx-mesa0 
+          sudo apt-get install -y libgl1 and libglx-mesa0
 
-      - name: Install Conda environment with Micromamba
-        uses: mamba-org/setup-micromamba@v1
+      - name: Install ipynb dependencies (pandoc)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y pandoc
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          environment-name: DeepForest
-          environment-file: environment.yml
-          create-args: "python=${{ matrix.python-version }}"
-          cache-environment: true
-          cache-downloads: true
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up Python
+        run: uv python install
 
       - name: Install package
-        run: pip install . -U
+        run: uv sync --all-extras --dev
 
       - name: Run pytest
-        run: pytest -v
+        run: uv run pytest -v
 
       - name: Check style
-        run: yapf -d --recursive src/deepforest/ --style=.style.yapf
+        run: uv run yapf -d --recursive src/deepforest/ --style=.style.yapf
 
       - name: Check notebook style
-        run: nbqa yapf --in-place docs/user_guide/examples/*.ipynb --style=.style.yapf
+        run: uv run nbqa yapf --in-place docs/user_guide/examples/*.ipynb --style=.style.yapf
 
       - name: Check notebook build
-        run: pytest --nbmake docs/**/*_test.ipynb
+        run: uv run pytest --nbmake docs/**/*_test.ipynb
 
       - name: Run docformatter
-        run: docformatter --check --recursive src/deepforest/
+        run: uv run docformatter --check --recursive src/deepforest/
 
       - name: Test Docs
         run: |
-          cd docs && make clean && make html SPHINXOPTS="-W"
+          cd docs && uv run make clean && uv run make html SPHINXOPTS="-W"
 
       - name: Test and check build artifacts
         run: |
-          pip install build && python -m build && twine check dist/*
+          uv pip install build && uv run python -m build && uv run twine check dist/*

pyproject.toml

@@ -72,5 +72,26 @@ dependencies = [
     "xmltodict",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "black",
+    "bump-my-version",
+    "docformatter",
+    "flake8",
+    "mypy",
+    "nbmake",
+    "nbsphinx",
+    "nbqa",
+    "pytest",
+    "pytest-cov",
+    "pytest-mock",
+    "pytest-xdist",
+    "sphinx_design",
+    "sphinx_markdown_tables",
+    "sphinx_rtd_theme",
+    "twine",
+    "yapf",
+]
+
 [tool.setuptools.packages.find]
 where = ["src"]