Use uv for dependency handling

.github/workflows/e2e-release.yml

@@ -23,6 +23,11 @@ jobs:
         with:
           python-version: 3.11
 
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/0.7.13/install.sh | sh
+          echo "$HOME/.cargo/bin" >> "$GITHUB_PATH"
+
       - name: Build package
         run: |
           make build

.github/workflows/make.yml

@@ -23,4 +23,8 @@ jobs:
         with:
           ruby-version: 3.3
       - run: gem install xcop
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/0.7.13/install.sh | sh
+          echo "$HOME/.cargo/bin" >> "$GITHUB_PATH"
       - run: make

.github/workflows/pylint.yml

@@ -19,5 +19,9 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: 3.11
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/0.7.13/install.sh | sh
+          echo "$HOME/.cargo/bin" >> "$GITHUB_PATH"
       - run: make requirements
       - run: make pylint

.github/workflows/ty.yml

@@ -18,21 +18,15 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Create venv
+      - name: Install uv (from Astral)
         run: |
-          python3 -m venv .venv
+          curl -LsSf https://astral.sh/uv/0.7.13/install.sh | bash
+          echo "$HOME/.cargo/bin" >> "$GITHUB_PATH"
 
       - name: Install aibolit dependencies
         run: |
-          source .venv/bin/activate
-          python -m pip install -r requirements.txt
-
-      - name: Install uv (from Astral)
-        run: |
-          curl -LsSf https://astral.sh/uv/install.sh | bash
-          echo "$HOME/.cargo/bin" >> "$GITHUB_PATH"
+          make requirements
 
       - name: Run Ty
         run: |
-          source .venv/bin/activate
           uvx ty==0.0.1-alpha.8 check

.rultor.yml

@@ -9,7 +9,9 @@ assets:
 architect:
   - yegor256
 install: |
-  python3 -m pip install twine
+  curl -LsSf https://astral.sh/uv/0.7.13/install.sh | sh
+  source $HOME/.local/bin/env
+  uv tool install twine
 merge:
   script: |
     make
@@ -18,8 +20,8 @@ release:
     sed -i "s/0\.0\.0/${tag}/g" aibolit/__init__.py
     git add aibolit/__init__.py
     git commit -am "${tag}"
-    python3 --version
-    python3 -m pip --version
+    uv run python --version
+    uv --version
     make
     make e2e
-    python3 -m twine upload dist/* -u __token__ -p $(cat ../twine_token)
+    uv run twine upload dist/* -u __token__ -p $(cat ../twine_token)

Makefile

@@ -14,18 +14,18 @@ all: requirements install test it lint xcop sphinx
 lint: flake8 pylint mypy
 
 requirements:
-	python3 -m pip install -r requirements.txt
+	uv sync
 
 install:
-	python3 -m pip install .
-	python3 aibolit --version
+	uv pip install -e .
+	uv run aibolit --version
 
 test:
-	python3 -m pytest --testmon --cov=aibolit/ test/
+	uv run pytest --cov=aibolit/ test/
 
 it:
-	python3 -m test.integration.test_patterns_and_metrics
-	python3 -m test.integration.test_model > /dev/null
+	uv run python -m test.integration.test_patterns_and_metrics
+	uv run python -m test.integration.test_model > /dev/null
 	./test/integration/test_recommend.sh
 
 xcop:
@@ -34,27 +34,27 @@ xcop:
 	done < <(find . -name '*.xml' -not -path './.venv/**' -not -path './wp/**')
 
 flake8:
-	python3 -m flake8 aibolit test scripts --exclude scripts/target/*
+	uv run flake8 aibolit test scripts --exclude scripts/target/*
 
 pylint:
-	python3 -m pylint aibolit test scripts --ignore=scripts/target
+	uv run pylint aibolit test scripts --ignore=scripts/target
 
 ruff:
-	python3 -m ruff check .
+	uv run ruff check .
 
 sphinx:
 	rm -rf sphinx html
-	sphinx-apidoc -o sphinx aibolit --full
-	sphinx-build sphinx html
+	uv run sphinx-apidoc -o sphinx aibolit --full
+	uv run sphinx-build sphinx html
 
 mypy:
-	python3 -m mypy aibolit
+	uv run mypy aibolit
 
 build: requirements
-	python3 -m build
+	uv build
 
 e2e: build
-	./test/e2e/test_e2e_release.sh
+	./test/e2e/test_e2e_release.sh dist
 
 clean:
 	rm -rf build

README.md

@@ -10,7 +10,7 @@
 Learn how Aibolit works in our [White Paper].
 
 First, you install it (you must have
-[Python 3.7.7](https://www.python.org/downloads/)
+[Python 3.11+](https://www.python.org/downloads/)
 and [Pip](https://pip.pypa.io/en/stable/installing/) installed):
 
 ```bash
@@ -316,12 +316,12 @@ aibolit train --java_folder=src/java --skip_collect_dataset
 
 First, you need to install:
 
-* [Python 3+](https://www.python.org/downloads/)
-* [Pip](https://pip.pypa.io/en/stable/installing/)
+* [Python 3.11+](https://www.python.org/downloads/)
+* [uv](https://docs.astral.sh/uv/)
 * Ruby 2.6+
 * [Xcop](https://github.com/yegor256/xcop)
 
-Install the following packages if you don't have:
+Install the following packages if you don't have them:
 
 ```bash
 apt-get install ruby-dev libz-dev libxml2

REUSE.toml

@@ -42,6 +42,7 @@ path = [
     "**/Gemfile.lock",
     "README.md",
     "renovate.json",
+    "uv.lock",
     ".xcop",
     ".flake8",
 ]

pyproject.toml

@@ -10,7 +10,28 @@ authors = [
 license = { text = "MIT" }
 readme = "README.md"
 requires-python = ">=3.11"
-dynamic = ["version", "dependencies", "optional-dependencies"]
+dynamic = ["version"]
+dependencies = [
+  "beautifulsoup4==4.13.4",
+  "build==1.2.2.post1",
+  "catboost==1.2.8",
+  "chardet==5.2.0",         # Replace cchardet with chardet for Python 3.12 compatibility
+  "deprecated==1.2.10",
+  "html5lib==1.1",
+  "javalang==0.13.0",
+  "lxml==5.4.0",
+  "matplotlib==3.10.3",
+  "networkx==3.2",          # Updated to be compatible with NumPy 2.0+
+  "numpy==2.2.5",
+  "packaging==25.0",        # For version parsing, updated for sphinx compatibility
+  "pandas==2.2.3",
+  "pebble==4.5.3",
+  "requests==2.32.4",
+  "scikit-learn==1.6.1",
+  "scipy==1.15.3",
+  "setuptools==80.7.1",
+  "tqdm==4.66.3",
+]
 
 classifiers = [
   "Programming Language :: Python",
@@ -36,8 +57,6 @@ aibolit = [
 
 [tool.setuptools.dynamic]
 version = { attr = "aibolit.__version__" }
-dependencies = { file = ["requirements.txt"] }
-optional-dependencies.test = { file = ["requirements.txt"] }
 
 [build-system]
 requires = ["setuptools>=61", "wheel"]
@@ -60,3 +79,18 @@ extend-select = [
 docstring-quotes = "double"
 inline-quotes = "single"
 multiline-quotes = "single"
+
+[dependency-groups]
+dev = [
+  "codecov==2.1.13",
+  "flake8-elegant-objects==1.1.1",
+  "flake8==7.2.0",
+  "mypy==1.16.1",                    # Update to a version compatible with Python 3.12
+  "pylint==3.3.7",
+  "pytest-cov==6.1.1",
+  "pytest-testmon==2.1.3",
+  "pytest==8.3.5",
+  "ruff==0.11.11",
+  "sphinx==8.2.3",
+  "types-requests==2.32.0.20250515",
+]

test/e2e/test_e2e_release.sh

@@ -4,9 +4,11 @@
 
 set -euo pipefail
 
+DIST_DIR=${1:-dist}
+
 echo "Starting e2e release test..."
 
-TEMP_VENV=$(mktemp -d)
+TEMP_VENV=$(mktemp -d --suffix=test-env)
 echo "Testing in temporary environment: $TEMP_VENV"
 
 cleanup() {
@@ -15,15 +17,13 @@ cleanup() {
 
 trap cleanup EXIT
 
-echo "Creating fresh virtual environment"
-pushd "$TEMP_VENV"
-python3 -m venv test-env
+echo "Creating fresh virtual environment with Python 3.11..."
+uv venv --seed --python 3.11 "$TEMP_VENV"
 # shellcheck disable=SC1091
-source test-env/bin/activate
+source "$TEMP_VENV/bin/activate"
 
 echo "Installing built package..."
-popd > /dev/null
-python3 -m pip install dist/*.whl
+python3 -m pip install "$DIST_DIR"/*.whl
 
 echo "Verifying aibolit command..."
 which aibolit > /dev/null