Merge pull request #25 from AllenInstitute/feature/switch-to-uv

Switch to using uv and ruff
AllenInstitute · Jan 15, 2025 · 3f88ff7 · 3f88ff7
2 parents f972fc6 + 877cd54
commit 3f88ff7
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -21,21 +21,38 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
+        uv-resolution: ["highest", "lowest"]
+        exclude:
+          - python-version: "3.10"
+            uv-resolution: "lowest"
+          - python-version: "3.11"
+            uv-resolution: "lowest"
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4        
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
+          python-version: ${{ github.event.inputs.python-version }}
       - name: Set up AllenInstitute Repo Authorization
         uses: ./.github/actions/configure-org-repo-authorization
         with:
           token: ${{ secrets.AI_PACKAGES_TOKEN }}
           ssh_private_key: ${{ secrets.AIBSGITHUB_PRIVATE_KEY }}
       - name: Run Release
         run: |
-          make release
+          if [ ${{ matrix.uv-resolution }} == "highest" ]; then
+            make release            
+          else
+            # Install dependencies
+            uv sync --frozen --group all --all-extras --resolution ${{ matrix.uv-resolution }}
+            
+            # Linting 
+            uv run ruff check
+            uv run mypy ./
+
+            # Testing
+            uv run pytest -vv --durations=10
+          fi
         shell: bash
       - name: Upload coverage reports
         if: |

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -41,11 +41,11 @@ jobs:
         uses: actions/checkout@v4
         with:
           ssh-key: ${{ secrets.AIBSGITHUB_PRIVATE_KEY }}
-      - name: Set up Python ${{ github.event.inputs.python-version }}
-        uses: actions/setup-python@v4        
+      - name: Install uv
+        id: setup-uv
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ github.event.inputs.python-version }}
-          cache: 'pip'
       - name: Set up AllenInstitute Repo Authorization
         uses: ./.github/actions/configure-org-repo-authorization
         with:
@@ -105,11 +105,11 @@ jobs:
       - uses: actions/checkout@v4
         with:
           ref: ${{ needs.bump.outputs.VERSION_TAG }}
-      - name: Set up Python ${{ github.event.inputs.python-version }}
-        uses: actions/setup-python@v4        
+      - name: Install uv
+        id: setup-uv
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ github.event.inputs.python-version }}
-          cache: 'pip'
       - name: Set up AllenInstitute Repo Authorization
         uses: ./.github/actions/configure-org-repo-authorization
         with:

diff --git a/Makefile b/Makefile
@@ -65,41 +65,41 @@ obliterate: clean-venv clean  ## alias to clean, clean-venv
 ##@ Installation Commands
 #########################
 
-create-venv: $(PYTHON)  ## Creates virtualenv
-$(PYTHON):
-	python3 -m venv $(VENV) --prompt $(shell basename $(PACKAGE_DIR))
-	$(PYTHON) -m pip install --upgrade pip
+.uv: ## Check that uv is installed
+	@uv -V || echo 'Please install uv: https://docs.astral.sh/uv/getting-started/installation/'
 
-install: $(INSTALL_STAMP) ## Installs package dependencies
-$(INSTALL_STAMP): $(PYTHON) $(DEP_FILES)
-	@. $(VENV_BIN)/activate;\
-	$(PIP) install -e .[dev]; 
-	@touch $(INSTALL_STAMP)
 
-install-release: clean-install-stamp $(PYTHON) $(DEP_FILES) ## Installs package for release
-	@. $(VENV_BIN)/activate;\
-	$(PIP) install .[release]
+install: .uv  ## Installs package dependencies
+	uv sync --frozen --all-extras
+
+
+rebuild-lockfile: .uv  ## Rebuilds the lockfile
+	uv lock --upgrade
+
+
+make install-release: .uv  ## Installs package dependencies
+	uv sync --frozen --group release
 
-install-force: clean-install-stamp install ## Force install package dependencies
 
 link-packages: ## Link local packages to virtualenv  
 	@parent_dir=$$(dirname $$(pwd)); \
 	local_packages=$$(ls $$parent_dir); \
-	dependencies=$$($(PIP) list --format freeze --exclude-editable | awk -F '==' '{print $$1}');\
+	dependencies=$$(uv pip list --format freeze --exclude-editable | awk -F '==' '{print $$1}');\
 	for local_package in $$local_packages; do \
 		for dependency in $$dependencies; do \
 			if [ $$local_package == $$dependency ]; then \
 				echo "Reinstalling $$local_package dependency to local override"; \
-				$(PIP) install -e $$parent_dir/$$local_package --no-deps; \
+				uv pip install -e $$parent_dir/$$local_package; \
 			fi \
 		done; \
 	done
 
+
 unlink-packages: ## Unlink local packages from virtualenv
 	@parent_dir=$$(dirname $$(pwd)); \
 	this_package=$$(basename $$(pwd)); \
 	local_packages=$$(ls $$parent_dir); \
-	dependencies=$$($(PIP) list --format freeze --editable | awk -F '==' '{print $$1}');\
+	dependencies=$$(uv pip list --format freeze --editable | awk -F '==' '{print $$1}');\
 	is_found=0; \
 	for local_package in $$local_packages; do \
 		for dependency in $$dependencies; do \
@@ -110,53 +110,42 @@ unlink-packages: ## Unlink local packages from virtualenv
 	done; \
 	if [ $$is_found == 1 ]; then \
 		echo "Found dependencies installed locally, reinstalling..."; \
-		make clean-install-stamp install; \
+		make install; \
 	fi
 
-.PHONY: create-venv install install-force link-packages unlink-packages
+.PHONY: .uv install install-release rebuild-lockfile link-packages unlink-packages
 
 #######################
 ##@ Formatting Commands
 #######################
 
-lint-black: $(INSTALL_STAMP) ## Run black (check only)
-	$(VENV_BIN)/black ./ --check
-
-lint-isort: $(INSTALL_STAMP) ## Run isort (check only) 
-	$(VENV_BIN)/isort ./ --check
-
-lint-mypy: $(INSTALL_STAMP) ## Run mypy
-	$(VENV_BIN)/mypy ./
+lint-ruff: .uv ## Run ruff checker
+	uv run ruff check
 
+lint-mypy: .uv ## Run mypy
+	uv run mypy ./
 
-lint: lint-isort lint-black lint-mypy  ## Run all lint targets (black, isort, mypy)
+lint: lint-ruff lint-mypy  ## Run all lint targets (ruff, mypy)
 
 
-format-black: $(INSTALL_STAMP) ## Format code using black
-	$(VENV_BIN)/black ./
+format-ruff: .uv ## Run ruff formatter 
+	uv run ruff check --fix
+	uv run ruff format
 
-format-isort: $(INSTALL_STAMP) ## Format code using isort
-	$(VENV_BIN)/isort ./
+format: format-ruff  ## Run all formatters (ruff) 
 
-
-format: format-isort format-black  ## Run all formatters (black, isort) 
-
-.PHONY: lint-isort lint-black lint-mypy lint format-lint format-black format-mypy format
+.PHONY: lint-ruff lint-mypy lint format-ruff format-mypy format
 
 #####################
 ##@ Testing Commands
 #####################
 
-pytest: $(INSTALL_STAMP)  ## Run test (pytest)
-	$(VENV_BIN)/pytest -vv --durations=10
-
-tox: $(INSTALL_STAMP)  ## Run Test in tox environment
-	$(VENV_BIN)/tox
+pytest: install  ## Run test (pytest)
+	uv run pytest -vv --durations=10
 
 test: pytest  ## Run Standard Tests
 
-.PHONY: pytest tox test
-
+.PHONY: pytest test
 
 #####################
 ##@ Inspect Commands
@@ -165,22 +154,28 @@ test: pytest  ## Run Standard Tests
 coverage-server: $(INSTALL_STAMP) ## Run coverage server
 	$(PYTHON) -m http.server $(COVERAGE_SERVER_PORT) -d $(COVERAGE_DIR)
 
+.PHONY: coverage-server
 
 #####################
-##@ Packaging Commands
+##@ Docker Commands
 #####################
 
-package: $(INSTALL_STAMP)  ## Build package distribution
-	$(PIP) install -U build
-	$(PYTHON) -m build
+docker-build: ## Build docker image
+	@docker build 									\
+		--ssh default 								\
+		--platform linux/amd64  					\
+		--tag aibs-informatics-core:latest			\
+		--file $(PACKAGE_DIR)/docker/Dockerfile		\
+		$(PACKAGE_DIR)
+
+.PHONY: docker-build
 
 #####################
 ##@ Release Commands
 #####################
 
 dist: install-release ## Build source and wheel package
-	@. $(VENV_BIN)/activate;\
-	$(PYTHON) -m build;
+	uv build
 
 reinstall: obliterate install ## Recreate environment and install
 
@@ -190,4 +185,5 @@ post-build: lint test  ## Run linters and tests
 release: pre-build build post-build  ## Runs pre-build, build, post-build
 run: release
 
-.PHONY: reinstall pre-build build post-build release run
+.PHONY: dist reinstall pre-build build post-build release run
+
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,14 +1,35 @@
 FROM public.ecr.aws/lts/ubuntu:22.04_stable
 
+ARG PYTHON_VERSION=3.11
+ARG UV_VERSION=0.5.18
+
 # Update and install deps
-RUN apt-get update -y && apt-get install -y \
-    python3.9 \
+# uv installer requires curl (and certificates) to download the release archive
+RUN apt-get update -y && apt-get install -y --no-install-recommends \
+    curl \
+    ca-certificates \
+    python${PYTHON_VERSION} \
     python3-pip
 
+# Download the latest installer
+# ENV UV_INSTALL_DIR="/opt/.uv" 
+# ENV UV_UNMANAGED_INSTALL="/opt/.uv"
+RUN if [ -n "$UV_VERSION" ]; then \
+    curl -sSL "https://astral.sh/uv/${UV_VERSION}/install.sh" -o /uv-installer.sh; \
+else \
+    curl -sSL "https://astral.sh/uv/install.sh" -o /uv-installer.sh; \
+fi
+
+# Run the installer then remove it
+RUN env UV_INSTALL_DIR='/opt/.uv' UV_UNMANAGED_INSTALL="/opt/.uv" sh /uv-installer.sh \
+    && rm /uv-installer.sh
+
 COPY . /opt/python/aibs-informatics-core/
 
 WORKDIR /opt/python/aibs-informatics-core
-RUN pip3 install --no-cache-dir .
+RUN /opt/.uv/uv pip install --system .
 WORKDIR /
 
+RUN rm -rf /opt/.uv
+
 CMD ["python3"]
diff --git a/pyproject.toml b/pyproject.toml
@@ -31,12 +31,35 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "aibs-informatics-test-resources[all]~=0.0.4",
+    "aibs-informatics-test-resources~=0.1",
 ]
+
+[dependency-groups]
+
+dev = [
+    { include-group = 'linting' },
+    { include-group = 'typing' },
+]
+
 release = [
-    "build",
+    { include-group = 'bump' },
+    { include-group = 'build' }    
+]
+
+linting = [
+    "ruff~=0.9",
+]
+
+typing = [
+    "mypy~=1.13",
+]   
+
+bump = [
     "bump-my-version",
-    "twine",
+]
+
+build = [
+    "build",
     "wheel",
 ]
 
@@ -58,6 +81,13 @@ Homepage = "https://github.com/AllenInstitute/aibs-informatics-core/"
 Issues = "https://github.com/AllenInstitute/aibs-informatics-core/issues"
 Repository = "https://github.com/AllenInstitute/aibs-informatics-core/"
 
+# -----------------------------------------------------------------------------
+##  astral-uv Configurations
+#   https://docs.astral.sh/uv/getting-started/
+# -----------------------------------------------------------------------------
+
+[tool.uv]
+
 
 # -----------------------------------------------------------------------------
 ##  Pyright Configurations
@@ -200,25 +230,17 @@ ignore_errors = false
 
 
 # -----------------------------------------------------------------------------
-##  Black Configurations
-#   https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#what-on-earth-is-a-pyproject-toml-file
+##  ruff Configurations
+#   https://beta.ruff.rs/docs/configuration/
 # -----------------------------------------------------------------------------
 
-
-[tool.black]
+[tool.ruff]
 line-length = 99
-include = '\.pyi?$'
-
-# -----------------------------------------------------------------------------
-##  isort Configurations
-#   https://pycqa.github.io/isort/docs/configuration/config_files.html
-# -----------------------------------------------------------------------------
+src = ["src", "test"]
 
-[tool.isort]
-# required for compatibility with black:
-line_length = 99
-profile = "black"
-src_paths = ["src", "test"]
+[tool.ruff.lint]
+select = ["E", "F", "W", "C90"]
+# ignore = ["E501"]
 
 # -----------------------------------------------------------------------------
 ##  bumpversion Configurations