Merge pull request #7 from AllenInstitute/feature/switch-to-uv

Switch to use uv instead of pip

.github/workflows/build.yml

@@ -24,22 +24,40 @@ 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"
     env:
       PYTHON_VERSION: ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4        
+      - name: Install uv
+        id: setup-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/setup-ai-github-urls
         with:
           token: ${{ secrets.AI_PACKAGES_TOKEN }}
       - 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: |

.github/workflows/release.yml

@@ -39,11 +39,11 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      - 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/setup-ai-github-urls
         with:
@@ -61,7 +61,7 @@ jobs:
       - name: Bump version with bumpversion
         run: |
           source .venv/bin/activate  
-          bump-my-version bump ${{ github.event.inputs.part }}
+          uvx --from bump-my-version bump-my-version bump ${{ github.event.inputs.part }}
       - name: Commit and push with tags
         if: ${{ github.event.inputs.dry-run == 'false' }}
         run: |
@@ -103,11 +103,11 @@ 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/setup-ai-github-urls
         with:

Makefile

@@ -65,98 +65,94 @@ 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
 
-install: $(INSTALL_STAMP) ## Installs package dependencies
-$(INSTALL_STAMP): $(PYTHON) $(DEP_FILES)
-	@. $(VENV_BIN)/activate;\
-	$(PIP) install -e .[all]; 
-	@touch $(INSTALL_STAMP)
+.uv: ## Check that uv is installed
+	@uv -V || echo 'Please install uv: https://docs.astral.sh/uv/getting-started/installation/'
 
-install-release: clean-install-stamp $(PYTHON) $(DEP_FILES) ## Installs package for release
-	@. $(VENV_BIN)/activate;\
-	$(PIP) install .[release]
+.PHONY: .uv
 
-install-force: clean-install-stamp install ## Force install package dependencies
+install: .uv  ## Installs package dependencies
+	uv sync --frozen --all-extras
+
+.PHONY: install
+
+rebuild-lockfile: .uv  ## Rebuilds the lockfile
+	uv lock --upgrade
+
+.PHONY: rebuild-lockfiles
+
+make install-release: .uv  ## Installs package dependencies
+	uv sync --frozen --group release
+
+.PHONY: install-release
 
 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/$$local_package --no-deps; \
+				uv add -v --editable --frozen $$parent_dir/$$local_package; \
 			fi \
 		done; \
 	done
 
+.PHONY: link-packages
+
 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 \
 			if [ $$local_package == $$dependency ] && [ $$local_package != $$this_package ]; then \
 				is_found=1; \
+				uv remove --frozen $$local_package; \
 			fi; \
 		done \
 	done; \
 	if [ $$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-ruff: .uv ## Run ruff checker
+	uv run ruff check
 
-lint-isort: $(INSTALL_STAMP) ## Run isort (check only) 
-	$(VENV_BIN)/isort ./ --check
+lint-mypy: .uv ## Run mypy
+	uv run mypy ./
 
-lint-mypy: $(INSTALL_STAMP) ## Run mypy
-	$(VENV_BIN)/mypy ./
+lint: lint-ruff lint-mypy  ## Run all lint targets (ruff, mypy)
 
 
-lint: lint-isort lint-black lint-mypy  ## Run all lint targets (black, isort, mypy)
+format-ruff: .uv ## Run ruff formatter 
+	uv run ruff check --fix
+	uv run ruff format
 
+format: format-ruff  ## Run all formatters (ruff) 
 
-format-black: $(INSTALL_STAMP) ## Format code using black
-	$(VENV_BIN)/black ./
-
-format-isort: $(INSTALL_STAMP) ## Format code using isort
-	$(VENV_BIN)/isort ./
-
-
-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
@@ -165,14 +161,14 @@ 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
 
 #####################
 ##@ 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
 
@@ -182,4 +178,4 @@ 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

pyproject.toml

@@ -26,26 +26,50 @@ dependencies = [
 
 [project.optional-dependencies]
 all = [
-    "aibs-informatics-test-resources[formatting]",
+    "aibs-informatics-test-resources[linting]",
     "aibs-informatics-test-resources[typing]",
 ]
 
-formatting = [
-    "black==23.11.0",
-    "flake8~=6.1.0",
+linting = [
+    "black~=23.11.0",
     "isort~=5.10",
+    "ruff~=0.9",
 ]
 
 typing = [
     "mypy~=1.6",
 ]
 
+[dependency-groups]
+
+dev = [
+    { include-group = 'linting' },
+    { include-group = 'typing' },
+]
+
 release = [
-    "build",
+    { include-group = 'bump' },
+    { include-group = 'build' }    
+]
+
+linting = [
+    "ruff~=0.9",
+]
+
+typing = [
+    "mypy",
+]   
+
+bump = [
     "bump-my-version",
+]
+
+build = [
+    "build",
     "wheel",
 ]
 
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
@@ -58,6 +82,14 @@ Homepage = "https://github.com/AllenInstitute/aibs-informatics-test-resources/"
 Issues = "https://github.com/AllenInstitute/aibs-informatics-test-resources/issues"
 Repository = "https://github.com/AllenInstitute/aibs-informatics-test-resources/"
 
+
+# -----------------------------------------------------------------------------
+##  astral-uv Configurations
+#   https://docs.astral.sh/uv/getting-started/
+# -----------------------------------------------------------------------------
+
+[tool.uv]
+
 # -----------------------------------------------------------------------------
 ##  Pyright Configurations
 #   https://github.com/microsoft/pyright/blob/main/docs/configuration.md
@@ -187,25 +219,16 @@ 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"]
 
 # -----------------------------------------------------------------------------
 ##  bumpversion Configurations
@@ -232,4 +255,4 @@ tag_name = "v{new_version}"
 [[tool.bumpversion.files]]
 filename = "src/aibs_informatics_test_resources/__version__.py"
 search = "__version__ = \"{current_version}\""
-replace = "__version__ = \"{new_version}\""
+replace = "__version__ = \"{new_version}\""

src/aibs_informatics_test_resources/base.py

@@ -1,3 +1,8 @@
+__all__ = [
+    "BaseTest",
+    "does_not_raise",
+]
+
 import json
 import os
 import re
@@ -7,7 +12,7 @@
 from contextlib import nullcontext as does_not_raise
 from copy import deepcopy
 from pathlib import Path
-from typing import Any, Callable, ClassVar, List, Optional, Tuple, Union, cast
+from typing import Any, ClassVar, List, Optional, Tuple, Union
 from unittest.mock import MagicMock, patch
 
 import pytest