Update build to use uv and fix publishing issues

bbglab · Dec 7, 2024 · 24b822f · 24b822f
1 parent ba4a4e0
commit 24b822f
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Showing 4 changed files with 918 additions and 48 deletions.
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -12,7 +12,6 @@ permissions:
 
 env:
   TERM: xterm
-  PYTHON_VERSION: 3.12
 
 jobs:
   packages-build:
@@ -27,23 +26,23 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: "pyproject.toml"
 
-      - uses: eifinger/setup-rye@v4
+      - uses: astral-sh/setup-uv@v4
 
       - name: Check format
         run: |
           make check-format || true
           BOLDRED=$(tput bold && tput setaf 1)
           RESET=$(tput sgr0)
-          echo "${BOLDRED}==> We won't fail on formatting errors for the time being, but we will in the future.${RESET}"
+          echo "${BOLDRED}==> We won't penalise formatting errors for the time being, but we will in the future.${RESET}"
       
       - name: Check lint
         run: |
           make check-lint || true
           BOLDRED=$(tput bold && tput setaf 1)
           RESET=$(tput sgr0)
-          echo "${BOLDRED}==> We won't fail on lint errors for the time being, but we will in the future.${RESET}"
+          echo "${BOLDRED}==> We won’t enforce linting errors for the time being, but we will in the future.${RESET}"
 
       - name: Build packages
         run: make build-dist
@@ -64,9 +63,9 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: "pyproject.toml"
 
-      - uses: eifinger/setup-rye@v4
+      - uses: astral-sh/setup-uv@v4
 
       - name: Check Dockerfile
         run: make check-docker
@@ -92,9 +91,9 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: "pyproject.toml"
 
-      - uses: eifinger/setup-rye@v4
+      - uses: astral-sh/setup-uv@v4
 
       - name: Check version matching the tag
         run: make check-version
@@ -112,9 +111,9 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: "pyproject.toml"
 
-      - uses: eifinger/setup-rye@v4
+      - uses: astral-sh/setup-uv@v4
 
       - name: Download packages
         uses: actions/download-artifact@v4
@@ -143,9 +142,9 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ env.PYTHON_VERSION }}
+          python-version-file: "pyproject.toml"
 
-      - uses: eifinger/setup-rye@v4
+      - uses: astral-sh/setup-uv@v4
 
       - name: Login to DockerHub
         if: ${{ env.DOCKER_USERNAME != '' }}

diff --git a/Makefile b/Makefile
@@ -2,12 +2,17 @@ ROOT_DIR := $(shell echo $(dir $(lastword $(MAKEFILE_LIST))) | sed 's|/*$$||')
 
 SHELL := /bin/bash
 
-VERSION = $(shell rye version)
+define version
+$(shell uv run python -c "from oncodriveclustl import __version__; print(__version__)")
+endef
 
-GIT_TAG_OR_SHA = $(shell git describe --tags --exact-match 2>/dev/null || git rev-parse --short HEAD)
+define git_tag_or_sha
+$(shell git describe --tags --exact-match 2>/dev/null || git rev-parse --short HEAD)
+endef
 
-IMAGE_TAG = $(VERSION)
-IMAGE := bbglab/oncodriveclustl:$(IMAGE_TAG)
+define image
+bbglab/oncodriveclustl:$(call version)
+endef
 
 BOLDRED := $(shell tput bold && tput setaf 1)
 BOLDGREEN := $(shell tput bold && tput setaf 2)
@@ -34,28 +39,37 @@ help:
 	@echo "$(BOLDGREEN)  clean        $(WHITE)-> Clean the working directory (build files, virtual environments, caches)"
 	@echo "$(RESET)"
 
-.PHONY: rye-installed
-rye-installed:
-	@if ! which rye > /dev/null; then \
-		echo "$(BOLDRED)This project build is managed by $(BOLDYELLOW)rye$(BOLDRED), which is not installed.$(RESET)"; \
+.PHONY: uv-installed
+uv-installed:
+	@if ! which uv > /dev/null; then \
+		echo "$(BOLDRED)This project build is managed by $(BOLDYELLOW)uv$(BOLDRED), which is not installed.$(RESET)"; \
 		echo "$(LIGHTBLUE)Please follow these instructions to install it:$(RESET)"; \
-		echo "$(LIGHTBLUE)--> $(BOLDBLUE)https://rye.astral.sh/guide/installation/$(RESET)"; \
+		echo "$(LIGHTBLUE)--> $(BOLDBLUE)https://docs.astral.sh/uv/#getting-started$(RESET)"; \
 		exit 1; \
 	fi
 
+.PHONY: ruff-installed
+ruff-installed: uv-installed
+	@if ! which ruff > /dev/null; then \
+		echo "$(BOLDRED)This project requires $(BOLDYELLOW)ruff$(BOLDRED), which is not installed.$(RESET)"; \
+		echo "$(LIGHTBLUE)Installing it with $(BOLDYELLOW)uv tool install ruff$(RESET)"; \
+		uv tool install ruff; \
+		ruff --version; \
+	fi
+
 .PHONY: checks
 checks: check-format check-lint check-docker
 
 .PHONY: check-format
-check-format: rye-installed
+check-format: ruff-installed
 	@echo "$(BOLDGREEN)Checking code format ...$(RESET)"
-	rye fmt --check
+	ruff format --check
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: check-lint
-check-lint: rye-installed
+check-lint: ruff-installed
 	@echo "$(BOLDGREEN)Checking lint ...$(RESET)"
-	rye lint
+	ruff check
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: check-docker
@@ -69,47 +83,47 @@ check-docker:
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: check-version
-check-version: rye-installed
+check-version: uv-installed
 	@echo "$(BOLDGREEN)Checking that the version matches the tag ...$(RESET)"
-	@if [ "$(VERSION)" != "$(GIT_TAG_OR_SHA)" ]; then \
-	    echo "$(BOLDRED)==> Version $(BOLDYELLOW)$(VERSION)$(BOLDRED) doesn't match the git tag $(BOLDYELLOW)$(GIT_TAG_OR_SHA)$(BOLDRED) !!!$(RESET)"; \
+	@if [ "$(call version)" != "$(call git_tag_or_sha)" ]; then \
+	    echo "$(BOLDRED)==> Version $(BOLDYELLOW)$(call version)$(BOLDRED) doesn't match the git tag $(BOLDYELLOW)$(call git_tag_or_sha)$(BOLDRED) !!!$(RESET)"; \
 		echo "$(BOLDRED)==> Please update the $(BOLDYELLOW)__version__$(BOLDRED) in $(BOLDYELLOW)oncodrivefml/__init__.py$(BOLDRED) and re-create the tag.$(RESET)"; \
 	    exit 1; \
 	fi
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: format
-format: rye-installed
+format: ruff-installed
 	@echo "$(BOLDGREEN)Formatting code ...$(RESET)"
-	rye fmt
+	ruff format
 
 .PHONY: build-dist
-build-dist: rye-installed
+build-dist: uv-installed
 	@echo "$(BOLDGREEN)Building packages ...$(RESET)"
-	rye build
+	uv build
 
 .PHONY: publish-dist
-publish-dist: rye-installed
-	@echo "$(BOLDGREEN)Publishing OncodriveCLUSTL $(BOLDYELLOW)$(VERSION)$(BOLDGREEN) to PyPI ...$(RESET)"
+publish-dist: uv-installed
+	@echo "$(BOLDGREEN)Publishing OncodriveCLUSTL $(BOLDYELLOW)$(call version)$(BOLDGREEN) to PyPI ...$(RESET)"
 	@[[ -z "$(PYPI_TOKEN)" ]] && (echo "$(BOLDRED)==> Missing PyPI token !!!$(RESET)"; exit 1)
-	rye publish --token $(PYPI_TOKEN)
+	uv publish --token $(PYPI_TOKEN)
 
 .PHONY: build-image
-build-image: rye-installed
-	@echo "$(BOLDGREEN)Building Docker image $(BOLDYELLOW)$(IMAGE)$(BOLDGREEN) ...$(RESET)"
-	docker build --progress=plain -t $(IMAGE) .
+build-image: uv-installed
+	@echo "$(BOLDGREEN)Building Docker image $(BOLDYELLOW)$(call image)$(BOLDGREEN) ...$(RESET)"
+	docker build --progress=plain -t $(call image) .
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: build-image
-push-image: rye-installed
+push-image: uv-installed
 	@echo "$(BOLDGREEN)Pushing the Docker image into the DockerHub ...$(RESET)"
-	docker push $(IMAGE)
+	docker push $(call image)
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"
 
 .PHONY: run-example
-run-example: rye-installed
+run-example: uv-installed
 	@echo "$(BOLDGREEN)Running example ...$(RESET)"
-	rye run oncodriveclustl \
+	uv run oncodriveclustl \
 		-i example/PAAD.tsv.gz -r example/cds.hg19.regions.gz -o example/output \
 		-sw 15 -cw 15 -simw 35 -sim region_restricted --concatenate --clustplot -e KRAS
 	@echo "$(BOLDGREEN)==> Success!$(RESET)"

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,7 @@ dependencies = [
     "tqdm==4.66.5",
 ]
 readme = "README.md"
-requires-python = ">=3.5,<3.13"
+requires-python = ">=3.10,<3.13"
 license = { file = "LICENSE" }
 
 [project.scripts]
@@ -32,10 +32,6 @@ license = { file = "LICENSE" }
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
-[tool.rye]
-managed = true
-dev-dependencies = []
-
 [tool.hatch.version]
 path = "oncodriveclustl/__init__.py"