diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 102a0c2..067c270 100644 --- 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 index 4b29b29..d2c09f5 100644 --- 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 index ed3ce4b..f5295b7 100644 --- 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" diff --git a/uv.lock b/uv.lock new file 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