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chris-zenchris-zen
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Upgrading versions and adding Continuous Integration and Delivery
1 parent 2b3842e commit 264abe9

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‎.dockerignore

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.venv/
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dist/
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example/
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oncodriveclustl.egg-info/

‎.github/workflows/build.yaml

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name: Build and Publish
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on:
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push:
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tags:
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- "**"
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branches:
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- "**"
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permissions:
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contents: read
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env:
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TERM: xterm
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jobs:
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packages-build:
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name: Build packages
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runs-on: ubuntu-latest
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env:
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RUFF_FORMAT: github
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- uses: astral-sh/setup-uv@v4
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- name: Check format
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run: |
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make check-format || true
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BOLDRED=$(tput bold && tput setaf 1)
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RESET=$(tput sgr0)
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echo "${BOLDRED}==> We won't penalise formatting errors for the time being, but we will in the future.${RESET}"
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- name: Check lint
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run: |
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make check-lint || true
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BOLDRED=$(tput bold && tput setaf 1)
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RESET=$(tput sgr0)
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echo "${BOLDRED}==> We won’t enforce linting errors for the time being, but we will in the future.${RESET}"
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- name: Build packages
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run: make build-dist
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- name: Upload packages
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uses: actions/upload-artifact@v4
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with:
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name: python-packages
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path: dist
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docker-build:
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name: Build Docker image
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- uses: astral-sh/setup-uv@v4
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- name: Check Dockerfile
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run: make check-docker
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- name: Build Docker image
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run: make build-image
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# TODO: Enable this when we figure out how to run it without having to download several Gigabytes of data.
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# - name: Test Docker image
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# run: make run-example
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check-version:
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name: Check version
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/')
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needs:
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- packages-build
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- docker-build
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- uses: astral-sh/setup-uv@v4
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- name: Check version matching the tag
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run: make check-version
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packages-publish:
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name: Publish packages
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runs-on: ubuntu-latest
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if: startsWith(github.ref, 'refs/tags/')
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needs:
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- check-version
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- uses: astral-sh/setup-uv@v4
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- name: Download packages
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uses: actions/download-artifact@v4
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with:
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name: python-packages
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- name: Publish to PyPI
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env:
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PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
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if: ${{ env.PYPI_TOKEN != '' }}
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run: make publish-dist
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docker-push:
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name: Push Docker image
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if: startsWith(github.ref, 'refs/tags/')
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runs-on: ubuntu-latest
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env:
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DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
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needs:
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- check-version
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steps:
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- if: ${{ env.DOCKER_USERNAME != '' }}
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version-file: "pyproject.toml"
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- uses: astral-sh/setup-uv@v4
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- name: Login to DockerHub
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if: ${{ env.DOCKER_USERNAME != '' }}
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run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
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- name: Push Docker image
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if: ${{ env.DOCKER_USERNAME != '' }}
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run: make push-image

‎.gitignore

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Distance_mutations.ipynb
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oncodriveclustl/count_mutations.py
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oncodriveclustl/mutations_intogen_local.txt
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example/output
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# Singularity images
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*.simg
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*~
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# Python bytecode
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__pycache__
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*.pyc
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*.egg-info/
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dist/
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# rye files
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.venv/
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requirements-dev.lock
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requirements.lock
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‎.hadolint.yaml

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ignored:
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- DL3003

‎.python-version

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3.12.4

‎Dockerfile

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FROM python:3.12-slim
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# hadolint ignore=DL3042
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RUN --mount=type=cache,target=/root/.cache/pip \
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--mount=type=bind,target=/project,rw \
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cd /project && pip install .
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RUN oncodriveclustl --help
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ENTRYPOINT [ "/usr/local/bin/oncodriveclustl" ]

‎MANIFEST.in

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This file was deleted.

‎Makefile

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ROOT_DIR := $(shell echo $(dir $(lastword $(MAKEFILE_LIST))) | sed 's|/*$$||')
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SHELL := /bin/bash
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define version
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$(shell uv run python -c "from oncodriveclustl import __version__; print(__version__)")
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endef
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define git_tag_or_sha
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$(shell git describe --tags --exact-match 2>/dev/null || git rev-parse --short HEAD)
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endef
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define image
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bbglab/oncodriveclustl:$(call version)
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endef
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BOLDRED := $(shell tput bold && tput setaf 1)
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BOLDGREEN := $(shell tput bold && tput setaf 2)
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BOLDYELLOW := $(shell tput bold && tput setaf 3)
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BOLDBLUE := $(shell tput bold && tput setaf 4)
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LIGHTBLUE := $(shell tput setaf 6)
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WHITE := $(shell tput sgr0 && tput setaf 7)
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RESET := $(shell tput sgr0)
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.PHONY: help
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help:
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@echo "$(BOLDYELLOW)Available targets:$(RESET)"
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@echo
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@echo "$(BOLDGREEN) checks $(WHITE)-> Run all the checks (format and lint)"
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@echo "$(BOLDGREEN) check-format $(WHITE)-> Check for formatting errors"
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@echo "$(BOLDGREEN) check-lint $(WHITE)-> Check for lint errors"
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@echo "$(BOLDGREEN) check-docker $(WHITE)-> Check the Dockerfile"
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@echo "$(BOLDGREEN) format $(WHITE)-> Format source code"
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@echo "$(BOLDGREEN) build-dist $(WHITE)-> Build source and wheel distribution files"
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@echo "$(BOLDGREEN) build-image $(WHITE)-> Build the Docker image"
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@echo "$(BOLDGREEN) push-image $(WHITE)-> Push the Docker image into DockerHub"
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@echo "$(BOLDGREEN) run-example $(WHITE)-> Run the included example using the Docker image"
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@echo "$(BOLDGREEN) clean $(WHITE)-> Clean the working directory (build files, virtual environments, caches)"
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@echo "$(RESET)"
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.PHONY: uv-installed
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uv-installed:
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@if ! which uv > /dev/null; then \
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echo "$(BOLDRED)This project build is managed by $(BOLDYELLOW)uv$(BOLDRED), which is not installed.$(RESET)"; \
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echo "$(LIGHTBLUE)Please follow these instructions to install it:$(RESET)"; \
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echo "$(LIGHTBLUE)--> $(BOLDBLUE)https://docs.astral.sh/uv/#getting-started$(RESET)"; \
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exit 1; \
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fi
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.PHONY: ruff-installed
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ruff-installed: uv-installed
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@if ! which ruff > /dev/null; then \
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echo "$(BOLDRED)This project requires $(BOLDYELLOW)ruff$(BOLDRED), which is not installed.$(RESET)"; \
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echo "$(LIGHTBLUE)Installing it with $(BOLDYELLOW)uv tool install ruff$(RESET)"; \
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uv tool install ruff; \
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ruff --version; \
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fi
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.PHONY: checks
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checks: check-format check-lint check-docker
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.PHONY: check-format
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check-format: ruff-installed
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@echo "$(BOLDGREEN)Checking code format ...$(RESET)"
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ruff format --check
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: check-lint
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check-lint: ruff-installed
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@echo "$(BOLDGREEN)Checking lint ...$(RESET)"
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ruff check
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: check-docker
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check-docker:
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@echo "$(BOLDGREEN)Checking Dockerfile ...$(RESET)"
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docker run --rm -i \
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-v $$(pwd):/project \
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hadolint/hadolint hadolint \
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--config /project/.hadolint.yaml \
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/project/Dockerfile
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: check-version
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check-version: uv-installed
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@echo "$(BOLDGREEN)Checking that the version matches the tag ...$(RESET)"
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@if [ "$(call version)" != "$(call git_tag_or_sha)" ]; then \
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echo "$(BOLDRED)==> Version $(BOLDYELLOW)$(call version)$(BOLDRED) doesn't match the git tag $(BOLDYELLOW)$(call git_tag_or_sha)$(BOLDRED) !!!$(RESET)"; \
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echo "$(BOLDRED)==> Please update the $(BOLDYELLOW)__version__$(BOLDRED) in $(BOLDYELLOW)oncodrivefml/__init__.py$(BOLDRED) and re-create the tag.$(RESET)"; \
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exit 1; \
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fi
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: format
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format: ruff-installed
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@echo "$(BOLDGREEN)Formatting code ...$(RESET)"
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ruff format
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.PHONY: build-dist
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build-dist: uv-installed
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@echo "$(BOLDGREEN)Building packages ...$(RESET)"
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uv build
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.PHONY: publish-dist
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publish-dist: uv-installed
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@echo "$(BOLDGREEN)Publishing OncodriveCLUSTL $(BOLDYELLOW)$(call version)$(BOLDGREEN) to PyPI ...$(RESET)"
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@if [ -z "$(PYPI_TOKEN)" ]; then \
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echo "$(BOLDRED)==> Missing PyPI token !!!$(RESET)"; \
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exit 1; \
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fi
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uv publish --token $(PYPI_TOKEN)
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.PHONY: build-image
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build-image: uv-installed
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@echo "$(BOLDGREEN)Building Docker image $(BOLDYELLOW)$(call image)$(BOLDGREEN) ...$(RESET)"
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docker build --progress=plain -t $(call image) .
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: build-image
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push-image: uv-installed
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@echo "$(BOLDGREEN)Pushing the Docker image into the DockerHub ...$(RESET)"
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docker push $(call image)
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: run-example
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run-example: uv-installed
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@echo "$(BOLDGREEN)Running example ...$(RESET)"
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uv run oncodriveclustl \
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-i example/PAAD.tsv.gz -r example/cds.hg19.regions.gz -o example/output \
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-sw 15 -cw 15 -simw 35 -sim region_restricted --concatenate --clustplot -e KRAS
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@echo "$(BOLDGREEN)==> Success!$(RESET)"
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.PHONY: clean
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clean:
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@echo "$(BOLDGREEN)Cleaning the repository ...$(RESET)"
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rm -rf ./oncodriveclustl.egg-info ./dist ./.ruff_cache ./.venv
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find . -name "__pycache__" -type d -exec rm -r {} +

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