Upgrading versions and adding Continuous Integration and Delivery

.dockerignore

@@ -0,0 +1,4 @@
+.venv/
+dist/
+example/
+oncodriveclustl.egg-info/

.github/workflows/build.yaml

@@ -0,0 +1,156 @@
+name: Build and Publish
+
+on:
+  push:
+    tags:
+      - "**"
+    branches:
+      - "**"
+
+permissions:
+  contents: read
+
+env:
+  TERM: xterm
+  PYTHON_VERSION: 3.12
+
+jobs:
+  packages-build:
+    name: Build packages
+    runs-on: ubuntu-latest
+    env:
+      RUFF_FORMAT: github
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: eifinger/setup-rye@v4
+
+      - name: Check format
+        run: |
+          make check-format || true
+          BOLDRED=$(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.${RESET}"
+
+      - name: Check lint
+        run: |
+          make check-lint || true
+          BOLDRED=$(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}"
+
+      - name: Build packages
+        run: make build-dist
+
+      - name: Upload packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-packages
+          path: dist
+
+  docker-build:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: eifinger/setup-rye@v4
+
+      - name: Check Dockerfile
+        run: make check-docker
+
+      - name: Build Docker image
+        run: make build-image
+
+      # TODO: Enable this when we figure out how to run it without having to download several Gigabytes of data.
+      # - name: Test Docker image
+      #   run: make run-example
+
+  check-version:
+    name: Check version
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - packages-build
+      - docker-build
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: eifinger/setup-rye@v4
+
+      - name: Check version matching the tag
+        run: make check-version
+
+  packages-publish:
+    name: Publish packages
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - check-version
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: eifinger/setup-rye@v4
+
+      - name: Download packages
+        uses: actions/download-artifact@v4
+        with:
+          name: python-packages
+
+      - name: Publish to PyPI
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+        if: ${{ env.PYPI_TOKEN != '' }}
+        run: make publish-dist
+
+  docker-push:
+    name: Push Docker image
+    if: startsWith(github.ref, 'refs/tags/')
+    runs-on: ubuntu-latest
+    env:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+    needs:
+      - check-version
+
+    steps:
+      - if: ${{ env.DOCKER_USERNAME != '' }}
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: eifinger/setup-rye@v4
+
+      - name: Login to DockerHub
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
+
+      - name: Push Docker image
+        if: ${{ env.DOCKER_USERNAME != '' }}
+        run: make push-image

.gitignore

@@ -15,6 +15,7 @@ dataset_randomizator.py
 Distance_mutations.ipynb
 oncodriveclustl/count_mutations.py
 oncodriveclustl/mutations_intogen_local.txt
+example/output
 
 # Singularity images
 *.simg
@@ -35,7 +36,13 @@ oncodriveclustl/mutations_intogen_local.txt
 *~
 
 # Python bytecode
+__pycache__
 *.pyc
 *.egg-info/
 dist/
 
+# rye files
+.venv/
+requirements-dev.lock
+requirements.lock
+

.hadolint.yaml

@@ -0,0 +1,2 @@
+ignored:
+  - DL3003

.python-version

@@ -0,0 +1 @@
+3.12.4

Dockerfile

@@ -0,0 +1,10 @@
+FROM python:3.12-slim
+
+# hadolint ignore=DL3042
+RUN --mount=type=cache,target=/root/.cache/pip \
+    --mount=type=bind,target=/project,rw \
+    cd /project && pip install .
+
+RUN oncodriveclustl --help
+
+ENTRYPOINT [ "/usr/local/bin/oncodriveclustl" ]

Makefile

@@ -0,0 +1,121 @@
+ROOT_DIR := $(shell echo $(dir $(lastword $(MAKEFILE_LIST))) | sed 's|/*$$||')
+
+SHELL := /bin/bash
+
+VERSION = $(shell rye version)
+
+GIT_TAG_OR_SHA = $(shell git describe --tags --exact-match 2>/dev/null || git rev-parse --short HEAD)
+
+IMAGE_TAG = $(VERSION)
+IMAGE := bbglab/oncodriveclustl:$(IMAGE_TAG)
+
+BOLDRED := $(shell tput bold && tput setaf 1)
+BOLDGREEN := $(shell tput bold && tput setaf 2)
+BOLDYELLOW := $(shell tput bold && tput setaf 3)
+BOLDBLUE := $(shell tput bold && tput setaf 4)
+LIGHTBLUE := $(shell tput setaf 6)
+WHITE := $(shell tput sgr0 && tput setaf 7)
+RESET := $(shell tput sgr0)
+
+
+.PHONY: help
+help:
+	@echo "$(BOLDYELLOW)Available targets:$(RESET)"
+	@echo
+	@echo "$(BOLDGREEN)  checks       $(WHITE)-> Run all the checks (format and lint)"
+	@echo "$(BOLDGREEN)  check-format $(WHITE)-> Check for formatting errors"
+	@echo "$(BOLDGREEN)  check-lint   $(WHITE)-> Check for lint errors"
+	@echo "$(BOLDGREEN)  check-docker $(WHITE)-> Check the Dockerfile"
+	@echo "$(BOLDGREEN)  format       $(WHITE)-> Format source code"
+	@echo "$(BOLDGREEN)  build-dist   $(WHITE)-> Build source and wheel distribution files"
+	@echo "$(BOLDGREEN)  build-image  $(WHITE)-> Build the Docker image"
+	@echo "$(BOLDGREEN)  push-image   $(WHITE)-> Push the Docker image into DockerHub"
+	@echo "$(BOLDGREEN)  run-example  $(WHITE)-> Run the included example using the Docker image"
+	@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)"; \
+		echo "$(LIGHTBLUE)Please follow these instructions to install it:$(RESET)"; \
+		echo "$(LIGHTBLUE)--> $(BOLDBLUE)https://rye.astral.sh/guide/installation/$(RESET)"; \
+		exit 1; \
+	fi
+
+.PHONY: checks
+checks: check-format check-lint check-docker
+
+.PHONY: check-format
+check-format: rye-installed
+	@echo "$(BOLDGREEN)Checking code format ...$(RESET)"
+	rye fmt --check
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: check-lint
+check-lint: rye-installed
+	@echo "$(BOLDGREEN)Checking lint ...$(RESET)"
+	rye lint
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: check-docker
+check-docker:
+	@echo "$(BOLDGREEN)Checking Dockerfile ...$(RESET)"
+	docker run --rm -i \
+		-v $$(pwd):/project \
+		hadolint/hadolint hadolint \
+		--config /project/.hadolint.yaml \
+		/project/Dockerfile
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: check-version
+check-version: rye-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)"; \
+		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!$(RESET)"
+
+.PHONY: format
+format: rye-installed
+	@echo "$(BOLDGREEN)Formatting code ...$(RESET)"
+	rye fmt
+
+.PHONY: build-dist
+build-dist: rye-installed
+	@echo "$(BOLDGREEN)Building packages ...$(RESET)"
+	rye build
+
+.PHONY: publish-dist
+publish-dist: rye-installed
+	@echo "$(BOLDGREEN)Publishing OncodriveCLUSTL $(BOLDYELLOW)$(VERSION)$(BOLDGREEN) to PyPI ...$(RESET)"
+	@[[ -z "$(PYPI_TOKEN)" ]] && (echo "$(BOLDRED)==> Missing PyPI token !!!$(RESET)"; exit 1)
+	rye 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 $(IMAGE) .
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: build-image
+push-image: rye-installed
+	@echo "$(BOLDGREEN)Pushing the Docker image into the DockerHub ...$(RESET)"
+	docker push $(IMAGE)
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: run-example
+run-example: rye-installed
+	@echo "$(BOLDGREEN)Running example ...$(RESET)"
+	rye run oncodriveclustl \
+		-i example/PAAD.tsv.gz -r example/cds.hg19.regions.gz -o example/output \
+		-sw 15 -cw 15 -simw 35 -sim region_restricted --concatenate --clustplot -e KRAS
+	@echo "$(BOLDGREEN)==> Success!$(RESET)"
+
+.PHONY: clean
+clean:
+	@echo "$(BOLDGREEN)Cleaning the repository ...$(RESET)"
+	rm -rf ./oncodriveclustl.egg-info ./dist ./.ruff_cache ./.venv
+	find . -name "__pycache__" -type d -exec rm -r {} +