Merge pull request #14 from NCI-GDC/feat/multistage-build-test

Feat/multistage build test

Author: czyszCTDS

Dockerfile.multistage

@@ -0,0 +1,28 @@
+FROM quay.io/ncigdc/bio-python:3.6 as builder
+
+COPY ./ /opt
+
+WORKDIR /opt
+
+RUN python3 setup.py build \
+	&& mkdir -p dist/ \
+	&& cp -r build/lib/* dist/ \
+	&& cp -r bin/ dist/ \
+	&& cp -f Makefile requirements.txt dev-requirements.txt README.md setup.py dist/
+
+FROM quay.io/ncigdc/bio-python:3.6
+
+COPY --from=builder /opt/dist/ /opt
+
+ENV BINARY=aliquotmaf
+
+WORKDIR /opt
+
+RUN python3 -m pip install -r requirements.txt -r dev-requirements.txt \
+	&& python3 setup.py develop \
+	&& ln -s /opt/bin/${BINARY} /bin/${BINARY} \
+	&& chmod +x /bin/${BINARY}
+
+ENTRYPOINT ["/bin/aliquotmaf"]
+
+CMD ["--help"]

Jenkinsfile

@@ -17,29 +17,13 @@ pipeline {
 	TWINE_PASSWORD = credentials('twine_password')
 	QUAY_USERNAME = credentials('QUAY_USERNAME')
 	QUAY_PASSWORD = credentials('QUAY_PASSWORD')
-	http_proxy = "$PROXY"
-	https_proxy = "$PROXY"
   }
   options {
     disableConcurrentBuilds()
     skipStagesAfterUnstable()
   }
 
   stages {
-    stage('Init') {
-      steps {
-        vbash 'make version'
-
-	script {
-	  GIT_HASH = sh(script: 'git rev-parse HEAD', returnStdout: true).trim()
-	  VERSION = sh(script: "make print-version BRANCH_NAME=${BRANCH_NAME}", returnStdout: true).trim()
-	  PYPI_VERSION = sh(script: "make print-pypi", returnStdout: true).trim()
-	  currentBuild.displayName = "#${currentBuild.number} - ${VERSION}"
-	}
-
-	echo "Version: ${VERSION}"
-      }
-    }
     stage('Docker Build') {
       steps {
         vbash "make build-docker PROXY=${PROXY}"
@@ -50,44 +34,18 @@ pipeline {
         sh 'make test-docker'
       }
     }
-    stage('Docker Publish Staging') {
-      when {
-        anyOf {
-	  branch 'feat*'
-	  branch 'develop'
-	  branch 'hotfix/*'
-	  branch 'release/*'
-	}
-      }
+    stage('Docker Publish') {
       steps {
-        sh 'make publish-staging'
-      }
-    }
-    stage('Docker Publish Release') {
-      when {
-        anyOf {
-	  branch 'main'
+        script {
+          DOCKER_TAG = sh(script: "make version-docker-tag", returnStdout: true).trim()
 	}
-      }
-      steps {
-        sh 'make publish-release'
+        sh "make publish-docker DOCKER_TAG=${DOCKER_TAG}"
       }
     }
-    stage('PyPI Publish Branch') {
-      when { 
-        anyOf {
-	  branch 'main'
-	  branch 'develop'
-	  branch 'hotfix/*'
-	  branch 'release/*'
-	}
-      }
-      steps {
-	echo "Building PyPI Version: ${PYPI_VERSION}"
-        sh "pip install --user twine wheel"
-        vbash "make build-pypi"
-        vbash "make publish-pypi"
-      }
+  }
+  post {
+    always {
+      sh 'make clean'
     }
   }
 }

Makefile

@@ -1,30 +1,25 @@
-# UPDATE ME
 REPO = aliquot-maf-tools
 
-# UPDATE ME
 MODULE = aliquotmaf
 
-GIT_SHORT_HASH:=$(shell git rev-parse --short HEAD)
-
-PYPI_VERSION:=$(shell python3 setup.py -q print_version --pypi)
-DOCKER_VERSION:=$(shell python3 setup.py -q print_version --docker)
-COMMIT_HASH:=$(shell python3 setup.py -q print_version --hash)
+COMMIT_HASH:=$(shell git rev-parse HEAD 2>/dev/null)
 
 DOCKER_REPO := quay.io/ncigdc
-DOCKER_IMAGE := ${DOCKER_REPO}/${REPO}:${DOCKER_VERSION}
 DOCKER_IMAGE_COMMIT := ${DOCKER_REPO}/${REPO}:${COMMIT_HASH}
 DOCKER_IMAGE_LATEST := ${DOCKER_REPO}/${REPO}:latest
 
-TWINE_REPOSITORY_URL?=""
+TWINE_REPOSITORY_URL?=
 PIP_EXTRA_INDEX_URL?=
 
 .PHONY: version version-* print-*
 version:
 	@echo --- VERSION: ${PYPI_VERSION} ---
 
 version-docker:
-	@echo ${DOCKER_IMAGE}
-	@echo ${DOCKER_IMAGE_COMMIT}
+	@python setup.py -q print_version --docker
+
+version-docker-tag:
+	@docker run --rm --entrypoint="make" ${DOCKER_IMAGE_LATEST} "version-docker"
 
 .PHONY: docker-login
 docker-login:
@@ -87,17 +82,11 @@ build: build-docker
 build-docker:
 	@echo
 	@echo -- Building docker --
-	python3 setup.py build
-	mkdir -p dist
-	cp -r build/lib/* dist/
-	cp -r bin/ dist/
-	cp -f Makefile requirements.txt dev-requirements.txt README.md setup.py dist/
 	docker build . \
-		--file ./Dockerfile \
+		--file ./Dockerfile.multistage \
 		--build-arg http_proxy=${PROXY} \
 		--build-arg https_proxy=${PROXY} \
 		-t "${DOCKER_IMAGE_COMMIT}" \
-		-t "${DOCKER_IMAGE}" \
 		-t "${DOCKER_IMAGE_LATEST}"
 
 build-pypi:
@@ -121,10 +110,11 @@ test-docker:
 	@echo -- Running Docker Test --
 	docker run --rm ${DOCKER_IMAGE_LATEST} test
 
-.PHONY: publish publish-*
-publish:
+.PHONY: publish-*
+publish-docker:
+	docker tag ${DOCKER_IMAGE_COMMIT} ${DOCKER_REPO}/${REPO}:${DOCKER_TAG}
 	docker push ${DOCKER_IMAGE_COMMIT}
-	docker push ${DOCKER_IMAGE}
+	docker push ${DOCKER_REPO}/${REPO}:${DOCKER_TAG}
 
 publish-pypi: dist/*.whl
 	@echo

setup.py

@@ -15,7 +15,7 @@
 GIT_REPO_URL = "https://github.com/NCI-GDC/{}".format(GIT_REPO)
 
 INSTALL_REQUIRES = [
-    "bioinf-maflib>=1.1.0",
+    "bioinf-maflib",
     "pysam",
 ]