From d842bbfe847ef7adea42097c4c571a03a18af729 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Sun, 10 Jul 2022 13:21:07 +0000
Subject: [PATCH] ci: add Conda tests and refactor
---
.gitlab-ci.yml | 65 +++++++++++++++++++++++++++++++++++++------------
environment.yml | 1 +
2 files changed, 50 insertions(+), 16 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 51ca7c9..d8329a8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,27 +6,60 @@ workflow:
rules:
- if: $CI_PIPELINE_SOURCE == "push"
-test:
- rules:
- - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+stages:
+ - build
+ - test
+ - publish
+
+build_conda:
+ stage: build
+ script:
+ - mamba env create --force -f environment.yml
+ - echo $CONDA_DEFAULT_ENV
+
+build_docker:
+ stage: build
+ before_script:
+ - export IMAGE="${DOCKER_ORG}/${DOCKER_REPO}"
+ - export BUILD_TAG="build"
+ - echo "IMAGE=$IMAGE" >> build.env
+ - echo "BUILD_TAG=$BUILD_TAG" >> build.env
+ script:
+ - docker build -t ${IMAGE}:${BUILD_TAG} .
+ artifacts:
+ reports:
+ dotenv: build.env
+
+test_conda:
+ stage: test
+ needs:
+ job: build_conda
+ before_script:
+ - conda activate ascii-alignment-pileup
+ script:
+ - tests/test.sh
+
+test_docker:
+ stage: test
+ needs:
+ - job: build_docker
+ artifacts: true
script:
- - export IMAGE="${DOCKER_ORG}/${DOCKER_REPO}:latest"
- - docker build -t $IMAGE .
- - docker run --rm $IMAGE tests/test.sh
+ - docker run --rm ${IMAGE}:${BUILD_TAG} tests/test.sh
-test_and_publish:
+publish_docker:
+ stage: publish
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
- script:
+ needs:
+ - job: build_docker
+ artifacts: true
+ - job: test_docker
+ before_script:
- export VERSION=$(grep 'version <-' ascii_alignment_pileup.R | cut -f2 -d'"')
- - export IMAGE="${DOCKER_ORG}/${DOCKER_REPO}"
- - |
- docker build \
- -t ${IMAGE}:${VERSION} \
- --build-arg version=$VERSION \
- .
- - docker run --rm ${IMAGE}:${VERSION} tests/test.sh
+ script:
- echo "${DOCKER_TOKEN}" | docker login -u "${DOCKER_USER}" --password-stdin
- - docker tag ${IMAGE}:${VERSION} ${IMAGE}:latest
+ - docker tag ${IMAGE}:${BUILD_TAG} ${IMAGE}:${VERSION}
+ - docker tag ${IMAGE}:${BUILD_TAG} ${IMAGE}:latest
- docker push ${IMAGE}:${VERSION}
- docker push ${IMAGE}:latest
diff --git a/environment.yml b/environment.yml
index 3452990..cc5c4d6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,6 +1,7 @@
name: ascii-alignment-pileup
channels:
- bioconda
+ - conda-forge
dependencies:
- r-optparse=1.7.1
- bioconductor-rtracklayer=1.54.0
--
GitLab