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- test # this checks the viability of the code
- assets # this builds assets to be included in documentation and distribution binaries
- documentation # this processes the documentation
- test-compat # this runs many additional compatibility tests
GIT_STRATEGY: clone
DOCKER_DRIVER: overlay2
DOCKER_TLS_CERTDIR: ""
DOCKER_GHCR_TAG: "ghcr.io/lcsb-biocore/docker/cobrexa.jl"
#
# Predefined conditions for triggering jobs
#
.global_trigger_pull_request: &global_trigger_pull_request
- if: $CI_COMMIT_BRANCH == "develop"
when: never
- if: $CI_COMMIT_BRANCH == "master"
when: never
- if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
.global_trigger_build_doc: &global_trigger_build_doc
- if: $CI_EXTERNAL_PULL_REQUEST_TARGET_BRANCH_NAME == "master" && $CI_EXTERNAL_PULL_REQUEST_SOURCE_BRANCH_NAME == "develop"
- if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
when: never
- if: $CI_COMMIT_BRANCH == "develop"
- if: $CI_COMMIT_TAG =~ /^v/
.global_trigger_full_tests: &global_trigger_full_tests
- if: $CI_COMMIT_BRANCH == "develop"
- if: $CI_COMMIT_BRANCH == "master"
- if: $CI_COMMIT_TAG =~ /^v/
.global_trigger_compat_tests: &global_trigger_compat_tests
rules:
- if: $CI_COMMIT_BRANCH == "master"
- if: $CI_EXTERNAL_PULL_REQUEST_TARGET_BRANCH_NAME == "master"
.global_trigger_test_containers: &global_trigger_test_containers
rules:
- if: $CI_PIPELINE_SOURCE == "external_pull_request_event"
when: never
- if: $CI_COMMIT_BRANCH == "develop"
.global_trigger_release_containers: &global_trigger_release_containers
rules:
- if: $CI_COMMIT_TAG =~ /^v/
#
# Test environment & platform settings
#
.global_dind: &global_dind
image: docker:20.10.12
tags:
- privileged
services:
- name: docker:20.10.12-dind
command: ["--tls=false", "--mtu=1458", "--registry-mirror", "https://docker-registry.lcsb.uni.lu"]
before_script:
- docker login -u $CI_USER_NAME -p $GITLAB_ACCESS_TOKEN $CI_REGISTRY
.global_julia16: &global_julia16
.global_env_linux: &global_env_linux
- $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/bin/julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
.global_env_win: &global_env_win
script:
- $global:LASTEXITCODE = 0 # Note the global prefix.
- Invoke-Expression $Env:ARTENOLIS_SOFT_PATH"\julia\"$Env:JULIA_VER"\bin\julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'"
- exit $LASTEXITCODE
.global_env_win8: &global_env_win8
.global_env_win10: &global_env_win10
.global_env_mac: &global_env_mac
- $ARTENOLIS_SOFT_PATH/julia/$JULIA_VER/Contents/Resources/julia/bin/julia --inline=yes --check-bounds=yes --color=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = true)'
name: "quay.io/singularity/singularity:$APPTAINER_DOCKER_TAG"
# the image entrypoint is the singularity binary by default
entrypoint: ["/bin/sh", "-c"]
tags:
- privileged
#
# TESTS
#
# The "basic" required test that gets triggered for the basic testing, runs in
# any available docker and current julia
#
stage: test
image: $CI_REGISTRY/r3/docker/julia-custom
script:
- julia --check-bounds=yes --inline=yes --project=@. -e "import Pkg; Pkg.test(; coverage = true)"
after_script:
- julia --project=test/coverage test/coverage/coverage-summary.jl
#
# The required compatibility test to pass on branches&tags before the docs get
# built & deployed
#
<<: *global_env_linux
linux:julia1.6:
stage: test
<<: *global_env_linux
#
# Additional platform&environment compatibility tests
#
<<: *global_env_win8
<<: *global_julia16
<<: *global_env_win10
mac:julia1.6:
stage: test-compat
<<: *global_env_mac
#
- |
docker run -v "$PWD":/project $CI_REGISTRY/r3/docker/julia-custom julia -e 'using JuliaFormatter; format("/project", verbose=true);'
- |
if [ `docker run -i -v "$PWD":/git alpine/git status -s | wc -l` -ne 0 ] ; then
GITHUB_COMMENT=":red_square: Commit ${CI_COMMIT_SHORT_SHA} requires formatting!\
"$'\n\n'"Required formatting changes summary:\
"$'\n```\n'"`docker run -i -v \"$PWD\":/git alpine/git diff --stat`"$'\n```'
GITHUB_COMMENT=":green_circle: Commit ${CI_COMMIT_SHORT_SHA} is formatted properly."
- |
export GITHUB_TOKEN="${GITHUB_ACCESS_TOKEN_FORMATTER}"
export GITHUB_OWNER="lcsb-biocore"
export GITHUB_REPO="cobrexa.jl"
export GITHUB_COMMENT_TYPE=pr
export GITHUB_PR_ISSUE_NUMBER="${CI_EXTERNAL_PULL_REQUEST_IID}"
export GITHUB_COMMENT_FORMAT=""
-e GITHUB_TOKEN \
-e GITHUB_OWNER \
-e GITHUB_REPO \
-e GITHUB_COMMENT_TYPE \
-e GITHUB_PR_ISSUE_NUMBER \
-e GITHUB_COMMENT_FORMAT \
-e GITHUB_COMMENT \
cloudposse/github-commenter
# ASSETS
# This builds the development history gif using gource, and some containers.
gource:
stage: assets
needs: [] # allow faster start
- docker run -v "$PWD":/visualization $CI_REGISTRY/r3/docker/gource
paths: ['output.gif']
apptainer-test:
stage: assets
script: |
alias apptainer=singularity
apptainer build cobrexa-test.sif cobrexa.def
<<: *global_build_apptainer
<<: *global_trigger_test_containers
apptainer-release:
alias apptainer=singularity
apptainer build cobrexa.sif cobrexa.def
- |
alias apptainer=singularity
export SINGULARITY_DOCKER_USERNAME="$GITHUB_ACCESS_USERNAME"
export SINGULARITY_DOCKER_PASSWORD="$GITHUB_ACCESS_TOKEN"
apptainer push cobrexa.sif "oras://ghcr.io/$APPTAINER_GHCR_TAG:latest"
apptainer push cobrexa.sif "oras://ghcr.io/$APPTAINER_GHCR_TAG:$CI_COMMIT_TAG"
<<: *global_build_apptainer
<<: *global_trigger_release_containers
<<: *global_trigger_test_containers
- docker build -t "$DOCKER_HUB_TAG:latest" .
# alias and push to docker hub
- docker tag "$DOCKER_HUB_TAG:latest" "$DOCKER_HUB_TAG:$CI_COMMIT_TAG"
- echo "$DOCKER_IO_ACCESS_TOKEN" | docker login --username "$DOCKER_IO_USER" --password-stdin
- docker push "$DOCKER_HUB_TAG:latest"
- docker push "$DOCKER_HUB_TAG:$CI_COMMIT_TAG"
# make 2 extra aliases and push to GHCR
- docker tag "$DOCKER_HUB_TAG:latest" "$DOCKER_GHCR_TAG:latest"
- docker tag "$DOCKER_HUB_TAG:latest" "$DOCKER_GHCR_TAG:$CI_COMMIT_TAG"
- echo "$GITHUB_ACCESS_TOKEN" | docker login ghcr.io --username "$GITHUB_ACCESS_USERNAME" --password-stdin
- docker push "$DOCKER_GHCR_TAG:latest"
- docker push "$DOCKER_GHCR_TAG:$CI_COMMIT_TAG"
<<: *global_trigger_release_containers
# DOCUMENTATION TESTS
#
# In pull requests, triggered after the tests succeed to avoid unnecessary
# double failure. In normal branch testing, these get triggered with normal
# tests (the error should be visible ASAP). We avoid a separate stage to keep
# the pipeline parallelizable.
image: $CI_REGISTRY/r3/docker/julia-custom
script:
- julia --project=@. -e 'import Pkg; Pkg.instantiate();'
- julia --project=@. --color=yes test/doctests.jl
stage: documentation
<<: *global_doctests
stage: test
<<: *global_doctests
<<: *global_trigger_full_tests
- gource
# Note: This dependency is also implied by the stage ordering, but let's
# be sure. As of Nov 2021, the assets are not used directly, but referred
# to externally from the docs.
image: $CI_REGISTRY/r3/docker/julia-custom
script:
# resolve and build packages from the docs/Project.toml file
- julia --project=docs -e 'using Pkg; Pkg.resolve(); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
# build and deploy docs (this doesn't upload the gource animation asset)
# move to the directory to be picked up by Gitlab pages (with assets)
- mv docs/build public
# EXTERNAL REPOSITORIES
#
# This trigger the test pipeline in external repo as defined by gitlab
# variables.
Laurent Heirendt
committed
trigger:
- curl --silent --output /dev/null -X POST -F token=$EXTERNAL_REPO_TOKEN -F ref=$EXTERNAL_REPO_BRANCH $EXTERNAL_REPO