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gitlab-ci.yml
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gitlab-ci.yml
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stages:
- tools
- build
- check
- knitr
- figures
- exports
- pdf
variables:
R_BUILD_DIR: "package"
KNITR_OUTPUT_DIR: "knitr"
TEX_DIR: "Paper"
OVERLEAF_ARTIFACTS_DIR: "overleaf"
REVIEW_ARTIFACTS_DIR: "pspline-inference"
COMPOSE_FILES: --file docker-compose.yml --file docker-compose-gitlab.yml
.docker:
tags:
- docker
services:
- docker:18.09.7-dind
variables:
DOCKER_HOST: tcp://docker:2375/
DOCKER_DRIVER: overlay2
DOCKER_TLS_CERTDIR: ""
image: ${CI_REGISTRY}/ci-utilities/ci-commands/gitlab-docker-compose-ci
tools:
stage: tools
extends:
- .docker
script:
- gitlab-docker-compose ${COMPOSE_FILES} --cache-from main package-tools paper-tools
.build:
stage: build
extends:
- .docker
variables:
R_PACKAGE_SOURCE: .
script:
- docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
- docker-compose ${COMPOSE_FILES} run package-build
- export R_PACKAGE_ARCHIVE=`ls "${R_BUILD_DIR}"/pspline.inference*.tar.gz | head -n1`
- printenv | grep '^R_PACKAGE_ARCHIVE=' >> build.env
artifacts:
name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-package"
paths:
- "${R_BUILD_DIR}"
- build.env
when: always
build:
extends: .build
variables:
R_BUILD_VIGNETTES: "TRUE"
rules:
- if: '$CI_COMMIT_REF_NAME =~ /^[Pp]aper([\/-].*)?$/ || $CI_COMMIT_REF_NAME =~ /^validation(-.*)?$/'
when: manual
- when: always
⚡️ build:
extends: .build
variables:
R_BUILD_VIGNETTES: "FALSE"
check:
stage: check
extends:
- .docker
script:
- docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
- docker-compose ${COMPOSE_FILES} run package-check
rules:
- if: '$CI_COMMIT_REF_NAME =~ /^[Pp]aper([\/-].*)?$/ || $CI_COMMIT_REF_NAME =~ /^validation(-.*)?$/'
when: manual
- when: always
needs:
- build
.knitr:
stage: knitr
extends:
- .docker
script:
- docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
- docker-compose ${COMPOSE_FILES} run paper-knit
needs:
- ⚡️ build
artifacts:
name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-knitr"
paths:
- "${KNITR_OUTPUT_DIR}"
knitr:
extends: .knitr
tags:
- docker-cpu:comp8
variables:
KNITR_RUN_VALIDATION: "TRUE"
rules:
- if: '$CI_COMMIT_REF_NAME =~ /^validation(-.*)?$/'
when: always
- when: manual
⚡️ knitr:
extends: .knitr
tags:
- docker-mem:3
variables:
KNITR_RUN_VALIDATION: "FALSE"
# figures:
# stage: figures
# extends:
# - .docker
# script:
# - docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
# - docker-compose ${COMPOSE_FILES} run paper-figures
# artifacts:
# name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-figures"
# paths:
# - "${KNITR_OUTPUT_DIR}/figures/*.pdf"
# - "${KNITR_OUTPUT_DIR}/figures/*.tif"
overleaf:
stage: exports
extends:
- .docker
script:
- docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
- docker-compose ${COMPOSE_FILES} run paper-overleaf
needs:
- ⚡️ knitr
artifacts:
name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-overleaf"
paths:
- "${OVERLEAF_ARTIFACTS_DIR}"
# plos-comp-biol:
# stage: exports
# extends:
# - .docker
# script:
# - docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
# - docker-compose ${COMPOSE_FILES} run paper-plos-comp-biol
# artifacts:
# name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-plos-comp-biol"
# paths:
# - '${REVIEW_ARTIFACTS_DIR}/*.tex'
# - '${REVIEW_ARTIFACTS_DIR}/Fig*.tif'
# - '${REVIEW_ARTIFACTS_DIR}/*.pdf'
pdf:
stage: pdf
extends:
- .docker
script:
- docker login --username "${CI_REGISTRY_USER}" --password "${CI_REGISTRY_PASSWORD}" "${CI_REGISTRY}"
- docker-compose ${COMPOSE_FILES} run paper-pdf
- mv "${OVERLEAF_ARTIFACTS_DIR}/PSplineInference.pdf" .
needs:
- overleaf
artifacts:
name: "${CI_PROJECT_NAME}-${CI_COMMIT_REF_SLUG}-${CI_COMMIT_SHORT_SHA}-pdf"
paths:
- "PSplineInference.pdf"