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.gitlab-ci.yml
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.gitlab-ci.yml
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###########################################################################
# This file defines the build process for fsl-mrs, as hosted at:
#
# https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
#
# The build pipeline currently comprises the following stages:
#
# 1. style: Check coding style - allowed to fail
#
# 2. test: Unit tests
#
# 3. validate: Fitting validation and upload fo test results
# to https://github.com/wtclarke/lcm_validation/
#
# 4. doc: Building user documentation which appears at:
# https://open.win.ox.ac.uk/pages/fsl/fsl_mrs/
#
# 5. build
# & deploy: Build conda package in three stages fsl-ci-pre,
# fsl-ci-build, fsl-ci-deploy (fsl-ci-test is not
# used in this repository).
#
#
# A custom docker image is used for the test job - images are
# available at:
#
# https://hub.docker.com/u/wtclarke/
#
# Stage run conditions:
# Style is run in all cases, but allowed to fail.
# Test is run in all cases.
# Doc is only run on master branches.
# Build stages are run according to the rules associated
# with https://git.fmrib.ox.ac.uk/fsl/conda/fsl-ci-rules
#
###########################################################################
include:
- project: fsl/conda/fsl-ci-rules
file: .gitlab-ci.yml
stages:
- style
- test
- validate
- doc
- fsl-ci-pre
- fsl-ci-build
- fsl-ci-test
- fsl-ci-deploy
####################################
# These anchors are used to restrict
# when and where jobs are executed.
# Copied from the fsl/fsleyes yaml file.
####################################
.except_releases: &except_releases
except:
- tags
.test_rules: &test_rules
rules:
# Releases are just tags on a release
# branch, so we don't need to test them.
- if: '$CI_COMMIT_TAG != null'
when: never
# Don't test if "[skip-tests]"
# is in the commit message
- if: '$CI_COMMIT_MESSAGE =~ /\[skip-tests\]/'
when: never
- if: '$CI_PIPELINE_SOURCE == "push"'
when: on_success
.validate_rules: &validate_rules
rules:
# Validate on tag / release in upstream (fsl/fsl_mrs) repo
- if: ( $CI_COMMIT_TAG != null ) && ( $CI_PROJECT_PATH == "fsl/fsl_mrs" )
when: on_success
# if "[validate]" is in the commit message
# AND it is to the forked (wclarke/fsl_mrs) repo
# AND the branch isn't master
- if: ($CI_COMMIT_MESSAGE =~ /\[validate\]/ ) && ( $CI_PROJECT_PATH == "wclarke/fsl_mrs" ) && ($CI_COMMIT_BRANCH != "master")
when: on_success
# ############
# # 1. style
# ############
flake8:
<<: *except_releases
image: python:3.9-slim-buster
stage: style
before_script:
- python --version
- pip install flake8==4.0.1
script:
- flake8 fsl_mrs
- flake8 fsl_mrs/scripts/*
allow_failure: true
############
# 2. test
############
pytest:
<<: *test_rules
image: wtclarke/fsl_mrs_tests:latest
stage: test
variables:
GIT_SUBMODULE_STRATEGY: normal
before_script:
- micromamba create -n fsl_mrs -c conda-forge -y python=3.9
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate fsl_mrs
- micromamba install -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge fsl-flirt fsl-flameo fsl-avwutils fsl-fugue
- export FSLOUTPUTTYPE="NIFTI_GZ"
- export FSLDIR="/opt/conda/envs/fsl_mrs"
- micromamba install -y -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ --file requirements.txt
- micromamba install -y -c conda-forge pytest
- pip install .
script:
- pytest fsl_mrs/tests
- pytest fsl_mrs/denmatsim/tests
############
# 3. Validate
############
fit-validate:
<<: *validate_rules
image: wtclarke/fsl_mrs_tests:latest
stage: validate
variables:
GIT_STRATEGY: clone
GIT_SUBMODULE_STRATEGY: normal
DEPLOY_CURL_COMMAND_BODY: "'{\"title\":\"New FSL-MRS version\",\"body\":\"Version '$$FSL_MRS_VERSION' \",\"head\":\"fsl_mrs_updates_'$$FSL_MRS_VERSION'\",\"base\":\"main\"}'"
DEPLOY_CURL_COMMAND: 'curl -X POST -H "Accept: application/vnd.github+json" -H "Authorization: Bearer $GITHUB_PAT" https://api.github.com/repos/wtclarke/lcm_validation/pulls -d $DEPLOY_CURL_COMMAND_BODY'
before_script:
# Create an environment to work in
- micromamba create -n fsl_mrs -c conda-forge -y python=3.9
- eval "$(micromamba shell hook --shell bash)"
- micromamba activate fsl_mrs
# Install all the FSL tools needed
- micromamba install -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge fsl-flirt fsl-flameo fsl-avwutils fsl-fugue
- export FSLOUTPUTTYPE="NIFTI_GZ"
- export FSLDIR="/opt/conda/envs/fsl_mrs"
# Get the git tags.
- git config --global --add safe.directory /builds/wclarke/fsl_mrs
- git config --global --add safe.directory /builds/fsl/fsl_mrs
- git fetch --tags
- git status
- micromamba install -y -c conda-forge -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ --file requirements.txt
- pip install .
# Setup ssh communication with the github instance
# https://docs.gitlab.com/ee/ci/ssh_keys/#ssh-keys-when-using-the-docker-executor
- eval $(ssh-agent -s)
- echo "$LCM_VALIDATION_KEY" | tr -d '\r' | ssh-add -
- mkdir -p ~/.ssh
- chmod 700 ~/.ssh
- ssh-keyscan -H github.com >> ~/.ssh/known_hosts
script:
- FSL_MRS_VERSION=`fsl_mrs --version` && export FSL_MRS_VERSION
- echo $FSL_MRS_VERSION
- git clone git@github.com:wtclarke/lcm_validation.git
- cd lcm_validation
- git config --global user.name "wtclarke"
- git config --global user.email "william.clarke@ndcn.ox.ac.uk"
- git checkout -b "fsl_mrs_updates_${FSL_MRS_VERSION}" main
- python ../validation/mrs_challenge.py --mh_samples 20 results $FSL_MRS_VERSION
- ls results/fsl_mrs_newton
- git add *
- git commit -m "Results for FSL-MRS ${FSL_MRS_VERSION}"
- git push origin "fsl_mrs_updates_${FSL_MRS_VERSION}"
- echo $DEPLOY_CURL_COMMAND
- 'eval "$DEPLOY_CURL_COMMAND"'
allow_failure: true
############
# 4. doc
############
pages:
variables:
GIT_LFS_SKIP_SMUDGE: "1"
GIT_STRATEGY: clone
only:
- branches@wclarke/fsl_mrs
- tags@fsl/fsl_mrs
image: python:3.9
stage: doc
script:
- git describe --tag --dirty
- pip install -U "h5py<3.11" sphinx sphinx_rtd_theme
- pip install .
- sphinx-build -b html ./docs/user_docs public
artifacts:
paths:
- public