CoreMS/.gitlab-ci.yml at master · EMSL-Computing/CoreMS · GitHub

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include:
  - remote: 'https://raw.githubusercontent.com/pnnl-miscscripts/gitlab-lib/v1/gitlab-lib.yaml'


services:
  - postgres:13

variables:
  POSTGRES_DB: molformula
  POSTGRES_USER: coremsdb
  POSTGRES_PASSWORD: coremsmolform
  POSTGRES_HOST_AUTH_METHOD: trust
  COREMS_DATABASE_URL: postgresql://coremsdb:coremsmolform@postgres:5432/molformula
  PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"

stages:
  - Pytest
  - Test Notebooks
  - Build Python Package
  - Push to PyPi
  - Push to Gitlab Registry
  # - Push to Docker Hub

test-source:
  image: code-registry.emsl.pnl.gov/mass-spectrometry/corems/corems-base-310-dotnet6:2.5.3-1005
  stage: Pytest
  tags:
    - k8s
    - rzr
    - codebuilds
  script:
    - python3 -V  # Print out python version for debugging
    - python3 -m pip install --upgrade pip
    - python3 -m pip install -r requirements.txt
    - python3 -m pip install pytest pytest-cov
    - python3 -m pip install psycopg2
    - export COREMS_LIPIDOMICS_SQLITE_PATH="$CI_PROJECT_DIR/tests/tests_data/lcms/202412_lipid_ref.sqlite"
    - make download-lipidomics-db LIPIDOMICS_SQLITE_PATH="$COREMS_LIPIDOMICS_SQLITE_PATH"
    - python3 -c "import pathlib; [p.unlink() for p in pathlib.Path('.').rglob('tests/win_only/__init__.py')]"
    - export PYTHONNET_RUNTIME=coreclr
    - pytest --cache-clear

  artifacts:
    paths:
      - doc/coverage_html_report

test-notebooks:
  image: code-registry.emsl.pnl.gov/mass-spectrometry/corems/corems-base-310-dotnet6:2.5.3-1005
  stage: Test Notebooks
  tags:
    - k8s
    - rzr
    - codebuilds
  script:
    - python3 -V  # Print out python version for debugging
    - python3 -m pip install --upgrade pip
    - python3 -m pip install -r requirements.txt
    - python3 -m pip install jupyter nbconvert
    - python3 -m pip install psycopg2
    - python3 -m pip install -e .
    - export PYTHONNET_RUNTIME=coreclr
    - cd examples && python3 test_notebooks.py

  artifacts:
    when: on_failure
    paths:
      - /tmp/*_test.ipynb

build:

  stage: Build Python Package
  image: code-registry.emsl.pnl.gov/mass-spectrometry/corems/corems-base-310-dotnet6:2.5.3-1005
  tags:
    - k8s
    - rzr
    - codebuilds

  script:

    - apt-get install libpq-dev -y
    - python3 -V  # Print out python version for debugging
    - python3 -m pip install twine
    - python3 setup.py sdist
    - python3 -m pip install dist/*
    # run the command here

  artifacts:
    paths:
      - dist/*

#pypi:

#  stage: Push to PyPi
#  tags:
#    - corems
#    - k8s
#    - rzr

#  script:
#    - twine upload dist/*

#  only:
#    - tags


# build-base-image:
#   extends: .pnnllib-gitlab-build-container-image
#   stage: Push to Gitlab Registry
#   image: gcr.io/kaniko-project/executor:debug@sha256:71d8cf6012b67979960f5b15b85408438132d87eef599926d8931f348d045957
#   tags:
#   - k8s
#   - rzr
#   - codebuilds
#   only:
#     - master
#   variables:
#     KANIKO_EXTRA_ARGS: "--cache=true --cache-copy-layers=true --destination $CI_REGISTRY_IMAGE:latest"
#     CONTEXT: $CI_PROJECT_DIR
#     DOCKERFILE: Dockerfile_py310_dotnet_base_clean
#     KUBERNETES_CPU_REQUEST: 100m
#     KUBERNETES_CPU_LIMIT: "2"
#     KUBERNETES_MEMORY_REQUEST: 2Gi
#     KUBERNETES_MEMORY_LIMIT: 8Gi
#     CONTAINER_TAG: "2.0.0-1005"

# deployment:

#   stage: Push to Gitlab Registry
#   tags:
#     - k8s
#     - rzr
#     - codebuilds

#   image:

#     name: gcr.io/kaniko-project/executor:debug
#     entrypoint: [""]

#   script:

#     - export DOCKER_CONFIG=/kaniko/.docker/
#     - export GOOGLE_APPLICATION_CREDENTIALS=/kaniko/.docker/config.json
#     - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
#     - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile_py310_dotnet_base --destination $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG

#   only:
#     - master
#docker push:

#  stage: Push to Docker Hub
#  tags:
#    - corems
#    - k8s
#    - rzr

#  image:

#    name: gcr.io/kaniko-project/executor:debug
#    entrypoint: [""]

#  script:
#    - export DOCKER_CONFIG=/kaniko/.docker/
#    - export GOOGLE_APPLICATION_CREDENTIALS=/kaniko/.docker/config.json
#    - echo "{\"auths\":{\"$DOCKER_HUB_REGISTRY\":{\"username\":\"$DOCKER_HUB_USER\",\"password\":\"$DOCKER_HUB_PASSWORD\"}}}" > /kaniko/.docker/config.json
#    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --destination $MAJOR_VER

#  only:
#    - master


#pages:
#  script:
#    - pip install sphinx sphinx-rtd-theme
#    - cd doc ; make html
#    - mv build/html/ ../public/
#  artifacts:
#    paths:
#      - public
#  only:
#    - master