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'

workflow:
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
    - if: '$CI_PIPELINE_SOURCE == "push" && $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS'
      when: never
    - if: '$CI_PIPELINE_SOURCE == "push"'
    - if: '$CI_COMMIT_TAG'
    - if: '$CI_PIPELINE_SOURCE == "schedule" || $CI_PIPELINE_SOURCE == "web" || $CI_PIPELINE_SOURCE == "pipeline"'
    - when: never

# ---------------------------------------------------------------------------
# Global configuration
# ---------------------------------------------------------------------------
default:
  image: python:3.13-slim
  tags:
    - k8s
    - rzr
    - codebuilds

services:
  - postgres:18

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"
  PIP_ROOT_USER_ACTION: ignore
  # Avoids libicu dependency crash when .NET initialises in a slim container
  DOTNET_SYSTEM_GLOBALIZATION_INVARIANT: "1"
  # Kubernetes runner pod sizing — undersized defaults are a common cause of
  # slow CI wall time. Override per-job if a stage needs more/less.
  KUBERNETES_CPU_REQUEST: "2"
  KUBERNETES_CPU_LIMIT: "4"
  KUBERNETES_MEMORY_REQUEST: 4Gi
  KUBERNETES_MEMORY_LIMIT: 8Gi

cache:
  key: "$CI_COMMIT_REF_SLUG"
  paths:
    - .cache/pip
    - tests/tests_data/lcms/202412_lipid_ref.sqlite

stages:
  - test
  - build
  - publish
  - publish-image

# ---------------------------------------------------------------------------
# Helpers
# ---------------------------------------------------------------------------
.install-dotnet: &install-dotnet
  - apt-get update -qq && apt-get install -y --no-install-recommends curl ca-certificates libssl3 libkrb5-3 zlib1g gcc python3-dev make
  - curl -sSL https://dot.net/v1/dotnet-install.sh -o /tmp/dotnet-install.sh
  - chmod +x /tmp/dotnet-install.sh
  - /tmp/dotnet-install.sh --runtime dotnet --channel 8.0 --install-dir /usr/local/dotnet
  - export DOTNET_ROOT=/usr/local/dotnet
  - export PATH="$PATH:/usr/local/dotnet"
  - rm /tmp/dotnet-install.sh

.test_job_rules: &test_job_rules
  - if: '$CI_PIPELINE_SOURCE == "push" || $CI_PIPELINE_SOURCE == "merge_request_event"'
    changes:
      - corems/**/*
      - tests/**/*
      - examples/**/*
      - db/**/*
      - ext_lib/**/*
      - support_code/**/*
      - Dockerfile*
      - docker-compose*.yml
      - Makefile
      - setup.py
      - pyproject.toml
      - pytest.ini
      - conftest.py
      - .gitlab-ci.yml
  - if: '$CI_PIPELINE_SOURCE == "schedule" || $CI_PIPELINE_SOURCE == "web" || $CI_PIPELINE_SOURCE == "pipeline"'
  - if: '$CI_COMMIT_TAG'
  - when: never

# ---------------------------------------------------------------------------
# Test
# ---------------------------------------------------------------------------
test-source:
  stage: test
  rules: *test_job_rules
  script:
    - *install-dotnet
    - make ci-test-source LIPIDOMICS_SQLITE_PATH="$CI_PROJECT_DIR/tests/tests_data/lcms/202412_lipid_ref.sqlite"

# ---------------------------------------------------------------------------
# Notebook tests
# ---------------------------------------------------------------------------
test-notebooks:
  stage: test
  rules: *test_job_rules
  script:
    - *install-dotnet
    - make ci-test-notebooks LIPIDOMICS_SQLITE_PATH="$CI_PROJECT_DIR/tests/tests_data/lcms/202412_lipid_ref.sqlite"

  artifacts:
    when: on_failure
    paths:
      - /tmp/*_test.ipynb
    expire_in: 3 days

# ---------------------------------------------------------------------------
# Build sdist + wheel
# ---------------------------------------------------------------------------
build-package:
  stage: build
  script:
    - python3 -m pip install --upgrade pip build
    - python3 -m build

  artifacts:
    paths:
      - dist/
    expire_in: 7 days

# ---------------------------------------------------------------------------
# Publish to PyPI  (version tags on the default branch only, e.g. v3.11.0)
# ---------------------------------------------------------------------------
publish-pypi:
  stage: publish
  needs: [build-package]
  rules:
    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+/'
    - if: '$CI_PIPELINE_SOURCE == "web"'
      when: manual
  script:
    - python3 -m pip install --upgrade twine
    - TWINE_USERNAME=__token__ TWINE_PASSWORD="$PYPI_TOKEN" twine upload dist/*
  environment:
    name: pypi
    url: https://pypi.org/project/CoreMS/

# ---------------------------------------------------------------------------
# Build and push the base container image to the GitLab registry
# (runs only on the default branch or version tags)
# ---------------------------------------------------------------------------
publish-image:
  extends: .pnnllib-gitlab-build-container-image
  stage: publish-image
  rules:
    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+/'
  variables:
    KANIKO_EXTRA_ARGS: "--cache=true --cache-copy-layers=true --destination $CI_REGISTRY_IMAGE:$CI_COMMIT_SHORT_SHA --destination $CI_REGISTRY_IMAGE:latest"
    CONTEXT: $CI_PROJECT_DIR
    DOCKERFILE: Dockerfile
    KUBERNETES_CPU_REQUEST: 100m
    KUBERNETES_CPU_LIMIT: "2"
    KUBERNETES_MEMORY_REQUEST: 2Gi
    KUBERNETES_MEMORY_LIMIT: 8Gi