.gitlab-ci.yml

# Copyright © 2023 German Cancer Research Center (DKFZ), Division of Medical Image Computing
#
# SPDX-License-Identifier: Apache-2.0

stages:
  - lint
  - test 

license_compliance:
  image: python:3.10
  stage: lint
  before_script:
    - pip install --upgrade pip
    - pip install reuse
  script:
    - reuse lint
  allow_failure: true
  rules:
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH

.default_before_script: &default_before_script
  - apt-get update && apt-get install libgl1 git-lfs -y
  - pip install --upgrade pip
  - pip install numpy # actually installed via pyproject.toml but pyradiomics requires it already during installation
  - pip install pytest

test_pytest:
  image: python:${VERSION}
  parallel:
    matrix:
      - VERSION: ["3.9", "3.10", "3.11"] #, "3.12", "latest" ]
  stage: test
  before_script:
    - *default_before_script
  script:
    - pip install .
    - pytest  -v -s tests/ # -k "features"
  #artifacts:
  #  paths:
  #    - tests/test_results/
  rules:
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH

test_run_parcellate:
 extends: test_pytest
 before_script:
   - *default_before_script
   - pip install .
   - mkdir tests/test_results/ -p
 script:
   - radtract_parcellate --streamlines tests/test_data/test_tract.trk --envelope tests/test_data/test_tract_envelope.nii.gz --start tests/test_data/test_tract_b.nii.gz --num_parcels 5 --output tests/test_results/hyperplane_parcellation_command.nii.gz
   - radtract_features --parcellation tests/test_results/hyperplane_parcellation_command.nii.gz --map tests/test_data/test_map.nii.gz --output tests/test_results/hyperplane_parcellation_command.csv