.gitlab-ci.yml

# This workflow will install Python dependencies, run tests, and write documentation

variables:
  GIT_STRATEGY: clone # clone entire repo instead of reusing workspace
  GIT_DEPTH: "0" # avoid shallow clone to give sonar all the info it needs

stages:
  - test
  - deploy

# Install python dependencies and run python tests with pytest and the CLI test script
.test:
  stage: test
  before_script:
    - python --version  # For debugging python version
    - wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo
    - wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft
    - export PATH=$PATH:$PWD/mafft-linux64/mafftdir/bin/:$PWD
    - export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/
    - clustalo --version  # For debugging clustalo version
    - mafft --version  # For debugging mafft version
    #    - pip config set global.index-url https://pypi.org/simple/
    #    - pip config set global.extra-index-url https://test.pypi.org/simple/
    - python -m pip install ".[full]" --no-cache-dir
    - python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version
    - python -m pip install pytest
    - python -m pip install jupyterlab
    - python -m pip freeze # For debugging environment
  script:
    - cd testing && QSPPRED_TEST_SPLIT_UNITS=true QSPRPRED_VERBOSE_LOGGING=true ./run.sh

# Run tests on the recent Python (linux image)
test:python3.12:
  extends: .test
  image: python:3.12