.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
      - 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:
      - pytest qsprpred
      - cd clitest && ./run.sh
      - cd ../tutorial && ./run_all.sh

# # Run tests on Python version 11 (linux image)
# test:python3.11:
#    extends: .test
#    image: python:3.11

# Run tests on Python version 10 (linux image)
test:python3.10:
   extends: .test
   image: python:3.10

# Write documentation on main branch
pages:
   stage: deploy
   image: python:3.10
   before_script:
      - python -m pip install -U sphinx
      - python -m pip install sphinx-rtd-theme
   script:
      - mkdir public
      - sphinx-build -b html ./docs public
   artifacts:
      paths:
      - public
   only:
      - main