pytests.yml

# This is testing the python versions *other than* the
#   one in the QUIP Docker, which is 3.7.10 at the time
#   of writing this. Coverage is disabled.

name: Python Package and tests

# on all push actions AND can be triggered manually as well
on:
  workflow_dispatch:
  pull_request:

jobs:
  build-and-test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [ "3.9" ]
      max-parallel: 5
    env:
      coverage-on-version: "3.9"
      use-mpi: True
      PIP_CONSTRAINT: pip_constraint.txt
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - uses: actions/checkout@v4

      - name: Set up python ${{ matrix.python-version }} via conda
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}

      - name: Check python version
        run: |
          which python3
          python3 --version

      - name: Install dependencies from pip
        run: |
          echo "numpy<2" >> $PIP_CONSTRAINT
          python3 -m pip install wheel setuptools numpy scipy click matplotlib pyyaml spglib rdkit flake8 pytest pytest-cov requests

      - name: Install latest ASE from pypi
        run: |
          echo PIP_CONSTRAINT $PIP_CONSTRAINT
          python3 -m pip install ase 
          echo -n "ASE VERSION "
          python3 -c "import ase; print(ase.__file__, ase.__version__)"

      - name: Install intel-oneapi-mkl for phono3py
        run: |
          # based on
          #   https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-download.html?operatingsystem=linux&distributions=aptpackagemanager
          # download the key to system keyring
          wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
          # add signed entry to apt sources and configure the APT client to use Intel repository:
          echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
          sudo apt update
          sudo apt install intel-oneapi-mkl
          sudo apt install intel-oneapi-mkl-devel

      - name: Install phono3py from source
        run: |
            # find mklvars
            for pkg in $( apt list --installed | fgrep "installed" | fgrep "mkl" | sed "s#/.*##" ); do
                if dpkg -L $pkg | egrep -q 'env/vars.sh$'; then
                    mklvars=$( dpkg -L $pkg | egrep 'env/vars.sh$' )
                    break
                fi
            done
            if [ $( echo $mklvars | wc -w ) != 2 ]; then
                echo "wrong number of  mkl setvars.sh '$mklvars'" 1>&2
                exit 1
            fi
            source $mklvars intel64

            export PIP_CONSTRAINT=$PWD/$PIP_CONSTRAINT

            git clone https://github.com/phonopy/phonopy
            cd phonopy
            echo python3 -m pip install -e . -vvv
            python3 -m pip install -e . -vvv
            cd ..

            git clone https://github.com/phonopy/phono3py
            cd phono3py
            python3 -m pip install -e . -vvv
            cd ..

      - name: Install Quippy from PyPI
        run: python3 -m pip install quippy-ase

      - name: Install xTB (before things that need pandas like MACE and wfl, since it will break pandas-numpy compatibility by downgrading numpy)
        run: |
          conda install -c conda-forge xtb-python
          python3 -m pip install typing-extensions
          # install pandas now to encourage compatible numpy version after conda regressed it
          python3 -m pip install pandas

      - name: MACE
        run: |
          echo "search for torch version"
          set +o pipefail
          torch_version=$( python3 -m pip install torch== 2>&1 | fgrep 'from versions' | sed -e 's/.* //' -e 's/)//' )
          echo "found torch version $torch_version, installing cpu-only variant"
          python3 -m pip install torch==${torch_version}+cpu -f https://download.pytorch.org/whl/torch_stable.html
          echo "installing mace"
          python3 -m pip install git+https://github.com/ACEsuit/mace.git@main
          python3 -c "import mace; print(mace.__file__)"

      - name: Julia and ace fit
        run: |
          python3 -m pip install threadpoolctl
          wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz
          tar xzf julia-1.8.1-linux-x86_64.tar.gz
          # note that this hardwires a particular compatible ACE1pack version
          echo 'using Pkg; pkg"registry add https://github.com/JuliaRegistries/General"; pkg"registry add https://github.com/JuliaMolSim/MolSim.git"; pkg"add ACE1pack@0.0, ACE1, JuLIP, IPFitting, ASE"' > ace1pack_install.jl
          ${PWD}/julia-1.8.1/bin/julia ace1pack_install.jl

      - name: Install wfl (expyre and universalSOAP are dependencies)
        run: python3 -m pip install .

      - name: Install Quantum Espresso
        run: |
          sudo apt-get install --no-install-recommends quantum-espresso

      - name: Install MOPAC
        run: |
          wget https://github.com/openmopac/mopac/releases/download/v22.0.6/mopac-22.0.6-linux.tar.gz
          tar -xzvf mopac-22.0.6-linux.tar.gz

      - name: add mopac to path
        run: echo $GITHUB_WORKSPACE/mopac-22.0.6-linux/bin >> $GITHUB_PATH

      - name: Install buildcell
        run: |
          sudo apt-get install gfortran
          wget https://www.mtg.msm.cam.ac.uk/system/files/documents/airss-0.9.1.tgz
          tar xzf airss-0.9.1.tgz
          cd airss-0.9.1
          make buildcell
          mkdir -p $HOME/bin
          cp src/buildcell/src/buildcell $HOME/bin/
          cd ..

      - name: Add buildcell to system path
        run: |
          echo $HOME/bin >> $GITHUB_PATH

      - name: Install MPI dependencies
        if: env.use-mpi
        run: |
          # this can eaily be turned off if needed
          conda install -c conda-forge mpi4py openmpi pytest-mpi
          python3 -m pip install mpipool

      - name: Install and configure slurm and ExPyRe
        run: |
          sudo apt-get install -u slurm-wlm mailutils
          echo "SLURM apt-get done, doing local configuration"
          host_s=$( hostname -s )
          if [ -f /etc/slurm/slurm.conf ]; then sudo mv /etc/slurm/slurm.conf /etc/slurm/slurm.conf.orig; fi
          sudo bash -c 'gzip -cd /usr/share/doc/slurmd/examples/slurm.conf.simple.gz > /etc/slurm/slurm.conf'
          # sudo sed -E -i -e "s/^\s*ClusterName\s*=.*/ClusterName=github_expyre_test/" /etc/slurm/slurm.conf
          sudo bash -c 'sed -E -i -e "s/^\s*SlurmctldHost\s*=.*/SlurmctldHost=_HOST_/" /etc/slurm/slurm.conf'
          # sudo sed -E -i -e "s/^\s*DefaultStorageHost\s*=.*/DefaultStorageHost=none" /etc/slurm/slurm.conf
          sudo bash -c 'echo "NodeName=_HOST_ CPUs=2 Weight=1 Sockets=1 CoresPerSocket=2 ThreadsPerCore=1 RealMemory=1000" >> /etc/slurm/slurm.conf'
          sudo bash -c 'echo "PartitionName=standard Default=YES AllocNodes=_HOST_ Nodes=ALL State=UP" >> /etc/slurm/slurm.conf'
          sudo sed -i -e "s/_HOST_/$host_s/g" /etc/slurm/slurm.conf
          sudo mkdir -p /var/log/slurm
          sudo mkdir -p /var/spool/slurmd
          sudo service slurmd start
          sudo service slurmctld start
          sleep 5
          echo "sinfo -s --long"
          sinfo -s --long
          mkdir $HOME/.expyre
          cp .github/workflows_assets/config.json $HOME/.expyre

      - name: Set up pw.x for running in wfl
        run: |
          echo "which pw.x"
          which pw.x
          ls -l /usr/bin/pw.x
          export PYTEST_WFL_ASE_ESPRESSO_COMMAND=pw.x

      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8 wfl/ --count --select=E9,F63,F7,F82 --show-source --statistics
          # exit-zero treats all errors as warnings.
          flake8 wfl/ --count --exit-zero --max-complexity=20 --max-line-length=140 --ignore=E127,E128 --statistics

      - name: Test with pytest - plain
        if: env.coverage-on-version != matrix.python-version
        run: |
          rm -rf $HOME/pytest_plain
          mkdir $HOME/pytest_plain
          #
          export EXPYRE_PYTEST_SYSTEMS=github
          export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell
          export WFL_NUM_PYTHON_SUBPROCESSES=2
          export OMP_NUM_THREADS=1
          export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia
          pytest --runremote --basetemp $HOME/pytest_plain -rxXs

      - name: Test with pytest - coverage
        if: env.coverage-on-version == matrix.python-version
        run: |
          rm -rf $HOME/pytest_cov
          mkdir $HOME/pytest_cov
          #
          export EXPYRE_PYTEST_SYSTEMS=github
          export WFL_PYTEST_BUILDCELL=$HOME/bin/buildcell
          export WFL_NUM_PYTHON_SUBPROCESSES=2
          export OMP_NUM_THREADS=1
          export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia
          pytest -v --cov=wfl --cov-report term --cov-report html --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --runremote --basetemp $HOME/pytest_cov -rxXs

      # # DEBUGGING
      # - name: Setup tmate session
          # if: failure()
          # uses: mxschmitt/action-tmate@v3
          # timeout-minutes: 15

      - name: MPI tests -- plain
        if: ${{ env.use-mpi && env.coverage-on-version != matrix.python-version}}
        run: |
          # envvar and test run - No coverage
          export WFL_MPIPOOL=2
          export WFL_NUM_PYTHON_SUBPROCESSES=2
          export OMP_NUM_THREADS=1
          mpirun -n 2 pytest --with-mpi -k mpi

      - name: MPI tests -- coverage
        if: ${{ env.use-mpi && env.coverage-on-version == matrix.python-version}}
        run: |
          # envvar and coverage Appended to the previous
          export WFL_MPIPOOL=2
          export WFL_NUM_PYTHON_SUBPROCESSES=2
          export OMP_NUM_THREADS=1
          export WFL_JULIA_COMMAND=${PWD}/julia-1.8.1/bin/julia
          mpirun -n 2 pytest --cov=wfl --cov-report term --cov-config=tests/.coveragerc --cov-report term-missing --cov-report term:skip-covered --with-mpi -k mpi --cov-append

      - name: 'Upload Coverage Data'
        uses: actions/upload-artifact@v2
        if: env.coverage-on-version == matrix.python-version
        with:
          name: coverage-html-${{ matrix.python-version }}
          path: coverage-html/
          retention-days: 7