Cron compilers

.github/workflows/gh-ci-cron.yaml

@@ -0,0 +1,223 @@
+name: GH Actions Cron CI
+on:
+  push:
+    branches:
+      - cron-compilers
+
+        #  schedule:
+        #    - cron:  '*/10 * * * *'
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+env:
+  MDA_CONDA_MIN_DEPS: "pip pytest==6.1.2 mmtf-python biopython networkx cython matplotlib-base scipy griddataformats hypothesis gsd codecov"
+  MDA_CONDA_EXTRA_DEPS: "seaborn>=0.7.0 clustalw=2.1 netcdf4 scikit-learn joblib>=0.12 chemfiles tqdm>=4.43.0 tidynamics>=1.0.0 rdkit>=2020.03.1 h5py==2.10.0"
+  MDA_PIP_MIN_DEPS: 'coveralls coverage<5 pytest-cov pytest-xdist'
+  MDA_PIP_EXTRA_DEPS: 'duecredit parmed'
+  OMP_NUM_THREADS: 1
+
+
+jobs:
+  numpy_dev:
+    runs-on: ubuntu-latest
+    env:
+      CYTHON_TRACE_NOGIL: 1
+      MPLBACKEND: agg
+    steps:
+    - uses: actions/checkout@v2
+    - name: setup_compilers
+      run: |
+        echo "CC=gcc-10" >> $GITHUB_ENV
+        echo "CXX=g++-10" >> $GITHUB_ENV
+        echo "FC=gfortran-10" >> $GITHUB_ENV
+
+    - name: setup_miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: 3.8
+        auto-update-conda: true
+        channel-priority: flexible
+        channels: biobuilds, conda-forge
+        add-pip-as-python-dependency: true
+        mamba-version: "*"
+        architecture: x64
+
+    - name: build_numpy
+      run: |
+        git clone https://github.com/numpy/numpy.git
+        (cd numpy && pip install .)
+
+    - name: install_deps
+      env:
+        MDA_CONDA_FULL_DEPS: "${{ env.MDA_CONDA_MIN_DEPS }}"
+        MDA_PIP_FULL_DEPS: "${{ env.MDA_PIP_MIN_DEPS }}"
+      run: |
+        conda_deps=${MDA_CONDA_MIN_DEPS}
+        pip_deps=${MDA_PIP_MIN_DEPS}
+        mamba install ${conda_deps}
+        pip install ${pip_deps}
+
+    - name: check_setup
+      run: |
+        # Check OS and python setup
+        echo "OS: ${{ matrix.os }}"
+        which python
+        which pip
+        pip list
+        conda info
+        conda list
+
+    - name: install_mda
+      run: |
+        (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install)
+
+    - name: run_tests
+      run: |
+        pytest -n 2 testsuite/MDAnalysisTests --durations=50
+
+  # long term separate clang and gcc once ubuntu+clang is fixed
+  compiler_sweep:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+          os: [ubuntu-latest, ]
+          python-version: [3.8, ]
+          compiler-version: [7, 8, 9, 10]
+          compiler: [gcc, ]
+          include:
+            - name: ubuntu-18-gcc6
+              os: ubuntu-18.04
+              python-version: 3.8
+              compiler-version: 7
+              compiler: gcc
+            - name: ubuntu-16-gcc5
+              os: ubuntu-16.04
+              python-version: 3.8
+              compiler-version: 5
+              compiler: gcc
+            - name: macOS-Catalina-clang12
+              os: macOS-10.15
+              python-version: 3.8
+              compiler-version: 12
+              compiler: clang
+            - name: macOS-Catalina-clang11
+              os: macOS-10.15
+              python-version: 3.8
+              compiler-version: 11
+              compiler: clang
+    env:
+      CYTHON_TRACE_NOGIL: 1
+      MPLBACKEND: agg
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: setup_osx
+      if: startsWith(matrix.os, 'macOS')
+      run: |
+        echo "MACOSX_DEPLOYMENT_TARGET=10.9" >> $GITHUB_ENV
+        ulimit -S -n 2048
+
+      # clang macOS definitions are different than the ubuntu runners
+    - name: setup_osx_clang
+      if: startsWith(matrix.os, 'macOS') && startsWith(matrix.compiler, 'clang')
+      run: |
+        if [[ ${{ matrix.compiler-version }} == 11 ]]; then
+          $(brew --prefix llvm)/bin/clang --version
+          echo "CC=$(brew --prefix llvm)/bin/clang" >> $GITHUB_ENV
+          $(brew --prefix llvm)/bin/clang++ --version
+          echo "CXX=$(brew --prefix llvm)/bin/clang++" >> $GITHUB_ENV
+        else
+          # clang-12 isn't defined for some reason
+          clang --version
+          echo "CC=clang" >> $GITHUB_ENV
+          clang++ --version
+          echo "CXX=clang++" >> $GITHUB_ENV
+        fi
+
+        # no clang fortran compiler, default to gfortran 10
+        if gfortran-10 --version &> /dev/null
+        then
+          echo "HOLE2=true" >> $GITHUB_ENV
+          echo "FC=$GFORT" >> $GITHUB_ENV
+        else
+          echo "HOLE2=false" >> $GITHUB_ENV
+        fi
+
+    - name: setup_gcc_compilers
+      if: startsWith(matrix.compiler, 'gcc')
+      env:
+        GCC: "gcc-${{ matrix.compiler-version }}"
+        GXX: "g++-${{ matrix.compiler-version }}"
+        GFORT: "gfortran-${{matrix.compiler-version }}" 
+      run: |
+        # Set OS specific vars and compiler flags
+        $GCC --version
+        echo "CC=${GCC}" >> $GITHUB_ENV
+        $GXX --version
+        echo "CXX=${GXX}" >> $GITHUB_ENV
+        if $GFORT --version &> /dev/null
+        then
+          echo "HOLE2=true" >> $GITHUB_ENV
+          echo "FC=$GFORT" >> $GITHUB_ENV
+        else
+          echo "HOLE2=false" >> $GITHUB_ENV
+        fi
+
+    - name: setup_miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+        auto-update-conda: true
+        channel-priority: flexible
+        channels: biobuilds, conda-forge
+        add-pip-as-python-dependency: true
+        mamba-version: "*"
+        architecture: x64
+
+    - name: install_deps
+      env:
+        MDA_CONDA_FULL_DEPS: "${{ env.MDA_CONDA_MIN_DEPS }} ${{ env.MDA_CONDA_EXTRA_DEPS }}"
+        MDA_PIP_FULL_DEPS: "${{ env.MDA_PIP_MIN_DEPS }} ${{ env.MDA_PIP_EXTRA_DEPS }}"
+      run: |
+        # NOTE: vars need to be re-assigned
+        # NOTE: set matrix.numpy to pin to a specific numpy version
+        conda_deps="numpy ${MDA_CONDA_FULL_DEPS}"
+        pip_deps=${MDA_PIP_FULL_DEPS}
+        mamba install ${conda_deps}
+        pip install ${pip_deps}
+
+    - name: check_setup
+      run: |
+        # Check OS and python setup
+        echo "OS: ${{ matrix.os }}"
+        which python
+        which pip
+        pip list
+        conda info
+        conda list
+
+    - name: install_hole
+      if : ${{ env.HOLE2 == 'true' }}
+      run: |
+        # We manually build hole2 to avoid OS incompatibilities
+        git clone https://github.com/MDAnalysis/hole2.git
+        cd hole2/src
+        source ../source.apache
+        (make FC=${FC}) && (make PREFIX=${HOME}/hole2 FC=${FC} install)
+        source ../source.unset
+        echo "HOLE_BINDIR=${HOME}/hole2/bin" >> $GITHUB_ENV
+        echo "${HOME}/hole2/bin" >> $GITHUB_PATH
+
+    - name: install_mda
+      run: |
+        (cd package/ && python setup.py develop) && (cd testsuite/ && python setup.py install)
+
+    - name: run_tests
+      run: |
+        PYTEST_FLAGS="--disable-pytest-warnings --durations=50"
+        echo $PYTEST_FLAGS
+        pytest -n 2 testsuite/MDAnalysisTests $PYTEST_FLAGS