add t-distribution to SpatialKernel, fix up kernel code #952
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| # It's useful to use yamllint to find problems with this file; | |
| # pip install --user yamllint, python3 -m yamllint <file> | |
| # | |
| # It is quite aggressive by default, though, so I've disabled some rules | |
| # | |
| # yamllint disable rule:document-start | |
| # yamllint disable rule:line-length | |
| # yamllint disable rule:brackets | |
| # yamllint disable rule:braces | |
| name: tests | |
| on: [push, pull_request] # yamllint disable-line rule:truthy | |
| jobs: | |
| canceller: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Cancel previous runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| CLI: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Ubuntu with the oldest supported GCC (used to be 4.8, but with 20.04 it is 7, sadly). | |
| - os: ubuntu-20.04 | |
| gcc: 7 | |
| python: 3.8 | |
| # Ubuntu with the most recent GCC (on 22.04, that is 12). | |
| - os: ubuntu-22.04 | |
| gcc: 12 | |
| python: 3.9 | |
| # macOS, oldest supported version (macos-10.15 was removed by GitHub) | |
| - os: macos-11 | |
| python: 3.8 | |
| # macOS, newest supported version (macos-13 does not work yet) | |
| - os: macos-12 | |
| python: 3.9 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Choose GCC | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| # Install specific GCC version as the default. | |
| sudo apt-get install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }} | |
| sudo update-alternatives \ | |
| --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc }} 100 \ | |
| --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc }} | |
| - name: Cache conda and dependancies | |
| id: cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| c:\Miniconda\envs\anaconda-client-env | |
| /usr/share/miniconda/envs/anaconda-client-env | |
| ~/osx-conda | |
| ~/.profile | |
| key: ${{ runner.os }}-${{ matrix.python }}-conda-v13-${{ hashFiles('treerec/tests/conda-requirements.txt') }}-${{ hashFiles('treerec/tests/pip-requirements.txt') }} | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: anaconda-client-env | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| channel-priority: strict | |
| auto-update-conda: true | |
| use-only-tar-bz2: true | |
| - name: Install conda deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} # We need a login shell to get conda | |
| run: conda install --yes --file=treerec/tests/conda-requirements.txt | |
| - name: Install pip deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| pip3 install -r treerec/tests/pip-requirements.txt | |
| - name: Fix OSX Cache Write # OSX Won't let the cache restore due to file perms | |
| if: steps.cache.outputs.cache-hit != 'true' && startsWith(matrix.os, 'macos') | |
| run: | | |
| cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda | |
| - name: Fix OSX Cache Restore | |
| if: steps.cache.outputs.cache-hit == 'true' && startsWith(matrix.os, 'macos') | |
| run: | | |
| sudo mkdir -p /usr/local/miniconda/envs | |
| sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env | |
| - name: Install pyslim | |
| shell: bash -l {0} | |
| run: | | |
| # TODO: uncomment when pyslim 1.0 on conda | |
| source ~/.profile | |
| # conda activate anaconda-client-env | |
| # pip install pyslim | |
| git clone https://github.com/tskit-dev/pyslim.git | |
| cd pyslim | |
| pip3 install . | |
| - name: Build (Debug) | |
| run: | | |
| mkdir Debug | |
| cd Debug | |
| cmake -D CMAKE_BUILD_TYPE=Debug .. | |
| make -j 2 | |
| - name: Test (Debug) | |
| run: | | |
| cd Debug | |
| ./eidos -testEidos | |
| ./slim -testEidos | |
| ./slim -testSLiM | |
| - name: Build (Release) | |
| run: | | |
| mkdir Release | |
| cd Release | |
| cmake -D CMAKE_BUILD_TYPE=Release .. | |
| make -j 2 | |
| - name: Test (Release) | |
| run: | | |
| cd Release | |
| ./eidos -testEidos | |
| ./slim -testEidos | |
| ./slim -testSLiM | |
| - name: Treesequence tests | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| export PATH=$PATH:$PWD/Release | |
| echo $PATH | |
| cd treerec/tests && python -m pytest -xv | |
| GUI: | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| CXXFLAGS: -D NO_QT_VERSION_ERROR | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Ubuntu with the oldest supported Qt and GCC. | |
| - os: ubuntu-20.04 | |
| qt: 5.9.5 | |
| gcc: 7 | |
| # Ubuntu with the most recent Qt and GCC. | |
| - os: ubuntu-20.04 | |
| qt: 5.15.2 | |
| gcc: 11 | |
| # Ubuntu with the most recent Qt and GCC. | |
| - os: ubuntu-22.04 | |
| qt: 5.15.2 | |
| gcc: 12 | |
| # old macOS with oldest supported Qt. | |
| - os: macos-11 | |
| qt: 5.9.5 | |
| # new macOS with most recent Qt (macos-13 does not work yet) | |
| - os: macos-12 | |
| qt: 5.15.2 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Choose GCC | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| sudo apt-get install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }} | |
| sudo update-alternatives \ | |
| --install /usr/bin/gcc gcc /usr/bin/gcc-${{ matrix.gcc }} 100 \ | |
| --slave /usr/bin/g++ g++ /usr/bin/g++-${{ matrix.gcc }} | |
| - name: Install Qt | |
| uses: jurplel/install-qt-action@v3 | |
| with: | |
| version: ${{ matrix.qt }} | |
| setup-python: true | |
| - name: Build (cmake) | |
| run: | | |
| # Just do a release build. | |
| mkdir Release | |
| cd Release | |
| cmake -D BUILD_SLIMGUI=ON -D CMAKE_BUILD_TYPE=Release .. | |
| make -j 2 | |
| - name: Build (qmake) | |
| run: | | |
| mkdir QtSLiM_QMAKE | |
| cd QtSLiM_QMAKE | |
| qmake .. | |
| make -j 2 | |
| # test windows-latest compilation | |
| tests-windows-latest-CLI: | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { sys: mingw64, env: x86_64, python: 3.8 } | |
| - { sys: ucrt64, env: ucrt-x86_64, python: 3.8 } | |
| name: Windows CLI (${{ matrix.sys }}, ${{ matrix.env }}) | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: ${{matrix.sys}} | |
| update: true | |
| install: >- | |
| git | |
| base-devel | |
| msys2-devel | |
| mingw-w64-${{matrix.env}}-toolchain | |
| mingw-w64-${{matrix.env}}-cmake | |
| - name: Cache conda and dependancies | |
| id: cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| c:\Miniconda\envs\anaconda-client-env | |
| ~/.bash_profile | |
| ~/.profile | |
| key: ${{ runner.os }}-${{ matrix.python}}-conda-v16-${{ hashFiles('treerec/tests/conda-requirements.txt') }}-${{ hashFiles('treerec/tests/pip-requirements.txt') }} | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: anaconda-client-env | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| channel-priority: strict | |
| auto-update-conda: true | |
| use-only-tar-bz2: true | |
| - name: Install conda deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| conda install --yes --file=treerec/tests/conda-requirements.txt | |
| - name: Install pip deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r treerec/tests/pip-requirements.txt | |
| - name: Install pyslim | |
| shell: bash -l {0} | |
| run: | | |
| # TODO: uncomment when pyslim 1.0 is on conda | |
| # conda install -c conda-forge pyslim | |
| git clone https://github.com/tskit-dev/pyslim.git | |
| cd pyslim | |
| pip3 install . | |
| - name: Debug | |
| run: | | |
| cd windows_compat/gnulib | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in | |
| cd ../.. | |
| mkdir Debug | |
| cd Debug | |
| cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Debug .. | |
| make -j 2 | |
| - name: Build (Release) | |
| run: | | |
| cd windows_compat/gnulib | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in | |
| cd ../.. | |
| mkdir Release | |
| cd Release | |
| cmake -G"MSYS Makefiles" -DCMAKE_BUILD_TYPE=Release .. | |
| make -j 2 | |
| - name: Test (Release) | |
| run: | | |
| cd Release | |
| ./eidos -testEidos | |
| ./slim -testEidos | |
| ./slim -testSLiM | |
| - name: Treesequence tests | |
| shell: bash -l {0} | |
| run: | | |
| export PATH=$PATH:$(pwd)/Release | |
| cd treerec/tests | |
| python -m pytest -xv | |
| tests-windows-latest-GUI: | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { sys: mingw64, env: x86_64 } | |
| - { sys: ucrt64, env: ucrt-x86_64 } | |
| name: Windows GUI (${{ matrix.sys }}, ${{ matrix.env }}) | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: ${{matrix.sys}} | |
| update: true | |
| install: >- | |
| git | |
| base-devel | |
| msys2-devel | |
| mingw-w64-${{matrix.env}}-toolchain | |
| mingw-w64-${{matrix.env}}-cmake | |
| mingw-w64-${{matrix.env}}-qt5-base | |
| - name: Build (cmake) | |
| run: | | |
| cd . | |
| cd windows_compat/gnulib | |
| touch --date="`date`" aclocal.m4 Makefile.am configure configure.ac config.h.in Makefile.in | |
| cd ../.. | |
| # Just do a release build. | |
| mkdir Release | |
| cd Release | |
| cmake -G"MSYS Makefiles" -DBUILD_SLIMGUI=ON -DCMAKE_BUILD_TYPE=Release .. | |
| make -j 2 | |
| tests-windows-latest-pacman: | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { sys: mingw64, env: x86_64 } | |
| - { sys: ucrt64, env: ucrt-x86_64 } | |
| name: Windows pacman (${{ matrix.sys }}, ${{ matrix.env }}) | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - name: 'Checkout' | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: true | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: ${{matrix.sys}} | |
| update: true | |
| install: >- | |
| mingw-w64-${{matrix.env}}-slim-simulator | |
| - name: Test | |
| run: | | |
| eidos -testEidos | |
| slim -testEidos | |
| slim -testSLiM |