fix missed glfo merge call #282
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| name: Build and Test | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main, dev ] | |
| jobs: | |
| docker: | |
| runs-on: ubuntu-latest | |
| env: | |
| ACTIONS_ALLOW_UNSECURE_COMMANDS: true | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Checkout tags | |
| run: git fetch --unshallow origin +refs/tags/*:refs/tags/* | |
| - name: Set git branch variable | |
| run: echo ::set-env name=BRANCH::$(git branch --show-current) | |
| - name: Set git tag variable | |
| run: if [ $BRANCH == "main" ];then echo ::set-env name=TAG::$(git describe --tags);else echo ::set-env name=TAG::$BRANCH;fi | |
| - name: Checkout submodules | |
| shell: bash | |
| run: | | |
| auth_header="$(git config --local --get http.https://github.com/.extraheader)" | |
| git submodule sync --recursive | |
| git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1 | |
| - name: Build the Docker image | |
| run: docker build . -t quay.io/matsengrp/partis:$TAG | |
| # - name: Run tests in the Docker image # eh, would need to install simulation stuff to do this, and not worth it at the moment (the quick test is run at the end of the docker build above) | |
| # run: docker run quay.io/matsengrp/partis:$TAG /bin/bash -c "/partis/test/test.py --run-all" | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-15-intel] # this is the last intel build, will be deprecated dec 2027, and atm we can't run on non-intel macs: https://github.com/psathyrella/partis/issues/330 | |
| python-version: ['3.12'] | |
| install-method: ['pip', 'pipx'] | |
| fail-fast: false | |
| env: | |
| TERM: xterm | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Checkout ham submodule | |
| if: matrix.install-method == 'pip' | |
| run: | | |
| git submodule update --init packages/ham | |
| - name: Checkout ig-sw submodule | |
| if: matrix.install-method == 'pip' | |
| run: | | |
| git submodule update --init packages/ig-sw | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install system dependencies (Ubuntu) | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt update | |
| sudo apt install -y python3 python3-pip python-is-python3 pipx build-essential cmake libgsl-dev libyaml-cpp-dev scons mafft ncurses-base ncurses-bin r-base | |
| # sudo apt install libbpp-core libbpp-seq # which packages do i actually have to write here? | |
| - name: Install system dependencies (macOS) | |
| if: startsWith(matrix.os, 'macos') | |
| run: | | |
| brew install gsl yaml-cpp scons mafft r | |
| # brew tap jydu/homebrew-biopp | |
| # brew install libbpp-core bppsuite # which packages do i actually have to write here? | |
| brew install --cask font-lato | |
| # - name: Set Homebrew paths for ARM64 Mac # not used atm, but we'll want these if we manage to fix the emmintrin.h/SSE2 issue, so leaving in | |
| # if: matrix.os == 'macos-14' | |
| # run: | | |
| # echo "CPPFLAGS=-I/opt/homebrew/include" >> $GITHUB_ENV | |
| # echo "LDFLAGS=-L/opt/homebrew/lib" >> $GITHUB_ENV | |
| # - name: Install R tree generation packages # could turn this back on, but it's really slow and not super important (and is unnecessary with --no-tree-gen arg below), although note we're still installing R above | |
| # run: | | |
| # R --slave -e 'dir.create(c(Sys.getenv("R_LIBS_USER")), recursive=TRUE); install.packages(c("TreeSim", "TreeSimGM", "geiger", "MASS"), repos="http://cran.rstudio.com/", dependencies=TRUE, lib=c(Sys.getenv("R_LIBS_USER")))' | |
| - name: Install with pip | |
| if: matrix.install-method == 'pip' | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e . -v | |
| - name: Install with pipx | |
| if: matrix.install-method == 'pipx' | |
| run: | | |
| pipx install partis-bcr | |
| - name: Test partis help | |
| run: | | |
| partis --help | |
| - name: Test scripts work | |
| run: | | |
| split-loci.py --help | |
| - name: Run quick test | |
| run: | | |
| partis-test.py --quick | |
| - name: Run full test | |
| run: | | |
| # if [[ "${{ matrix.install-method }}" == "pipx" || "${{ matrix.os }}" == macos* ]]; then | |
| if [[ "${{ matrix.os }}" == macos* ]]; then | |
| partis-test.py --no-simu | |
| partis-test.py --paired --no-simu | |
| else | |
| partis-test.py --no-per-base-mutation --no-tree-gen | |
| partis-test.py --paired --no-per-base-mutation --no-tree-gen | |
| fi | |
| - name: Build and publish to PyPI | |
| if: matrix.install-method == 'pip' && github.event_name == 'push' # && github.ref == 'refs/heads/main' # && matrix.os == 'ubuntu-latest' | |
| run: | | |
| python -m pip install build twine | |
| if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then | |
| python setup.py bdist_wheel --plat-name manylinux1_x86_64 | |
| python -m build --sdist 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/' | |
| python -m twine check dist/* | |
| python -m twine upload dist/* | |
| else | |
| python -m build --wheel 2>&1 | grep -v 'adding .test/\|adding .data/\|creating partis_bcr.*/test/\|copying docs/\|copying data/\|copying packages/\|copying python/.*/test/\|copying build/.*/test/' | |
| python -m twine check dist/*.whl | |
| python -m twine upload dist/*.whl | |
| fi | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} |