diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e786557..b9af934 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -16,26 +16,40 @@ jobs: if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository steps: - - uses: actions/checkout@v2 - - - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v1 + - uses: actions/checkout@v4 with: - python-version: ${{ matrix.python }} + fetch-depth: 0 - - run: pip install -U pip setuptools + - name: cache conda + uses: actions/cache@v3 + env: + CACHE_NUMBER: 0 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} - - name: Setup conda - uses: s-weigand/setup-conda@v1 + - name: setup conda + uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 with: - activate-conda: true + auto-update-conda: true + python-version: 3.9 + channels: conda-forge,bioconda + miniforge-variant: Mambaforge + miniforge-version: latest + use-mamba: true + mamba-version: "*" + activate-environment: sourmash_dev + auto-activate-base: false + use-only-tar-bz2: true + - run: conda env update -n base -f environment.yml - name: Install coverage dependencies - run: pip install pytest-cov pytest-dependency + run: pip install pytest-cov pytest-dependency setuptools - - name: Build - run: python setup.py build_ext --inplace +# - name: Build +# run: python setup.py build_ext --inplace - name: Install charcoal run: pip install -e . diff --git a/setup.py b/setup.py index 2e00da5..5d9ba89 100644 --- a/setup.py +++ b/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup, find_packages +from setuptools import setup CLASSIFIERS = [ "Environment :: Console", @@ -22,7 +22,7 @@ author="C. Titus Brown and Taylor Reiter", author_email="titus@idyll.org,tereiter@ucdavis.edu", license="BSD 3-clause", - packages = find_packages(), + packages = ["charcoal"], classifiers = CLASSIFIERS, entry_points = {'console_scripts': [ 'charcoal = charcoal.__main__:main' @@ -30,6 +30,5 @@ }, include_package_data=True, package_data = { "charcoal": ["Snakefile", "*.yml", "*.ipynb"] }, - setup_requires = [ "setuptools>=68.2.2" ], install_requires = ['snakemake==7.32.4', 'click>=7,<8'] )