diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6774da5..c0c44b6 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,7 +1,6 @@ name: spora -# Controls when the workflow will run on: push: branches: @@ -14,21 +13,25 @@ jobs: build: name: spora test on ${{ matrix.os }} runs-on: ${{ matrix.os }} + env: + CONDA_OVERRIDE_CUDA: "11.8" strategy: matrix: os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.8"] + python-version: ["3.9"] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + - if: runner.os == 'Linux' + run: sudo apt-get -y update && sudo apt-get install -y libgl1-mesa-dev libglfw3-dev - uses: conda-incubator/setup-miniconda@v2 with: environment-file: environments/environment.yml activate-environment: ncov_spora channels: conda-forge,bioconda,defaults,r - mamba-version: "*" - - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} + miniconda-version: "latest" - name: Install spora run: pip install . - name: Check spora version diff --git a/environments/environment.yml b/environments/environment.yml index 99ffbd0..dce6d6b 100644 --- a/environments/environment.yml +++ b/environments/environment.yml @@ -13,11 +13,12 @@ dependencies: - fasttree=2.1.10 - iqtree=2.1.2 - mafft=7.480 - - numpy=1.20.3 + - numpy==1.24.3 - pandas=1.2.4 - pandoc=>2.1.3 - pango=1.48.5 - pip=21.1.2 + - pulp==2.7.0 - pytest=6.2.4 - python=3.8.10 - raxml=8.2.12 diff --git a/setup.py b/setup.py index 2151ea6..bae8368 100644 --- a/setup.py +++ b/setup.py @@ -21,12 +21,12 @@ }, license='', author='Matthew Watson', - author_email='matthew.watson@oahpp.ca', + author_email='matt.sd.watson@gmail.com', description='spora: Streamlined Phylogenomic Outbreak Report Analysis', long_description_content_type="text/markdown", long_description = long_description, - install_requires = ["pandas>=1.1.5", "numpy>=1.19", "biopython>=1.79", "snakemake>=7.0.0", "pypandoc>=1.8", - "pytest>=7.1.2", "click>=8.0.3"], + install_requires = ["pandas>=1.1.5", "numpy>=1.24.3", "biopython>=1.79", "snakemake>=7.0.0", "pypandoc>=1.8", + "pytest>=7.1.2", "click>=8.0.3", "pulp==2.7.0"], entry_points=""" [console_scripts] {program} = spora.main:main diff --git a/spora/__init__.py b/spora/__init__.py index bd29a78..a4ce392 100644 --- a/spora/__init__.py +++ b/spora/__init__.py @@ -1,2 +1,2 @@ _program = "spora" -__version__ = "0.7.0" +__version__ = "0.7.1"