From 5fc419ee98a2286a4be5c340a6a74cc827e96746 Mon Sep 17 00:00:00 2001 From: John Sterrett Date: Thu, 5 Sep 2024 14:49:53 -0600 Subject: [PATCH] reorder the conda installs andcreate a conda environment --- .github/workflows/main.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index bc11140..3d1c684 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -32,10 +32,12 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install pytest + sudo apt-get update + sudo apt-get install -y conda + conda create -n test-env python=${{ matrix.python-version }} -y + conda activate test-env + conda install -c bioconda -c conda-forge pip pytest fastspar>=0.0.7 armadillo=8 "scipy<=1.10.1,>=1.8.0" numpy networkx biom-format pandas scikit-bio statsmodels h5py if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - conda install -c bioconda -c conda-forge "fastspar>=0.0.7" armadillo=8 "scipy<=1.10.1,>=1.8.0" python setup.py install - name: Test with pytest