From a69328c3d7347f13029cea91c34c09fda9ec4ec3 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Mon, 27 Nov 2023 17:56:04 +0100 Subject: [PATCH] improve conda install in gh action --- .github/workflows/main.yml | 16 +++++++--------- ppanggolin_env.yaml | 23 +++++++++++++++++++++++ 2 files changed, 30 insertions(+), 9 deletions(-) create mode 100644 ppanggolin_env.yaml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9297851c..3989b363 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,19 +20,17 @@ jobs: python-version: ['3.8', '3.9', '3.10'] steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - # Setting up miniconda + - uses: actions/checkout@v3 + # Install requirements with miniconda - uses: conda-incubator/setup-miniconda@v2 with: - condarc-file: .condarc.yml - activate-environment: test python-version: ${{ matrix.python-version }} - # Install the dependencies - - name: Set up test environment - shell: bash -l {0} + channels: conda-forge,bioconda,defaults + environment-file: ppanggolin_env.yaml + activate-environment: ppanggolin + - name: Install ppanggolin run: | - conda install -y --file requirements.txt - pip install .[test] + pip install . # Check that it is installed and displays help without error - name: Check that PPanGGOLiN is installed shell: bash -l {0} diff --git a/ppanggolin_env.yaml b/ppanggolin_env.yaml new file mode 100644 index 00000000..0cb20b18 --- /dev/null +++ b/ppanggolin_env.yaml @@ -0,0 +1,23 @@ +name: ppanggolin +channels: + - bioconda + - defaults + - conda-forge +dependencies: + - tqdm>=4.64 + - pytables>=3.7 + - pyrodigal>=3.0.1 + - networkx>=3.0 + - dataclasses>=0.8 + - scipy>=1.10.0 + - plotly>=4.14.3 + - gmpy2>=2.1.2 + - pandas>=2.0 + - colorlover>=0.3 + - numpy>=1.24 + - bokeh>=3.1 + # Tool that are not in python + - infernal>=1.1.4 + - aragorn>=1.2.41 + - mmseqs2>=13.45111 + - mafft>=7.505 \ No newline at end of file