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main.yml
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name: Python package build
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
workflow_dispatch:
branches: [ main ]
jobs:
test_python_3_10:
name: Test Python 3.10
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.10
uses: actions/setup-python@v4
with:
python-version: "3.10"
- uses: s-weigand/setup-conda@v1
with:
python-version: "3.10"
activate-conda: true
- run: conda --version
- run: which python
- name: Show working dir
shell: bash
run: ls
- name: Add reademption bin to PATH
shell: bash
run: echo "bin" >> $GITHUB_PATH
- name: Conda info
shell: bash
run: conda info
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
python -m pip install matplotlib
python -m pip install biopython
python -m pip install pysam
python -m pip install pandas
python -m pip install seaborn
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Update
shell: bash
run: sudo apt-get update
- name: Install packages
shell: bash
run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
- name: Conda info
shell: bash
run: conda info
- name: Conda install segemehl
shell: bash
run: conda install -c bioconda segemehl=0.3.4
- name: Conda list
shell: bash
run: conda list
- name: List conda bin
run: ls $CONDA/bin
- name: Add conda bin (segemehl.x) to PATH
shell: bash
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install DESEQ2
shell: bash
run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" | sudo R --no-save
- name: Show python version
shell: bash
run: python --version
- name: Test with pytest
run: |
pytest
test_python_3_9:
name: Test Python 3.9
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.9
- uses: s-weigand/setup-conda@v1
with:
python-version: 3.9
activate-conda: true
- run: conda --version
- run: which python
- name: Show working dir
shell: bash
run: ls
- name: Add reademption bin to PATH
shell: bash
run: echo "bin" >> $GITHUB_PATH
- name: Conda info
shell: bash
run: conda info
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
python -m pip install matplotlib
python -m pip install biopython
python -m pip install pysam
python -m pip install pandas
python -m pip install seaborn
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Update
shell: bash
run: sudo apt-get update
- name: Install packages
shell: bash
run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
- name: Conda info
shell: bash
run: conda info
- name: Conda install segemehl
shell: bash
run: conda install -c bioconda segemehl=0.3.4
- name: Conda list
shell: bash
run: conda list
- name: List conda bin
run: ls $CONDA/bin
- name: Add conda bin (segemehl.x) to PATH
shell: bash
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install DESEQ2
shell: bash
run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" | sudo R --no-save
- name: Show python version
shell: bash
run: python --version
- name: Test with pytest
run: |
pytest
test_python_3_8:
name: Test Python 3.8
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Set up Python 3.8
uses: actions/setup-python@v4
with:
python-version: 3.8
- uses: s-weigand/setup-conda@v1
with:
python-version: 3.8
activate-conda: true
- run: conda --version
- run: which python
- name: Show working dir
shell: bash
run: ls
- name: Add reademption bin to PATH
shell: bash
run: echo "bin" >> $GITHUB_PATH
- name: Conda info
shell: bash
run: conda info
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
python -m pip install matplotlib
python -m pip install biopython
python -m pip install pysam
python -m pip install pandas
python -m pip install seaborn
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Update
shell: bash
run: sudo apt-get update
- name: Install packages
shell: bash
run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
- name: Conda info
shell: bash
run: conda info
- name: Conda install segemehl
shell: bash
run: conda install -c bioconda segemehl=0.3.4
- name: Conda list
shell: bash
run: conda list
- name: List conda bin
run: ls $CONDA/bin
- name: Add conda bin (segemehl.x) to PATH
shell: bash
run: echo "$CONDA/bin" >> $GITHUB_PATH
- name: Install DESEQ2
shell: bash
run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" | sudo R --no-save
- name: Show python version
shell: bash
run: python --version
- name: Test with pytest
run: |
pytest