remove getopt #39
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| name: install and test | |
| on: | |
| push: | |
| paths: | |
| - '**.py' | |
| - '**.sh' | |
| - '.github/workflows/thefirst.yml' | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| # os: ['ubuntu-latest', 'macos-latest', 'windows-latest'] | |
| # align-it in conda is only for linux 64 bit https://anaconda.org/bioconda/align_it/files | |
| os: ['ubuntu-18.04', 'ubuntu-20.04'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: install miniconda and run tests | |
| shell: bash | |
| run: | | |
| echo "---------Fetching miniconda---------" | |
| wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh | |
| bash ~/miniconda.sh -b -p $HOME/miniconda | |
| echo "---------Setting up---------" | |
| conda env list | |
| conda env create -f conda-environment.yml | |
| conda init bash --dry-run --verbose | |
| echo "Adding path" | |
| export XDG_CONFIG_HOME=$HOME/.config | |
| export PATH="$PATH:$HOME/.dotnet/tools" | |
| export PATH="$PATH:$HOME/.config/composer/vendor/bin" | |
| __conda_setup="$('/usr/share/miniconda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" | |
| if [ $? -eq 0 ]; then | |
| eval "$__conda_setup" | |
| else | |
| if [ -f "/usr/share/miniconda/etc/profile.d/conda.sh" ]; then | |
| . "/usr/share/miniconda/etc/profile.d/conda.sh" | |
| else | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| fi | |
| fi | |
| unset __conda_setup | |
| echo "---------Activate---------" | |
| conda activate annapurna | |
| echo "---------Run tests---------" | |
| ./annapurna.py --help | |
| ./annapurna-tests.sh |