changing the cwd

I’m trying to use setup-miniconda with my python package setup. The default github workflow for python package ci was working:

name: traitar3

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:

    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7, 3.8]

    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    - name: Test with pytest
      run: |
        pytest -s --script-launch-mode=subprocess

…and here’s my yaml when incorporating setup-miniconda:

name: traitar3

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:
    name: build (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7, 3.8]
    steps:
    - uses: goanpeca/setup-miniconda@v1
      with:
        miniconda-version: 'latest'
        auto-update-conda: true
        python-version: ${{ matrix.python-version }}
        channels: conda-forge,bioconda
        activate-environment: traitar3
    - name: conda env create
      shell: bash -l {0}
      run: |
        conda info -a
        conda install python=${{ matrix.python-version }} bioconda::hmmer scipy pandas numpy matplotlib
    - name: package install
      run: |
        python -m pip install --upgrade pip
        pip install pytest pytest-dependency pytest-console-scripts
        python setup.py install
    - name: Test with pytest
      run: |
        pytest -s --script-launch-mode=subprocess

The setup-miniconda version always throws the error: python: can't open file 'setup.py': [Errno 2] No such file or directory. I’m guessing that either uses: goanpeca/setup-miniconda@v1 or shell: bash -l {0} is changing the working directory, so then setup.py cannot be found. I’ve been trying to debug this for a while with a number of approaches and haven’t found a solution. Any help would be appreciated.

It would be helpful to include python package setup in one of the setup-miniconda examples.

[goanpeca]

See: https://github.com/actions/checkout

[goanpeca]

Glad you got it working 👍🏼