Run pytest as module

[RMeli]

I just spent a few hours debugging a ModuleNotFoundError with GitHub Actions. My installed module was not picked up by pytest for some reason and running pytest as a module solved the issue.

Since my GitHub Action was strongly inspired by this one, I think running pytest as a module could be a safer option here as well?

[RMeli]

Pinging @jaimergp as the author of #95

[jaimergp]

Hi! Thanks for the report! May I see your GHA implementation? Maybe there's something else going on because we haven't seen this problem in several projects we are using this in!

[RMeli]

Sure, here it is:

name: pytest

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

jobs:
  test:

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

    steps:
    - uses: actions/checkout@v2

    - name: Build infos
      shell: bash
      run: |
        uname -a
        df -h
        ulimit -a

    # More info on options: https://github.com/goanpeca/setup-miniconda
    - uses: goanpeca/setup-miniconda@v1
      with:
        python-version: ${{ matrix.python-version }}
        environment-file: conda.yml
        activate-environment: test
        miniconda-version: "latest"
        auto-update-conda: true
        auto-activate-base: false
        show-channel-urls: true

    - name: Install package
      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        cd code
        python -m pip install . --no-deps
        python -c "import ael; print(ael)"

    - name: conda infos
      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        conda info
        conda list
        conda env list

    - name: Run tests
      # conda setup requires this special shell
      shell: bash -l {0}
      run: |
        cd code
        python -m pytest -v --cov=ael --color=yes tests

As I mentioned I did not use the cookiecutter for this particular project, therefore it is very likely I did something wrong in my GHA. However, I think using python -m never hurts.

[jaimergp]

I think using python -m never hurts.

Absolutely! We can probably integrate this without much discussion. I don't see anything obviously wrong in your yml so, yep, CI stuff 🤷

Let's see what the MolSSI devs think!

[janash]

I would like to understand the problem/why it occurred. Running pytest as a module adds the current directory to sys.path, so this seems like some kind of package installation issue. I'm not sure of the other consequences of using -m, but am hesitant to add anything without understanding the problem we're solving. Do you have links to the GHA logs?

[RMeli]

@janash I completely understand. Unfortunately I could not troubleshoot why this problem was happening (but the reason it's very likely unrelated to this repository). I don't have a direct link to the GHA log since it's in a private repository, I'll see if I can copy-paste it here.

I tried to troubleshoot the issue for a long time and I observed the following:

• pip installation was always successful
• The working directory was the same in which I run test locally (with pytest only)
• python -c "import ael; print(ael)" always worked after installation, under all name sections
• My package was always present in conda list after installation

I thought as well about installation issues but what puzzles me is that python -c "import ael; print(ael)" was working.

[RMeli]

(Since this is likely unrelated with the cookiecutter, please feel free to close the PR at any time. I mainly wanted to leave a comment somewhere in case other people encounter similar problems in the future.)