`tox` warning when running default configuration

[Alexandru Coca]

Hello,

I am testing this as a potential way to structure a project I'm working on. First of all - awesome job.

I've set up my repository and made a few changes to the environment files and so on and I tested to see that tox works with some dummy test file and dummy test function before adding my code to the repository. When I run the command tox, the test passes but I get the following warning:

The way I understand this is that the extras field under [testenv] basically means that tox executes pip install[testing] since extras is bound to testing and there is an entry in the setup.cfg to install the dependencies. Hence, I don't understand exactly what tox complains about? Should I go and explicitly add deps to [testenv] ?

Many thanks for great work, it's a massive help!

Relevant testenv config.

[testenv]
description = invoke pytest to run automated tests
isolated_build = True
setenv =
    TOXINIDIR = {toxinidir}
passenv =
    HOME
extras =
    testing
commands =
    pytest {posargs}

Relevant part of setup.cfg

[options.extras_require]
# Add here additional requirements for extra features, to install with:
# `pip install sgd-utils[PDF]` like:
# PDF = ReportLab; RXP

# Add here test requirements (semicolon/line-separated)
testing =
    setuptools
    pytest>=6.2.3, <7.0.0
    pytest-cov

Please provide any additional information below.
I created my environment using the command:

conda env create -f environment.yml

where the environment file is

name: my_package_name
channels:
  - defaults
  - conda-forge
  - pytorch
  # - fastai
dependencies:
  - python>=3.8, <3.9
  - pip
  # BASICS
  # VISUALIZATION
  - matplotlib
  - seaborn
  # OTHER TOOLS
  - pip:
     - -e .  # install git checkout of sgd-utils in editable mode
     # add here only pip-packages that are not available in conda/conda-forge!
     # or use if your preferred way of installing packages is pip in a conda env :)

and then updating with

conda env update -f dev_environment.yml

where the dev_environment.yml file is

name: my_package_name
channels:
  - defaults
  - conda-forge
  - pytorch
dependencies:
  - pip:
    #   - jupyterlab
    - pytest>=6.2.3, <7.0.0
    - pytest-cov
    - tox
    - pre_commit
    - nbdime
    #- nbstripout
    - sphinx
    - recommonmark
    - flake8>=3.9.1, <4.0.0

Versions and main components

• PyScaffold Version: 4.0.1
• dsproject extension: 0.6.1
• Python Version: 3.8.8
• Operating system: Windows 10 (but working in WSL 1)
• How did you install PyScaffold: pip

[Florian Wilhelm]

Hi @alexcoca, my best guess is that it has something to do with the fact that you are using the pip version of tox, pyscaffold and all the other tools instead of the conda equivalents. There are subtle differences in those packages between conda and pip, especially for packages that do some environment magic like tox. With the default environment.yml which comes with PyScaffold dsproject extension I could not reproduce these errors. Here is what I did in detail:

conda activate test # some new and totally clean conda environment with Python 3.8
conda install -c conda-forge pyscaffoldext-dsproject
putup --dsproject test_dsproject
cd test_dsproject
conda env create -f environment.yml
conda activate test_dsproject
vim tests/test_sth.py # imported test_dsproject and wrote some dummy unit test
tox # does not show any warnings

Could you change dev_environment.yml that it reflects the default environment.yml in terms of tox, pytest, etc.?

[Alexandru Coca]

Hi @FlorianWilhelm,

Apologies for the delay, was snowed under. I will do early next week and update here! Thanks so much for your support!

[Florian Wilhelm]

Hi @alexcoca, any news on this issue? Have you had time to test it out again?

[Alexandru Coca]

Hi @FlorianWilhelm,

I have not had time but I am setting a new project as we speak and intend to have the dev requirements separately. I will follow the instructions and report back with findings!

[Alexandru Coca]

@FlorianWilhelm, I have followed your advice and put the development dependencies under -dependencies rather than -pip. tox now runs warning free 👍! Thank you so much for your help and sorry for the delay.

Your work is very valuable for machine learning research.

[Florian Wilhelm]

Thanks for reporting back. I'll close this issue now.