Pytest coverage not adding src files into report on DOCKER container

Question

I am trying to setup tests with multiple version with .tox

I finally solved all the other strange issues that were coming up, however I am not sure why coverage won't report test coverage on anything inside the src directory. On my local machine, it works okay. But not on Docker.

I am using a debian-based image with a layer on top that installs tox and several python versions. I already managed to setup the project for another repo where it worked ok in the end, but not now.

Here's how it looks like on both local and docker:

On a docker container with tox

---------- coverage: platform linux, python 3.10.2-final-0 -----------
Name                                           Stmts   Miss Branch BrPart  Cover
--------------------------------------------------------------------------------
setup.py                                          10     10      6      0     0%
src/bla.py                                         2      2      0      0     0%
src/core_file.py                                 701    701    243      0     0%
src/resources/stuff.py                            42     42      4      0     0%
src/resources/utils.py                             6      6      2      0     0%
tests/conftest.py                                 89      9      8      0    89%
tests/test_bla.py                                  3      0      0      0   100%
tests/test_core_file.py                          625     14    104      0    97%
tests/test_stuff.py                               26      0      0      0   100%
tests/test_utils.py                               38      1      4      0    98%
--------------------------------------------------------------------------------
TOTAL                                           1542    785    371      0    45%

Local machine

Name                                           Stmts   Miss Branch BrPart  Cover
--------------------------------------------------------------------------------
__init__.py                                        0      0      0      0   100%
setup.py                                          10     10      4      0     0%
src/__init__.py                                    0      0      0      0   100%
src/bla.py                                         2      0      0      0   100%
src/core_file.py                                 701    137    205     43    78%
src/resources/__init__.py                          0      0      0      0   100%
src/resources/stuff.py                            41      0     10      0   100%
src/resources/utils.py                             6      0      2      0   100%
tests/__init__.py                                  0      0      0      0   100%
tests/conftest.py                                 72      9      2      0    85%
tests/test_bla.py                                  3      0      0      0   100%
tests/test_core_file.py     5                     74     14     18      0    98%
tests/test_stuff.py                               26      0      0      0   100%
tests/test_utils.py                               38      1      6      0    98%
--------------------------------------------------------------------------------
TOTAL                                           1473    171    247     43    86%

I have the following files set:

setup.cfg

[tool:pytest]
addopts =
    # Configure pytest to verbose output
    -v
    # Configure pytest-cov to report coverage for src
    --cov=.
    # Configure pytest-cov to output coverage results to stdout
    --cov-report term
     # Configure pytest-cov to generate an html report in /htmlcov
     --cov-report html
    # Configure pytest-cov to fail, if the under coverage falls under the value below
    --cov-fail-under=87
testpaths = tests/

tox.ini

[tox]
envlist = 3.6.15, 3.10.2

[testenv]
deps =
    -rrequirements.test.txt
    -rrequirements.txt
commands =
    pytest tests/ -k "not tobefixed"
    coverage report

[testenv:clean]
deps = coverage
skip_install = true
commands = coverage erase

setup.py

from os.path import splitext, basename
from pathlib import Path

import os
from setuptools import setup, find_packages
from setuptools.glob import glob

VERSION = '2.16.0'

setup(
    python_requires='>=3.6',
    description='[OMITTED]',
    keywords='[OMITTED]',
    name='[OMITTED]',
    version=VERSION,
    url='[OMITTED]',
    classifiers=[
        # Python versions supported.
        'Programming Language :: Python :: 3.6',
        'Programming Language :: Python :: 3.10',
    ],
    packages=find_packages('src'),
    package_dir={'': 'src'},
    py_modules=[splitext(basename(path))[0] for path in glob('src/*.py')],
    package_data={'[OMITTED]': ['py.typed']},
    include_package_data=True,
    zip_safe=False,
    install_requires=[
        'requests~=2.25',
        'importlib-metadata >= 1.0 ; python_version > "3.6"',  # Backport used in _version.py
    ],
    extras_require={
        'dev': [
            'flake8-bugbear ~= 20.11',
            'flake8-import-order ~= 0.18.1',
            'flake8-logging-format ~= 0.6.0',
            'flake8 ~= 3.8',
            'isort ~= 5.6',
            'tox-pyenv',
            'tox ~= 3.25',
            'pytest-cov',
            'pytest',
            'freezegun==1.1.0',
            'pytest-freezegun==0.4.2',
            'twine',
        ]
    })

---

Any ideas what might be wrong? I tried adding a .coveragerc but then it only shows zeros at the src files and only 2 test files, instead of everything, so not sure what's wrong.

Thanks!