title: .coveragerc unable to locate files I want omitted
body: <p>I am using <code>tox</code> to automatically run my tests using <code>pytest</code> and <code>pytest-cov</code> plugin. However, I'm getting coverage reports for the files I omitted in <code>.coveragerc</code>:</p>
  
  <pre><code>(env) alex@smartalex-pc:~/.repos/codelib/github/project$ tox
  
  [...]
  
  ../../../tests/test_module1.py::test_func PASSED  [  3%]
  
  [...]
  
  ../../../tests/test_module2.py::test_func PASSED  [100%]
  
  ----------- coverage: platform linux, python 3.6.7-final-0 -----------
  Name                                                                                                   Stmts   Miss  Cover
  --------------------------------------------------------------------------------------------------------------------------
  /home/alex/.repos/codelib/github/project/.tox/py36/lib/python3.6/site-packages/package/__init__.py             0      0   100%
  /home/alex/.repos/codelib/github/project/.tox/py36/lib/python3.6/site-packages/package/__main__.py             2      2     0%
  /home/alex/.repos/codelib/github/project/.tox/py36/lib/python3.6/site-packages/package/application.py         40      0   100%
  /home/alex/.repos/codelib/github/project/.tox/py36/lib/python3.6/site-packages/package/core.py                73      0   100%
  /home/alex/.repos/codelib/github/project/.tox/py36/lib/python3.6/site-packages/package/user_interface.py      45      0   100%
  --------------------------------------------------------------------------------------------------------------------------
  TOTAL                                                                                                        160      2    99%
  </code></pre>
  
  <p>It seems that <code>tox</code> does not use my <code>.coveragerc</code>. I tried to explicitly specify the config file with <code>--cov-config={toxinidir}/.coveragerc</code>, but I get the same result again. </p>
  
  <p>Simplified project structure:</p>
  
  <pre><code>package/
      __init__.py
      __main__.py
      application.py
      core.py
      user_interface.py
  tests/
      test_module1.py
      test_module2.py
  .coveragerc
  pytest.ini
  setup.py
  tox.ini
  </code></pre>
  
  <p>This is my <code>tox.ini</code>:</p>
  
  <pre><code>[tox]
  envlist = py36
  
  [testenv]
  changedir = {envtmpdir}
  deps = 
      trio
      -r dev-requirements.txt
  commands =
      pytest -v {toxinidir}/tests --cov=package --cov-config={toxinidir}/.coveragerc
  </code></pre>
  
  <p>This is my <code>.coveragerc</code>:</p>
  
  <pre><code>[run]
  omit =
      package/__main__.py
      package/__init__.py
  </code></pre>
  
  <p>This is my <code>pytest.ini</code>:</p>
  
  <pre><code>[pytest]
  trio_mode = true
  </code></pre>
  
  <p>I think this is enough but let me know if you need more output/information. </p>
  
  <p>How can I overcome the issue?</p>