KeyError __init__.py not found on sqldata.py

[iroussos]

Describe the bug
Since v5.0 was released on PyPi, we are getting the following error:

... .... ...
690 INTERNALERROR> Traceback (most recent call last):
691 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/_pytest/main.py", line 209, in wrap_session
692 INTERNALERROR>     session.exitstatus = doit(config, session) or 0
693 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/_pytest/main.py", line 249, in _main
694 INTERNALERROR>     config.hook.pytest_runtestloop(session=session)
695 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pluggy/hooks.py", line 284, in __call__
696 INTERNALERROR>     return self._hookexec(self, self.get_hookimpls(), kwargs)
697 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pluggy/manager.py", line 67, in _hookexec
698 INTERNALERROR>     return self._inner_hookexec(hook, methods, kwargs)
699 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pluggy/manager.py", line 61, in <lambda>
700 INTERNALERROR>     firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
701 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pluggy/callers.py", line 203, in _multicall
702 INTERNALERROR>     gen.send(outcome)
703 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pytest_cov/plugin.py", line 229, in pytest_runtestloop
704 INTERNALERROR>     self.cov_controller.finish()
705 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/pytest_cov/engine.py", line 167, in finish
706 INTERNALERROR>     self.cov.stop()
707 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/coverage/control.py", line 651, in combine
708 INTERNALERROR>     combine_parallel_data(self._data, aliases=aliases, data_paths=data_paths, strict=strict)
709 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/coverage/data.py", line 117, in combine_parallel_data
710 INTERNALERROR>     data.update(new_data, aliases=aliases)
711 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/coverage/sqldata.py", line 705, in update
712 INTERNALERROR>     for (file, context), numbits in lines.items()
713 INTERNALERROR>   File "/usr/local/lib/python3.6/site-packages/coverage/sqldata.py", line 705, in <listcomp>
714 INTERNALERROR>     for (file, context), numbits in lines.items()
715 INTERNALERROR> KeyError: '/builds/meltano/meltano/src/meltano/__init__.py'

To Reproduce

How can we reproduce the problem? Please be specific.

1. What version of Python are you using?

Python 3.6

1. What version of coverage.py are you using? The output of coverage debug sys is helpful.

Latest on PyPi --> 5.0 (coverage-5.0-cp36-cp36m-manylinux1_x86_64.whl)

1. What versions of what packages do you have installed? The output of pip freeze is helpful.

You can check our full pip install '.[dev]' log in our runner's log together with the pytests and the coverage run afterwards:

https://gitlab.com/meltano/meltano/-/jobs/379770331

1. What code are you running? Give us a specific commit of a specific repo that we can check out.

https://gitlab.com/meltano/meltano/blob/master/.gitlab/ci/test.gitlab-ci.yml#L46

1. What commands did you run?

We are running coveragepy as part of our automated tests after our pytests are done:

    - pytest -v --cov-report= --cov meltano -m "$PYTEST_MARKERS"
    - coverage combine .coverage
    - coverage report
    - coverage html

Expected behavior
This was running without issues on the latest pre v5.0 stable release.

[nedbat]

Thanks. I worked through how to get the latest versions of everything, and found a single test that reproduces the problem (below). @ionelmc can you take a look to figure out why pytest-cov gets this error when "coverage combine" doesn't?

cd /tmp

mkdir bug881a

cd bug881a

mktmpenv -p python3.6 -n

Running virtualenv with interpreter /usr/local/bin/python3.6
Using base prefix '/usr/local/pythonz/pythons/CPython-3.6.9'
New python executable in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/bin/python3.6
Also creating executable in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/bin/python
Installing setuptools, pip, wheel...done.
Requirement already up-to-date: pip in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (19.3.1)
Requirement already up-to-date: setuptools in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (42.0.2)
This is a temporary environment. It will be deleted when you run 'deactivate'.

git clone git@gitlab.com:meltano/meltano.git

Cloning into 'meltano'...
remote: Enumerating objects: 44002, done.
remote: Counting objects: 100% (44002/44002), done.
remote: Compressing objects: 100% (13918/13918), done.
remote: Total 44002 (delta 29365), reused 43668 (delta 29063)
Receiving objects: 100% (44002/44002), 56.93 MiB | 7.43 MiB/s, done.
Resolving deltas: 100% (29365/29365), done.

cd meltano

git checkout 2f8eee90b6b0548f2019b94ac9a94269ca7ad37e

Note: switching to '2f8eee90b6b0548f2019b94ac9a94269ca7ad37e'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 2f8eee90 Merge branch 'update-meltanodata-guide' into 'master'

pip install '.[dev]'

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Building wheels for collected packages: meltano
  Building wheel for meltano (setup.py) ... done
  Created wheel for meltano: filename=meltano-1.11.2-cp36-none-any.whl size=1276590 sha256=96d0e574b2c309a4e6bd8cb55422ba125b6b653f967cc5c1913bb8265fa6294b
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Successfully built meltano
Installing collected packages: aenum, idna, asn1crypto, idna-ssl, chardet, multidict, yarl, attrs, async-timeout, aiohttp, MarkupSafe, Mako, six, python-dateutil, sqlalchemy, python-editor, alembic, atomicwrites, urllib3, certifi, requests, pycparser, cffi, cryptography, authlib, backoff, bcrypt, Cerberus, click, click-default-group, colorama, smmap2, gitdb2, gitpython, gunicorn, jsonschema, markdown, decorator, networkx, pytz, numpy, pandas, psycopg2, psutil, pyhumps, pypika, python-dotenv, pyyaml, future, azure-nspkg, azure-common, azure-storage, jmespath, docutils, botocore, ijson, s3transfer, boto3, pyasn1, pyasn1-modules, pyjwt, pycryptodomex, pyOpenSSL, snowflake-connector-python, snowflake-sqlalchemy, monotonic, fasteners, Werkzeug, Jinja2, itsdangerous, flask, flask-cors, flask-executor, flask-sqlalchemy, aniso8601, flask-restful, flask-jwt-extended, pathlib2, flatten-dict, speaklater, Babel, Flask-BabelEx, blinker, Flask-Principal, WTForms, Flask-WTF, Flask-Mail, passlib, Flask-Login, meltano-flask-security, pyparsing, pyhocon, python-gitlab, simplejson, sqlparse, pathtools, argh, watchdog, asynctest, toml, appdirs, black, bumpversion, changelog-cli, coverage, freezegun, more-itertools, py, zipp, importlib-metadata, pluggy, pytest, pytest-asyncio, requests-mock, pygments, ptyprocess, pexpect, parso, jedi, wcwidth, prompt-toolkit, pickleshare, appnope, backcall, ipython-genutils, traitlets, ipython, pytest-cov, meltano
Successfully installed Babel-2.7.0 Cerberus-1.2 Flask-BabelEx-0.9.3 Flask-Login-0.4.1 Flask-Mail-0.9.1 Flask-Principal-0.4.0 Flask-WTF-0.14.2 Jinja2-2.10.3 Mako-1.1.0 MarkupSafe-1.1.1 WTForms-2.2.1 Werkzeug-0.16.0 aenum-2.1.2 aiohttp-3.4.4 alembic-1.0.11 aniso8601-8.0.0 appdirs-1.4.3 appnope-0.1.0 argh-0.26.2 asn1crypto-0.24.0 async-timeout-3.0.1 asynctest-0.12.2 atomicwrites-1.2.1 attrs-19.3.0 authlib-0.10 azure-common-1.1.23 azure-nspkg-2.0.0 azure-storage-0.36.0 backcall-0.1.0 backoff-1.8.0 bcrypt-3.1.6 black-18.9b0 blinker-1.4 boto3-1.8.9 botocore-1.11.9 bumpversion-0.5.3 certifi-2019.11.28 cffi-1.13.2 changelog-cli-0.6.2 chardet-3.0.4 click-7.0 click-default-group-1.2.1 colorama-0.3.9 coverage-4.5.4 cryptography-2.8 decorator-4.4.1 docutils-0.15.2 fasteners-0.15 flask-1.1.1 flask-cors-3.0.7 flask-executor-0.9.2 flask-jwt-extended-3.17.0 flask-restful-0.3.7 flask-sqlalchemy-2.3.2 flatten-dict-0.1.0 freezegun-0.3.12 future-0.18.2 gitdb2-2.0.6 gitpython-2.1.11 gunicorn-19.9.0 idna-2.7 idna-ssl-1.1.0 ijson-2.5.1 importlib-metadata-1.3.0 ipython-7.5.0 ipython-genutils-0.2.0 itsdangerous-1.1.0 jedi-0.15.1 jmespath-0.9.4 jsonschema-2.6.0 markdown-3.0.1 meltano-1.11.2 meltano-flask-security-0.1.0 monotonic-1.5 more-itertools-8.0.2 multidict-4.7.1 networkx-2.2 numpy-1.17.4 pandas-0.24.1 parso-0.5.2 passlib-1.7.2 pathlib2-2.3.5 pathtools-0.1.2 pexpect-4.7.0 pickleshare-0.7.5 pluggy-0.13.1 prompt-toolkit-2.0.10 psutil-5.6.3 psycopg2-2.7.7 ptyprocess-0.6.0 py-1.8.0 pyOpenSSL-19.1.0 pyasn1-0.4.8 pyasn1-modules-0.2.7 pycparser-2.19 pycryptodomex-3.9.4 pygments-2.5.2 pyhocon-0.3.51 pyhumps-0.4.0 pyjwt-1.7.1 pyparsing-2.4.5 pypika-0.25.1 pytest-4.3.1 pytest-asyncio-0.10.0 pytest-cov-2.6.1 python-dateutil-2.8.1 python-dotenv-0.10.1 python-editor-1.0.4 python-gitlab-1.8.0 pytz-2019.3 pyyaml-3.13 requests-2.22.0 requests-mock-1.6.0 s3transfer-0.1.13 simplejson-3.16.0 six-1.13.0 smmap2-2.0.5 snowflake-connector-python-1.6.10 snowflake-sqlalchemy-1.1.2 speaklater-1.3 sqlalchemy-1.2.12 sqlparse-0.3.0 toml-0.10.0 traitlets-4.3.3 urllib3-1.23 watchdog-0.9.0 wcwidth-0.1.7 yarl-1.4.2 zipp-0.6.0

pip install coverage==5.0 pytest-cov==2.8.1

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Requirement already satisfied: pytest>=3.6 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest-cov==2.8.1) (4.3.1)
Requirement already satisfied: py>=1.5.0 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (1.8.0)
Requirement already satisfied: pluggy>=0.7 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (0.13.1)
Requirement already satisfied: setuptools in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (42.0.2)
Requirement already satisfied: more-itertools>=4.0.0; python_version > "2.7" in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (8.0.2)
Requirement already satisfied: atomicwrites>=1.0 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (1.2.1)
Requirement already satisfied: six>=1.10.0 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (1.13.0)
Requirement already satisfied: attrs>=17.4.0 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pytest>=3.6->pytest-cov==2.8.1) (19.3.0)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from pluggy>=0.7->pytest>=3.6->pytest-cov==2.8.1) (1.3.0)
Requirement already satisfied: zipp>=0.5 in /usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest>=3.6->pytest-cov==2.8.1) (0.6.0)
Installing collected packages: coverage, pytest-cov
  Found existing installation: coverage 4.5.4
    Uninstalling coverage-4.5.4:
      Successfully uninstalled coverage-4.5.4
  Found existing installation: pytest-cov 2.6.1
    Uninstalling pytest-cov-2.6.1:
      Successfully uninstalled pytest-cov-2.6.1
Successfully installed coverage-5.0 pytest-cov-2.8.1

rm -f .coverage .coverage.*

zsh: no matches found: .coverage.*

pytest -v --cov-report= --cov meltano -k sql_controller

===================================================================== test session starts ======================================================================
platform darwin -- Python 3.6.9, pytest-4.3.1, py-1.8.0, pluggy-0.13.1 -- /usr/local/virtualenvs/tmp-25c2776e1dd6d267/bin/python3.6
cachedir: .pytest_cache
rootdir: /private/tmp/bug881a/meltano, inifile: pytest.ini
plugins: asyncio-0.10.0, cov-2.8.1, requests-mock-1.6.0
collected 161 items / 160 deselected / 1 selected

tests/meltano/api/controllers/test_sql_controller.py::TestSqlController::test_get_sql ERROR                                                              [100%]
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/_pytest/main.py", line 209, in wrap_session
INTERNALERROR>     session.exitstatus = doit(config, session) or 0
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/_pytest/main.py", line 249, in _main
INTERNALERROR>     config.hook.pytest_runtestloop(session=session)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR>     return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pluggy/manager.py", line 93, in _hookexec
INTERNALERROR>     return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pluggy/manager.py", line 87, in <lambda>
INTERNALERROR>     firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pluggy/callers.py", line 203, in _multicall
INTERNALERROR>     gen.send(outcome)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pytest_cov/plugin.py", line 254, in pytest_runtestloop
INTERNALERROR>     self.cov_controller.finish()
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/pytest_cov/engine.py", line 197, in finish
INTERNALERROR>     self.cov.stop()
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/coverage/control.py", line 651, in combine
INTERNALERROR>     combine_parallel_data(self._data, aliases=aliases, data_paths=data_paths, strict=strict)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/coverage/data.py", line 117, in combine_parallel_data
INTERNALERROR>     data.update(new_data, aliases=aliases)
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/coverage/sqldata.py", line 705, in update
INTERNALERROR>     for (file, context), numbits in lines.items()
INTERNALERROR>   File "/usr/local/virtualenvs/tmp-25c2776e1dd6d267/lib/python3.6/site-packages/coverage/sqldata.py", line 705, in <listcomp>
INTERNALERROR>     for (file, context), numbits in lines.items()
INTERNALERROR> KeyError: '/private/tmp/bug881a/meltano/src/meltano/__init__.py'

=========================================================== 160 deselected, 1 error in 8.06 seconds ============================================================