report.py Tries to parse non-existent files

[adam-grant-hendry]

Describe the bug

After uninstalling PyQt5 and installing PySide6 in my virtual environment (using poetry add/remove), coverage reports warnings that it cannot parse some non-existent files. It is looking for site-packages pyscript, shibokensupport, and signature_bootstrap.py as if they are in my local folder, when they are actually in my .venv/Lib/site-packages folder:

myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\pyscript': No source for code: 'Myproj\pyscript'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\__init__.py': No source for code: 'Myproj\shibokensupport\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\feature.py': No source for code: 'Myproj\shibokensupport\feature.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\__init__.py': No source for code: 'Myproj\shibokensupport\signature\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\errorhandler.py': No source for code: 'Myproj\shibokensupport\signature\errorhandler.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\importhandler.py': No source for code: 'Myproj\shibokensupport\signature\importhandler.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\layout.py': No source for code: 'Myproj\shibokensupport\signature\layout.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\lib\__init__.py': No source for code: 'Myproj\shibokensupport\signature\lib\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\lib\enum_sig.py': No source for code: 'Myproj\shibokensupport\signature\lib\enum_sig.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\lib\pyi_generator.py': No source for code: 'Myproj\shibokensupport\signature\lib\pyi_generator.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\lib\tool.py': No source for code: 'Myproj\shibokensupport\signature\lib\tool.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\loader.py': No source for code: 'Myproj\shibokensupport\signature\loader.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\mapping.py': No source for code: 'Myproj\shibokensupport\signature\mapping.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\shibokensupport\signature\parser.py': No source for code: 'Myproj\shibokensupport\signature\parser.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
myproj\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse 'Myproj\signature_bootstrap.py': No source for code: 'Myproj\signature_bootstrap.py'. (couldnt-parse)       
  coverage._warn(msg, slug="couldnt-parse")

To Reproduce
How can we reproduce the problem? Please be specific. Don't link to a failing CI job. Answer the questions below:

1. What version of Python are you using? 3.8.10
2. What version of coverage.py shows the problem? The output of coverage debug sys is helpful. 6.4
3. What versions of what packages do you have installed? The output of pip freeze is helpful.

[tool.poetry.dependencies]
appdirs = "^1.4.4"
h5py = "^3.6.0"
hypothesis = "^6.46.2"
ipython = "^8.3.0"
matplotlib = "^3.5.2"
merry = "^0.3.0"
meshio = "^5.3.4"
ninja = "^1.10.2"
numpy = "^1.22.3"
opencv-python = "^4.5.5.64"
pyembree = "^0.2.11"
pykdtree = "^1.3.4"
pymeshfix = "^0.15.0"
pyqtgraph = "^0.12.4"
PySide6 = "^6.3.0"
pytest-xdist = "^2.5.0"
python = "3.8"
pyvista = "^0.34.1"
pyvistaqt = "^0.9.0"
QtPy = "^2.1.0"
Rtree = "^1.0.0"
trimesh = "^3.11.2"
vtk = "^9.1.0"

[tool.poetry.dev-dependencies]
bandit = {extras = ["toml"], version = "^1.7.4"}
beautifulsoup4 = "4.11.1"
black = "^22.3.0"
bump2version = "^1.0.1"
check-jsonschema = "^0.14.3"
codecov = "^2.1.12"
codespell = "^2.1.0"
commitizen = "^2.27.0"
Cython = "^0.29.28"
docformatter = "^1.4"
flake8 = "^4.0.1"
flake8-docstrings = "^1.6.0"
flake8-quotes = "^3.3.1"
html5lib = "^1.1"
isort = "^5.10.1"
lxml = "^4.8.0"
memory-profiler = "^0.60.0"
MonkeyType = "^22.2.0"
mypy = "^0.950"
myst-parser = "^0.17.2"
pep8-naming = "^0.12.1"
pre-commit = "^2.18.1"
pydocstyle = "^6.1.1"
pyinstaller = "^5.1"
pylint = "^2.13.8"
pytest = "^7.1.2"
pytest-doctestplus = "^0.12.0"
pytest-env = "^0.6.2"
pytest-memprof = "^0.2.0"
pytest-qt = "^4.0.2"
pytest-randomly = "^3.11.0"
requests = "^2.27.1"
rstcheck = "^5.0.0"
Sphinx = "^4.5.0"
sphinx-rtd-theme = "^1.0.0"
sphinxcontrib-email = "^0.3.5"
sphinxcontrib-napoleon = "^0.7"
toml = "^0.10.2"
tox = "^3.25.0"
tqdm = "^4.64.0"
vulture = "^2.3"
wheel = "^0.37.1"
pytest-cov = "^3.0.0"
coverage = {extras = ["toml"], version = "^6.4"}

4. What code shows the problem? Give us a specific commit of a specific repo that we can check out. If you've already worked around the problem, please provide a commit before that fix.
   Not a specific code example as this is an internal warning.

5. What commands did you run?

pytest --cov --cov-report term-missing --cov-report html --cov-report xml

Expected behavior
A clear and concise description of what you expected to happen.
These warnings should not occur because these are non-existent file paths.

Additional context
Add any other context about the problem here.

I deleted every single __pycache__ and *.pyc, as well as the .coverage file in the project, but the problem persists.

[nedbat]

I'm not sure how to help without a way to reproduce this. Can you try setting COVERAGE_DEBUG=trace in your environment? It will show tracing decisions that might provide clues.

[adam-grant-hendry]

@nedbat Yes, I'll do this. One sec.

[adam-grant-hendry]

I've attached the debug log. As you can see, it is trying to trace files that don't exist (they are not in myproj):

Tracing 'pyscript' as '%USERPROFILE%\\Code\\myproj\\pyscript'
Tracing 'signature_bootstrap.py' as '%USERPROFILE%\\Code\\myproj\\signature_bootstrap.py'
Tracing 'shibokensupport/__init__.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\__init__.py'
Tracing 'shibokensupport/signature/__init__.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\__init__.py'
Tracing 'shibokensupport/signature/loader.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\loader.py'
Tracing 'shibokensupport/feature.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\feature.py'
Tracing 'shibokensupport/signature/mapping.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\mapping.py'
Tracing 'shibokensupport/signature/errorhandler.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\errorhandler.py'
Tracing 'shibokensupport/signature/layout.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\layout.py'
Tracing 'shibokensupport/signature/lib/__init__.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\lib\\__init__.py'
Tracing 'shibokensupport/signature/parser.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\parser.py'
Tracing 'shibokensupport/signature/lib/tool.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\lib\\tool.py'
Tracing 'shibokensupport/signature/importhandler.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\importhandler.py'
Tracing 'shibokensupport/signature/lib/enum_sig.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\lib\\enum_sig.py'
Tracing 'shibokensupport/signature/lib/pyi_generator.py' as '%USERPROFILE%\\Code\\myproj\\shibokensupport\\signature\\lib\\pyi_generator.py'
Tracing 'config.py' as '%USERPROFILE%\\Code\\myproj\\config.py'
Tracing 'config-3.py' as '%USERPROFILE%\\Code\\myproj\\config-3.py'

Specifying source to myproj/ in my pyproject.toml will result in the debug saying "Not Tracing", but coverage shouldn't be looking for non-existent files in the first place. This is clearly a bug.

debug_log.txt

[adam-grant-hendry]

I'm not sure how to help without a way to reproduce this

System

OS: Windows 10
Python: 3.8.10
VSCode: 1.67.2
coverage: 6.4 (with toml extra)

To reproduce,

Minimum Reproducible Example (MRE)

1. Create and activate a virtual environment

   PS> py -m venv .venv
   PS> .venv/Scripts/Activate.ps1

   and ensure vscode sees the Python Interpreter (use Ctrl+Shift+p and set).

2. Create a new poetry project

   PS> poetry init

3. Install pytest, pytest-cov, pytest-env, pytest-qt, pyqt5, and qtpy

   PS> poetry add pytest pytest-cov pytest-qt pyqt5 qtpy

4. Update the pyproject.toml and then run poetry install to make a local (editable) install

   [tool.poetry]
   name = "coverage-issue-1392"
   version = "0.1.0"
   description = ""
   authors = ["Hendry, Adam <adam.grant.hendry@gmail.com>"]
   packages = [
       {include = "myproj"},
       {include = "tests"}
   ]
   
   [tool.poetry.dependencies]
   PyQt5 = "^5.15.6"
   pytest = "^7.1.2"
   pytest-cov = "^3.0.0"
   pytest-env = "^0.6.2"
   pytest-qt = "^4.0.2"
   python = "3.8"
   QtPy = "^2.1.0"
   
   [tool.poetry.dev-dependencies]
   
   [build-system]
   requires = ["poetry-core>=1.0.0"]
   build-backend = "poetry.core.masonry.api"
   
   [tool.pytest.ini_options]
   minversion = "7.0"
   addopts = """\
   --last-failed --last-failed-no-failures all \
   -p no:faulthandler \
   --import-mode=importlib \
   --cov \
   --cov-report term-missing \
   --cov-report html \
   --cov-report xml \
   """
   testpaths = [
       "tests",
   ]
   qt_api = "pyqt5"
   env = [
       "D:COVERAGE_DEBUG=trace",
       "D:COVERAGE_DEBUG_FILE=debug_log.txt"
   ]

5. Create a dummy Qt project

   myproj/main.py

   from qtpy import QtWidgets
   
   
   class MainApp(QtWidgets.QMainWindow):
       """The main window."""
   
   if __name__ == '__main__':
       app = QtWidgets.QApplication([])
       window = MainApp()
       window.show()
       app.exec_()

6. Create a dummy test

   test/test_window.py

   import pytest
   from myproj.main import MainApp
   
   
   @pytest.fixture(name='app', scope='function')
   def fixture_app(qtbot):
       window = MainApp()
       window.show()
   
       qtbot.addWidget(window)
   
       yield window
   
   def test_window_appears(app) -> None:
       assert app.isVisible()

7. Run pytest

   PS> pytest

8. Add pyside6 and remove pyqt5

      PS> poetry add pyside6
      PS> poetry remove pyqt5

   NOTE: Before doing this, be sure to set python exactly to 3.8 in the pyproject.toml:

   python = "3.8"

9. Change qt_api in pyproject.toml:

   [tool.pytest.ini_options]
   qt_api = "pyside6"

10. Update project with new toml

    PS> poetry update

11. Re-run pytest

    PS> pytest

This results in the error messages mentioned in this issue:

%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\pyscript': No source for code: '%userprofile%\Code\coverage-issue-1392\pyscript'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\__init__.py': No source for 
code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\feature.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\feature.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\__init__.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\errorhandler.py': 
No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\errorhandler.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\importhandler.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\importhandler.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\layout.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\layout.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\__init__.py': 
No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\__init__.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\enum_sig.py': 
No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\enum_sig.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\pyi_generator.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\pyi_generator.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\tool.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\lib\tool.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\loader.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\loader.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\mapping.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\mapping.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\parser.py': No source for code: '%userprofile%\Code\coverage-issue-1392\shibokensupport\signature\parser.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")
%userprofile%\code\coverage-issue-1392\.venv\lib\site-packages\coverage\report.py:87: CoverageWarning: Couldn't parse '%userprofile%\Code\coverage-issue-1392\signature_bootstrap.py': No source for code: '%userprofile%\Code\coverage-issue-1392\signature_bootstrap.py'. (couldnt-parse)
  coverage._warn(msg, slug="couldnt-parse")

[nedbat]

This seems to be due to pyside using "shiboken6", which imports files from a zip file, reporting file names that don't exist on the file system. I don't see how coverage.py could know that they shouldn't be attempted.

You can tell reporting to omit those files using settings like this in pyproject.toml:

[tool.coverage.report]
omit = [
    "shibokensupport/*",
    "pyscript",
    "signature_bootstrap.py",
]

Or you can suppress that warning entirely with:

[tool.coverage.run]
disable_warnings = ["couldnt-parse"]

Either way, you will not be bothered with those messages.

[nedbat]

Feel free to reopen this if you have an idea about how coverage.py could do something more here.

[nedbat]

BTW, simpler reproduction steps, due to @SnoopJeDi:

pyproject.toml:

[tool.pytest.ini_options]
minversion = "7.0"
addopts = """\
--last-failed --last-failed-no-failures all \
-p no:faulthandler \
--import-mode=importlib \
--cov \
--cov-report term-missing \
--cov-report html \
--cov-report xml \
"""

requirements.txt:

pytest==7.1.2
pytest-cov==3.0.0
pyside6==6.3.0
qtpy==2.1.0

test_repro.py:

from qtpy import QtWidgets

Then in a Python3.8 environment, run:

python3 -m pip install -r requirements.txt
python3 -m pytest

[adam-grant-hendry]

This seems to be due to pyside using "shiboken6", which imports files from a zip file

How were you able to see that it imports from a zip file?

[nedbat]

Actually, I'm guessing where the file came from. But I know it didn't exist because I added some debugging lines to coverage/inorout.py to log whether the claimed file exists.

[SnoopJ]

This seems to be due to pyside using "shiboken6", which imports files from a zip file

How were you able to see that it imports from a zip file?

If you print the contents of sys.modules after the import that causes these warnings, the offending modules indicate that they are instances of EmbeddableZipImporter objects (which are specific to pyside6) in their repr:

Input:

from pprint import pprint
import sys

from qtpy import QtWidgets

pprint(sys.modules)

Output:

{'PySide6': <module 'PySide6' from '/home/snoopjedi/repos/coveragepy-src/.direnv/python-3.8.12/lib/python3.8/site-packages/PySide6/__init__.py'>,       
 'PySide6.QtCore': <module 'PySide6.QtCore' from '/home/snoopjedi/repos/coveragepy-src/.direnv/python-3.8.12/lib/python3.8/site-packages/PySide6/QtCore.abi3.so'>,
 'PySide6.QtDataVisualization': <module 'PySide6.QtDataVisualization' from '/home/snoopjedi/repos/coveragepy-src/.direnv/python-3.8.12/lib/python3.8/site-packages/PySide6/Qt
DataVisualization.abi3.so'>,
# ... snipped ...
 'shiboken6': <module 'shiboken6' from '/home/snoopjedi/repos/coveragepy-src/.direnv/python-3.8.12/lib/python3.8/site-packages/shiboken6/__init__.py'>,
 'shiboken6.Shiboken': <module 'shiboken6.Shiboken' from '/home/snoopjedi/repos/coveragepy-src/.direnv/python-3.8.12/lib/python3.8/site-packages/shiboken6/Shiboken.abi3.so'>
,
 'shibokensupport': <module 'shibokensupport' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.feature': <module 'PySide6.support.__feature__' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature': <module 'PySide6.support.signature' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.errorhandler': <module 'PySide6.support.signature.errorhandler' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.importhandler': <module 'PySide6.support.signature.importhandler' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.layout': <module 'PySide6.support.signature.layout' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.lib': <module 'PySide6.support.signature.lib' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.lib.enum_sig': <module 'PySide6.support.signature.lib.enum_sig' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.lib.pyi_generator': <module 'PySide6.support.signature.lib.pyi_generator' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>
,
 'shibokensupport.signature.lib.tool': <module 'PySide6.support.signature.lib.tool' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.loader': <module 'shibokensupport.signature.loader' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.mapping': <module 'PySide6.support.signature.mapping' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
 'shibokensupport.signature.parser': <module 'PySide6.support.signature.parser' (<signature_bootstrap.EmbeddableZipImporter object at 0x7f9009ae1430>)>,
# ... snipped ...

[adam-grant-hendry]

Actually, I'm guessing where the file came from. But I know it didn't exist because I added some debugging lines to coverage/inorout.py to log whether the claimed file exists.

I believe you are right. I dug deeper into a similar problem posted on SO and it does appear shiboken6 imports from a zip file.

I know I used to see a private . folder cached in my top-level project directory before, but I can't seem to find it.

[adam-grant-hendry]

If you print the contents of sys.modules after the import that causes these warnings, the offending modules indicate that they are instances of EmbeddableZipImporter objects (which are specific to pyside6) in their repr:

Thank you! Great tip.

The bug on the PySide tracker (PYSIDE-932) does note that their solution was to embed everything now. That makes sense.

[adam-grant-hendry]

FWIW future readers (a tip), I've added a note in my pyproject.toml regarding this since newcomers to my codebase might scratch their heads when they see that a non-existent folder is being omitted:

# `shiboken6`, which creates the python bindings for `Qt` C++ source, imports from a
# `zip` file into the top-level directory at runtime. These files are deleted after
# running, but `coverage` attempts to look at their source after they're gone, causing
# warnings to appear. Namely, it looks for these modules/files:
#
#    myproj/pysrcript
#    myproj/shibokensupport
#    myproj/signature_bootstrap.py
#
# To avoid this error, `source` is specified to the package subdirectory. However, this
# can also be avoided by explicitly omitting these folders in the `omit` section.
#
# See https://github.com/nedbat/coveragepy/issues/1392

[SnoopJ]

It's conceivable that PySide could adjust the filenames of things provided by EmbeddableZipImporter to start with "<" which would cause coverage to ignore them, but I don't know if that would impact any of the other usage in their little ecosystem. Might be worth asking them about it, though.

[adam-grant-hendry]

It's conceivable that PySide could adjust the filenames of things provided by EmbeddableZipImporter to start with "<" which would cause coverage to ignore them, but I don't know if that would impact any of the other usage in their little ecosystem. Might be worth asking them about it, though.

I'm comfortable in my own project, for the timebeing, commenting what's happening in my pyproject.toml.

If this surfaces into a bigger issue, I can open a request on their tracker later.

[jaraco]

I also encountered this issue in pytest-dev/pytest-cov#538 and in jaraco/zipp#93.

For example, this code triggers a warning when (test) can't be parsed:

https://github.com/jaraco/zipp/blob/a730c30dd4c2c9fe0c5a5374481adcaf984bfd37/tests/test_zipp.py#L271-L282

Probably that test is going to get removed soon, as it appears to be there for Python 2 compatibility. That doesn't change the fact that someone might want to invoke compile on inline logic. Is there a special value the user should supply to the filename parameter of compile to avoid triggering these warnings?

In other cases, warnings were emitted for temporary files loaded when processing temp files that were no longer available in a later scope.

It sounds as if the best recommendation is to blocklist the unwanted paths or disable the warnings altogether. I'll probably end up doing the latter.

[SnoopJ]

Is there a special value the user should supply to the filename parameter of compile to avoid triggering these warnings?

I believe that if the filename starts with <, then coverage will ignore it (seen in the code here) so perhaps you could use <test> instead of (test) there.

It sounds as if the best recommendation is to blocklist the unwanted paths or disable the warnings altogether. I'll probably end up doing the latter.

The former strikes me as the better option because the offending code can be quarantined with good granularity, but either of these imposes fewer constraints on the downstream consumer of coverage and are in that sense 'better' than restricting yourself to a special filename.

[rbm-radius]

For what it's worth, I am running into a similar problem, but I don't think it's coming from a zip file.

code/xx/venv/lib/python3.9/site-packages/coverage/report.py:113: CoverageWarning: Couldn't parse 'code/xx/_run_request_middleware': No source for code: 'code/xx/_run_request_middleware'. (couldnt-parse)

(and a few similar errors with different paths)

That spurious path (_run_request_middleware) is only found in the code in the Sanic package installed in a virtual environment at code/venv. There is no file named _run_request_middleware anywhere. This happens whether I delete that __pycache__ directory or not.

$ grep -r _run_request_middleware *
Binary file venv/lib/python3.9/site-packages/sanic/__pycache__/app.cpython-39.pyc matches
venv/lib/python3.9/site-packages/sanic/app.py:        "_run_request_middleware",
venv/lib/python3.9/site-packages/sanic/app.py:            response = await self._run_request_middleware(request, middleware)
venv/lib/python3.9/site-packages/sanic/app.py:                response = await self._run_request_middleware(
venv/lib/python3.9/site-packages/sanic/app.py:    async def _run_request_middleware(

My .coveragerc is set to omit virtual env directories, __pycache__, and .pyc files:

[run]
command_line = -m pytest -W ignore::DeprecationWarning -W ignore::UserWarning --cov=xx --cov-reset --cov-report=html tests/unit/ops
omit = */tests/*,./*/*.pyc,*/venv/*,*/__pycache__/*

[report]
# Regexes for lines to exclude from consideration
exclude_lines =
    # Have to re-enable the standard pragma
    pragma: no cover

    # Don't complain about missing debug-only code:
    def __repr__
    if self\.debug

    # Don't complain if tests don't hit defensive assertion code:
    raise NotImplementedError

    # Don't complain about abstract methods, they aren't run:
    @(abc\.)?abstractmethod

ignore_errors = True

No warnings are thrown during coverage run but they do appear when I run coverage xml

I tried adding the disable_warnings directive to .coveragerc in the [run] and [report] sections to no avail.

[tool.coverage.run]
disable_warnings = ["couldnt-parse"]

Any ideas?

Thanks.

[SnoopJ]

There is no file named _run_request_middleware anywhere.

Looks like sanic does some code generation at runtime as part of its "touchup" process (which is invoked because of the declaration here), so there isn't any source file for coverage to locate, but coverage doesn't know that because the code object's filename isn't distinguishable from a "real" filename.

See sanic-org/sanic#2345 for a downstream report of the same issue which points out that

these functions … are rewritten at startup time based upon your application's code.

Looks like sanic uses the name of the method being touched-up as the filename for the resulting code object. I don't know if they have load-bearing reasons for doing that, but if they used a filename starting with <, then coverage would ignore the generated code. It may be worth filing a downstream issue for this change.

I'm not sure about your other questions, it sounds like there may be a separate issue going on with your attempt to use disable_warnings to squelch this, maybe something is forcing the warning back on? I'll leave those other matters for @nedbat 😅

[rbm-radius]

@SnoopJ nice detective work on the sanic-related issue. I will file an issue there.

As to why disable_warnings is ignored, that is indeed a mystery.

[bersbersbers]

Sorry for excavating this old thread, but how is

a filename starting with <

supposed to work on Windows? < is not allowed in Windows filenames, compare https://stackoverflow.com/q/1976007/.

[nedbat]

Sorry for excavating this old thread, but how is

a filename starting with <

supposed to work on Windows? < is not allowed in Windows filenames, compare https://stackoverflow.com/q/1976007/.

If you are referring to this earlier comment:

I believe that if the filename starts with <, then coverage will ignore it (seen in the code here) so perhaps you could use instead of (test) there.

This should be "if a reported filename starts with <, then it isn't actually a file name, it's a synthetic placeholder like <memory>."