Coverage sees deleted files?

[HalfWhitt]

I've tried scouring all the bytecode folders, passing -r so tox rebuilds its environment, manually deleting the entire .tox folder, and starting a new Python virtual environment, but so far I haven't found a way — short of starting from a fresh clone of the repo — to get coverage to ignore files that used to exist, but have been deleted.

Name                                                                                                        Stmts   Miss Branch BrPart  Cover   Missing
-------------------------------------------------------------------------------------------------------------------------------------------------------
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/__future__.py                 8      8      0      0   0.0%   3-10
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/__init__.py                  26     26     14      0   0.0%   5-46
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/abc.py                        3      3      0      0   0.0%   1-5
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/builtins.py                  12     12      0      0   0.0%   1-30
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/collections/__init__.py       1      1      0      0   0.0%   1
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/collections/abc.py           10     10      2      0   0.0%   21-51
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/contextlib.py                56     56     12      0   0.0%   1-113
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/dataclasses.py               10     10      2      0   0.0%   1-26
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/enum.py                       7      7      0      0   0.0%   1-14
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/functools.py                 20     20      6      0   0.0%   1-26
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/importlib/__init__.py         3      3      0      0   0.0%   1-7
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/importlib/metadata.py         8      8      0      0   0.0%   1-17
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/traceback.py                 16     16      2      0   0.0%   3-38
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/typing.py                     5      5      2      0   0.0%   1-22
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/compat/warnings.py                   5      5      0      0   0.0%   3-11
/Users/charles/toga_dev/toga/.tox/py-cov/lib/python3.13/site-packages/toga/widgets/canvas.py                  579    579     52      0   0.0%   1-1744
src/toga/style/pack.py                                                                                        386      1    164      1  99.6%   182
-------------------------------------------------------------------------------------------------------------------------------------------------------
TOTAL                                                                                                        6287    770   135

Does anyone know where the heck it's keeping information on these ghost files?

[mhsmith]

Maybe in some hidden .coverage* files.

[johnzhou721]

but so far I haven't found a way — short of starting from a fresh clone of the repo

My two cents: Try removing the gitignore file, removing all the things you've tried removing that did not solve the problem, add, commit, then diff against a fresh commit bee-fore you deleted the gitignore, to find things you may-bee forgot to delete.

[rmartin16]

@freakboy3742 remembered the root cause and detailed it in Discord.

@HalfWhitt I think I saw a comment go past recently about getting stray coverage misses that looked like they were from a .tox folder that no longer exists (toga/compat). I can't find the comment now - but I just hit the same thing, and had a sudden recollection of the cause.

The issue is stale content in the core/build folder. When you create a tox install, it creates a wheel; that wheel populates a bunch of cache/intermediate content in the build folder for the project. If a module is ever deleted from the actual project, the build directory retains those cached files - and so they can continue to appear if you use the same build directory to create an updated wheel.

Delete the core/build folder and run tox with -r to rebuild the environment, and the problem goes away.