Make list_paths() include dotfiles

[jwodder]

I realized while investigating dandi/dandi-archive#1336 that list_paths() is ignoring dotfiles & dotdirs, which could theoretically lead to a test not behaving properly when such files are present in a Dandiset or Zarr.

[codecov]

Codecov Report

Base: 88.08% // Head: 88.05% // Decreases project coverage by -0.03% ⚠️

Coverage data is based on head (da14e11) compared to base (08a2a26).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1142      +/-   ##
==========================================
- Coverage   88.08%   88.05%   -0.04%     
==========================================
  Files          73       73              
  Lines        8586     8586              
==========================================
- Hits         7563     7560       -3     
- Misses       1023     1026       +3     

Flag	Coverage Δ
unittests	88.05% <100.00%> (-0.04%)	⬇️

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Impacted Files	Coverage Δ
dandi/utils.py	82.20% <100.00%> (ø)
dandi/support/threaded_walk.py	92.85% <0.00%> (-1.79%)	⬇️
dandi/organize.py	82.81% <0.00%> (-0.45%)	⬇️

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[yarikoptic]

Tests seems to fail, need a look.

Note: we use this helper only in the tests

❯ git grep 'list_paths'
dandi/tests/test_dandiapi.py:from ..utils import list_paths
dandi/tests/test_dandiapi.py:    paths = list_paths(tmp_path)
dandi/tests/test_dandiapi.py:    assert list_paths(tmp_path) == [
dandi/tests/test_dandiapi.py:    assert list_paths(tmp_path) == [
dandi/tests/test_delete.py:from ..utils import list_paths
dandi/tests/test_delete.py:    assert list_paths(tmp_path) == [
dandi/tests/test_delete.py:    assert list_paths(tmp_path) == [
dandi/tests/test_delete.py:    assert list_paths(tmp_path) == [
dandi/tests/test_delete.py:    assert list_paths(tmp_path) == [
dandi/tests/test_download.py:from ..utils import list_paths
dandi/tests/test_download.py:    assert list_paths(dsdir, dirs=True) == [
dandi/tests/test_download.py:    assert list_paths(dsdir, dirs=True) == [dsdir / "dandiset.yaml"]
dandi/tests/test_download.py:    assert list_paths(dsdir, dirs=True) == [
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [tmp_path / "coconut.txt"]
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [tmp_path / "coconut.txt"]
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [tmp_path / "coconut.txt"]
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [tmp_path / "apple.txt"]
dandi/tests/test_download.py:    assert list_paths(tmp_path, dirs=True) == [
dandi/tests/test_upload.py:from ..utils import list_paths, yaml_dump
dandi/tests/test_upload.py:        p for p in list_paths(organized_nwb_dir) if p.name != dandiset_metadata_file
dandi/tests/test_upload.py:    assert list_paths(tmp_path) == [
dandi/tests/test_upload.py:    assert list_paths(tmp_path) == [
dandi/utils.py:def list_paths(dirpath: Union[str, Path], dirs: bool = False) -> List[Path]:

so generally should be ok to change its default behavior - I was afraid that it might be used in some other location, where then listing of .git and others wouldn't be desired.

[jwodder]

@yarikoptic The test failures are due to dandi/dandi-archive#1336.

[jwodder]

@yarikoptic The tests are now passing.

[yarikoptic]

ok, before addressing #1146 we better proceed with this change.