Follow symlinks recursively #56
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The current implementation did not follow symlink directories, only files. The built-in flag 'recurse_symlinks' was not introduced until py3.13. This commit adds a method for safely recursing directories for local paths (assumes we don't have to worry about symlinks for cloudpaths) Wil need to add some proper tests, but interactive testing suggests this fix works. Eventually, this method can be dropped in favor of path.rglob(*, recurse_symlinks=True) when only py3.13+ is supported.
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nx10
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Jun 11, 2025
| @pytest.fixture | ||
| def symlink_dataset(tmp_path: Path, sub: str = "sub-001", ses: str = "ses-001") -> Path: | ||
| data = tmp_path / "data" | ||
| data.mkdir() |
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Does this need to be cleaned up?
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When you say "cleaned up" do you mean the code for the fixture or like the directory itself?
nx10
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Jun 11, 2025
- Use built-in method for ClouthPath's since `glob.glob` does not properly recurse through sub-directories. If it is a local path, just fall back to `glob.glob`. Alternatively, could just check for Python version and only run this if <py3.13. - The built-in rglob methods have slightly different parameters so need different calls for them.
nx10
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Aug 13, 2025
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@clane9, wondering if you have any thoughts about this before I merge? Might be misremembering, but I think we might have chatted about this briefly at some point. |
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looks fine to me! |
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Resolves #55
The
path.globthat was used didn't follow directories that were symlinked.In py3.13,From what I was able to figure out, this was only needed when indexing a subject directory. I also added a (I admit messy) pytest fixture for testing indexing with symlinks.recurse_symlinksargument was introduced, but this is still an issue in py3.11 and py3.12. This introduces a method that performs similarly to py3.13 to recurse symlinks as well viaos.walk.I wonder if there is a better fix / way to do this.Turns out yes...the changes stem from trying to unifypathlib.path.globwithglob.glob(see python/cpython#117589). For now, this is falling back onglob.globwith a recursive pattern to support <py3.13.@nx10 - mind taking a look? My brain is doing circles trying to sort out this symlinking stuff.