feat: create parent dirs when writing into h5ad

[marcfranquesa]

Solves the following error raised when writing an h5ad file if a parent directory does not exist:

FileNotFoundError: [Errno 2] Unable to synchronously create file (unable to open file: name = 'dir1/dir2/adata.h5ad', errno = 2, error message = 'No such file or directory', flags = 13, o_flags = 242)

It is specifically raised by the following line

anndata/src/anndata/_io/h5ad.py

Line 79 in 920f8a9

with h5py.File(filepath, mode) as f:

I am not sure if this is the general desired behavior, if not, I would happily modify the implementation (e.g. adding a new function argument to write_h5ad).

I believe it makes more sense to create the directories by default. Let me know otherwise. I will happily add a test if this behavior is desired.

[ilan-gold]

Hmm @marcfranquesa I generally hesitate to introduce more "magic" file behavior. What happens if the writing of the h5ad file fails? Then you have a magically created directory. I wonder if this somehow could break something else unexpectedly. I don't see any reason mdkir -p would not be threadsafe, but that was just a first glance. So that isn't an issue.

I believe it makes more sense to create the directories by default.

What's the use-case here? Just convenience?

[marcfranquesa]

Hi Ilan, thank you for the reply and explanation.

What's the use-case here? Just convenience?

Yes.

The PR can be closed.

[ilan-gold]

@flying-sheep any thoughts?