Avoid filesystem writes when there are no bytes to write.

Description

https://github.com/astropy/astropy/blob/main/astropy/io/fits/hdu/table.py#L939 which pads FITS binary tables that variable-length columns out to the necessary multiple of 2880, can be triggered even when data._gap == 0. That is, fileobj.write(b'') is not a no-op.

This padding may also be needed if a table or image is not itself an exact multiple of 2880 bytes, so it may be possible to trigger this even when there are no variable-length columns.

Expected behavior

Don’t trigger a filesystem write if there is nothing to write:

if data._gap > 0:
    fileobj.write((data._gap * '\0').encode('ascii'))

Actual behavior

The Lustre filesystem has a known issue that is triggered when zero-length writes are attempted. This bug report is an attempt to provide a workaround, and in general raise consciousness of corner cases that can happen in certain filesystems.

EDIT: Permalink to the code below

https://github.com/astropy/astropy/blob/3f8cf27b87f2e10f7389190971651cd33178bd7d/astropy/io/fits/hdu/table.py#L939

[weaverba137]

In principle the fix is petty simple:

if data._gap > 0:
    fileobj.write((data._gap * '\0').encode('ascii'))

The trick will be to write a unit test that exercises this. That’s been holding me up.

[dhomeier]

The Python docs say the standard open is in fact an alias to io.open; anyway fits.open also works with filehandles like

import io
fh = io.open('file.fits', mode='r+b')
hdulist = fits.open(fh, mode='u')

so if you replace fh with a handle created by such a custom opener, you should be done – ideally 😉