replace fasteners

[orbeckst]

The fasteners package is licensed under the Apache 2.0 license, which is incompatible with our target license LGPLv2.1+. We therefore need to replace it with a compatible alternative.

Reason

Further background on why this change is necessary:
https://www.mdanalysis.org/2023/09/22/licensing-update/#why-the-interim-gpl-v3-and-lgpl-v3-package-licenses-the-issue-with-apache-20

Alternatives to fasteners

One possibility is py-filelock but others could be explored, too.

Background

• fasteners is used exclusively in coordinates/XDR.py

  mdanalysis/package/MDAnalysis/coordinates/XDR.py

  Line 41 in c48962e

  import fasteners

• see Issues Error loading XDR files with corrupted offset files #3230, Problem with loading XTC offsets in parallel #1988, PR On loading the same XTC offset in parallel #3375 for why we need it.

[orbeckst]

When someone is looking at the XDR offsets code, please scrutinize the line

mdanalysis/package/MDAnalysis/coordinates/XDR.py

Lines 202 to 204 in c48962e

	warnings.warn(f"Cannot write lock/offset file in same location as "
	f"{self.filename}. Using slow offset calculation.")
	self._read_offsets(store=True)

Is it possible that this ought to be

self._read_offsets(store=False) 

because we just determined that we cannot write to the location? This may save a warning from _read_offsets. However, I only briefly glanced at the code and because this is all subtle, I don't want to jump to conclusions. Just look at it carefully.

[talagayev]

I would tackle this one if it is fine :)

py-filelock does work from local testing, as for alternatives I looked portalocker looks
also as an option, but would need more code refactoring, so I would tend towards py-filelock, other than that didn't find any good alternatives.

[orbeckst]

Put up a PR! Thanks!

[yuxuanzhuang]

When someone is looking at the XDR offsets code, please scrutinize the line

mdanalysis/package/MDAnalysis/coordinates/XDR.py

Lines 202 to 204 in c48962e

	warnings.warn(f"Cannot write lock/offset file in same location as "
	f"{self.filename}. Using slow offset calculation.")
	self._read_offsets(store=True)

Is it possible that this ought to be

self._read_offsets(store=False) 

because we just determined that we cannot write to the location? This may save a warning from _read_offsets. However, I only briefly glanced at the code and because this is all subtle, I don't want to jump to conclusions. Just look at it carefully.

Yes. I think self._read_offsets(store=False) makes much more sense and is not breaking anything here.