Refactor script discretization/discrete_pos.py; Fix function mdtools.check.bins; Fix function mdtools.structure.discrete_pos_trj

[andthum]

Refactor script discretization/discrete_pos.py; Fix function mdtools.check.bins; Fix function mdtools.structure.discrete_pos_trj

Type of change

• Change of core package.
• Change of scripts.

• Bug fix.
• New feature.
• Code refactoring.
• Dependency update.
• Documentation update.
• Maintenance.
• Other: Description.

• Non-breaking (backward-compatible) change.
• Breaking (non-backward-compatible) change.

Proposed changes

Bug Fixes:

• Fix the function mdtools.structure.discrete_pos_trj by setting the bin edges to the return value of the function mdtools.check.bin_edges. Before, the bin edges were checked but not changed if they were erroneous.
• Fix a bug in the function mdtools.check.bins that was introduced in commit f69d2fc (Pull Request New script subvolume_charge.py #119). In this commit an if condition was changed such that although the variable step might be None it is compared to an integer which raises a TypeError.

New Features:

• Script discretization/discrete_pos.py: Add new command-line option --tol with which the user can specify the tolerance value that is added to the box length to account for the right-open bin interval of the last bin.
• Function mdtools.file_handler.save_dtrj: Add a new argument rename. If set to True and a file with the given file name already exists, rename it to fname.bak_timestamp to back it up.

PR checklist

• I followed the guidelines in the Developer's guide.
• New/changed code is properly tested.
• New/changed code is properly documented.
• The CI workflow is passing.