v. 3.5.1

This is a minor release that fixes several minor bugs and add some minor functionality (e.g. the possibility of computing the stress tensor on GPUs)

• Add the stress tensor calculation on GPUs for DNA
• Improve the performance and memory consumption of the DNA and RNA interactions
• Improve the numerical stability of the CUDA RNA and DNA codes
• Make the StressAutocorrelation observable output also the bulk and longitudinal ACFs
• Remove some unnecessary checks on the required keys from the MC backend
• Add a pivot move to the MC2 backend
• Add the possibility of disabling JSON support at compile time (-DJSON_ENABLED=Off)
• Fix a bug whereby a DNA force was sometimes incorrectly evaluated on GPU
• Fix two minor bugs in the CUDARNA interaction [0112a3e]
• Fix a bug whereby the code would sometimes segfault due to plugins [b6ed721]

oxpy

• Make the metad interface set more default input options

oat

• Completely rewrote oxDNA/ANM -> PDB converter
  • Now works with RNA as well as DNA and proteins
  • No longer depends on Biopython (removed from oat dependencies).
  • More control over output files.
• All oat utilities that don't involve oxpy have compete and correct type annotations
• Many doctoring updates.
• Better error messages when something that isn't a configuration file is passed to the configuration parser.
• Update the dot-bracket parser to accept pseudoknotted structures
• bugfixes:
  • Decimal in particle IDs no longer break forces2pairs.
  • Extra spaces in the header of the topology parser no longer crash it.