v. 3.6.0

This release includes support for a new topology file format and a new interaction that can simulate DNA/RNA hybrids.

• Add 6 more tests to the run level; these tests use the new topology and check that the DNA, RNA and NA interactions compute the right energies for a short nicked duplex
• Add support for a "new" topology format where nucleotides are listed in the 5' -> 3' order, which is the standard in the community
• Add the NA interaction, which can be used to simulated hybrid DNA/RNA systems (by @eryykr, see #68 )
• Add a old<->new topology converter to the utils folder
• Add an option stiff_rate to the mutual_trap force
• Remove a few warnings when compiling with CUDA
• Fix the computation of the stress tensor on the GPU

oxpy

• Update pybind version from 2.2 to 2.11 to make oxpy compatible with Python 3.11
• Deprecate support for Python versions < 3.8 (see here if an older version is still needed)
• Add (undocumented) support for -Dpython=On and -DPYTHON=On

oat

• Add support for the new topology format
• Fixed an error in the oxDNA_PDB CLI parser
• Added error handling for truncated trajectories in the oat parser (see #67)