Prepare the repo for the new release

CHANGELOG

@@ -1,4 +1,49 @@
-v. 3.6.1
+v. 3.7.0
+	- Add two new options to manage the format of the numerical output of some observables [6d03f40]
+	- Deprecate many old plugins in the contrib/rovigatti folder [95bd2e0]
+	- Add compiler flags to support Ampere GPUs [21d7e48]
+	- Update generate-sa.py to support generation of dsDNA with sticky ends and add an example to show its functionalities [08dcc2c]
+	- Add an attraction plane that constrains particles to stay on one side of it while attracting them with a constant force (`type = attraction_plane`).  Documentation is also included [f0e0c9d]
+	- Port the ANNaMo interaction to CUDA [3568256]
+	- Make it possible to print the kinetic and total energies with any precision [f42d61d]
+	- Make the NA interaction support custom bases (fix #129) [306a276]
+	- Make it possible to simulate arbitrary LJ binary mixtures [b191c3d]
+	- DPS: Add an optional Yukawa repulsion to the model [dbdc726]
+	- DPS: Add an input file key to disable three body interaction [2d62ba7]
+	- DPS: Fix a bug whereby species with 0 particles would not be handled correctly [2d33bcc]
+	- Fix a bug whereby the CUDA code would crash for particular initial configurations made by nucleotides aligned along z (#120) [2b69edf]
+	- Fix an example (#123) [f4853f9]
+	- Fix a bug whereby the code would hang if bases_file (used by HBEnergy) was not readable [a20df96]
+	- Fix a bug that made VMMC simulate the wrong model when used with the DNA2 interaction [6096fdb]
+	- Improve the docs (see *e.g.* #116)
+	oxpy:
+	  - Fix #97 (FFS Simulation Type Fails to Log Correctly When Running Consecutive Processes) [2b93f63]
+	  - Add a workaround documentation to a known oxpy bug [960a8c5]
+	  - Fix #138: make oxpy's get_bool() to handle non-lowercase booleans [208049d]
+	  - Improve the docs
+	oat:
+	  - Duplex angle plotter now works with ANY nucleotide id in the duplex [eb17a42]
+	  - Fixed bug where output_bonds would fail instead of exiting normally when no plot was requested [c287226]
+	  - Fixed bug where duplexes were detected as longer than they should be if they became unpaired [e1580e6]
+	  - Fixed bug where inboxing would always center the structure, center=False works now [b23bdb7]
+	  - Fixed parser and data type errors in oxDNA_PDB [d951742]
+	  - Fixed bug where strands would sometimes be backwards in converted PDBs and fixed bug where the box center was incorrect during inboxing [2f179ad]
+	  - In oxview.py, now from_path supports multiple systems loading [0050492]
+	  - Updated bond_analysis to be able to drop data files [27d2fbb]
+	  - Added __len__ methods to System and Strand [ac5e632]
+	  - Changed read_force_file to interpret particle IDs as ints rather than floats [e7f6818]
+	  - Make oxDNA_PDB callable from scripting interface [a20207b]
+	  - Improved consistency in oat cli calls [3d628eb]
+	  - Updated oat superimpose to allow separate index files for each configuration [8a6ed9d]
+	  - Removal of now removed 'center' keywords from align function call [1cb3b40]
+	  - Fix error in input file parsing (#119) [bca41ab]
+	  - Created forces/pairs to dot-bracket converters and a skeleton script for trajectory analysis [cce8009]
+	  - Fixed bugs in pdb output file naming and improved RNA detection [e753007]
+	  - Fix parsing error for strand circularity in oat's new topology reader [a168f8d]
+	  - Faster linear version of decimate script [adbba3c]
+	  - Added PDB -> oxDNA converter to oat [e0084bc]
+
+v. 3.6.1 [6854eec]
 	- Fix some bugs and docs errors due to the DRH -> NA change (see #81) [79728d3 and 7cf4b94]
 	- Add and document an option to control the DH cut-off (see #83) [95a9f0d]
 	- Make the MPI VMMC backend runnable once again, after it had been broken for years (see #85) [8becd5f]

README.md

@@ -28,7 +28,7 @@ The `analysis/paper_examples` folder contains examples for `oxDNA_analysis_tools
 
 **Q: Can oxDNA be run on multiple CPU cores or GPUs?**
 
-**A:** No, oxDNA can run simulations on single cores or single GPUs only.
+**A:** No, oxDNA can run simulations on single cores or single GPUs only. However, the Python bindings (`oxpy`) can be used to implement parallel algorithms on top of `oxDNA`. See for instance `examples/METADYNAMICS` and `examples/OXPY_REMD`.
 
 **Q: How is the oxDNA force field defined?**