Deprecations and Breaking Changes

Entries for Gaussian-related utilities (formchk, unfchk, rwfdump) in .pysisyphusrc must be updated. Please see the documentation. For the above mentioned commands the trailing _cmd has been dropped (fchk_cmd=[path to fchk] is now only fchk=[path to fchk]). Alternatively, if the binaries are available on $PATH they should be found automatically by pysisyphus and their addition to .pysisyphusrc is not required. Whether the binaries are found is easily checked by executing pysisrc on the command line.

Addition

Ability to dump calculations results to JSON (provide dump: true to calculator in YAML input)
Remote calculator to execute calculations on external machines using Fabric
pysisreplace entry point to substitute atoms in existing geometries with new residues, e.g, OEt, OMe or Ph. Idea from 10.1002/wcms.1510
pysisrc entry point to check available software and to generate a proper .pysisyphusrc
An additional block can be given in barrier block for calculation of solvated energies (see examples/complex/08_trispericyclic)
scripts/aciddrain.py for batch calculation of pKa-values using luigi and LFER fitting (linear free energy relationship)
EnergyMin calculator to optimize to allow, e.g., different multiplicities along a COS, see 10.1063/5.0021923
Methods to center and randomly rotate geometries (Geometry.center() and Geometry.rotate())
Formed/broken bonds are now reported along an IRC integration

TDEN overlaps are much faster
Fixed several deprecation warnings
Update Github action workflows
Improved integration with thermoanalysis and fixed calculation of wavenumbers of normal modes
Amound of requested memory is now checked and adjusted if too much was requested
endopt can now be requested without previous IRC run
Gathered more global configuration values in config.py, e.g., default temperature and pressure, default sub-directory to store external QC program logs
Disabled long running tests in CI to save time in the test suite
@sheepforce updated nix-related files
Parsing of TURBOMOLE Hessians for bigger systems was faulty (fixes #173)