eljost/pysisyphus: Robustness fixes

Addition

• Linesearch in min and max subspaces for RSPRFO (disabled be default). Use min_line_search: True, max_line_search: True to enable it
• AFIR enhancments:
  • Support for arbitrary number of fragments
  • Different rhos (push/pull) and gammas can now be specified for every fragment pair
  • Hydrogens are ignored by default. Use ignore_hydrogen: False to enable AFIR forces on hydrogens
• pysistrj [input] --topdb converts geometries to PDB with automated fragment detection
• quiet mode for XTB calculator (prevents creation of log files etc.)
• Enabled minimum dynamic path from YAML input (still undocumented, see `examples/mdp/01_trispericyclic)
• run_tsopt_from_cos now supports coord_type: cart|dlc (default dlc)
• Basic test suite that ships with a pysisyphus installation (execut with pytest --pyargs pysisyphus.tests -v)
• Enabled QCEngine calculator from YAML input
• On-the-fly internal coordinate rebuilding for GrowingString
• After endopt not only RMSDs are compared, but also bond matrices, making it easier to judge if a COS/TSOpt/IRC/EndOpt run was successful
• Basic Dalton calculator using daltonproject (energies & gradient)
• MO re-normalization for TDEN overlaps when AO overlaps are reconstructed from MO coefficients (disabled by default, use mo_renorm: True)
• Ability to select which set of MO coefficients (reference/current) is used to recover AO overlaps (default cur, use mos_ref: cur|ref)

• Nix build of wfoverlap failed
• Disabled Eckart projection in hessian saving of analytical potentials
• Orthogonal direction for LinearBend and LinearDisplacement is now kept throughout the lifetime of the coordinate
• Allow pysis [yaml] --cp [dest] to be run outside the dir [yaml] resides in
• Dihedral generation in situations with 4 collinear atoms
• Generation of 3N-6 DLCs is now enforced
• More reasonable threshold for inverting WIlson B-matrix (1e-7 for eigenvalues of G matrix, corresponding to 3.16e-4 for singular values)

• No more "hand-coded" constants, now the scipy.constants package is used
• Double damping is now enabled by default in StringOptimizer (double_damp: true)