Convert config.pkl to config.yml

[zhonge]

Starting in cryodrgn version 2.x, we should save the config.pkl as a config.yml file so that the configuration file is human readable. We can then deprecate the cryodrgn_utils view_config command.

We probably want to support reading from both config.pkl and config.yml files so we maintain backwards compatibility.

[vineetbansal]

So I suppose this is what it's going to look like (I took a sample config from a train_vae run on EMPIAR 10076):

dataset_args:
  ctf: /home/vineetb/cryodrgn/cryodrgn_empiar/empiar10076/inputs/ctf.pkl
  datadir: null
  do_pose_sgd: false
  ind: null
  invert_data: false
  keepreal: false
  norm:
  - 0
  - 278.5937805175781
  particles: /media/vineetb/t5/10076_128/particles.128.txt
  poses: /home/vineetb/cryodrgn/cryodrgn_empiar/empiar10076/inputs/poses.pkl
  window: true
  window_r: 0.85
lattice_args:
  D: 129
  extent: 0.5
  ignore_DC: true
model_args:
  activation: relu
  domain: fourier
  enc_mask: 64
  encode_mode: resid
  feat_sigma: 0.5
  pdim: 1024
  pe_dim: null
  pe_type: gaussian
  players: 3
  qdim: 1024
  qlayers: 3
  zdim: 8
seed: 12345

Should we throw a DeprecationWarning when reading a config if it is in the .pkl format? That'll give us some runway for removing it in a future release.

[zhonge]

Do .yml files handle None and tuples (for dataset_args.norm) gracefully? Otherwise, looks good to me, and agree, the DeprecationWarning is a good idea!

[vineetbansal]

Yes - seems to work correctly (write + read back) in both cases.

Tuple:

  norm:
  - 0
  - 278.5937805175781

None:

pe_dim: null