Move installation to toml based.

[crangelsmith]

• Move from setup.cfg to pyproject.toml
• Update precommit and test workflows
• Some markdown files changed as extra reformatting was added to precommit.

Issue opened for a next PR in #250

To approve this PR it would be great if both @marjanfamili and @jolaem are able to run the installation, precommits and tests as described here: https://github.com/alan-turing-institute/affinity-vae/blob/e3c44807ac9a472844dbe94e0a319fd7ff5d5af2/README.md?plain=1#L27 and here https://github.com/alan-turing-institute/affinity-vae/blob/e3c44807ac9a472844dbe94e0a319fd7ff5d5af2/README.md?plain=1#L37

Run tests locally with:
https://github.com/alan-turing-institute/affinity-vae/blob/e842398dd94e8977c602a7b05389e2e391d38fae/.github/workflows/tests.yml#L18

[jolaem]

Since the venv is running from python3 endpoint maybe update this to pyton3 too? or set both to python for consistency.

[crangelsmith]

yes, good catch!

[jolaem]

Testing both via python3 -m pip install -e . and python -m pip install -e ."[test]" installs ok outside Baskerville system. Tests run ok too.

$ python
Python 3.8.10 (default, May 26 2023, 14:05:08) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from avae.model_b import AffinityVAE
>>> vae = AffinityVAE(capacity=8, depth=4, input_size=(32, 32), latent_dims=7)
>>> print(vae)
AffinityVAE(
  (encoder): Encoder(
    (conv_enc): ModuleList(
      (0): Conv2d(1, 8, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1))
      (1): Conv2d(8, 16, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1))
      (2): Conv2d(16, 24, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1))
      (3): Conv2d(24, 32, kernel_size=(3, 3), stride=(2, 2), padding=(1, 1))
    )
    (norm_enc): ModuleList(
      (0): BatchNorm2d(8, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (2): BatchNorm2d(24, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (3): BatchNorm2d(32, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
    (fc_mu): Linear(in_features=128, out_features=7, bias=True)
    (fc_logvar): Linear(in_features=128, out_features=7, bias=True)
  )
  (decoder): Decoder(
    (conv_dec): ModuleList(
      (0): ConvTranspose2d(32, 24, kernel_size=(4, 4), stride=(2, 2), padding=(1, 1))
      (1): ConvTranspose2d(24, 16, kernel_size=(4, 4), stride=(2, 2), padding=(1, 1))
      (2): ConvTranspose2d(16, 8, kernel_size=(4, 4), stride=(2, 2), padding=(1, 1))
      (3): ConvTranspose2d(8, 1, kernel_size=(4, 4), stride=(2, 2), padding=(1, 1))
    )
    (norm_dec): ModuleList(
      (0): BatchNorm2d(24, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (1): BatchNorm2d(16, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (2): BatchNorm2d(8, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
      (3): BatchNorm2d(1, eps=1e-05, momentum=0.1, affine=True, track_running_stats=True)
    )
    (fc): Linear(in_features=7, out_features=128, bias=True)
  )
)
>>> 

[marjanfamili]

All good for me. I installed and tested everything with python3 and on Mac M1.

[crangelsmith]

Merging this now!