Plenoptic: A platform for synthesizing model-optimized visual stimuli

We are now starting the changes suggested in the pyOpenSci review.

A lot of the changes since the last release are bugfixes and documentation updates. The non-documentation, non-bugfix changes are:

• Images can now be accessed using the plenoptic.data module (e.g., po.data.einstein()), which means that the example notebooks can be downloaded and run directly!

• The Portilla-Simoncelli model has been refactored and made more efficient!

• We're now on conda and can be installed with conda install plenoptic -c conda-forge (no Windows support for conda, unfortunately).

• All FrontEnd models (e.g., po.simul.LinearNonlinear) now have a pretrained argument, which loads in the parameters used in Alex Berardino's thesis.

• Deprecates a variety of functions and objects. Most importantly, Geodesic is deprecated and will be removed soon, because it needs more work to be as stable and robust as the other methods. Work will continue in the new geodesics repo.

• The included models now use register_buffers, so that you can call e.g.,

  ps = po.simul.PortillaSimoncelli((256, 256))
  ps.cuda()
  

  (in addition to ps.to('cuda')

What's Changed

• Add PortillaSimoncelliMinimal to tutorial get original paper's statistics by @dherrera1911 in https://github.com/plenoptic-org/plenoptic/pull/216
• Adds info about pip minimum version by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/228
• Citation.cff by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/231
• Updates installation instructions and CONTRIBUTING by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/230
• Switch models to using register_buffers by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/232
• Citation update by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/249
• Fix failing urlchecker by using nbstripout by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/253
• Adds description of torch/pyrtools dependencies by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/248
• fix for test_stop_criterion by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/251
• Adds repo status badge by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/255
• Clarify what model means by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/250
• Small citation update by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/256
• Updates action versions, change how notebooks are tested by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/257
• Updates python versions and trove classifiers by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/254
• 235 include example data by @BalzaniEdoardo in https://github.com/plenoptic-org/plenoptic/pull/252
• Refactor Portilla-Simoncelli model by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/225
• Update deploy by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/258
• Torch tensor replacements by @hmd101 in https://github.com/plenoptic-org/plenoptic/pull/260
• Update Deprecated PyTorch Functions to torch.linalg Namespace by @hmd101 in https://github.com/plenoptic-org/plenoptic/pull/261
• Fix Minor Typos in Documentation by @hmd101 in https://github.com/plenoptic-org/plenoptic/pull/267
• small update to quickstart text by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/272
• Updates matplotlib config for animations by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/274
• Fix links in documentation index, updates CCN logo by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/275
• Dynamically Adjust Number of Columns in plot_representation Based on Number of Loss Plots by @hmd101 in https://github.com/plenoptic-org/plenoptic/pull/276
• Adds conda install instructions by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/278
• adds Hanna to citation.cff by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/280
• Avoid unnecessary computation of magnitude variance in Portilla-Simoncelli model by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/281
• adds Edoardo to citation by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/282
• Updates github org name by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/285
• Fix jenkins by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/286
• Small restructure of how we use importlib.resources by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/289
• Make penalize_range more efficient by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/287
• Deprecations by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/288
• Specify docutils version by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/290
• Improvements to FrontEnd models by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/291
• Fix broken to method, test non-standard models/metrics, don't assume dtype by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/292
• Updates binder link to 1.1.0 by @billbrod in https://github.com/plenoptic-org/plenoptic/pull/293

New Contributors

• @dherrera1911 made their first contribution in https://github.com/plenoptic-org/plenoptic/pull/216
• @BalzaniEdoardo made their first contribution in https://github.com/plenoptic-org/plenoptic/pull/252
• @hmd101 made their first contribution in https://github.com/plenoptic-org/plenoptic/pull/260

Full Changelog: https://github.com/plenoptic-org/plenoptic/compare/1.0.2...1.1.0