SURE-tools 2.2.1__tar.gz → 2.2.2__tar.gz

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Files changed (30) hide show
  1. {sure_tools-2.2.1 → sure_tools-2.2.2}/PKG-INFO +1 -1
  2. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/DensityFlow.py +2 -2
  3. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/SURE.py +6 -6
  4. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/PKG-INFO +1 -1
  5. {sure_tools-2.2.1 → sure_tools-2.2.2}/setup.py +1 -1
  6. {sure_tools-2.2.1 → sure_tools-2.2.2}/LICENSE +0 -0
  7. {sure_tools-2.2.1 → sure_tools-2.2.2}/README.md +0 -0
  8. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/__init__.py +0 -0
  9. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.2.1 → sure_tools-2.2.2}/setup.cfg +0 -0
{sure_tools-2.2.1 → sure_tools-2.2.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.2.1
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+ Version: 2.2.2
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/DensityFlow.py RENAMED
@@ -64,8 +64,8 @@ class DensityFlow(nn.Module):
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  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
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  loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
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  inverse_dispersion: float = 10.0,
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- use_zeroinflate: bool = False,
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- hidden_layers: list = [300],
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+ use_zeroinflate: bool = True,
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+ hidden_layers: list = [500],
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  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
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  nn_dropout: float = 0.1,
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  post_layer_fct: list = ['layernorm'],
{sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/SURE.py RENAMED
@@ -99,17 +99,17 @@ class SURE(nn.Module):
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  cell_factor_size: int = 0,
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  supervised_mode: bool = False,
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  z_dim: int = 10,
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- z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
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- loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
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+ z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
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+ loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
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  inverse_dispersion: float = 10.0,
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  use_zeroinflate: bool = True,
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- hidden_layers: list = [300],
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+ hidden_layers: list = [500],
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  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
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  nn_dropout: float = 0.1,
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  post_layer_fct: list = ['layernorm'],
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  post_act_fct: list = None,
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  config_enum: str = 'parallel',
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- use_cuda: bool = False,
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+ use_cuda: bool = True,
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  seed: int = 42,
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  dtype = torch.float32, # type: ignore
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  ):
@@ -817,7 +817,7 @@ class SURE(nn.Module):
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  us = None,
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  ys = None,
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  zs = None,
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- num_epochs: int = 200,
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+ num_epochs: int = 500,
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  learning_rate: float = 0.0001,
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  batch_size: int = 256,
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  algo: Literal['adam','rmsprop','adamw'] = 'adam',
@@ -826,7 +826,7 @@ class SURE(nn.Module):
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  decay_rate: float = 0.9,
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  config_enum: str = 'parallel',
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  threshold: int = 0,
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- use_jax: bool = False):
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+ use_jax: bool = True):
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  """
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  Train the SURE model.
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{sure_tools-2.2.1 → sure_tools-2.2.2}/SURE_tools.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.2.1
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+ Version: 2.2.2
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.2.1 → sure_tools-2.2.2}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
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  setup(
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  name='SURE-tools',
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- version='2.2.1',
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+ version='2.2.2',
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  description='Succinct Representation of Single Cells',
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  long_description=long_description,
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  long_description_content_type="text/markdown",
{sure_tools-2.2.1 → sure_tools-2.2.2}/LICENSE RENAMED
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{sure_tools-2.2.1 → sure_tools-2.2.2}/README.md RENAMED
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{sure_tools-2.2.1 → sure_tools-2.2.2}/SURE/__init__.py RENAMED
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{sure_tools-2.2.1 → sure_tools-2.2.2}/setup.cfg RENAMED
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