SURE-tools 2.1.49__tar.gz → 2.1.51__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of SURE-tools might be problematic. Click here for more details.
- {sure_tools-2.1.49 → sure_tools-2.1.51}/PKG-INFO +2 -1
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/PerturbFlow.py +2 -2
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/PKG-INFO +2 -1
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/requires.txt +1 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/setup.py +2 -2
- {sure_tools-2.1.49 → sure_tools-2.1.51}/LICENSE +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/README.md +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/SURE.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/assembly/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/assembly/assembly.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/assembly/atlas.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/atac/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/atac/utils.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/codebook/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/codebook/codebook.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/flow/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/flow/flow_stats.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/flow/plot_quiver.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/perturb/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/perturb/perturb.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/utils/__init__.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/utils/custom_mlp.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/utils/queue.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE/utils/utils.py +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/SOURCES.txt +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/dependency_links.txt +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/entry_points.txt +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/SURE_tools.egg-info/top_level.txt +0 -0
- {sure_tools-2.1.49 → sure_tools-2.1.51}/setup.cfg +0 -0
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: SURE-tools
|
|
3
|
-
Version: 2.1.
|
|
3
|
+
Version: 2.1.51
|
|
4
4
|
Summary: Succinct Representation of Single Cells
|
|
5
5
|
Home-page: https://github.com/ZengFLab/SURE
|
|
6
6
|
Author: Feng Zeng
|
|
@@ -20,6 +20,7 @@ Requires-Dist: numpy
|
|
|
20
20
|
Requires-Dist: scikit-learn
|
|
21
21
|
Requires-Dist: pandas
|
|
22
22
|
Requires-Dist: pyro-ppl
|
|
23
|
+
Requires-Dist: jax[cuda12]
|
|
23
24
|
Requires-Dist: leidenalg
|
|
24
25
|
Requires-Dist: python-igraph
|
|
25
26
|
Requires-Dist: networkx
|
|
@@ -64,7 +64,7 @@ class PerturbFlow(nn.Module):
|
|
|
64
64
|
z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
|
|
65
65
|
loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
|
|
66
66
|
inverse_dispersion: float = 10.0,
|
|
67
|
-
use_zeroinflate: bool =
|
|
67
|
+
use_zeroinflate: bool = False,
|
|
68
68
|
hidden_layers: list = [300],
|
|
69
69
|
hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
|
|
70
70
|
nn_dropout: float = 0.1,
|
|
@@ -933,7 +933,7 @@ class PerturbFlow(nn.Module):
|
|
|
933
933
|
decay_rate: float = 0.9,
|
|
934
934
|
config_enum: str = 'parallel',
|
|
935
935
|
threshold: int = 0,
|
|
936
|
-
use_jax: bool =
|
|
936
|
+
use_jax: bool = True):
|
|
937
937
|
"""
|
|
938
938
|
Train the PerturbFlow model.
|
|
939
939
|
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: SURE-tools
|
|
3
|
-
Version: 2.1.
|
|
3
|
+
Version: 2.1.51
|
|
4
4
|
Summary: Succinct Representation of Single Cells
|
|
5
5
|
Home-page: https://github.com/ZengFLab/SURE
|
|
6
6
|
Author: Feng Zeng
|
|
@@ -20,6 +20,7 @@ Requires-Dist: numpy
|
|
|
20
20
|
Requires-Dist: scikit-learn
|
|
21
21
|
Requires-Dist: pandas
|
|
22
22
|
Requires-Dist: pyro-ppl
|
|
23
|
+
Requires-Dist: jax[cuda12]
|
|
23
24
|
Requires-Dist: leidenalg
|
|
24
25
|
Requires-Dist: python-igraph
|
|
25
26
|
Requires-Dist: networkx
|
|
@@ -5,14 +5,14 @@ with open("README.md", "r") as fh:
|
|
|
5
5
|
|
|
6
6
|
setup(
|
|
7
7
|
name='SURE-tools',
|
|
8
|
-
version='2.1.
|
|
8
|
+
version='2.1.51',
|
|
9
9
|
description='Succinct Representation of Single Cells',
|
|
10
10
|
long_description=long_description,
|
|
11
11
|
long_description_content_type="text/markdown",
|
|
12
12
|
author='Feng Zeng',
|
|
13
13
|
author_email='zengfeng@xmu.edu.cn',
|
|
14
14
|
packages=find_packages(),
|
|
15
|
-
install_requires=['dill==0.3.8','scanpy','pytorch-ignite','datatable','scipy','numpy','scikit-learn','pandas','pyro-ppl',
|
|
15
|
+
install_requires=['dill==0.3.8','scanpy','pytorch-ignite','datatable','scipy','numpy','scikit-learn','pandas','pyro-ppl', "jax[cuda12]",
|
|
16
16
|
'leidenalg','python-igraph','networkx','matplotlib','seaborn','fa2-modified'],
|
|
17
17
|
classifiers=[
|
|
18
18
|
'Programming Language :: Python :: 3',
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|