updating imports for pip install

demos/ieeg_seizure.py

@@ -6,8 +6,8 @@
 import scipy.io as sio
 
 import mdp # for incremental sfa, ica, pca
-from proSVD.proSVD import proSVD
-from proSVD.utils import get_derivs
+from proSVD import proSVD
+from pro_utils import get_derivs
 
 # %% data from http://ieeg-swez.ethz.ch/
 # sampled at 512 hz, each file is 3 mins before seizure, seizure, 3 mins after

demos/pandarinath2018_reaching.py

@@ -4,8 +4,8 @@
 import scipy.io as sio
 from scipy.ndimage import gaussian_filter1d
 
-from proSVD.proSVD import proSVD
-from proSVD.utils import get_streamingSVD, get_derivs
+from proSVD import proSVD
+from pro_utils import get_streamingSVD, get_derivs
 
 import os
 

demos/rp_benchmark.py

@@ -10,8 +10,8 @@
 from scipy.stats import sem
 from scipy.spatial.distance import pdist
 
-from proSVD.proSVD import proSVD
-from proSVD.utils import embed_data, generate_stable_LDS, get_stable_dynamics_mat
+from proSVD import proSVD
+from pro_utils import embed_data, generate_stable_LDS, get_stable_dynamics_mat
 
 np.set_printoptions(precision=4)
 #%% reduction functions
@@ -219,7 +219,6 @@ def get_accuracy_6_dim(X, dists, rp_range, k=6, form='traut', iters=20):
 plt.plot(X_low.T)
 
 #%% running distortion
-%%time
 iters = 2           # iters for RP
 # rp_range = np.array([10, 50, 100, 500, 1000, 5000])
 # rp_range = np.ceil(np.logspace(1, 4, 30)).astype('int')

demos/stringer2019_ephys.py

@@ -10,7 +10,7 @@
 from scipy.ndimage import gaussian_filter1d
 from sklearn import random_projection as rp
 
-from proSVD.proSVD import proSVD
+from proSVD import proSVD
 
 #%% loading processed matlab data
 # one mouse
@@ -68,9 +68,7 @@ def reduce_sparseRP(X, comps=100, eps=0.1, transformer=None):
 
 
 #%% running proSVD
-%%time
-
-k = 10  
+k = 10 
 l1 = k      # cols to init
 l = 1       # num cols processed per iter (1 datapoint)
 decay = 1   # 'forgetting' 

demos/toy_examples.py

@@ -6,7 +6,7 @@
 from scipy.ndimage import gaussian_filter1d
 
 from proSVD import proSVD
-# from proSVD.utils import get_streamingSVD
+from pro_utils import get_streamingSVD
 
 #%% switching between different spectral regimes
 np.random.seed(100)

pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "proSVD"
+version = "0.0.1"
+description = "Code for streaming dimension reduction with stability"
+authors = [{name = "Pranjal Gupta"}]
+
+readme = "README.md"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+requires-python = ">=3.7"
+keywords = ["streaming", "SVD"]
+dependencies = [
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "scikit-learn"
+]
+
+[tool.setuptools]
+py-modules = ["proSVD", "pro_utils"]
+
+[project.optional-dependencies]
+related-methods = ["pymdptoolbox"]