From 9b7f77c66948389beb067240b83d66f69685922b Mon Sep 17 00:00:00 2001
From: Pranjal Gupta <pranjal.gupta@duke.edu>
Date: Tue, 8 Aug 2023 16:08:27 -0400
Subject: [PATCH] updating imports for pip install

---
 demos/ieeg_seizure.py             |  4 ++--
 demos/pandarinath2018_reaching.py |  4 ++--
 demos/rp_benchmark.py             |  5 ++---
 demos/stringer2019_ephys.py       |  6 ++----
 demos/toy_examples.py             |  2 +-
 utils.py => pro_utils.py          |  0
 pyproject.toml                    | 31 +++++++++++++++++++++++++++++++
 requirements.txt                  |  5 -----
 setup.py                          | 17 -----------------
 9 files changed, 40 insertions(+), 34 deletions(-)
 rename utils.py => pro_utils.py (100%)
 create mode 100644 pyproject.toml
 delete mode 100644 requirements.txt
 delete mode 100644 setup.py

diff --git a/demos/ieeg_seizure.py b/demos/ieeg_seizure.py
index 31d622b..891bd5c 100644
--- a/demos/ieeg_seizure.py
+++ b/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
diff --git a/demos/pandarinath2018_reaching.py b/demos/pandarinath2018_reaching.py
index 4652479..633c58f 100644
--- a/demos/pandarinath2018_reaching.py
+++ b/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
 
diff --git a/demos/rp_benchmark.py b/demos/rp_benchmark.py
index 6aa64ea..c49636b 100644
--- a/demos/rp_benchmark.py
+++ b/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')
diff --git a/demos/stringer2019_ephys.py b/demos/stringer2019_ephys.py
index 192d344..6373127 100644
--- a/demos/stringer2019_ephys.py
+++ b/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' 
diff --git a/demos/toy_examples.py b/demos/toy_examples.py
index f86d27c..108bcff 100644
--- a/demos/toy_examples.py
+++ b/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)
diff --git a/utils.py b/pro_utils.py
similarity index 100%
rename from utils.py
rename to pro_utils.py
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..63d229e
--- /dev/null
+++ b/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"]
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 254ecce..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-numpy
-matplotlib
-scipy
-sklearn
-jupyter
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 4a16850..0000000
--- a/setup.py
+++ /dev/null
@@ -1,17 +0,0 @@
-import setuptools
-
-with open("README.md", "r") as fh:
-	long_description = fh.read()
-
-setuptools.setup(
-	name="proSVD",
-	version='0.0.1',
-	author="Pranjal Gupta",
-	author_email="pranjal.gupta@duke.edu",
-	description="Streaming dimension reduction tools for neural data",
-	long_description=long_description,
-	long_description_content_type="text/markdown",
-	url="https://github.com/pearsonlab/proSVD",
-	packages=setuptools.find_packages(),
-
-)
\ No newline at end of file