florisvb · florisvb · May 30, 2025 · May 28, 2025 · May 28, 2025 · May 28, 2025
diff --git a/.gitignore b/.gitignore
@@ -116,3 +116,4 @@ __pycache__
 dist
 *.whl
 .vscode
+docs/build
diff --git a/README.md b/README.md
@@ -9,8 +9,6 @@ Python methods for numerical differentiation of noisy data, including multi-obje
 </p>
 
 <p align="center">
-    <a href="#travis" alt="Travis Build Status">
-        <img src="https://travis-ci.com/florisvb/PyNumDiff.svg?branch=master"/></a>
     <a href='https://pynumdiff.readthedocs.io/en/master/?badge=master'>
         <img src='https://readthedocs.org/projects/pynumdiff/badge/?version=master' alt='Documentation Status' /></a>
     <a href="https://badge.fury.io/py/pynumdiff">
@@ -86,9 +84,8 @@ For more details, refer to [this paper](https://doi.org/10.1109/ACCESS.2020.3034
             |- index.rst
             |- ...
       |- .gitignore
-      |- .travis.yml
       |- LICENSE.txt
-      |- requirements.txt
+      |- pyproject.toml
 
 ## Citation
 
@@ -125,7 +122,7 @@ See CITATION.cff file as well as the following references.
 ### Prerequisite
 
 PyNumDiff requires common packages like `numpy`, `scipy`, `matplotlib`, `pytest` (for unittests), `pylint` 
-(for PEP8 style check). For a full list, you can check the file [requirements.txt](requirements.txt)
+(for PEP8 style check). For a full list, you can check the file [pyproject.toml](pyproject.toml)
 
 In addition, it also requires certain additional packages for select functions, though these are not required for a successful install of PyNumDiff:
 * Total Variation Regularization methods: [`cvxpy`](http://www.cvxpy.org/install/index.html)

diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/LICENSE.rst b/docs/source/LICENSE.rst
@@ -6,6 +6,7 @@ The MIT License (MIT)
 Copyright (c) 2021
 Floris van Breugel, The University of Nevada, Reno, Mechanical Engineering Department
 Yuying Liu, The University of Washington Applied Math Department
+Pavel Komarov, Univerity of Washington Electrical and Computer Engineering
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -20,8 +20,8 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PyNumDiff'
-copyright = '2021, Floris van Breugel, Yuying Liu'
-author = 'Floris van Breugel, Yuying Liu'
+copyright = '2025, Floris van Breugel, Yuying Liu, Pavel Komarov'
+author = 'Floris van Breugel, Yuying Liu, Pavel Komarov'
 
 # The full version, including alpha/beta/rc tags
 release = '0.1.2'

diff --git a/docs/source/finite_difference.rst b/docs/source/finite_difference.rst
@@ -1,7 +1,5 @@
 finite_difference
 =================
 
-.. toctree::
-   :maxdepth: 1
-
-   finite_difference/_finite_difference
+.. automodule:: pynumdiff.finite_difference
+    :members:
diff --git a/docs/source/finite_difference/_finite_difference.rst b/docs/source/finite_difference/_finite_difference.rst
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -81,9 +81,8 @@ Structure
             |- ...
       |- setup.py
       |- .gitignore
-      |- .travis.yml
       |- LICENSE.txt
-      |- requirements.txt
+      |- pyproject.toml
 
 Getting Started
 ---------------

diff --git a/docs/source/kalman_smooth.rst b/docs/source/kalman_smooth.rst
@@ -1,7 +1,5 @@
 kalman_smooth
 =============
 
-.. toctree::
-   :maxdepth: 1
-
-   kalman_smooth/_kalman_smooth
+.. automodule:: pynumdiff.kalman_smooth
+    :members:
diff --git a/docs/source/kalman_smooth/_kalman_smooth.rst b/docs/source/kalman_smooth/_kalman_smooth.rst
diff --git a/docs/source/linear_model.rst b/docs/source/linear_model.rst
@@ -1,7 +1,5 @@
 linear_model
 ============
 
-.. toctree::
-   :maxdepth: 1
-
-   linear_model/_linear_model
+.. automodule:: pynumdiff.linear_model
+    :members:
diff --git a/docs/source/linear_model/_linear_model.rst b/docs/source/linear_model/_linear_model.rst
diff --git a/docs/source/smooth_finite_difference.rst b/docs/source/smooth_finite_difference.rst
@@ -1,7 +1,5 @@
 smooth_finite_difference
 ========================
 
-.. toctree::
-   :maxdepth: 1
-
-   smooth_finite_difference/_smooth_finite_difference
+.. automodule:: pynumdiff.smooth_finite_difference
+    :members:
diff --git a/docs/source/smooth_finite_difference/_smooth_finite_difference.rst b/docs/source/smooth_finite_difference/_smooth_finite_difference.rst
diff --git a/docs/source/total_variation_regularization.rst b/docs/source/total_variation_regularization.rst
@@ -1,7 +1,5 @@
 total_variation_regularization
 ==============================
 
-.. toctree::
-   :maxdepth: 1
-
-   total_variation_regularization/_total_variation_regularization
+.. automodule:: pynumdiff.total_variation_regularization
+    :members:
diff --git a/docs/source/total_variation_regularization/_total_variation_regularization.rst b/docs/source/total_variation_regularization/_total_variation_regularization.rst
diff --git a/paper.bib b/paper.bib
@@ -225,7 +225,3 @@ @Misc{findiff
   year =      {2018},
   url = "https://github.com/maroba/findiff"
 }
-
-
-
-
diff --git a/paper.md b/paper.md
@@ -29,7 +29,7 @@ bibliography: paper.bib
 
 # Statement of need
 
-The numerical computation of derivatives is ubiquitous in every scientific discipline and engineering application because derivatives express fundamental relationships among many quantities of interest. As a result, a large number of diverse algorithms have been developed to differentiate numerical data.  These efforts are challenging because, in reality, practitioners  often have sparse and noisy measurements and data, which undermine the ability to estimate accurate derivatives.  Among the diversity of mathematical approaches that have been formulated, many are ad hoc in nature and require significant bespoke tuning of multiple parameters to produce reasonable results. Thus, at a practical level, it is often unclear which method should be used, how to choose parameters, and how to compare results from different methods. 
+The numerical computation of derivatives is ubiquitous in every scientific discipline and engineering application because derivatives express fundamental relationships among many quantities of interest. As a result, a large number of diverse algorithms have been developed to differentiate numerical data. These efforts are challenging because, in reality, practitioners often have sparse and noisy measurements and data, which undermine the ability to estimate accurate derivatives. Among the diversity of mathematical approaches that have been formulated, many are ad hoc in nature and require significant bespoke tuning of multiple parameters to produce reasonable results. Thus, at a practical level, it is often unclear which method should be used, how to choose parameters, and how to compare results from different methods.
 
 Regardless of application domain, scientists of various levels of mathematical expertise would benefit from a unified toolbox for differentiation techniques and parameter tuning. To address these needs, we built the open-source package `PyNumDiff`, with two primary goals in mind: (1) to develop a unified source for a diversity of differentiation methods using a common API, and (2) to provide an objective approach for choosing optimal parameters with a single universal hyperparameter (`gamma`) that functions similarly for all differentiation methods [@van2020numerical]. By filling these needs, `PyNumdiff` facilitates easy computations of derivatives on diverse time-series data sets.
 

diff --git a/pynumdiff/finite_difference/__init__.py b/pynumdiff/finite_difference/__init__.py
@@ -1,5 +1,5 @@
+"""This module implements some common finite difference schemes
 """
-Import useful functions from _finite_difference module
-"""
-from pynumdiff.finite_difference._finite_difference import first_order
-from pynumdiff.finite_difference._finite_difference import second_order
+from ._finite_difference import first_order, second_order
+
+__all__ = ['first_order', 'second_order'] # So these get treated as direct members of the module by sphinx
-Original file line number
+Diff line change
@@ Expand Up / @@ -116,3 +116,4 @@ __pycache__ @@
     dist
     *.whl
     .vscode
+    docs/build
Original file line number	Diff line number	Diff line change
Expand Up		@@ -225,7 +225,3 @@ @Misc{findiff
		year = {2018},
		url = "https://github.com/maroba/findiff"
		}