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Proceedings of the 21st Python in Science Conference (SciPy 2022)

Meghann Agarwal, Chris Calloway, Dillon Niederhut, David Shupe

July 11 - July 17

Austin, Texas


Organizers | Posters and Slides | Sponsored Students


The Advanced Scientific Data Format (ASDF): An Update 1
Perry Greenfield, Edward Slavich, William Jamieson, Nadia Dencheva

Semi-Supervised Semantic Annotator (S3A): Toward Efficient Semantic Labeling 7
Nathan Jessurun, Daniel E. Capecci, Olivia P. Dizon-Paradis, Damon L. Woodard, Navid Asadizanjani

Galyleo: A General-Purpose Extensible Visualization Solution 13
Rick McGeer, Andreas Bergen, Mahdiyar Biazi, Matt Hemmings, Robin Schreiber

USACE Coastal Engineering Toolkit and a Method of Creating a Web-Based Application 22
Amanda Catlett, Theresa R. Coumbe, Scott D. Christensen, Mary A. Byrant

Search for Extraterrestrial Intelligence: GPU Accelerated TurboSETI 26
Luigi Cruz, Wael Farah, Richard Elkins

Experience report of physics-informed neural networks in fluid simulations: pitfalls and frustration 28
Pi-Yueh Chuang, Lorena A. Barba

atoMEC: An open-source average-atom Python code 37
Timothy J. Callow, Daniel Kotik, Eli Kraisler, Attila Cangi

Automatic random variate generation in Python 46
Christoph Baumgarten, Tirth Patel

Utilizing SciPy and other open source packages to provide a powerful API for materials manipulation in the Schrödinger Materials Suite 52
Alexandr Fonari, Farshad Fallah, Michael Rauch

A Novel Pipeline for Cell Instance Segmentation, Tracking and Motility Classification of Toxoplasma Gondii in 3D Space 60
Seyed Alireza Vaezi, Gianni Orlando, Mojtaba Fazli, Gary Ward, Silvia Moreno, Shannon Quinn

The myth of the normal curve and what to do about it 64
Allan Campopiano

Python for Global Applications: teaching scientific Python in context to law and diplomacy students 69
Anna Haensch, Karin Knudson

Papyri: better documentation for the scientific ecosystem in Jupyter 75
Matthias Bussonnier, Camille Carvalho

Bayesian Estimation and Forecasting of Time Series in statsmodels 83
Chad Fulton

Python vs. the pandemic: a case study in high-stakes software development 90
Cliff C. Kerr, Robyn M. Stuart, Dina Mistry, Romesh G. Abeysuriya, Jamie A. Cohen, Lauren George, Michał Jastrzebski, Michael Famulare, Edward Wenger, Daniel J. Klein

Pylira: deconvolution of images in the presence of Poisson noise 98
Axel Donath, Aneta Siemiginowska, Vinay Kashyap, Douglas Burke, Karthik Reddy Solipuram, David van Dyk

Codebraid Preview for VS Code: Pandoc Markdown Preview with Jupyter Kernels 105
Geoffrey M. Poore

Incorporating Task-Agnostic Information in Task-Based Active Learning Using a Variational Autoencoder 110
Curtis Godwin, Meekail Zain, Nathan Safir, Bella Humphrey, Shannon P Quinn

Awkward Packaging: building Scikit-HEP 115
Henry Schreiner, Jim Pivarski, Eduardo Rodrigues

Keeping your Jupyter notebook code quality bar high (and production ready) with Ploomber 121
Ido Michael

Likeness: a toolkit for connecting the social fabric of place to human dynamics 125
Joseph V. Tuccillo, James D. Gaboardi

poliastro: a Python library for interactive astrodynamics 136
Juan Luis Cano Rodríguez, Jorge Martínez Garrido

A New Python API for Webots Robotics Simulations 147
Justin C. Fisher

pyAudioProcessing: Audio Processing, Feature Extraction, and Machine Learning Modeling 152
Jyotika Singh

Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2 159
Aleksandr Koshkarov, Wanlin Li, My-Linh Luu, Nadia Tahiri

Global optimization software library for research and education 167
Nadia Udler

Temporal Word Embeddings Analysis for Disease Prevention 171
Nathan Jacobi, Ivan Mo, Albert You, Krishi Kishore, Zane Page, Shannon P. Quinn, Tim Heckman

Design of a Scientific Data Analysis Support Platform 179
Nathan Martindale, Jason Hite, Scott Stewart, Mark Adams

The Geoscience Community Analysis Toolkit: An Open Development, Community Driven Toolkit in the Scientific Python Ecosystem 187
Orhan Eroglu, Anissa Zacharias, Michaela Sizemore, Alea Kootz, Heather Craker, John Clyne

popmon: Analysis Package for Dataset Shift Detection 194
Simon Brugman, Tomas Sostak, Pradyot Patil, Max Baak

pyDAMPF: a Python package for modeling mechanical properties of hygroscopic materials under interaction with a nanoprobe 202
Willy Menacho, Gonzalo Marcelo Ramírez-Ávila, Horacio V. Guzman

Improving PyDDA's atmospheric wind retrievals using automatic differentiation and Augmented Lagrangian methods 210
Robert Jackson, Rebecca Gjini, Sri Hari Krishna Narayanan, Matt Menickelly, Paul Hovland, Jan Hückelheim, Scott Collis

RocketPy: Combining Open-Source and Scientific Libraries to Make the Space Sector More Modern and Accessible 217
João Lemes Gribel Soares, Mateus Stano Junqueira, Oscar Mauricio Prada Ramirez, Patrick Sampaio dos Santos Brandão, Adriano Augusto Antongiovanni, Guilherme Fernandes Alves, Giovani Hidalgo Ceotto

Wailord: Parsers and Reproducibility for Quantum Chemistry 226
Rohit Goswami

Variational Autoencoders For Semi-Supervised Deep Metric Learning 231
Nathan Safir, Meekail Zain, Curtis Godwin, Eric Miller, Bella Humphrey, Shannon P Quinn

A Python Pipeline for Rapid Application Development (RAD) 240
Scott D. Christensen, Marvin S. Brown, Robert B. Haehnel, Joshua Q. Church, Amanda Catlett, Dallon C. Schofield, Quyen T. Brannon, Stacy T. Smith

Monaco: A Monte Carlo Library for Performing Uncertainty and Sensitivity Analyses 244
W. Scott Shambaugh

Enabling Active Learning Pedagogy and Insight Mining with a Grammar of Model Analysis 251
Zachary del Rosario

Low Level Feature Extraction for Cilia Segmentation 259
Meekail Zain, Eric Miller, Shannon P Quinn, Cecilia Lo