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Proceedings of the 19th Python in Science Conference (SciPy 2020)

Meghann Agarwal, Chris Calloway, Dillon Niederhut, David Shupe

July 6 - July 12

Austin, Texas


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Preface 1
Meghann Agarwal, Julie Hollek, Dillon Niederhut

Securing Your Collaborative Jupyter Notebooks in the Cloud using Container and Load Balancing Services 2
Haw-minn Lu, Adrian Kwong, José Unpingco

Quasi-orthonormal Encoding for Machine Learning Applications 11
Haw-minn Lu

Fluctuation X-ray Scattering real-time app 18
Antoine Dujardin, Elliott Slaugther, Jeffrey Donatelli, Peter Zwart, Amedeo Perazzo, Chun Hong Yoon

HOOMD-blue version 3.0 A Modern, Extensible, Flexible, Object-Oriented API for Molecular Simulations 24
Brandon L. Butler, Vyas Ramasubramani, Joshua A. Anderson, Sharon C. Glotzer

Compyle: a Python package for parallel computing 32
Aditya Bhosale, Prabhu Ramachandran

Netlist Analysis and Transformations Using SpyDrNet 40
Dallin Skouson, Andrew Keller, Michael Wirthlin

Introduction to Geometric Learning in Python with Geomstats 48
Nina Miolane, Nicolas Guigui, Hadi Zaatiti, Christian Shewmake, Hatem Hajri, Daniel Brooks, Alice Le Brigant, Johan Mathe, Benjamin Hou, Yann Thanwerdas, Stefan Heyder, Olivier Peltre, Niklas Koep, Yann Cabanes, Thomas Gerald, Paul Chauchat, Bernhard Kainz, Claire Donnat, Susan Holmes, Xavier Pennec

Network visualizations with Pyvis and VisJS 58
Giancarlo Perrone, Jose Unpingco, Haw-minn Lu

Boost-histogram: High-Performance Histograms as Objects 63
Henry Schreiner, Hans Dembinski, Shuo Liu, Jim Pivarski

Learning from evolving data streams 70
Jacob Montiel

Awkward Array: JSON-like data, NumPy-like idioms 78
Jim Pivarski, Ianna Osborne, Pratyush Das, Anish Biswas, Peter Elmer

High-performance operator evaluations with ease of use: libCEED's Python interface 85
Valeria Barra, Jed Brown, Jeremy Thompson, Yohann Dudouit

Spectral Analysis of Mitochondrial Dynamics: A Graph-Theoretic Approach to Understanding Subcellular Pathology 91
Marcus Hill, Mojtaba Fazli, Rachel Mattson, Meekail Zain, Andrew Durden, Allyson T Loy, Barbara Reaves, Abigail Courtney, Frederick D Quinn, S Chakra Chennubhotla, Shannon P Quinn

Matched Filter Mismatch Losses in MPSK and MQAM Using Semi-Analytic BEP Modeling 98
Mark Wickert, David Peckham

Having your cake and eating it: Exploiting Python for programmer productivity and performance on micro-core architectures using ePython 107
Maurice Jamieson, Nick Brown, Sihang Liu

pandera: Statistical Data Validation of Pandas Dataframes 116
Niels Bantilan

Combining Physics-Based and Data-Driven Modeling for Pressure Prediction in Well Construction 125
Oney Erge, Eric van Oort

Pydra - a flexible and lightweight dataflow engine for scientific analyses 132
Dorota Jarecka, Mathias Goncalves, Christopher J. Markiewicz, Oscar Esteban, Nicole Lo, Jakub Kaczmarzyk, Satrajit Ghosh

Leading magnetic fusion energy science into the big-and-fast data lane 140
Ralph Kube, R Michael Churchill, Jong Youl Choi, Ruonan Wang, Scott Klasky, CS Chang, Minjun J. Choi, Jinseop Park

SHADOW: A workflow scheduling algorithm reference and testing framework 148
Ryan W. Bunney, Andreas Wicenec, Mark Reynolds

Software Engineering as Research Method: Aligning Roles in Econ-ARK 156
Sebastian Benthall, Mridul Seth

Falsify your Software: validating scientific code with property-based testing 162
Zac Hatfield-Dodds

Towards an Unsupervised Spatiotemporal Representation of Cilia Video Using A Modular Generative Pipeline 166
Meekail Zain, Sonia Rao, Nathan Safir, Quinn Wyner, Isabella Humphrey, Alex Eldridge, Chenxiao Li, BahaaEddin AlAila, Shannon Quinn