Merge branch 'scipy-conference:2024' into Gagnon_Kebe_Tahiri

README.md

@@ -508,6 +508,7 @@ Editors should come to a final 'ready', 'unready' decision before the **Final Ed
    2. Posters presented at the poster session (posters)
    3. 30-minute talk slide decks (slides)
    4. SciPy tools plenary slide decks (tools)
+   5. 45-minute keynote slide decks (keynote)
 5. Choose the appropriate folder, and make a new directory inside it (it needs a unique name)
 6. Copy your slide deck or poster into the directory, and add a file called `info.json` with the following fields needed for uploading to Zenodo (using an empty string for author orcid or
    affiliation if these cannot be provided):

presentations/keynote/barnes-elizabeth/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942222
+  doi: 10.25080/yhec5334
+  id: fc57f03b-55fb-47d7-84e2-05b694a1958e
+  title: 'Explainable AI for Climate Science: Opening the Black Box to Reveal Planet Earth'
+  authors:
+    - name: Elizabeth A. Barnes
+      affiliation: Colorado State University
+      orcid: 0000-0003-4284-9320
+  abstract: 'Earth’s climate is chaotic and noisy. Finding usable signals amidst all of the noise can be challenging: be it predicting if it will rain, knowing which direction a hurricane will go, understanding the implications of melting Arctic ice, or detecting the impacts of humans on the earth’s surface. Here, I will demonstrate how explainable artificial intelligence (XAI) techniques can sift through vast amounts of climate data and push the bounds of scientific discovery: allowing scientists to ask "why?" but now with the power of machine learning.'
+  downloads:
+    - title: Presentation
+      file: BARNES_SciPy_July_11_2024.pdf

presentations/keynote/cranmer-kyle/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942226
+  doi: 10.25080/rkcg9834
+  id: 9e80aadb-92e3-466b-a165-38e84ac415df
+  title: Particles, People, and Pull Requests
+  authors:
+    - name: Kyle Cranmer
+      affiliation: University of Wisconsin-Madison
+      orcid: 0000-0002-5769-7094
+  abstract: I will tell the story of how the statistical challenges in the search for the Higgs boson and exotic new physics at the Large Hadron Collider led to new approaches to collaborative, open science. The story centers around computational and sociological challenges where software and cyberinfrastructure play a key role. I will highlight a few important changes in perspective that were critical for progress including embracing declarative specifications, pivoting from reproducibility to reuse, and the abstraction that led to the field of simulation-based inference.
+  downloads:
+    - title: Presentation
+      file: Cranmer-Kyle-Keynote-SciPy-2024.pdf

presentations/keynote/silge-julia/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942230
+  doi: 10.25080/xwen4438
+  id: 3f27f4d7-7bd1-4dde-aa01-e23948d812b8
+  title: The Right Tool for the Job
+  authors:
+    - name: Julia Silge
+      affiliation: Posit PBC
+      orcid: 0000-0002-3671-836X
+  abstract: There are many programming languages that we might choose for scientific computing, and we each bring a complex set of preferences and experiences to such a decision. There are significant barriers to learning about other programming languages outside our comfort zone, and seeing another person or community make a different choice can be baffling. In this talk, hear about the costs that arise from exploring or using multiple programming languages, what we can gain by being open to different languages, and how curiosity and interest in other programming languages supports sharing across communities. We’ll explore these three points with practical examples from software built for flexible storage and model deployment, as well as a brand new project for scientific computing.
+  downloads:
+    - title: Presentation
+      file: silge-scipy-2024.pdf

presentations/lightning/deploying-python-environments-on-top-of-mt-rainier/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942232
+  doi: 10.25080/pyyu4582
+  id: 5c188d79-98e7-47de-93a4-56004e6fef94
+  title: Deploying Python environments on top of Mt. Rainier
+  authors:
+    - name: Benoit Hamelin
+      affiliation: Tutte Institute for Mathematics and Computing
+      orcid: 0000-0001-7333-5635
+  abstract: A process for building preparing artifacts that enable the deployment of a Python computing environment in a place where there is no Internet access.
+  downloads:
+    - title: Presentation
+      file: Deploying Python Environments on top of Mt. Rainier.pdf

presentations/lightning/hello_project/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942234
+  doi: 10.25080/hxxk4957
+  id: 3d7cb8ab-ca5c-4c6c-87ee-8f651222d1ed
+  title: Hello Project!
+  authors:
+    - name: Hannah Aizenman
+      affiliation: matplotlib
+      orcid: 0000-0002-4622-4427
+  abstract: tips for onboarding into contributing to open source
+  downloads:
+    - title: Presentation
+      file: hello_project.pdf

presentations/lightning/josh_borrow/myst.yml

@@ -0,0 +1,17 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942236
+  doi: 10.25080/uncn2995
+  id: e1544942-b8cd-41b0-ad88-5cd4646f5284
+  title: 'swiftascmaps: A colour map library for swifties'
+  authors:
+    - name: Josh Borrow
+      affiliation: Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA, USA 19104
+      orcid: 0000-0002-1327-1921
+  abstract: A hopefully comedic talk about the colour map library swiftascmaps.
+  downloads:
+    - title: Presentation
+      file: lightning.pdf
+    - title: Keynote File
+      file: lightning.key

presentations/lightning/kerr_sciris/myst.yml

@@ -0,0 +1,21 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942240
+  doi: 10.25080/knjj9332
+  id: 4aa53d70-2bac-4267-a3ea-767403e22581
+  title: 'Sciris: Simplifying scientific Python'
+  authors:
+    - name: Cliff Kerr
+      affiliation: Bill & Melinda Gates Foundation
+      orcid: 0000-0003-2517-2354
+    - name: Paula Sanz-Leon
+      affiliation: Bill & Melinda Gates Foundation
+      orcid: 0000-0002-1545-6380
+    - name: Romesh Abeysuriya
+      affiliation: Burnet Institute
+      orcid: 0000-0002-9618-6457
+  abstract: Sciris aims to streamline the development of scientific Python code by making it easier to perform common tasks. This example illustrates how the same block of fairly typical scientific Python code -- which performs tasks like collecting data from a function running in parallel, saving and loading files, and 3D plotting -- looks like when written in 'vanilla Python' compared to using Sciris.
+  downloads:
+    - title: Presentation
+      file: kerr_sciris.pdf

presentations/lightning/matplotlib-slides/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942242
+  doi: 10.25080/wrvp6756
+  id: 0701ae97-90ba-43bd-b9c2-8060940b836b
+  title: Plotting Slides in Matplotlib
+  authors:
+    - name: Elliott Sales de Andrade
+      affiliation: Matplotlib
+      orcid: 0000-0001-7310-8942
+  abstract: Matplotlib makes easy things easy and hard things possible, like this silly idea of making slides in it.
+  downloads:
+    - title: Presentation
+      file: scipy2024-lightning-mpl-slide.pdf

presentations/lightning/python_evangelist/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942244
+  doi: 10.25080/hcya9443
+  id: b0a9bfa5-f253-4dd7-96d0-c7c89a5c3b61
+  title: For the python evangelist
+  authors:
+    - name: Christine Smit
+      affiliation: National Aeronautics and Space Administration
+      orcid: 0000-0002-3135-1191
+  abstract: Because clearly python needs to make music.
+  downloads:
+    - title: Presentation
+      file: Christine_lightening.pdf

presentations/lightning/renovate-automating-dependency-management/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942246
+  doi: 10.25080/tkky5633
+  id: 11d24ef3-1f88-4d19-9bfb-63472ddaff14
+  title: 'Renovate: Automating Dependency Management'
+  authors:
+    - name: Patrick J. Roddy
+      affiliation: University College London
+      orcid: 0000-0002-6271-1700
+  abstract: A brief introduction to Renovate, a tool for automating dependency management in software projects. The slides can be accessed at https://paddyroddy.github.io/talks/renovate-automating-dependency-management. Two example parent configurations I maintain are available at https://github.com/paddyroddy/.github/tree/main/renovate and https://github.com/UCL-ARC/.github/tree/main/renovate.
+  downloads:
+    - title: Presentation
+      file: renovate_automating_dependency_management.pdf

presentations/posters/Alireza_Vaezi/myst.yml

@@ -0,0 +1,18 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942248
+  doi: 10.25080/hfew4757
+  id: 6575c943-0901-4861-9f1a-cf3a5e3f806a
+  title: Training a Supervised Cilia Segmentation Model from Self-Supervision
+  authors:
+    - name: Seyed Alireza Vaezi
+      affiliation: University of Georgia
+      orcid: 0009-0000-2089-8362
+    - name: Shannon Quinn
+      affiliation: University of Georgia
+      orcid: 0000-0002-8916-6335
+  abstract: Understanding cilia behavior is essential in diagnosing and treating such diseases. But, the tasks of automatically analysing cilia are often a labor and time-intensive since there is a lack of automated segmentation. In this work we overcome this bottleneck by developing a robust, self-supervised framework exploiting the visual similarity of normal and dysfunctional cilia. This framework generates pseudolabels from optical flow motion vectors, which serve as training data for a semi-supervised neural network. Our approach eliminates the need for manual annotations, enabling accurate and efficient segmentation of both motile and immotile cilia.
+  downloads:
+    - title: Poster
+      file: Scipy_2024 Cilia Poster.pdf

presentations/posters/Domovyk_Multilingual Transliteration for Cyrillic Text/myst.yml

@@ -0,0 +1,15 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942250
+  doi: 10.25080/udkt5322
+  id: b137c86a-4875-4e44-bedd-8847110ee41a
+  title: 'Domovyk: Multilingual Transliteration for Cyrillic Text'
+  authors:
+    - name: Ian Goodale
+      affiliation: UT-Austin
+      orcid: 0000-0002-6685-2949
+  abstract: The Domovyk package provides transliteration to and from Cyrillic alphabets in a way that addresses some limitations in existing packages, providing multilingual functionality, support for composite Unicode characters, and support for languages not addressed in other packages, such as Church Slavonic and Carpatho-Rusyn. Domovyk aims to increase the accessibility of transliteration technologies for users working in these languages, focusing on use cases that require thorough and accurate transliteration.
+  downloads:
+    - title: Poster
+      file: Goodale_Domovyk_Poster.pdf

presentations/posters/KaufmanEtAl-ncompare/myst.yml

@@ -0,0 +1,21 @@
+version: 1
+extends: ../../proceedings.yml
+project:
+  zenodo: https://zenodo.org/records/13942252
+  doi: 10.25080/etnj4973
+  id: 5a265c77-7eab-4d75-96dd-57176d13420a
+  title: 'ncompare: A Python Package for Comparing netCDF Structures'
+  authors:
+    - name: Daniel E. Kaufman
+      affiliation: NASA Langley Research Center, Atmospheric Science Data Center, Hampton, VA, USA; Booz Allen Hamilton, Inc.
+      orcid: 0000-0002-1487-7298
+    - name: Walter E. Baskin
+      affiliation: NASA Langley Research Center, Atmospheric Science Data Center, Hampton, VA, USA; Adnet Systems, Inc.
+      orcid: 0000-0002-2241-3266
+    - name: Julia S. Lowndes
+      affiliation: Openscapes, Santa Barbara, California, USA
+      orcid: 0000-0003-1682-3872
+  abstract: As netCDF (Network Common Data Form) files are widely used in Earth science — with climate models, oceanographic or atmospheric reanalyses, and observational data — improved means of evaluating netCDF files can help enable a wide range of applications. We have developed a reusable open source approach through `ncompare`, which is a Python package for comparing netCDF structures. `ncompare` facilitates rapid comparisons by generating a formatted display of the matching and non-matching groups, variables, and associated metadata between two NetCDF datasets. The user has the option to colorize the terminal output for ease of viewing, and `ncompare` can optionally save comparison reports in text, comma-separated value (CSV), and/or Microsoft Excel formats.
+  downloads:
+    - title: Poster
+      file: Poster_for_SciPy_July2024_ncompare.pdf