February 2025 Project Updates

Sponsored Projects

PyBAMM

• We have published a new release 25.1.
• We had the very first PyBaMM conference 5th-6th of February in London. The conference had over 130 attendees from all over the world and seven plenary speakers from UK, US, Germany, China and Sweden.

Bokeh

• 3.6.3 released with some performance bugs resolved
• New CZI wrap-up blog post: https://blog.bokeh.org/bokeh-for-bioscience-1e8ec629dd5a
• 3.7 release coming later this month

MDAnalysis

• MDAnalysis has elected 3 new Core Developers: Brady Johnston, Egor Marin, and Paul Smith. An introduction to each of the new Core Developers and a description of the process for electing Core Developers are provided on our blog: https://www.mdanalysis.org/2025/02/14/new_coredevs/.
• A new technical writer, Namir Oues, has been hired to reorganize and consolidate MDAnalysis documentation as part of a project funded by a NumFocus Small Development Grant: https://www.mdanalysis.org/2025/02/11/sdg23-writer/.

One of MDAnalysis’s Google Summer of Code (GSoC) 2024 students, Luna Morrow, shared her GSoC accomplishments in a blog post: https://www.mdanalysis.org/2025/02/11/gsoc2024-final-lg/. MDAnalysis developers have been busy applying for consideration as a host organization for the GSoC 2025 program.

ITK

🎉 ITK 5.4.2 is Now Available!
🔑 Key Improvements

• Enhanced Segmentation Workflows: Improved LabelUniqueLabelMapFilter behavior for more reliable label map handling.
• Modern Library Compatibility: Updates for seamless integration with recent libtiff versions.
• High-Dimensional Data Support: Expanded VectorImage capabilities to optimize large dataset processing.
• Performance Boost: Resolved thread-based parallelism issues in the SLIC filter.
• Cross-Platform Stability: Build system updates and compiler fixes for smoother multi-environment workflows.

🚀 What’s Next?
The community is actively preparing for ITK 6, featuring architectural modernization and streamlined builds. Stay tuned for alpha/beta releases alongside continued 5.4.x maintenance.

🙌 Thank You!
A huge thanks to all contributors for their code, testing, and documentation efforts.

👉 Explore ITK 5.4.2:
• Release Notes: https://docs.itk.org/en/latest/releases/5.4.2.html
• GitHub Release: https://github.com/InsightSoftwareConsortium/ITK/releases/tag/v5.4.2

Affiliated Project Updates

Open2C

Updates:

• Open2C recently moved to Discord (from slack), here’s our invite link: https://discord.com/invite/qVfSbDYHNG
• Open2C was one of the host organizations for Google Summer of Code in 2024, hopefully will be hosting again in 2025, https://summerofcode.withgoogle.com/programs/2024/organizations/open-chromosome-collective
• Open2C was introduced at ISMB-BOSC 2024, https://www.youtube.com/watch?v=Fj8qoLirOfY

Open2C published three impactful articles

• Open2C, Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, et al. (2024) Pairtools: From sequencing data to chromosome contacts. PLOS Computational Biology 20(5): e1012164. https://doi.org/10.1371/journal.pcbi.1012164
• Open2C, Abdennur N, Abraham S, Fudenberg G, Flyamer IM, et al. (2024) Cooltools: Enabling high-resolution Hi-C analysis in Python. PLOS Computational Biology 20(5): e1012067. https://doi.org/10.1371/journal.pcbi.1012067
• Open2C, Abdennur N, Abraham S, Fudenberg G, Flyamer IM, et al. (2024) Bioframe: operations on genomic intervals in Pandas dataframes, Bioinformatics, Volume 40, Issue 2, February 2024, btae088, https://doi.org/10.1093/bioinformatics/btae088

Milestones for Open2C

As the year began, our four most popular packages were granted NumFOCUS affiliation.

• Bioframe brings genomic interval operations natively to Pandas DataFrames. This is in contrast to the file-centric approach of the canonical CLI program, bedtools. Bioframe is therefore similar to GenomicRanges in the R/Bioconductor ecosystem, but operates directly on data frames rather than specialized data structures or wrapper objects.
• Pairtools is a critical suite of command line tools for processing and interpreting sequence alignments from proximity ligation NGS assays, like Hi-C.
• Cooler is a scalable file format and support package for storing multi-scale contact matrices and other genomic interaction maps.
• Cooltools provides common downstream analysis for Hi-C data.

“2024 was an eventful year for Open2C. For those not in the know, the Open Chromosome Collective (Open2C) is a collaborative community that several colleagues and I spun out of the interconnected software packages we had co-developed, most of us originally as graduate students. Our libraries focus on the processing and analysis of data from Chromosome Conformation Capture (3C/Hi-C) and related 3D genomics technologies, leveraging the Python data ecosystem. We also develop tools to support functional genomics analysis more broadly.” — Nezar Abdennur, Assistant Professor of Genomics and Computational Biology at UMass Chan

Read more about Open2C Year-in-Review here

BOSC2024 S1f Vedat Yilmaz, Open2C: Advancing 3D and functional genomics research

PyLops

The PyLops development team has delivered 3 major releases at the end of 2024 and a number additional milestones have been achieved:

PyLops core library (v2.4.0)

• A new operator called PyTensorOperator has been introduced to convert any PyLops LinearOperator into a PyTensor Op, ultimately enabling users to perform probabilistic programming via PyMC.
• A new operator called ToCupy has been introduced to allow users to solve out-of-GPU inverse problems whist still applying some of the operator’s forward and adjoint computations on the GPU — more details can be found in this Medium blog post.
• A new operator called JaxOperator has been created allowing users to run almost any PyLop’s operators on JAX arrays.
• A N-Dimensional Wavelet operator called DWTND has been contributed by solldavid (first time contributor)
• The entire suite of PyLops’ sliding and patching operators have been revamped leading to more efficient and less memory hungry implementations — see https://github.com/PyLops/pylops_slidingpatching for a detailed benchmark.

PyProximal (v0.10.0):

• Added AndersonProximalGradient solver
• Added iPALM solver
• Added gradtest_proximal and gradtest_bilinear methods to help user’s checking for correctness of their gradient implementations for Proximal and Bilinear operators.

PyLops-mpi (v0.2.1):

• Added support for using CuPy arrays with PyLops-MPI — enabling users to solve their inverse problems on multi-GPU systems (see again our Medium blog post for details).
• Published paper describing the development of the library and main design choices in great details object.
• Introduced the UNSAFE_BROADCAST partition to give users an option to handle overflow in broadcast scenarios.
• Added dottest routine to check the validity of distributed operators.
• Enabled 2D-distribution using sub-communicators as detailed in this PR.

AiiDA

• We successfully completed a “hero run” on the new Swiss supercomputer, occupying it entirely for about 20 hours with calculations managed remotely by AiiDA’s software tools. [Learn more here].
• We have pre-released alpha version (24.10.0a7) of [AiiDAlab-QE], which uses AiiDA as its backend. This makes it possible for experimentalist to run complex material simulations directly from their browsers.
• We launched our new blog system and are publishing weekly technical posts about AiiDA at [this link]. Our latest post highlights how the AiiDA engine works and includes tips on debugging.

Mesa

Mesa — Agent Based Modeling in Python

For our February 2025 update Mesa is proud to release Mesa 3.1.4 and we have submitted our application for Google Summer of Code! We will know by February 26th, if we were selected. Interested in being a contributor? Check out our idea list.

Also of significance Mesa 3.1.4 had three new first time contributors!

Highlights

Mesa 3.1.4 contains various improvements and bug fixes to the matplotlib-based visualization of spaces. Hexgrids are now fully supported, including property layers. In making this possible, various minor bugs were encountered and also fixed. In addition to the visualization improvements, there are various minor convenience improvements to the docs

What’s Changed

🛠 Enhancements made

• Fixed hex-space draw function to avoid overlaps by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2609
• Fix: Property layer visualization for HexGrid by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2646
• Enhance DataCollector to validate model_reporters functions by @peter-kinger in https://github.com/projectmesa/mesa/pull/2605
• Implemented post_process in Altair based components by @sanika-n in https://github.com/projectmesa/mesa/pull/2641

🐛 Bugs fixed

• bugfix for draw_property_layer by @quaquel in https://github.com/projectmesa/mesa/pull/2639
• Uses array for hex grid property layer fix by @Sahil-Chhoker in https://github.com/projectmesa/mesa/pull/2651
• Update Binder environment to use latest Mesa version (#2652) by @aarav-shukla07 in https://github.com/projectmesa/mesa/pull/2655
• Change Hexgrid._connect_cells_2d to use x,y coordinates by @quaquel in https://github.com/projectmesa/mesa/pull/2632

🔍 Examples updated

• Added property layer viz to sugarscape by @sanika-n in https://github.com/projectmesa/mesa/pull/2653
• added color-bar for spice by @sanika-n in https://github.com/projectmesa/mesa/pull/2622

📜 Documentation improvements

• remove any reference to using — pre by @quaquel in https://github.com/projectmesa/mesa/pull/2618
• Updated Docs by @sanika-n in https://github.com/projectmesa/mesa/pull/2624
• Fixed 404 error for Examples Tab in Introductory Tutorial (#2662) by @aarav-shukla07 in https://github.com/projectmesa/mesa/pull/2664
• Documentation by @Spartan-71 in https://github.com/projectmesa/mesa/pull/2630
• Adding a copy option at the top of the code written in the docs by @PrashantChoudhary13579 in https://github.com/projectmesa/mesa/pull/2628
• Adding Mesa Extension page by @PrashantChoudhary13579 in https://github.com/projectmesa/mesa/pull/2627

🔧 Maintenance

• remove remnants of mesa cli by @quaquel in https://github.com/projectmesa/mesa/pull/2617
• benchmarks.yml: Install SciPy and use uv for pip install by @EwoutH in https://github.com/projectmesa/mesa/pull/2633

New Contributors

• PrashantChoudhary13579 made their first contribution in https://github.com/projectmesa/mesa/pull/2628
• aarav-shukla07 made their first contribution in https://github.com/projectmesa/mesa/pull/2655
• peter-kinger made their first contribution in https://github.com/projectmesa/mesa/pull/2605

Full Changelog: https://github.com/projectmesa/mesa/compare/v3.1.3...v3.1.4

Please reach out on our Matrix Channel

GeomScale

🔬 GeomScale is an open-source research and development project focused on cutting-edge algorithms at the intersection of data science, optimization, geometry, and statistical computing.

📰 Latest News

📣 Google Summer of Code 2025
📝 We’ve applied once again to participate as a mentoring organization in Google Summer of Code (GSoC) 2025!

• 📌 All activities will be coordinated through our wiki page: https://github.com/GeomScale/gsoc25/wiki
• 💡 Interested mentors? Help us expand our project ideas page: https://github.com/GeomScale/gsoc25/wiki/table-of-proposed-coding-projects

🎤 FOSDEM 2025 Talk
✅ We have participated in FOSDEM 2025 with a talk on “volesti: Sampling Efficiently from High-Dimensional Distributions.”
📂 Resources:

• 📄 Slides, tutorials, and the talk video are available here: https://fosdem.org/2025/schedule/event/fosdem-2025-5219-volesti-sampling-efficiently-from-high-dimensional-distributions/

💬 Stay Connected!
🌐 Explore our work on GitHub: https://github.com/GeomScale/

Code of Conduct

NumFOCUS’s new Code of Conduct (CoC) is officially in effect. This comes after the NumFOCUS Board of Directors approved the new CoC on September 4, 2024, and after we established the NumFOCUS Code of Conduct Working Group (NF CoC WG) on December 16, 2024. The new policy reaffirms our commitment to fostering a safe, equitable, and welcoming environment for all individuals, regardless of their background or identity.

Please take a look here.