BETSE 1.4.1: The Resurrection of BETSE

[leycec]

Welcome to BETSE 1.4.1, the first stable release of BETSE in (almost exactly) two years! Let's model some bioelectricity. 🥳

Install All this Good Stuff! 👇

Like all prior BETSE releases, BETSE 1.4.1 is publicly available via both pip + PyPI and conda + @conda-forge. Pick your open-source packaging poison solution:

• "I choose pip!" Excellent choice. Everyone feels peppy with pip:

  pip install --upgrade betse

• "I choose conda!" Also excellent. You can't go wrong with reptiles:

  conda config --add channels conda-forge
  conda install betse

Verify That BETSE Still Behaves Itself! 👌

After upgrading to any new BETSE version (including BETSE 1.4.1), it's a great idea to validate that BETSE still behaves itself. Just run the betse try subcommand from a temporary directory you don't particularly care about: e.g.,

cd /tmp
betse try

You should see an animated plot of a sample bioelectric simulation subject to a cut profile (i.e., sudden removal of cells mimicking a tissue wound). If you see something other than that, see the "B-b-but Nothing Works..." section below. 😮‍💨

What's So Good about BETSE 1.4.1, Anyway? 🤔

Everything. Literally everything. BETSE 1.4.1 is a whole new computational beast.

Prior versions of BETSE (like BETSE 1.3.0) no longer run under a modern Python workflow. Incompatibilities with recent scientific dependencies (like NumPy 2.0.0, SciPy 1.14.0, and Matplotlib 3.9.0) render prior versions of BETSE all but unusable.

BETSE 1.4.1 resolves all outstanding issues, deprecations, exceptions, and warnings by:

• Requiring a modern version of CPython: CPython ≥ 3.11. 🌝
• Requiring recent versions of most scientific dependencies, including:
  • NumPy ≥ 2.0.0. ✔️
  • SciPy ≥ 1.14.0. ✔️
  • Matplotlib ≥ 3.9.0. ✔️
  • @beartype ≥ 0.18.0. ✔️
• Refactoring the BETSE build system from the antiquated setuptools + setup.py ^🤮 to Hatch + pyproject.toml. ^🥂
• Runtime type-checking the entire BETSE codebase with @beartype – a hyper-fast standards-compliant type-checker designed from the ground-up for scientific workloads. 😮

"B-b-but Nothing Works, Everything Is Busted, and My Paper Is Due in 5 Minutes!"

Having issues... again? Seeing a slew of exceptions? Drowning in a deluge of warnings? Fear not. We are here for you and your exciting research. Please submit:

• All issues and feature requests directly to our friendly issue tracker here on GitHub. Let us assuage your valid problems.
• All scientific inquiries and collaborative inspiration directly to Dr. Alexis Pietak at ResearchGate. Science!

This Is Where We Thank You 👏

The principal authors of BETSE – Dr. Alexis Pietak (@pietakio) and Cecil Curry (@leycec) – humbly thank everyone for your renewed interest in BETSE. Together, we will model all the bioelectricity.

We'd also like to congratulate Dr. Andre Norfleet on his recent explosive Cells 2024 submission: "Identification of Distinct, Quantitative Pattern Classes from Emergent Tissue-Scale hiPSC Bioelectric Properties". This super-exciting paper leverages BETSE to validate experimental bioelectric findings. Due in large part to this paper's high-profile inclusion in the Cells 2024 Special Issue "Multiscale Studies of Cell Behavior", we've fielded a sudden uptick of interest in using BETSE to validate similar findings and concern over the future well-being of BETSE.

Allow us to now say:

BETSE is here to stay.

And BETSE 1.4.1 is the proof in the bioelectric pudding.