Release notes

Version 0.3.0

0.3.0 2026-01-20 Version 0.3.0 Has split the smftools dependencies into its core dependencies, as well as various optional dependencies depending on the user's intended use in order to keep the package as light as possible. The package can now use wither a CLI or a Python based backend for Samtools, Bedtools, and BedGraphToBigWig for smftools load functionality.

Version 0.2.3

0.2.3 2025-12-02 Version 0.2.3 provides the core smftools functionality through several command line commands (load, preprocess, spatial, hmm).

Version 0.2.1

0.2.1 2025-11-05 Version 0.2.1 makes the core workflow (smftools load) a command line tool that takes in an experiment_config.csv file for input/output and parameter management.

Version 0.1.6

0.1.6 2025-05-29 Informatics, preprocessing, tools, plotting modules have core functionality that is approaching stability on MacOS (Intel/Silicon) and Linux (Ubuntu). Documentation/tutorials are still being improved. The base PyTorch/Scikit-Learn ML-infrastructure is going through organizational changes to work with PyTorch Lightning, Hydra, and WanDB to facilitate scaling, multi-device usage, and logging.

Version 0.1.1

0.1.1 2024-09-09 The informatics module has been bumped to alpha-phase status. This module can deal with POD5s and unaligned BAMS from nanopore conversion and direct SMF experiments, as well as FASTQs from Illumina conversion SMF experiments. Primary output from this module is an AnnData object containing all relevant SMF data, which is compatible with all downstream smftools modules. The other modules are still in pre-alpha phase. Preprocessing, Tools, and Plotting modules should be promoted to alpha-phase within the next month or so.

Version 0.1.0

0.1.0 2024-08-30 smftools initial release. Pre-Alpha phase. J McKenna

Currently, this package (smftools-0.1.0) is going through rapid improvement (dependency handling accross Linux and Mac OS, testing, documentation, debugging) and is still too early in development for widespread use. The underlying functionality was originally developed as a collection of scripts for single molecule footprinting (SMF) experiments in our lab, but is being packaged/developed to facilitate the expansion of SMF to any lab that is interested in performing these styles of experiments/analyses. The alpha-phase package is expected to be available within a couple months, so stay tuned!