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AlexandrovLab / SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
BSD 2-Clause "Simplified" License
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Changelog #246

Open IanVermes opened 2 months ago

IanVermes commented 2 months ago

Would you consider including a changelog to describe the significant changes between each release (major release, minor and subversion). It would help with deciding the upgrade strategy for our installations of SPE in long running projects.

We are currently pinned to 1.1.21, a changelog would help determine whether we can upgrade or not.

Edit: Perhaps you could use your existing release notes to help write a changelog file?

mdbarnesUCSD commented 1 month ago

Hi @IanVermes,

Thanks for reaching about this. We have decided that we will introduce a changelog into our repositories to help communicate the changes across versions moving forward.

Regarding your pinned v1.1.21 SigProfilerExtractor version, here are some things worth noting: v1.1.22: SBS4608 plotting was added for de novo signatures v1.1.23: COSMIC v3.4 signatures parameters set by default v1.1.24: Input processing for matrices was added

Importantly too though, when SigProfilerAssignment was updated to v0.1.0 COSMIC v3.4 signatures were added. The v1.1.21 release of SigProfilerExtractor does not require this version, so in your installation you may be using an older version of SigProfilerAssignment.