v0.4.5

Changed

• Documentation and tutorials follow the current workflows. Standardize terminology,
  technical notation, citations, and DOI links; update supported search-tool information
  and framework figures. Add a Verification tutorial, start DE and PTM from processed
  checkpoints, and integrate FlashLFQ as an optional DDA-LFQ example. Remove Quick start
  and the standalone FlashLFQ tutorial.
• Expected processing diagnostics use DEBUG. Per-block normalization details and
  notices about SDRF columns that cannot be projected onto .obs no longer appear at
  the default logging level. Other warnings remain unchanged.

Fixed

• Loading H5MU preserves its recorded history. read_h5mu() no longer adds a
  processing event, computes provenance hashes, or collects the current environment.
• Relocating unchanged input files preserves newly recorded data hashes. Readers
  keep source locations in provenance instead of duplicating them in search-result
  .uns or SDRF DataFrame.attrs. Local string file inputs are declared explicitly
  with file_inputs; URLs and Path objects remain detected directly. Custom
  @mm.pv.log functions must declare local string file arguments with
  file_inputs=("argument_name",).

The msmu-v2 hashing policy is unchanged, but removing duplicated source-path metadata
changes the content of newly imported data. Replaying an older checkpoint with the new
readers can therefore fail its recorded output-hash check. Use the recorded original
environment or regenerate the reference with the current version. Existing hashes are
not rewritten.

Merged pull requests

What's Changed

• BID-374 Stop recording provenance for H5MU reads by @jlthepi in #68
• BID-384 Lower normalisation block diagnostics to DEBUG by @jlthepi in #70
• BID-385 Keep source paths only in provenance by @jlthepi in #71
• BID-383 Refresh documentation and streamline analysis tutorials by @jlthepi in #72
• BID-386 Prepare msmu 0.4.5 release by @jlthepi in #73
• BID-386 Release msmu 0.4.5 by @jlthepi in #74

Full Changelog: v0.4.4...v0.4.5