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refactor: residual coverage, uv, and migration - #2

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TomasBalak wants to merge 36 commits into

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refactor/residual-coverage-and-uv

Closed

refactor: residual coverage, uv, and migration #2
TomasBalak wants to merge 36 commits into
masterfrom
refactor/residual-coverage-and-uv

Commits on Jan 27, 2026
- refactor: replace coverage with number of examined and flagged pixels
  TomasBalak
  committed
  92d1e97
- docs: update documentation for residual artifacts
  TomasBalak
  committed
  1b53925
- chore: add link to the documentation
  TomasBalak
  committed
  ed64162
- fix: ruff errors in piqe.py
  TomasBalak
  committed
  18bec80
- chore: change staining lib branch to prevent resolution errors + proper python target in lock file
  TomasBalak
  committed
  68e4b6a
- chore: change version of the staining lib
  TomasBalak
  committed
  75180b6
- refactor: update to the staining library refactor
  TomasBalak
  committed
  940c689
- docs: cleanup and update the examples
  TomasBalak
  committed
  a61ce3b
- chore: increase version and extend author list
  TomasBalak
  committed
  f20b443
- chore: update staining library
  TomasBalak
  committed
  95fec26
- chore: change from pdm to uv
  TomasBalak
  committed
  3a85dff
- style: imports
  TomasBalak
  committed
  e74b68c
- docs: update instalation and fix formatting
  TomasBalak
  committed
  99c9518
- chore: change staining library branch to master (when the changes are merged)
  TomasBalak
  committed
  ddb4af0
- fix: typing
  TomasBalak
  committed
  0ce4d2e
- style: format
  TomasBalak
  committed
  44dbf6d
Commits on Jan 29, 2026
- chore: temporarily change version of the staining library
  TomasBalak
  committed
  b39b27e
Commits on Jan 30, 2026
- fix: typing
  TomasBalak
  committed
  b207bcb
- docs: guide for setting up a development environment
  TomasBalak
  committed
  7a86b4f
Commits on Feb 1, 2026
- feat: coverage numbers for blur
  TomasBalak
  committed
  f3b42f4
- chore: cleanup (version of the staining lib still needs to be changed)
  TomasBalak
  committed
  45be6ea
Commits on Feb 2, 2026
- chore: replace deprecated binary erosion/dilation
  TomasBalak
  committed
  add1310
- fix: typing in folding
  
  xsedlak4
  authored and
  TomasBalak
  committed
  ce3508c
- fix: typing in folding
  TomasBalak
  committed
  6a56df8
Commits on Feb 14, 2026
- chore: update version of the staining library
  TomasBalak
  committed
  baef23a
Commits on Feb 22, 2026
- refactor: unite mask name format and coverage information
  TomasBalak
  committed
  eac6357
- docs: update mask names and add required dependency
  TomasBalak
  committed
  ea33741
Commits on Mar 9, 2026
- ci: migrate from gitlab to github
  TomasBalak
  committed
  686e41e
- chore: update piqe path
  TomasBalak
  committed
  4907b71
- chore: update links
  TomasBalak
  committed
  82675bf
Commits on Mar 12, 2026
- chore: update the legacy ruff alias
  TomasBalak
  committed
  e9a242f
- chore: selected fixes from ai code review
  TomasBalak
  committed
  56829f9
Commits on Mar 17, 2026
- fix: issues detected by ai review (consulted with @xsedlak4)
  TomasBalak
  committed
  f01109b
- chore: fix spelling
  TomasBalak
  committed
  8bd6373
- chore: fix wording
  TomasBalak
  committed
  9bd2ef4
- chore: fix function shadowing
  TomasBalak
  committed
  69f6b54

Commits

Commits on Jan 27, 2026

Commits on Jan 29, 2026

Commits on Jan 30, 2026

Commits on Feb 1, 2026

Commits on Feb 2, 2026

Commits on Feb 14, 2026

Commits on Feb 22, 2026

Commits on Mar 9, 2026

Commits on Mar 12, 2026

Commits on Mar 17, 2026