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Efficiency updates - #9

Merged

robertsamples merged 24 commits into

mainfrom

dev

Jun 30, 2026

Commits on Jun 29, 2026
- Reword and reprioritize main.py TODO list
  robertsamples
  committed
  f3fe407
- Add search-tab run-check, clean up main.py's dead imports
  
  robertsamples
  and
  claude
  committed
  9feb9ec
- Add GroupSetModel.move() for groupset reordering (model layer only)
  
  robertsamples
  and
  claude
  committed
  b5a804c
- Clarify stale PCA TODO note
  
  robertsamples
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  claude
  committed
  504410f
- Merge remote-tracking branch 'origin/main' into todo-cleanup
  robertsamples
  committed
  f06a971
- Merge branch 'main' into todo-cleanup
  robertsamples
  committed
  e110fa1
- Add Qt-free multivariate ordination backend (PCA/NMDS/PLS-DA)
  
  robertsamples
  and
  claude
  committed
  c0c160c
- Rework the mislabeled "PCA" plot into a multivariate ordination tab
  
  robertsamples
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  claude
  committed
  9c15631
- Fix ordination feedback: scaling, axis limits, NMDS %explained, bar styling
  
  robertsamples
  and
  claude
  committed
  c7b6a01
- Add dendrogram purity coloring: technical/biological replicate QC view
  
  robertsamples
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  claude
  committed
  ede1968
- Dendrogram: polyphyletic branches in red, add a no-coloring option
  
  robertsamples
  and
  claude
  committed
  573cbfa
- Replace treemap/upset PNG round-trip with real canvas plots
  
  robertsamples
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  claude
  committed
  bab713d
- Dendrogram: bridge-only red coloring; move bootstrap/collapse checkboxes to per-plot bars
  
  robertsamples
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  claude
  committed
  3be44dc
- Fix dendrogram coloring: red = proven non-monophyly (label-set overlap)
  
  robertsamples
  and
  claude
  committed
  5ca9baf
- Dendrogram: add Use Sample/Group Names labels; fix AU/BP label scaling
  
  robertsamples
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  claude
  committed
  66b3e02
- Docs: update mkdocs guide for ordination rework and dendrogram improvements
  
  robertsamples
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  claude
  committed
  9697aa3
Commits on Jun 30, 2026
- correlation matrix control improvements
  robertsamples
  committed
  52c1d37
- Update tests.yml
  robertsamples
  committed
  6a28902
- bugfixes, docs update
  robertsamples
  committed
  03e6d22
- implement npatlas fetch, bug report, update mgmt
  robertsamples
  committed
  6a65373
- efficiency updates
  robertsamples
  committed
  698af6f
- Merge branch 'main' into dev
  robertsamples
  authored
  0caf396
- resolve ci errors on python 3.11 and 3.9 macos
  robertsamples
  committed
  5f9a119
- Merge branch 'dev' of https://github.com/robertsamples/mpact into dev
  robertsamples
  committed
  d9857e6

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Efficiency updates - #9

Efficiency updates#9
robertsamples merged 24 commits into
mainfrom
dev

Commits on Jun 29, 2026

Reword and reprioritize main.py TODO list

Add search-tab run-check, clean up main.py's dead imports

Add GroupSetModel.move() for groupset reordering (model layer only)

Clarify stale PCA TODO note

Merge remote-tracking branch 'origin/main' into todo-cleanup

Merge branch 'main' into todo-cleanup

Add Qt-free multivariate ordination backend (PCA/NMDS/PLS-DA)

Rework the mislabeled "PCA" plot into a multivariate ordination tab

Fix ordination feedback: scaling, axis limits, NMDS %explained, bar styling

Add dendrogram purity coloring: technical/biological replicate QC view

Dendrogram: polyphyletic branches in red, add a no-coloring option

Replace treemap/upset PNG round-trip with real canvas plots

Dendrogram: bridge-only red coloring; move bootstrap/collapse checkboxes to per-plot bars

Fix dendrogram coloring: red = proven non-monophyly (label-set overlap)

Dendrogram: add Use Sample/Group Names labels; fix AU/BP label scaling

Docs: update mkdocs guide for ordination rework and dendrogram improvements

Commits on Jun 30, 2026

correlation matrix control improvements

Update tests.yml

bugfixes, docs update

implement npatlas fetch, bug report, update mgmt

efficiency updates

Merge branch 'main' into dev

resolve ci errors on python 3.11 and 3.9 macos

Merge branch 'dev' of https://github.com/robertsamples/mpact into dev