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

robertsamples
and
claude
committed
Add GroupSetModel.move() for groupset reordering (model layer only)

robertsamples
and
claude
committed
Clarify stale PCA TODO note

robertsamples
and
claude
committed
Merge remote-tracking branch 'origin/main' into todo-cleanup
robertsamples
committed
Merge branch 'main' into todo-cleanup
robertsamples
committed
Add Qt-free multivariate ordination backend (PCA/NMDS/PLS-DA)

robertsamples
and
claude
committed
Rework the mislabeled "PCA" plot into a multivariate ordination tab

robertsamples
and
claude
committed
Fix ordination feedback: scaling, axis limits, NMDS %explained, bar styling

robertsamples
and
claude
committed
Add dendrogram purity coloring: technical/biological replicate QC view

robertsamples
and
claude
committed
Dendrogram: polyphyletic branches in red, add a no-coloring option

robertsamples
and
claude
committed
Replace treemap/upset PNG round-trip with real canvas plots

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

robertsamples
and
claude
committed
Fix dendrogram coloring: red = proven non-monophyly (label-set overlap)

robertsamples
and
claude
committed
Dendrogram: add Use Sample/Group Names labels; fix AU/BP label scaling

robertsamples
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claude
committed
Docs: update mkdocs guide for ordination rework and dendrogram improvements

robertsamples
and
claude
committed

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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