CI TESTING - #24

Draft

psavery wants to merge 291 commits into

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Commits on Apr 17, 2026

2-way binding of active node/port in pipelineStripWidget
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4a9e0af
bring back the ThresholdSink functionality
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8eb9e5c
bring back the ScaleCubeSink functionality
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17e3f7d
bring back the RulerSink functionality
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781f45e
bring back the SegmentSink functionality
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bf7fbfe
properly bring back molecule related logic
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b26d793
restore interactive transform of a port volume (and sink reaction)
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eb061cf
more fixes to sinks related to rotation/scaling and clipping
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dba16ae
tomviz_pipeline is now part of tomviz instead of a separate target
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23efbb6
more improvements and fixes to VolumePropertiesWidget
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9625829
improve node data and execution state
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a6d69e5
rework transform progress reporting and live updates
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c9db000
implement changes to pipeline widget suggested from ui/ux team
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488d922
add SinkGroupNode to the data model and pipeline widget
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918e324
add pipeline controls widget and improve pipeline pausing/stopping
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c8267e4
fix crash in about dialog
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5ef2575
fix behavior of the various sinks when we have multiple scalar arrays
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94a3558
bugfixes related to dynamic data updates and active scalars
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caed13d
optionally disable pipeline elements dimming on selection
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ab48cf8
minor fixes for wayland and paraview 6.1
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cc170b2
fix minor issue that was causing most reconstruction algorithms to fail
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d6ba52a
Prevent sinks from running without data
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e7e5e31
Put VolumePropertiesWidget in a scroll area
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b10b899
Show slice sink by default if data is tilt series
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0dd06f8
Don't block in ThreadedExecutor
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267aaff
Make edit widget in "properties" panel scrollable
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b1084af
Fix shift rotation center widget
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94683ec
Make TransformEditDialog size like master behavior
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e37d139
Enable executing in external conda env
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3a415eb

Commits on Apr 20, 2026

Merge pull request #1 from psavery/new-pipeline-fixes
alesgenova
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143ec18

Commits on Apr 21, 2026

Commits on Apr 22, 2026

fix a series of memory leaks, some of which were major
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committed
e7646ae

Commits on Apr 29, 2026

Commits on May 4, 2026

Update ITK API

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eaa03b1
Reorganize operators and add OperatorSearchDialog

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ba7d91b
Put logic to get main window instance in function

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7739999
Add interactive cylindrical crop widget

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890b268
Check for nullptr when reading CONDA_PREFIX

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8db666b
Use modern cmake import targets for TBB

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9a426a2
Don't use a hardcoded "Monospace" font

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44fa67d
Prevent ParaView plugin widgets from appearing

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bc5488b
Fix macosx bundle path for conda packages

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bcf630f
Fix import paths for build trees on Mac

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761c5bb
Write human-readable stack trace on Windows crash

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fcec98d
Remove Monospace from PythonTransformEditorWidget

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1a818c6
implement per-node external python environment execution
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db1e631
implement a series of minor usability updates
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f2f52b8

Commits on May 5, 2026

Fix compile-time warnings

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8542876
Increase vertical size of data properties tables

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b23c0d9
Add drag-n-drop support

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a5f4992
Add hyperspy format as an HDF5 format

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4c1ba23
Always auto-execute tvh5 pipelines

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b1ce428
Bring back scan IDs in pyxrf and ptycho workflows

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f13d761
Set tomviz_pipeline_env for custom operators

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7c1fff6
Fix Python console crash

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859c888
Initialize python synchronously

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7d8137a
add definition and infrascructure for a new version of python transforms and sources
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231eeca

Commits on May 6, 2026

Commits on May 11, 2026

Fix save data reaction

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75ca877
Update Ptycho workflow to use SourceNode

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dc4929d
Refactor PyXRF workflow to be a source node

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8570227
Fix default camera orbit animation

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467ce55
Fix animation helper to use new pipeline elements

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50953de
Disable changing opacity with B&C editor

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d031416
Disable panning the histogram opacity widget

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dd8e1f2
Fix "Monospace" font warning on macos

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ca0eda8
Fix Python editor jumping around

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658974f
Fix returns on empty lines in Python editor

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69c69d7
improve the custom transforms menu
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a6eb75f

Commits on May 14, 2026

implement transient/persistent port data infrastructure
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039178f
Add segmentation colormap generator

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501d410
refactor pipeline templates to work with the new pipeline
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9bbdf07

Commits on May 15, 2026

Fix ClipSink to avoid render in worker thread

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158d4c8
Add instructions for cylindrical crop

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38197c8
Add SIRT, ART, and TV to tomopy methods

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080d713
Change "Modules" to "Visualizations"

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4b700b6
Add ability to use GPU for tomopy SIRT and MLEM

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8ab146e
Update animation helper module animations

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9f53e47
Change Module->Visualization in animation helper

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c7ae472
Allow PyXRF workflow to load CSV also

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7fa17fb
Allow download skipping in PyXRF workflow

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b3e630e
add a LabelMap port type
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7ca8aaa
Allow setting versions for multiple rows

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e3f1832
Add .npy and .mat to list of common file types

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a165f5a
Add simple mrc writer

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374136b
Add simple DICOM writer/reader

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cd9cd0f
Populate volume scalars options after data available

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9cccacd
Add tests for new recent features

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ebc24f6
Fix existing test failures

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e24075a
Fix displayed version in dev environment

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ff196dd
Disable multi-volume for now

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6fd0b3a

Commits on May 19, 2026

greatly improve how node widgets that need input data behave
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400ef10
Update all label map operators with new port type

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463c73d
Updates to LabelMap volume settings

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ae7a9f8
Make PyXRF and Ptycho widgets embedded in operator

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896a55d
Hide slice sink until data arrives

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a9f0f87
Update colormaps for all sources after first

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c3e1814
Rename "Workflows" to "Sources"

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acca669
make the "select_scalars" parameter type work with the new pipeline
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d1f8dda
open edit dialog when manual link completes a new transform's inputs
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fe1ef0d
fix the breakpoint feature in the new pipeline
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f0fd2c4
partially remove dependencies from legacy classes
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07980f9
fix build and tests
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02f5b05
Build fixes for Windows and Mac
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8b0bf24
Ensure we use pip from conda
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406572f
Re-enable LegacyDataset tests
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0f42074

Commits on May 20, 2026

Update old python tests to use LegacyDataset
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fade44a
Try to avoid Windows store stub for Python version
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c9d3895
Fix "Custom Transform" and "Custom ITK Transform"
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38d63fa
Fix "Color By" other arrays for contour viz
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00bda27
Increase default operator dialog size
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b679c68
Fix occasional warning from SliceSink deletion
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6b1ae9b
Make default B&C editor width larger
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c36b2e0
Delete pipeline node on "Delete" key press
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480c3d1
Delete contents of sink node group
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30c43ba
Check if port data is valid before accessing
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baa75b1
Remove "too many unique values" warning
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1e90651
Fix warning when Clip or Slice is cleared
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112ccac
Ensure warning doesn't appear on slice/clip delete
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67648cb
Fix "Image Viewer Mode" to use new pipeline sinks
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e1362e3

Commits on May 21, 2026

Stage several old features for removal
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c0aea88
Simplify error printing in python transform
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e53f0a5
Stage registration operators for removal
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c85c870
Stronger guards against seg faults
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297e857
Make PortData::value<T>() non-throwing to prevent bad_any_cast crashes
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d7d3264
Allow "missing" entries to be checked
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948a415
Add "executeWhenIdle()" to prevent re-execution
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e0ffe5e
Allow missing scans to be checked and re-downloaded in PyXRF UI
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8222674
Guard against invalid JSON values
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9906d57
Ensure combo box is updated in main thread
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28c7da7

Commits on May 25, 2026

Trigger CI for PRs against branch 3.0
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1ceeecb

Commits on May 28, 2026

Merge pull request #26 from psavery/nsls2-q3
celiafish
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cc99279

Commits on May 29, 2026

Restore rescaling opacity to B&C editor
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1ec84e1

Commits on May 30, 2026

Get the progress dialog to appear on top for macos
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686754b
Hide "Monospace" font warning on macos
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38fb7ff
Auto update line chart bounds when plot is added
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77aab3e
Look for sample EMDs at runtime
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d2794b8
Put deferred "insert" operators in correct place
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f2628eb
Guard against empty port values
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c962310
Restore visualization on operator cancel
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4abd11a

Commits on Jun 1, 2026

Fix all compile-time warnings (for macos)
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394c800
Fix most Windows compile warnings
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f3f190f
Fix test runtime warnings
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3065db4
Update scipy import paths
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f981c17

Commits on Jun 8, 2026

Add support for volume bricking
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a50dea7

Commits on Jun 13, 2026

Use custom ComputeFiniteRange for histogram range
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7446154

Commits on Jun 15, 2026

Merge pull request #27 from psavery/fix-bc-rescale-opacity
celiafish
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a4b006e

Commits on Jun 17, 2026

Make PyXRF param setup more robust
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1e8c225
Print warnings when we fail to read PyXFF files
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ba3e94a

Commits on Jun 18, 2026

Add retry logic for data.kitware.com downloads
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cf7f745
Fix a couple of segmentation fault issues
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1f4f515
Fix file dialogs for macos dev build
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85bda9f

Commits on Jun 19, 2026

Merge pull request #28 from psavery/3.0
celiafish
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21bfb62

Commits on Jun 22, 2026

Fix deconv/denoise scaling
psavery
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76d89e9

Commits on Jun 24, 2026

Commits on Jun 25, 2026

Commits on Jun 29, 2026

Commits on Jun 30, 2026

Merge pull request #27 from alesgenova/3.0
psavery
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3d77880

Commits on Jul 7, 2026

Request discrete GPU on Windows hybrid graphics
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375880d
Fix slice plane drag with origin and transforms
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a701d2d
Make slice index extent-relative in plane widget
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63543e4

Commits on Jul 10, 2026

Fix pipeline persistence mode and icon bugs
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ace2178

Commits on Jul 11, 2026

Fix tomopy output ordering
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63c5951
Close node edit dialog when its node is removed
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c48d2b9
Fix brightness/contrast Auto and Reset buttons
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b214da7

Commits on Jul 22, 2026

better link selection and other quality of life improvements
alesgenova
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a14e396
Merge pull request #28 from alesgenova/better-link-selection
psavery
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70f4707
Scope pipeline stylesheet, stable nav sort
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77e69ca

Commits on Jul 25, 2026

Avoid importing from user site-packages directory
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33d04d0
Add MAINTENANCE.md for pyxrf-utils
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0cd46ed
Add externalOnly operator flag
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0b0de0c

Commits on Jul 26, 2026

Add SAM 2 segmentation operator
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f9cef1f
Add SAM 3 segmentation operator
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299c359

Commits on Jul 27, 2026

Remove duplicate description from operator dialogs
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728121a
Add back help URLs for Python operators
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718484c
Fix default SAM3 label to work with example data
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72ac12d
Tune SAM 3 defaults for weakly-detected features
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bbd5c53
Declare LabelMap output for the SAM operators
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7a53b3a
Add click-on-slice seed picker for SAM 2
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9d72969
Remember the external env path per operator type
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031aa9d
Fix widget tests on macOS and Windows
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a1f102c
Add drift cleanup to the SAM 2 operator
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36f82ea

Commits on Jul 28, 2026

Match the dataset colormap in the SAM 2 seed view
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87de4d3
Put the SAM 2 seed coordinates on one row
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abd1218
Don't show a volume prop before its mapper has data
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c6e40a0
Fix colormap edit buttons not enabling on selection
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b252f9d
Add erosion split for SAM3
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75bc2b8
Fix several bugs with segmentation colormaps
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579ac1c

Commits on Jul 29, 2026

Don't create a colormap from the SAM 2 seed view
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2c317dc
Apply output metadata before external outputs reach the ports
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0c6ed67
reimplement "Save Data" to be in line with the new pipeline
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9c31cce
Merge pull request #29 from alesgenova/save-data
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8110c1b
Require setuptools greater than 83
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3878e25

Commits on Jul 30, 2026

add an interactive/raw json editor for node definition
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c6c2f43
Merge pull request #30 from alesgenova/json-editor
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477831c
Add help URLs for documented operators
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08eb324
Fix node definition editor regressions
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4e2cc18
Report 3.0.0 as the version under development
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134e6aa
Bring back the Save Script button
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c122322
Close the read-back files before removing them
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7443425
Time out stalled test data downloads
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7f0a70e
Merge pull request #29 from psavery/3.0
celiafish
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5bc38c4

Commits on Jul 31, 2026

Update pybind11 to latest - 3.0.4
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a13c000
Merge pull request #30 from psavery/3.0
celiafish
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18e4ff7

Commits on Aug 10, 2026

Fix camera orbit after loading a state file
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8edcbf3
Refresh animation dialog ranges on execution
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5f2e6b4

Commits on Aug 13, 2026

Fix phantom left click from macOS trackpad
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79a4bb2
Serialize HDF5 access with a process-wide mutex
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9af65e5

Commits on Aug 17, 2026

Add volume lighting presets
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9e0e4c7

Commits on Aug 20, 2026

Fix animation progress for nonzero time ranges
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9a7d39f
Restore time series playback
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b6f1ee6
Add movie export dialog with MP4 support
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7811204
Add Gentle lighting preset and a shadows toggle
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c2b2730
Key the scattering guard on voxel count, not input MTime
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70c17b0
Do not time the first frame of a scattering configuration
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a9ef5fa
Fire the scattering safety valve on a measurement, not an extrapolation
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28d0bb3
Raise the still-frame budget to one second
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b44fe91
Give Full the same shadow reach as Soft
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7a82f00
Correct why the sharpening cap exists
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e490f65
Say so when the guard switches shadows off
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fa80075
Animate clip planes, opacity and camera viewpoints
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072f2a3
Save the animation setup with the state file
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7a62053
Show camera viewpoints as thumbnails
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8660c5f
Run a visualization animation over one leg of the camera path
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0503fa5
Add a Label Map visualization type
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30222fe
Carry the render estimate across a changed opacity curve
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643373f
Animate a volume between two opacity curves
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54bc6e9
Hold one render quality across an exported morph
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93fe67e
Let Rotate keep the original dimensions
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2756fbd
Overhaul the Animation Helper
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1d97e46
Keep label maps out of the animation surface
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0c6254e
Give an animation enough frames to play
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8d560aa
Load a captured opacity curve back into the editor
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5dfd493
Save the rest of the animation and label state
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0a4eae4
Point the pyxrf-utils fallback at the HXN shared deployment
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ec10b3e
Trim the animation header comments
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23520cd