Partial upgrade of libsedml, fixed cli plot bugs#1627

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CodeByDrescher wants to merge 30 commits intomasterfrom

bsiosim_visual_results_fixes

Commits on Apr 15, 2026

First pass at upgrade; mostly clean-up; also abstract "Plot" class
CodeByDrescher
committed
Restructuring of files for organization and clarity
CodeByDrescher
committed
[WIP] Adding features
CodeByDrescher
committed
Fixed label / axis titling by expanding + updating libsedml
CodeByDrescher
committed
Added algorithm to attempt to keep legend smaller
CodeByDrescher
committed
Semantic bug fixes, added cloning to sedml, fixed xml helper, etc.
CodeByDrescher
committed
Added model pruning and fixed bugs with writing models
CodeByDrescher
committed
Fixed NPE when mapping was null
CodeByDrescher
committed
Fixed bug where wrong variable type was created; wrong argument order
CodeByDrescher
committed
Fixed Plotting bug
CodeByDrescher
committed
Fixed comparing / hashing of SedBase + Change. Fixed another variable bug
CodeByDrescher
committed
Added logging
CodeByDrescher
committed
Added safeguards to renaming of variable
CodeByDrescher
committed
small bug fixes
CodeByDrescher
committed
Attempting to solve why test is failing on remote
CodeByDrescher
committed
Fixing overzealous refactor
CodeByDrescher
committed
Reducing require accuracy of pixels
CodeByDrescher
committed
Fixed bad renames, and ensuring preserved order of biomodels
CodeByDrescher
committed
Added Axis test (frist jlibsedml test!)
CodeByDrescher
committed
Jim review modifications
CodeByDrescher
committed
Jim review modifications II
CodeByDrescher
committed
Now using SSIM image comparison
CodeByDrescher
committed
Fixed incorrect formula
CodeByDrescher
committed
Making error clearer & findable
CodeByDrescher
committed
Visually inspected results; look correct, getting detailed breakdown
CodeByDrescher
committed
Attempting blurred solution
CodeByDrescher
committed
Accepting 90% accuracy MSSIM
CodeByDrescher
committed
Fixed edge case bugs with sedml import + spatial results bug
CodeByDrescher
committed
rebase fixes
CodeByDrescher
committed
Fix AI-Caught bug
CodeByDrescher
committed

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Partial upgrade of libsedml, fixed cli plot bugs#1627

Partial upgrade of libsedml, fixed cli plot bugs#1627
CodeByDrescher wants to merge 30 commits intomasterfrom
bsiosim_visual_results_fixes

Commits on Apr 15, 2026

First pass at upgrade; mostly clean-up; also abstract "Plot" class

Restructuring of files for organization and clarity

[WIP] Adding features

Fixed label / axis titling by expanding + updating libsedml

Added algorithm to attempt to keep legend smaller

Semantic bug fixes, added cloning to sedml, fixed xml helper, etc.

Added model pruning and fixed bugs with writing models

Fixed NPE when mapping was null

Fixed bug where wrong variable type was created; wrong argument order

Fixed Plotting bug

Fixed comparing / hashing of SedBase + Change. Fixed another variable bug

Added logging

Added safeguards to renaming of variable

small bug fixes

Attempting to solve why test is failing on remote

Fixing overzealous refactor

Reducing require accuracy of pixels

Fixed bad renames, and ensuring preserved order of biomodels

Added Axis test (frist jlibsedml test!)

Jim review modifications

Jim review modifications II

Now using SSIM image comparison

Fixed incorrect formula

Making error clearer & findable

Visually inspected results; look correct, getting detailed breakdown

Attempting blurred solution

Accepting 90% accuracy MSSIM

Fixed edge case bugs with sedml import + spatial results bug

rebase fixes

Fix AI-Caught bug