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[JOSS review] Manuscript feedback

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#127 In DaymudeLab/assembly-theory;

· amcandio opened on Nov 15, 2025

Remove and replace items in the cache

featureAn entirely new capabilityAn entirely new capability

Status: Open.

#120 In DaymudeLab/assembly-theory;

· Garrett-Pz opened on Oct 10, 2025

Reduce allocations when tree canonizing

optimizationAn optimization to existing implementationAn optimization to existing implementation

Status: Open.

#102 In DaymudeLab/assembly-theory;

· AgentElement opened on Jul 25, 2025

Allow long-running calculations to timeout and return an upper bound

featureAn entirely new capabilityAn entirely new capability

Status: Open.

#100 In DaymudeLab/assembly-theory;

· jdaymude opened on Jul 23, 2025

Bring <code>canonization</code> up to current commit and optimize.

algorithmA new or improved algorithmA new or improved algorithm

Status: Open.

#83 In DaymudeLab/assembly-theory;

· AgentElement opened on Jul 9, 2025

String &amp; Graph Assembly indices

featureAn entirely new capabilityAn entirely new capability

Status: Open.

#24 In DaymudeLab/assembly-theory;

· colemathis opened on Feb 4, 2025

Joint Assembly Indices/Spaces

featureAn entirely new capabilityAn entirely new capability

Status: Open.

#23 In DaymudeLab/assembly-theory;

· colemathis opened on Feb 4, 2025

Extract Assembly pathway

featureAn entirely new capabilityAn entirely new capability

Status: Open.

#22 In DaymudeLab/assembly-theory;

· colemathis opened on Feb 4, 2025