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Prepare 0.8.0rc0 prerelease for Zenodo DOI - #119

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1400073 wants to merge 254 commits into

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Prepare 0.8.0rc0 prerelease for Zenodo DOI#119
1400073 wants to merge 254 commits into
masterfrom
release/time-domain-zenodo

This pull request is big! We're only showing the most recent 250 commits

Commits on Nov 8, 2024
Commits on Nov 9, 2024
Commits on Nov 10, 2024
- just some minor things
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Commits on Nov 11, 2024
- "Added Waveguide Model, started time_circuit class"
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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- "Made the ideal models dictionary based"
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- "Made the ideal Models dictionary based"
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Commits on Nov 16, 2024
Commits on Nov 18, 2024
- Current changes in the pole residue response
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- "Added Time-network parser"
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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- Bug fix in example file
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Commits on Dec 2, 2024
- All my recent changes that need to still be reviewed
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- Again the changes made
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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Commits on Dec 9, 2024
- Just the file I have been using for the time-delay analysis and checking how it changes with regards to the system it shouldnt effect anything that has already been doen
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Commits on Dec 16, 2024
- Just some changes to the time delay
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- moving files into the correct folder
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Commits on Jan 2, 2025
- All Recent changes
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Commits on Jan 6, 2025
- Updates ideal models example script
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- m
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Commits on Jan 8, 2025
- Recent changes to test the phase modulator in the ideal.simphony
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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Commits on Jan 10, 2025
- Fixes to the bug from the waveguide issues and the phase modulator testing
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Commits on Jan 22, 2025
- All current changes including the otpimizer and timedomainsim which can be renamed as needed for ease of usage
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Commits on Jan 27, 2025
- Reconnecter is done with some testing not as robust as I would like
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Commits on Feb 4, 2025
- All changes that have been made to make the run sim program work
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Commits on Feb 6, 2025
- Finished TimeDomainSim and working test
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Commits on Feb 10, 2025
- Jsuta final change
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Commits on Feb 12, 2025
- Incorporating state tracking into time system objects
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Commits on Feb 13, 2025
- Added reset method to time system (fixes IIRtTmeSystem)
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Commits on Feb 22, 2025
- current work
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Commits on Feb 24, 2025
- Generalized changes to circuit
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- some quick changes to the timeresult class to conform to present usage
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Commits on Feb 28, 2025
- add changes to fix two major bugs
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- trying to send in everything
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- one final bug
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- fixed another bug
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- Chandler TimeSim file structure
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Commits on Mar 5, 2025
Commits on Mar 7, 2025
- Fixed bug with the beta value
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Commits on Apr 25, 2025
Commits on Apr 28, 2025
- Progress bar for user
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Commits on May 6, 2025
- some edits
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Commits on May 8, 2025
- changes to idea
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- my tests
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- delete_checkstuff
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- made changes
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Commits on May 13, 2025
- mmisandtqdmchanges
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Commits on May 14, 2025
- modified stuff
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- Modified method for least square approximation
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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- You broke the least squares, this fixes it
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Commits on May 15, 2025
Commits on May 16, 2025
- stuff
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- Merge branch 'time_domain' of https://github.com/BYUCamachoLab/simphony into time_domain
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Commits on May 29, 2025
- simplifications to simulation
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- just some attempts of optimization
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Commits on May 30, 2025
- Fixed syntax error in pyproject.toml
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- Converted dlsim functions to jax.numpy
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- removed max_size variable from build_model
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- Merge branch 'optimization' of https://github.com/BYUCamachoLab/simphony into optimization
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Commits on Jun 2, 2025
- changes for optimization
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Commits on Jun 3, 2025
- changes
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- Made changes to the optimization branch swapped the optimizer code into the simulation file as changes have been tested
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- deletion of optimizer code
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- time_system improvements
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Commits on Jun 4, 2025
- all changes
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  c86a099
- deletecheck because chandler is lazy
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Commits on Jun 5, 2025
Commits on Jun 6, 2025
Commits on Jun 9, 2025
- no passive components handle case
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Commits on Jun 10, 2025
- Added Simphony.Circuit
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- Merge branch 'block_mode' of https://github.com/BYUCamachoLab/simphony into block_mode
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- Added port types optical, electrical, and logic
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- Port connection validation
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Commits on Jun 11, 2025
- Ports are now stored as Class attributes
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Commits on Jun 12, 2025
- Now simphony.Circuit automatically converts sax callables into Component types
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Commits on Jun 13, 2025
- SParameterSimulation class now creates the s-parameter circuit and validates non-recursive electrical connections
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Commits on Jun 14, 2025
- Added multiple connections
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  15baa86
- Updated the change_settings method to include default settings from the netlist (if desired).
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- Split the settings method into two: reset_settings and add_settings
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- Completed commit
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Commits on Jun 17, 2025
- Added a jax-compatible type system for optical, electrical, and logic signals
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- Fixed ElectricalSignal default value
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Commits on Jun 27, 2025
Commits on Jun 28, 2025
- Completed the steady state functionality for the OpticalModulator
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- Added a method to Circuit that removes a list of components
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Commits on Jun 29, 2025
Commits on Jun 30, 2025
Commits on Jul 1, 2025
Commits on Jul 15, 2025
- Added a python based scan function for debugging sample mode simulations
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Commits on Aug 12, 2025
- I have not pushed in a whie and I am afraid
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Commits on Aug 21, 2025
- Fixed the vector fitting algorithms and clarified sign conventions
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Commits on Aug 26, 2025
Commits on Aug 27, 2025
- I think I got delay compensation working. It has to be specified manually in the s-parameter settings in the circuit
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Commits on Aug 30, 2025
- s_parameter elements through an error when vector fitting error exceeds user defined threshold
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Commits on Nov 8, 2025
- Added IIR filters
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Commits on Nov 9, 2025
- Changed port system in Circuit. Need to update the simulators
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Commits on Nov 18, 2025
- Flattened out unecessary modules
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- Finished flattening imports
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- Separated component module from circuit module
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Commits on Nov 20, 2025
- I have summarized the strategy for handling hierarhcical circuits. This commit is prior to actually implementing this functionality
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Commits on Nov 23, 2025
- Updated circuit object to handle hierachical circuits. I almost certainly broke the funcitonality of being able to remove components with the Circuit method
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- Circuit can now take flat netlists in addition to hierarchical
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Commits on Nov 26, 2025
- Fixed bug in which subcircuit name must match the instance name.
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Commits on Nov 30, 2025
- Started creating subcircuits
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Commits on Dec 20, 2025
- Getting ready to convert SParameter components to PCells
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- PCell not implemented
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Commits on Dec 22, 2025
- Finished FlatCircuit class, fixed libraries naming convention
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Commits on Jan 4, 2026
- Added significant progress to the SParameter PCell
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Commits on Jan 25, 2026
- Added MZI and MZILatticeFilter
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Commits on Jan 27, 2026
- Changed how sax models are interpreted and how components are instantiated.
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Commits on Feb 8, 2026
- Working PCELL collapsing logic
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- Began work on creating external port visualization
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Commits on Feb 9, 2026
- Added port visualization for external and unconnected ports
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- Standardized the shapes of ports, components, and pcells
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Commits on Feb 18, 2026
- Almost there
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Commits on Feb 23, 2026
- Altered the order of some arguments in instantiated circuit
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Commits on Feb 24, 2026
- Fixed bug that caused 2 different ports to display for ext ports
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- Fixed bug where the instantiated_circuit.graph object had the display port nodes
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Commits on Mar 17, 2026
- Began block mode simulator
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- Added Temporary Feature that Sanitizes graphs that have non-JSON serializable settings
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  fad3e24
- Implemented most of the block mode features
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Commits on Mar 20, 2026
- I reimplemented the vector fitting algorithm and dicrete time state space models so that they handle assymmetric systems.
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Commits on Mar 21, 2026
- Added cache-ing functionality for discrete time vector fitting algorithm
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- Started a system for saving global, precomputed models. Need to fill it in.
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- Summarized ideas for the
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- Optimized state_space_response_discrete
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Commits on Mar 31, 2026
Commits on Apr 8, 2026
- Current rendition of changes
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Commits on Apr 9, 2026
- Created a convenience function for creating multimode sax models
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Commits on Apr 12, 2026
- Merge branch 'instantiated_circuit' of https://github.com/BYUCamachoLab/simphony into instantiated_circuit
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Commits on Apr 30, 2026
- Added functionality to consolidate contiguous s_paremeter models
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- Missing
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- Matthew's Changes Filtered
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- Merge branch 'instantiated_circuit' of https://github.com/BYUCamachoLab/simphony into instantiated_circuit
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- merge fixes debugging
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Commits on May 1, 2026
- Fixed state space shaping
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  4d0b238
- Removed "wavelength" as an attribute of electrical signals
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- Made electricalsignals have the argument voltage instead of amplitude
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Commits on May 5, 2026
Commits on May 6, 2026
- Fixed s-parameter simulations and matched their order of magnitude convention to classic simphony
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Commits on May 8, 2026
- Fixes for missing Sax settings
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  4d80665
- Merge branch 'instantiated_circuit' of https://github.com/BYUCamachoLab/simphony into instantiated_circuit
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  ba48685
- extraneous gravis import removed
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  cbdaf44
- Created a jax powered sampled mode simulator
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- Merge branch 'instantiated_circuit' of github.com:BYUCamachoLab/simphony into instantiated_circuit
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  b079c14
- revert settings conflicts
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- Fixed CWLaser after changing it for testing
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- Did some bug fixing in sample mode
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- Fixed bug in s_parameters
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  2502b84
- Merge branch 'instantiated_circuit' of https://github.com/BYUCamachoLab/simphony into instantiated_circuit
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Commits on May 9, 2026
- Began integrating the gaussian process code into simphony
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- Merge branch 'instantiated_circuit' of github.com:BYUCamachoLab/simphony into instantiated_circuit
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Commits on May 10, 2026
- Finished implementing the delay compensation code for s parameter simulations
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Commits on May 11, 2026
- Added a gaussian process simulator and test script of a racetrack resonator
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Commits on May 18, 2026
- Documentation along with three new examples based on circuits used in the paper.
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Commits on May 20, 2026
Commits on May 22, 2026
Commits on May 28, 2026
- Attempted Memory fix/migrating optimized statespace
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Commits on May 29, 2026
- VVector-fitting memory removal of wavelength batching and bug fixing
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  bcce30d
- Cleaned-upcode in preparation of pre-release
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  defd9e8
- Delete miscellanous files
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  f89d507
- Update to dependencies
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  4cd9428
- Style updates to follow reuirements
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  ccbdd92
- fixes to the example ring_filter_dealy_example
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  86a2349
- Merge origin/master into release/time-domain-zenodo
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  ba8e939
- Prepare Zenodo prerelease metadata
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  0b74edb
- Prepare 0.8.0rc0 prerelease
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  a32e3a7
- Fix prerelease test imports
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  b89374b
- Fix prerelease lint compatibility
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  dee144b
- Some style clean-ups
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  139bd73
- Reduce z-domain vector fitting memory usage
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  bb9f339
Commits on Jun 1, 2026
- Expose mzi_lattice_passband ports
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  237c4f1
- Continued space and time complexity optimizations
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Commits on Jun 7, 2026
- decomplicating the structure
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  e0f1680
Commits on Jun 29, 2026
- Terminator bug output to output fixed
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  631ea92
Commits on Jul 10, 2026
- auto-termination bug fixed
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  51d6118

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