Fix: cascaded mzi notebook + tidy3d pluggin bug fixes

[David-GERARD]

Overview

The end of this notebook is commented-out as meant to have a bug. I took a look at it, and in the process founds more errors.

Currently, the Notebook runs successfully IF AND ONLY IF the test data is downloaded trough make test-data. Let me know if this is enough to merge.

Changelog

• Bumped the required version of gdsfactory to be able to run gf.gpdk.PDK.activate() without error. 97a5d69

Future work

• Update the Notebook in the docs/ folder and veryfy that the documentation builds.
• tidy3d.wed.run() has been changed from the version the pluggins expects. In version 2.8.5 (current requirements is "tidy3d>=2.8.2,<2.9"), it expects a mandatory task name. However, it seems that in newer versions this is no longer the case.
• I flagged another bug in commit b05d6e4 as web.run() no longer accepts an object of the ComponentModeler class.

In general, I think that the tidy3d pluggin might need some work that goes beyon just fixing this Notebook.

Summary by Sourcery

Fix the cascaded MZI workflow notebook to run end-to-end and align the tidy3d plugin with updated API requirements.

Bug Fixes:

• Enable generation and loading of S-parameters in the cascaded MZI notebook using batch simulation jobs.
• Pass a stable task name and correct output path when running tidy3d web simulations to restore S-parameter computation.

Enhancements:

• Update the cascaded MZI notebook kernel metadata to use the project’s gplugins environment.

Build:

• Bump the minimum gdsfactory version requirement to 9.29.1 to support the current PDK activation API.

[sourcery-ai]

Reviewer's Guide

Updates the cascaded MZI workflow notebook to compute and batch-run s‑parameter simulations programmatically, aligns the Tidy3D plugin with newer web.run semantics using hashed task names and output directories, and bumps the gdsfactory dependency version required to activate the PDK without errors.

Sequence diagram for updated write_sparameters and web.run interaction

sequenceDiagram
    participant User
    participant write_sparameters
    participant ComponentModeler as ComponentModeler
    participant web
    participant Filesystem

    User->>write_sparameters: call write_sparameters(component, dirpath, ...)
    write_sparameters->>ComponentModeler: create modeler from component and settings
    write_sparameters->>ComponentModeler: compute hash via _hash_self()
    ComponentModeler-->>write_sparameters: task_name
    write_sparameters->>Filesystem: build path_dir = pathlib.Path(dirpath) / task_name
    write_sparameters->>ComponentModeler: modeler = modeler.updated_copy()
    write_sparameters->>Filesystem: check if cached sparameters file exists
    alt cached sparameters exists
        write_sparameters->>Filesystem: load npz file
        Filesystem-->>write_sparameters: sparameters data
        write_sparameters-->>User: return cached sparameters
    else no cache
        write_sparameters->>web: run(modeler, task_name=task_name, verbose=verbose, path=path_dir / simulation.hdf5)
        web-->>write_sparameters: modeler_data
        write_sparameters->>write_sparameters: compute s = modeler_data.smatrix()
        write_sparameters->>Filesystem: save sparameters to filepath
        write_sparameters-->>User: return computed sparameters
    end

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Flow diagram for updated cascaded MZI notebook sparameter batch simulation

flowchart TD
    A_start[Start notebook] --> B_defineSimLengths[Define sim_lengths and other parameters]
    B_defineSimLengths --> C_buildJobs[Build jobs list for each length in sim_lengths]
    C_buildJobs -->|for each length| C1_jobItem[Create dict with component, filepath, layer_stack]
    C_buildJobs --> D_callBatch[Call gt.write_sparameters_batch with jobs]
    D_callBatch --> E_getFutures[Receive list of simulation futures sims]
    E_getFutures --> F_collectResults[Call result on each future to build s_params_list]
    F_collectResults --> G_postProcess[Compute wavelengths, drop, through, error metrics]
    G_postProcess --> H_plot[Plot coupler responses and fitting errors]
    H_plot --> I_continueNotebook[Continue with filter modeling and full system simulation]
    I_continueNotebook --> J_end[End notebook]

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File-Level Changes

Change	Details	Files
Fix cascaded MZI notebook to generate and consume s-parameter simulations via write_sparameters_batch instead of relying on precomputed files.	Remove the commented-out construction of s_params_list from pre-saved NPZ files and instead build it from simulation results. Create a jobs list of dicts (component, filepath, layer_stack) over sim_lengths and pass it to gt.write_sparameters_batch. Update the notebook’s kernel metadata to use the gplugins (3.11.14) environment and Python 3.11.14.	notebooks/workflow_3_cascaded_mzi.ipynb
Adjust Tidy3D component s-parameter writer to work with newer web.run API requirements, including explicit task naming and per-task directories.	Derive a task_name from modeler._hash_self() and use it to form the per-simulation output directory. Pass task_name and an updated path pointing into the task-specific directory to web.run so simulations have unique names and output files. Leave a TODO noting that web.run currently does not support ComponentModeler objects directly and will require conversion to the appropriate simulation type.	gplugins/tidy3d/component.py
Increase the minimum gdsfactory version to ensure PDK activation and compatibility with updated APIs.	Bump gdsfactory dependency from >=9.15.1 to >=9.29.1 in pyproject.toml. Regenerate uv.lock to reflect the new dependency graph.	pyproject.toml uv.lock

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[sourcery-ai]

Hey - I've left some high level feedback:

• The notebook metadata now hardcodes a local kernel name ("display_name": "gplugins (3.11.14)" and Python 3.11.14); consider reverting those fields so the notebook remains environment-agnostic for other users.
• In write_sparameters, the web.run call now includes a TODO about ComponentModeler not being supported; it may be better to either implement a minimal conversion or explicitly raise a clear error when a ComponentModeler instance is passed instead of relying on a comment that can be overlooked.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The notebook metadata now hardcodes a local kernel name (`"display_name": "gplugins (3.11.14)"` and Python 3.11.14); consider reverting those fields so the notebook remains environment-agnostic for other users.
- In `write_sparameters`, the `web.run` call now includes a TODO about `ComponentModeler` not being supported; it may be better to either implement a minimal conversion or explicitly raise a clear error when a `ComponentModeler` instance is passed instead of relying on a comment that can be overlooked.

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