fixes delta lengths and netlist patching for notebook workflow_3_cascaded_mzi.ipynb

[jonbenfri]

Fixes issue #677.

Summary by Sourcery

Update the cascaded MZI workflow notebook to correct MZI path length definitions and enable proper recursive netlist patching and simulation plotting.

New Features:

• Add a recursive netlist patching helper and use it to run and plot circuit simulations directly in the notebook.

Bug Fixes:

• Correct the MZI path length difference definitions and delta length values used in the layout generation.
• Fix netlist patching by filtering model settings correctly and handling recursive netlists when replacing components.

Documentation:

• Fix minor wording and typo issues in the notebook narrative to improve clarity.

Chores:

• Update notebook kernel metadata to use the current Python 3 ipykernel and version.

[sourcery-ai]

Reviewer's Guide

Updates the cascaded MZI workflow notebook to correct the MZI path length definitions, preserve signed delta lengths in the layout, and introduce a recursive netlist patching helper that is exercised in an active simulation cell, along with minor text and environment metadata cleanup.

Sequence diagram for using patch_netlist_mod in circuit simulation

sequenceDiagram
  actor User
  participant Notebook
  participant patch_netlist_mod
  participant sax
  participant circuit

  User->>Notebook: Run simulation cell
  Notebook->>Notebook: layout = gf.c.mzi_lattice(...)
  Notebook->>patch_netlist_mod: patch_netlist_mod(netlist=layout.get_netlist(recursive=True), models, models_to_patch)
  patch_netlist_mod-->>Notebook: patched_netlist, patched_models
  Notebook->>sax: circuit(patched_netlist, patched_models)
  sax-->>Notebook: circuit
  Notebook->>circuit: s = circuit(wl=lda)
  circuit-->>Notebook: scattering_parameters s
  Notebook->>Notebook: Plot responses o1->o3 and o1->o4
  Notebook-->>User: Display transmission spectra

Loading

File-Level Changes

Change	Details	Files
Correct MZI path-length sign conventions and propagate them through the simulation layout.	Update markdown description of MZI path length differences to match the intended sign convention and physical design Adjust mzi_deltas tuple to use signed length_delta values and new combination with L_pi Pass mzi_deltas directly into the mzi_lattice delta_lengths parameter instead of their absolute values	notebooks/workflow_3_cascaded_mzi.ipynb
Improve netlist patching logic and apply it to recursive netlists.	Fix typo in filtered settings variable name to avoid using an undefined variable during model instantiation Introduce patch_netlist_mod helper that iterates over recursive netlist models and instances, filters settings against the target model signature, and rewrites components to unique versioned names Use patch_netlist_mod in an active plotting cell to build a sax circuit from a recursive netlist and plot transmission responses with a marker at the central wavelength	notebooks/workflow_3_cascaded_mzi.ipynb
Minor documentation and environment metadata updates.	Fix textual typo from 'latter' to 'later' in the notebook intro description Update notebook kernelspec display name and Python version metadata	notebooks/workflow_3_cascaded_mzi.ipynb

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[sourcery-ai]

Hey - I've found 1 issue, and left some high level feedback:

• The new patch_netlist_mod function largely duplicates the logic in patch_netlist; consider refactoring into a single, more general helper (e.g., with a recursive flag or shared inner routine) to avoid divergence between the two implementations.
• In patch_netlist_mod, the loop variable model is reused both as the key for netlist[model] and then as the instance dict (model = instances[name]), which is confusing and error-prone; use distinct variable names for the key and the instance object.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The new `patch_netlist_mod` function largely duplicates the logic in `patch_netlist`; consider refactoring into a single, more general helper (e.g., with a `recursive` flag or shared inner routine) to avoid divergence between the two implementations.
- In `patch_netlist_mod`, the loop variable `model` is reused both as the key for `netlist[model]` and then as the instance dict (`model = instances[name]`), which is confusing and error-prone; use distinct variable names for the key and the instance object.

## Individual Comments

### Comment 1
<location path="notebooks/workflow_3_cascaded_mzi.ipynb" line_range="715-729" />
<code_context>
+    "    # For recursive netlist\n",
+    "    for model in netlist.keys():\n",
+    "        instances = netlist[model][\"instances\"]\n",
+    "        for name in instances:\n",
+    "            model = instances[name]\n",
+    "            if model[\"component\"] in models_to_patch:\n",
+    "                component = model[\"component\"]\n",
</code_context>
<issue_to_address>
**suggestion:** Avoid reusing `model` as both the outer key and the inner instance dict.

Reusing `model` for both the netlist key and the instance dict (`for model in netlist.keys():` then `model = instances[name]`) makes the code hard to follow and easy to misuse later (e.g., confusing the key with the instance data). Please use distinct names like `netlist_name` and `instance` to clarify what’s being iterated and mutated.

```suggestion
    "def patch_netlist_mod(netlist, models, models_to_patch):\n",
    "    # For recursive netlist\n",
    "    for netlist_name in netlist.keys():\n",
    "        instances = netlist[netlist_name][\"instances\"]\n",
    "        for name in instances:\n",
    "            instance = instances[name]\n",
    "            if instance[\"component\"] in models_to_patch:\n",
    "                component = instance[\"component\"]\n",
    "                i = 0\n",
    "                new_component = f\"{component}_v{i}\"\n",
    "                while new_component in models:\n",
    "                    i += 1\n",
    "                    new_component = f\"{component}_v{i}\"\n",
    "                settings = instance[\"settings\"]\n",
    "                settings_filtered = {\n",
```
</issue_to_address>

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