feat: Add NodeDict collection for named node mappings

[Copilot]

• Add NodeDict class to src/caskade/collection.py
• Export NodeDict from src/caskade/__init__.py
• Update Module.__setattr__ to auto-convert plain dicts of nodes to NodeDict
• Add tests for NodeDict to tests/test_collection.py
• Add test coverage for dynamic property
• Add test coverage for update with kwargs
• Add Node Collections section to docs/source/notebooks/AdvancedGuide.ipynb
• Wrap all NodeList and NodeDict mutation methods in try/finally so _link_nodes() is always called even when an error occurs

Original prompt

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This section details on the original issue you should resolve

<issue_title>feat: dictionary of nodes collection</issue_title>
<issue_description>Currently have list and tuple of nodes. A dictionary of nodes would also be potentially useful</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes feat: dictionary of nodes collection #26

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (e075e4b) to head (6ee3af7).
⚠️ Report is 1 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff            @@
##               dev       #80   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1612      1688   +76     
=========================================
+ Hits          1612      1688   +76     

Flag	Coverage Δ
unittests	100.00% <100.00%> (ø)

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[ConnorStoneAstro]

@copilot can you add unit tests for the dynamic property and for "update" with kwargs. Looks like those cases aren't covered.

[Copilot]

@copilot can you add unit tests for the dynamic property and for "update" with kwargs. Looks like those cases aren't covered.

Added in 9b605d4. test_node_dict_manipulation now includes:

• a dynamic/static property check (static after to_static, dynamic after to_dynamic)
• an update with kwargs test (passes a kwarg mkw=Module("mkw") and asserts the key is linked correctly)

[ConnorStoneAstro]

@copilot can you add a section to the advanced tutorial for the NodeTuple, NodeList and NodeDict collections? It should just demo basic behaviour while adding some commentary on what these are useful for. The use cases include creating subsets of params for Gibbs sampling to make dynamic/static, picking out a list of params of interest to single them out for saving/updating, to select collections of modules/params for quick printing, etc. Should mention that collections of nodes assigned to a Module will automatically be turned into an appropriate node collection. Should also mention that the get_values and set_values methods work the same for collections as they do for Modules.

[Copilot]

@copilot can you add a section to the advanced tutorial for the NodeTuple, NodeList and NodeDict collections? It should just demo basic behaviour while adding some commentary on what...

Added in b6f81d9. The new "Node Collections: NodeList, NodeTuple, and NodeDict" section in AdvancedGuide.ipynb (inserted after "Param groups") includes:

• An intro explaining the three types and when to use them
• A note on auto-conversion when assigned to a Module attribute
• Enumerated use-cases (Gibbs sampling, selective saving/updating, quick inspection)
• Four code cells demonstrating:
  1. Direct construction and attribute access
  2. Auto-conversion inside a Module (list→NodeList, dict→NodeDict) with graphviz display
  3. get_values / set_values on a collection subset
  4. Gibbs-style Param toggling (group_A.to_static() / group_B.to_dynamic())

[Copilot]

Pull request overview

This PR adds a NodeDict collection type to the caskade library, filling the gap between the existing NodeList (mutable, ordered) and NodeTuple (immutable, ordered) collections with a mutable, key-indexed (str → Node) collection that integrates fully into the caskade DAG. It also auto-promotes plain Python dict assignments on Module attributes to NodeDict, consistent with existing list→NodeList / tuple→NodeTuple promotion.

Changes:

• NodeDict implementation in collection.py: a dict subclass of NodeCollection with full mutation support and automatic link/unlink cycle management.
• Auto-promotion in module.py: Module.__setattr__ now converts plain dict of nodes to NodeDict.
• Tests and docs: comprehensive tests in test_collection.py and a new "Node Collections" section in AdvancedGuide.ipynb.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
src/caskade/collection.py	Adds the NodeDict class with all mutation methods
src/caskade/module.py	Extends __setattr__ to auto-convert dict of nodes to NodeDict
src/caskade/__init__.py	Exports NodeDict as part of the public API
tests/test_collection.py	Tests for creation, mutation, param values, and module auto-conversion
docs/source/notebooks/AdvancedGuide.ipynb	New "Node Collections" section with usage examples
.gitignore	Adds safety-net entries for graphviz intermediate test files

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[ConnorStoneAstro]

@copilot the review pointed out that if there is an error during one of the operations on the collection (i.e. update for the NodeDict) then the collection will be left in a invalid state since the nodes will not be re-linked together. Could you use a try - finally block to ensure that after whatever happens with the collection operation, the nodes will be re-linked to keep the state valid? Please make this change for all the collection objects as it affects each of them.

[Copilot]

@copilot the review pointed out that if there is an error during one of the operations on the collection (i.e. update for the NodeDict) then the collection will be left in a invalid state since the ...

Done in a87467e. Every mutating method in NodeList (append, insert, extend, clear, pop, remove, __setitem__, __delitem__, __iadd__) and NodeDict (__setitem__, __delitem__, update, pop) now wraps the raw data-structure call in a try/finally block, so _link_nodes() is always called regardless of whether the operation raises.