Fixing DEFAULT_ATTR_KEYS usage

[JoOkuma]

• check and fix node_id, source_id, etc.. usage in SQLGraph
• write tests non-default usage of node_id and source_id, etc.

[JoOkuma]

@yfukai This PR is related to #228; there are a couple of points that need to be addressed.
The SQLGraph code becomes a bit more complex, and it doesn't bring much joy. I need to consider whether there's a better alternative and if this truly resolves #228

[codecov-commenter]

Codecov Report

❌ Patch coverage is 68.18182% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.36%. Comparing base (daba108) to head (68dade0).

Files with missing lines	Patch %	Lines
src/tracksdata/graph/_sql_graph.py	66.66%	2 Missing and 2 partials ⚠️
src/tracksdata/graph/_rustworkx_graph.py	60.00%	1 Missing and 1 partial ⚠️
src/tracksdata/metrics/_visualize.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #234      +/-   ##
==========================================
- Coverage   88.37%   88.36%   -0.02%     
==========================================
  Files          55       55              
  Lines        3940     3935       -5     
  Branches      690      690              
==========================================
- Hits         3482     3477       -5     
  Misses        276      276              
  Partials      182      182              

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[yfukai]

Thanks! This makes sense a lot!

• If possible, I might stick to an option to bind the field names to the graph objects themselves rather than having them globally, since one might have graphs with different column names in a single script.
• Maybe we could also update ["z", "y", "x"].

[JoOkuma]

uhm... , ok, if we bind everything to the graph, then every default attr_key must be None and check the graph's default.
Do you see another way of implementing it?

[yfukai]

Right, in that sense, the current implementation looks better for me!
(Sorry I changed my mind) I agree with the current implementation (and changing those names can be discouraged except in special cases).
Maybe we could also update ["z", "y", "x"]?

[yfukai]

We also need to implement the attr name conversion in functions that read other file formats such as GEFF.

[JoOkuma]

Happy New Year @yfukai ,
I agree with you, I opened these PRs #239, #238
Do they fix your issue?
Any suggestions?