Address review comments on bbknn_ts

[rcannood]

Describe your changes

Applies @mumichae's review comments from openproblems-bio#84, so you don't have to. The generated integration code itself is untouched.

• renamed the component to era_combat_bbknn, after the ERA system and the two algorithms it combines
• method_types: [embedding, graph]: the custom kNN graph is evaluated as is. transform only recomputes a graph from the embedding when uns['neighbors'] is missing, so your graph was already the one the graph metrics saw
• preferred_normalization: counts: the method does its own normalisation, and this is how a component declares that the preprocessing is part of the method
• pass --n_pca_components, --n_neighbors_per_batch and --total_k_neighbors through to the integration code -- they were declared but never read, the hardcoded config dict won
• store a minimal output object instead of the mutated input: 3.7 MB -> 0.6 MB on the test resource, and that ratio gets worse on the large datasets
• updated the reference to the Nature paper, and the links to google-research/era -- the repo has been renamed and the old docs URL now 404s, which check_config flags as a hard test failure
• openproblems/base_python:1 and [hightime, highmem, midcpu], in line with the other methods

I verified that this doesn't change the results: running your component and this one on resources_test/task_batch_integration/cxg_immune_cell_atlas gives the same embedding and the same kNN graph. The only difference comes from the docker tag bump (:1.0.0 -> :1, numpy 2.2.6 -> 2.5.2, scanpy 1.10.4 -> 1.12.3), which is 2e-06 relative drift on X_emb and leaves the graph topologically identical -- same neighbours for every cell, connectivities bit-identical. The old tag isn't an option anyway, it fails check_config against the current common/ submodule.

viash test src/methods/era_combat_bbknn/config.vsh.yaml succeeds.

Note that the branch still needs a merge with main before it can go in -- run_benchmark has moved on quite a bit since September.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!