Set the new env for clusTCR

[julenmendieta]

Greptile Summary

The PR adds and publishes a focused Python 3.12.10 environment for the clusTCR Clustering block.

• Adds the 3.12.10-clustcr runtime package with pinned clusTCR, scientific-computing, FAISS, and Polars dependencies.
• Registers Linux x64/ARM64 and macOS x64/ARM64 builds in CI, the pnpm workspace, and the public runtime catalogue.
• Adds a changeset for the new runtime and catalogue release.
• Important touched terms:
  • Run environment — A packaged, platform-specific Python distribution consumed by Platforma blocks. This PR introduces the 3.12.10-clustcr environment.
  • clusTCR — A T-cell receptor clustering library distributed as immunewatch-clustcr and imported through imw_clustcr. Version 1.0.1 is added as the environment’s primary workload dependency.
  • noDeps — Builder policy that installs a selected package without resolving its declared dependencies. The new profile applies it to clusTCR so its Python-3.12-incompatible SciPy metadata does not control resolution.
  • Dependency closure — The complete set of packages needed by an application at runtime. The profile explicitly supplies clusTCR’s closure, including NumPy, SciPy, pandas, scikit-learn, NetworkX, and clustering utilities.
  • FAISS — A native similarity-search library used by clusTCR’s two-step and V-gene-aware paths. The environment adds faiss-cpu==1.15.0.
  • Strict missing resolution — Builder behavior that fails rather than omitting a package when no permitted artifact can be resolved. The new profile enables strictMissing.
  • Catalogue entrypoint — A stable public name mapped to a runtime package’s generated software descriptor. The catalogue gains 3.12.10-clustcr.
  • Platform root — The packaged environment directory selected for an OS/architecture pair. The new package declares two Linux and two macOS roots.

Confidence Score: 5/5

The PR appears safe to merge because its runtime package, supported platform roots, CI matrix, workspace registration, catalogue reference, and release metadata are internally aligned.

No concrete blocking or independently actionable non-blocking defect remains after checking dependency-resolution semantics and the package’s build and publication wiring.

Important Files Changed

Filename	Overview
python-3.12.10-clustcr/config.json	Defines the pinned clusTCR dependency profile, bypasses incompatible upstream dependency metadata, and enables strict package resolution.
python-3.12.10-clustcr/package.json	Defines the runtime package lifecycle and matching Linux and macOS environment roots.
catalogue/package.json	Adds an aligned catalogue entrypoint and workspace dependency for the new runtime.
.github/workflows/build.yaml	Adds CI jobs corresponding exactly to the four platform roots declared by the runtime package.
pnpm-workspace.yaml	Registers the clusTCR package in the release workspace.
.changeset/clustcr-runenv.md	Records release intent for the new runtime and its catalogue exposure.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
    Config[clusTCR dependency profile] --> Builder[Shared Python runtime builder]
    Builder --> LinuxX64[Linux x64 root]
    Builder --> LinuxArm64[Linux ARM64 root]
    Builder --> MacX64[macOS x64 root]
    Builder --> MacArm64[macOS ARM64 root]
    LinuxX64 --> Runtime[Published clusTCR runtime package]
    LinuxArm64 --> Runtime
    MacX64 --> Runtime
    MacArm64 --> Runtime
    Runtime --> Catalogue[3.12.10-clustcr catalogue entrypoint]
    Catalogue --> Block[clusTCR Clustering block]

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Context used (6)

• Context used - Terms is a types in codebase. Provide the list of ... (source)
• Knowledge Base — Python runtime distribution catalog
• Knowledge Base — Build configuration composition
• Knowledge Base — Automation and release management
• Knowledge Base — CI build workflow
• Knowledge Base — Workspace and release configuration