Add OLGA runenv

[kevindetry-milaboratories]

Greptile Summary

This PR adds a new Python 3.12.10 run environment (python-3.12.10-pgen) targeting the Generation Probability (pgen) block, bundling olga for V(D)J CDR3 generation probability, numpy, and polars-lts-cpu. The package is correctly wired into the monorepo workspace, catalogue, and pnpm lockfile.

• New runenv package (python-3.12.10-pgen): declares olga==1.3.0, polars-lts-cpu==1.33.1, and numpy==2.2.6 as pip dependencies; builds for linux-x64, linux-aarch64, macosx-aarch64, and windows-x64 only — macosx-x64 is intentionally omitted from roots because no llvmlite cp312 wheel exists for that platform.
• Catalogue registration: the 3.12.10-pgen entrypoint and workspace:* dependency are added to catalogue/package.json, following the same pattern as all existing runenvs.
• Changeset: marks a minor bump for both the new package and the runenv-python-3 catalogue, consistent with the project's versioning conventions.

Confidence Score: 5/5

Safe to merge — this is a purely additive change that introduces a new isolated runenv package without touching any existing build logic.

All registration steps (workspace, catalogue entrypoint, catalogue dependency, lockfile) are correctly wired and follow the same conventions as existing runenvs. The intentional omission of macosx-x64 from roots mirrors the torch-cuda package approach and is clearly documented. Dependencies are pinned to specific versions. No existing packages are modified.

No files require special attention.

Important Files Changed

Filename	Overview
python-3.12.10-pgen/config.json	Declares pip dependencies (olga, polars-lts-cpu, numpy) with pinned versions; skip/overrides/platformSpecific/buildWheel are all empty objects, matching the template pattern used by other runenvs.
python-3.12.10-pgen/package.json	Package metadata and block-software artifact declaration; correctly omits macosx-x64 from roots (same pattern as python-3.12.10-torch-cuda) to reflect the intentional platform exclusion due to missing llvmlite cp312 wheel.
catalogue/package.json	Adds 3.12.10-pgen block-software entrypoint and workspace dependency; follows exact same structure as all other runenv entries.
pnpm-workspace.yaml	Registers python-3.12.10-pgen as a workspace package; placed correctly between clustering and catalogue.
.changeset/pgen-runenv.md	Declares a minor version bump for both the new pgen package and the runenv-python-3 catalogue; changeset summary accurately describes the new environment and its platform constraints.
pnpm-lock.yaml	Lockfile correctly updated: adds pgen to the catalogue importer block and creates its own python-3.12.10-pgen importer entry with devDependencies only.
python-3.12.10-pgen/README.md	Documents the environment purpose, transitive numba/llvmlite bundling rationale, and macOS-Intel exclusion; clear and accurate.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[pnpm-workspace.yaml
python-3.12.10-pgen] --> B[python-3.12.10-pgen/package.json
v0.1.0]
    B --> C[python-3.12.10-pgen/config.json
dependencies: olga==1.3.0
polars-lts-cpu==1.33.1
numpy==2.2.6]
    B --> D{Platform roots}
    D --> E[linux-x64
./pydist/linux-x64]
    D --> F[linux-aarch64
./pydist/linux-aarch64]
    D --> G[macosx-aarch64
./pydist/macosx-aarch64]
    D --> H[windows-x64
./pydist/windows-x64]
    D -. intentionally omitted .-> I[macosx-x64
no llvmlite cp312 wheel]
    B --> J[catalogue/package.json
entrypoints: 3.12.10-pgen
dependencies: workspace:*]
    J --> K[block-software artifact
dist/tengo/software/main.sw.json]
    C --> L[transitive deps
numba + llvmlite
via olga]

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%%{init: {'theme': 'base', 'themeVariables': {"darkMode": true, "background": "#0d1117", "primaryColor": "#21262d", "primaryTextColor": "#e6edf3", "primaryBorderColor": "#8b949e", "lineColor": "#8b949e", "textColor": "#e6edf3", "edgeLabelBackground": "#161b22", "actorBkg": "#21262d", "actorBorder": "#8b949e", "actorTextColor": "#e6edf3", "actorLineColor": "#8b949e", "signalColor": "#8b949e", "signalTextColor": "#e6edf3", "noteBkgColor": "#373320", "noteBorderColor": "#d4a72c", "noteTextColor": "#f0e6c0", "labelBoxBkgColor": "#21262d", "labelBoxBorderColor": "#8b949e", "labelTextColor": "#e6edf3", "loopTextColor": "#e6edf3", "activationBkgColor": "#30363d", "activationBorderColor": "#8b949e"}}}%%
flowchart TD
    A[pnpm-workspace.yaml
python-3.12.10-pgen] --> B[python-3.12.10-pgen/package.json
v0.1.0]
    B --> C[python-3.12.10-pgen/config.json
dependencies: olga==1.3.0
polars-lts-cpu==1.33.1
numpy==2.2.6]
    B --> D{Platform roots}
    D --> E[linux-x64
./pydist/linux-x64]
    D --> F[linux-aarch64
./pydist/linux-aarch64]
    D --> G[macosx-aarch64
./pydist/macosx-aarch64]
    D --> H[windows-x64
./pydist/windows-x64]
    D -. intentionally omitted .-> I[macosx-x64
no llvmlite cp312 wheel]
    B --> J[catalogue/package.json
entrypoints: 3.12.10-pgen
dependencies: workspace:*]
    J --> K[block-software artifact
dist/tengo/software/main.sw.json]
    C --> L[transitive deps
numba + llvmlite
via olga]

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_{Reviews (1): Last reviewed commit: "Add OLGA runenv" | Re-trigger Greptile}

[gemini-code-assist]

Code Review

This pull request introduces a new Python 3.12.10 run environment (python-3.12.10-pgen) designed for the Generation Probability block, bundling olga, polars-lts-cpu, and numpy. The environment is registered across the workspace configuration files, including catalogue/package.json, pnpm-lock.yaml, and pnpm-workspace.yaml. There are no review comments, and I have no additional feedback to provide.

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