Upgrade SDK

[kevindetry-milaboratories]

Greptile Summary

This PR upgrades several @platforma-sdk and @milaboratories packages across the monorepo and removes "private": true from parse-h5ad and parse-seurat packages to enable their publication via changesets.

• SDK version bumps: @platforma-sdk/block-tools 2.11.5 → 2.11.6, @platforma-sdk/test 1.79.21 → 1.79.23, with transitive updates to @milaboratories/pl-drivers (1.16.2 → 1.16.3) and @milaboratories/pl-middle-layer (1.64.39 → 1.64.41).
• Publishability change: "private": true removed from both software sub-packages, aligned with new changeset entries for patch-level release.
• Lockfile corrections: rolldown-plugin-dts peer dependency now consistently resolves against typescript@5.9.3 instead of the previously mismatched typescript@5.6.3.

Touched Terms:

Term	Definition	Change
@platforma-sdk/block-tools	CLI and build tooling for Platforma SDK blocks	Bumped 2.11.5 → 2.11.6 (patch) in catalog and lockfile
@platforma-sdk/test	Vitest-based test harness for Platforma SDK packages	Bumped 1.79.21 → 1.79.23 (skipping .22) in catalog and lockfile
@milaboratories/pl-middle-layer	Platforma middle-layer runtime, manages block/driver lifecycle	Transitive bump 1.64.39 → 1.64.41 via @platforma-sdk/test and block-tools
@milaboratories/pl-drivers	Low-level platform I/O drivers	Transitive bump 1.16.2 → 1.16.3 via pl-middle-layer
obug	Utility for structured error/bug reporting in Vitest ecosystem	Transitive bump 2.1.1 → 2.1.3
private (package.json field)	npm field that prevents a package from being published	Removed from parse-h5ad and parse-seurat, enabling changeset-driven publishing
rolldown-plugin-dts	Rolldown plugin for TypeScript declaration bundling	Peer dependency resolved TypeScript version corrected from 5.6.3 → 5.9.3

Confidence Score: 5/5

Safe to merge — all changes are version bumps to patch-level SDK dependencies and the intentional removal of 'private': true to enable publishing of two sub-packages.

The diff is limited to dependency version bumps, lockfile reconciliation, and the deliberate exposure of parse-h5ad and parse-seurat for npm publication. The 'private' removal is clearly coordinated with the new changeset file, and the lockfile correctly resolves the typescript peer-dep inconsistency in rolldown-plugin-dts.

No files require special attention. The removal of 'private': true in both software package.json files is intentional and backed by the changeset entry.

Important Files Changed

Filename	Overview
.changeset/ripe-sites-do.md	New changeset entry registering patch bumps for parse-seurat, parse-h5ad, and the root samples-and-data package; straightforward and correct.
pnpm-workspace.yaml	Catalog entries bumped for @platforma-sdk/block-tools (2.11.5→2.11.6) and @platforma-sdk/test (1.79.21→1.79.23); no issues.
pnpm-lock.yaml	Lockfile reflects all catalog bumps plus transitive upgrades (pl-drivers, pl-middle-layer, obug); also fixes rolldown-plugin-dts peer dep from typescript@5.6.3 to typescript@5.9.3.
software/parse-h5ad/package.json	Removed 'private': true to allow npm publishing; intentional change aligned with the new changeset entry.
software/parse-seurat/package.json	Removed 'private': true to allow npm publishing; intentional change aligned with the new changeset entry.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    WS["pnpm-workspace.yaml\n(catalog)"]
    BT["@platforma-sdk/block-tools\n2.11.5 → 2.11.6"]
    TEST["@platforma-sdk/test\n1.79.21 → 1.79.23"]
    ML["@milaboratories/pl-middle-layer\n1.64.39 → 1.64.41"]
    DRV["@milaboratories/pl-drivers\n1.16.2 → 1.16.3"]
    OBUG["obug\n2.1.1 → 2.1.3"]
    H5AD["parse-h5ad\nremoved private:true"]
    SEURAT["parse-seurat\nremoved private:true"]
    CS[".changeset/ripe-sites-do.md\npatch release for 3 packages"]

    WS --> BT
    WS --> TEST
    TEST --> ML
    ML --> DRV
    TEST --> OBUG
    BT --> ML
    H5AD --> CS
    SEURAT --> CS

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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
    WS["pnpm-workspace.yaml\n(catalog)"]
    BT["@platforma-sdk/block-tools\n2.11.5 → 2.11.6"]
    TEST["@platforma-sdk/test\n1.79.21 → 1.79.23"]
    ML["@milaboratories/pl-middle-layer\n1.64.39 → 1.64.41"]
    DRV["@milaboratories/pl-drivers\n1.16.2 → 1.16.3"]
    OBUG["obug\n2.1.1 → 2.1.3"]
    H5AD["parse-h5ad\nremoved private:true"]
    SEURAT["parse-seurat\nremoved private:true"]
    CS[".changeset/ripe-sites-do.md\npatch release for 3 packages"]

    WS --> BT
    WS --> TEST
    TEST --> ML
    ML --> DRV
    TEST --> OBUG
    BT --> ML
    H5AD --> CS
    SEURAT --> CS

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_{Reviews (1): Last reviewed commit: "Upgrade SDK" | Re-trigger Greptile}

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[gemini-code-assist]

Code Review

This pull request upgrades several SDK dependencies, including @platforma-sdk/block-tools and @platforma-sdk/test, and updates the workspace catalog and lockfile accordingly. Additionally, it removes the private flag from the package.json files of parse-h5ad and parse-seurat software packages, and adds a changeset file for publishing. There are no review comments, so I have no feedback to provide.

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