Milab 4784 fix deduplication and update

[aiturbidemil]

No description provided.

[gemini-code-assist]

Summary of Changes

Hello @aiturbidemil, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request significantly enhances the dimensionality reduction block by introducing a more structured and maintainable workflow architecture through the adoption of Tengo templates. It expands the block's descriptive documentation to clearly outline its advanced capabilities, including PCA, t-SNE, UMAP, and Harmony batch correction. Additionally, the PR incorporates a broad set of dependency updates to ensure the project uses the latest stable versions of its underlying libraries.

Highlights

• Workflow Refactoring with Tengo Templates: The core dimensionality reduction and batch correction logic has been refactored into dedicated Tengo workflow templates (batch-correction.tpl.tengo and dim-reduction-calculation.tpl.tengo). The main workflow now utilizes these templates via render.create, significantly improving modularity and maintainability.
• Enhanced Dimensionality Reduction Capabilities: The dimensionality reduction block's description has been extensively updated to detail its support for Principal Component Analysis (PCA), t-distributed Stochastic Neighbor Embedding (t-SNE), Uniform Manifold Approximation and Projection (UMAP), and optional Harmony batch correction. This provides clearer insight into the block's functionality.
• Improved Trace Labeling: The trace labels generated by the workflow have been made more informative, now explicitly including 'Dimensionality Reduction' or 'Batch Corrected Dimensionality Reduction' along with the parameters (nPCs, nNeighbors) for better clarity in output visualization.
• Dependency Updates: Numerous dependencies across @platforma-sdk packages and other third-party libraries (e.g., @milaboratories, @vitest, commander, debug, es-module-lexer, expect-type, fdir, magic-string, picomatch, selfsigned, std-env, tinyglobby, tinyrainbow, tslib) have been updated, as reflected in pnpm-lock.yaml and pnpm-workspace.yaml.
• Version and Changelog Entry: A new changeset entry (famous-hounds-dress.md) indicates a minor version bump for @platforma-open/milaboratories.dimensionality-reduction.workflow and @platforma-open/milaboratories.dimensionality-reduction, alongside a description of enabling block deduplication and improving the trace label. Note: The block/package.json diff shows a version change from 1.2.16 to 1.2.15, which appears to be a version correction or specific release numbering rather than a direct increment.

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[gemini-code-assist]

Code Review

This pull request introduces several valuable improvements, including a significant refactoring of the workflow logic into modular Tengo templates, which greatly enhances readability and maintainability. The block's documentation and descriptions have also been substantially updated, providing clearer and more comprehensive explanations. However, there is a critical issue in block/package.json where the version number has been incorrectly decremented. Additionally, there are a few opportunities to improve maintainability by replacing hardcoded values for resource allocation and cache durations with named constants or variables.

[gemini-code-assist]

The package version has been decremented from 1.2.16 to 1.2.15. Package versions should follow Semantic Versioning and always be incremented for new changes. Please revert this to 1.2.16 and allow the automated release process to handle the version bump based on the changeset file.

Suggested change

	"version": "1.2.15",
	"version": "1.2.16",

[gemini-code-assist]

The cache duration is hardcoded as a magic number. To improve readability and maintainability, it's better to define this value as a named constant at the top of the file.

For example:

cacheDuration := 24 * 60 * 60 * 1000 // 24 hours

Then, you can use this constant here: cache(cacheDuration).

[gemini-code-assist]

The cache duration is hardcoded as a magic number. To improve readability and maintainability, it's better to define this value as a named constant at the top of the file.

For example:

cacheDuration := 24 * 60 * 60 * 1000 // 24 hours

Then, you can use this constant here: cache(cacheDuration).

[gemini-code-assist]

The memory (32GiB) and CPU (16) resources are hardcoded here and also in the batchCorrectionRender block. To improve maintainability and avoid duplication, consider defining these as constants at the top of the file and reusing them in both places.

For example:

// At the top of the file
defaultExecMem := "32GiB"
defaultExecCpu := 16

// ... then use them in the render blocks
mem: defaultExecMem,
cpu: defaultExecCpu