Update anndata version to suppport newer h5ad files

[mzueva]

Update anndata version to suppport newer h5ad files

[gemini-code-assist]

Summary of Changes

Hello @mzueva, 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 primarily focuses on enabling support for newer H5AD file formats by upgrading the anndata library and its associated Python environment. This core update necessitated a cascade of dependency version bumps across the project's pnpm lockfile and workspace configuration, ensuring all components remain compatible and up-to-date.

Highlights

• Anndata Version Update: The anndata library, crucial for handling H5AD files, has been updated from version 0.11.3 to >=0.12.6 in the software/parse-h5ad/src/requirements.txt file. This update is accompanied by the addition of pandas>=2.0.0 as a dependency.
• Python Environment Adjustment: The Python execution environment for the parse-h5ad software has been specifically updated in software/parse-h5ad/package.json from 3.12.10-sccoda to 3.12.10-h5ad, reflecting the new requirements for supporting modern H5AD file formats.
• Extensive Dependency Updates: Numerous other project dependencies across various @platforma-sdk and @milaboratories packages, as well as several third-party libraries (e.g., Babel, Vitest, Browserslist, Istanbul), have been updated to their latest compatible versions. This ensures overall project health and compatibility with the core anndata upgrade.

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[gemini-code-assist]

Code Review

This pull request updates the anndata library to support newer .h5ad file formats. The changes primarily involve updating dependency versions in pnpm-lock.yaml, pnpm-workspace.yaml, and requirements.txt. The core change is upgrading anndata and adding pandas as an explicit dependency. My review focuses on ensuring the stability and reproducibility of the Python environment. I've suggested using more restrictive version specifiers in requirements.txt to prevent potential breaking changes from future major version updates of the dependencies.