[k0stik]

Jira: SOF-8099
Platform change: mat3ra/web-app#3026. Merge and release this PR together with it.
Uses client.files from mat3ra/api-client#51, released as mat3ra-api-client 2026.11.4.post0.

Why

The platform no longer accepts file bodies: public POST files is removed, and every file goes straight to storage with a signed URL. The notebooks uploaded text through POST files, so they would break.

What changes

• Notebooks (custom_python_calculation.ipynb, custom_shell_calculation.ipynb): upload with one call to the API client, client.files.upload(files_to_upload, account_id=ACCOUNT_ID). Files are read as bytes and passed on as they are; the markdown no longer says text "travels inside the request".
• notebooks_utils/core/entity/file/api.py: keeps only to_object_storage_input. The upload itself (one files/signed-urls putObject request with each file's size and content type, then a PUT per file with the signed headers) now lives in mat3ra-api-client as FileEndpoints.upload, with its tests.

Dependency

pyproject.toml and config.yml (api, api_examples) require mat3ra-api-client>=2026.11.4.post0.

Testing

• pytest tests/py/unit: 143 passed with the client from api-client#51 (the earlier JobEndpoints.auth failure was an outdated client).
• client.files against a local web-app (S3): text and binary upload, download round-trip, folder delete.
• The JupyterLite path: in a browser worker with this repo's Pyodide 0.24.1 and pyodide-http, a binary requests.put to a signed S3 URL with the signed headers returns 200 and the object reads back byte for byte.
• Not run end to end yet: the web-app Cypress features api-examples/custom_python_calculation and custom_shell_calculation cover the notebooks.

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