Notebook: three code cells (1. Install, 2. Mount Google Drive, 3. Run preprocessing) - #267

Owner request of 10 November 2026. Like the lab's ZeroCostDL4Mic and NucleiSky notebooks, notebooks/MorphoBricks_Preprocessing.ipynb now has three code cells instead of one. Each cell sits under a Markdown heading that explains it.

Unchanged: RELEASE_TAG v0.5.0, RELEASE_REF fd7afd339bcaab7579c806a28a65bb7ecebe940c, the install target and extras, DEVELOPMENT_OVERRIDE, SETUP_RECORD, and PreprocessingNotebook(describe=True) with the same display(app). This PR changes only how the code is split into cells, the Markdown, and the docs and tests that describe them. The v0.5.1 release PR moves RELEASE_REF later.

The cells

1. # @title 1. Install MorphoBricks preprocessing: the previous bootstrap code without the Drive mount. It still checks for a nearby checkout, an installed package or the pinned GitHub install, sets EXTRAS to notebook,zarr on Colab, checks that notebook_ui imports, and prints the version report followed by "Next: run cell 2 …, then cell 3 …". It does not ask for a restart. Running it again installs nothing that is already there (tested).
2. # @title 2. Mount Google Drive: drive.mount("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/content/drive") inside the Colab guard, with the same refusal as before when the mount fails. Outside Colab it prints one line: "Not Google Colab: there is no Google Drive to mount here, so nothing was done." It raises no error there.
3. # @title 3. Run preprocessing: builds and displays the app.
   • If SETUP_RECORD was never filled, it stops with a RuntimeError saying "run cell 1 (Install MorphoBricks preprocessing) first". That covers a fresh kernel and a cell 1 that failed. It does not fail with an ImportError.
   • On Colab without /content/drive/MyDrive, it stops and names cell 2. Nothing falls back silently to the runtime's disk.
   • No cell runs another cell's code.

The code-cell metadata is copied from the old cell (source hidden, JupyterLab hide-code lock).

Tests

• tests/test_notebook_file.py:
  • The notebook layout: an introduction, then exactly three heading + code pairs in order, with these titles.
  • What each cell does: the install cell alone has the pin, pip and the version report. The Drive cell only mounts. The run cell only shows the app and never installs, mounts or calls _install_preprocessing.
  • RELEASE_CALLS and release_call() are kept. Exactly one PreprocessingNotebook(...) call across all cells, and it is in cell 3.
  • A new AST check: /content strings and google imports appear only inside the Colab guard. No magics.
  • Real-kernel runs (nbclient): all three cells outside Colab, where cell 2 must print its single line; all three with a faked google.colab; and cell 3 alone in a fresh kernel, which must give a RuntimeError naming cell 1.
• tests/test_notebook_setup.py:
  • All the existing bootstrap tests are kept. They now run the cells in one shared namespace, and /content/drive is replaced by a temporary folder that the fake drive.mount fills.
  • New tests:
    • cell 1 neither mounts Drive nor shows the app;
    • cell 1 run twice installs once;
    • cell 2 outside Colab prints one line and does nothing;
    • cell 2 alone on Colab only mounts;
    • cell 3 without cell 1 names cell 1, on and off Colab;
    • cell 3 after a failed cell 1 still names cell 1;
    • cell 3 on Colab without Drive names cell 2, and works once cell 2 has run;
    • cell 3 outside Colab needs no cell 2.

Docs

• docs/colab-release-check.md section A: the smoke check now covers the three cells, including running them out of order and running cell 1 twice.
• docs/user_guide.md §1 and its Colab section, README.md, AGENTS.md (Notebook target row, the notebook-file tests, §7 code cells), the plan's Q58 amendment and a CHANGELOG "Unreleased" entry.

Verification

• python tools/check.py on f67bea0 (main 78cda50 merged in, including SWEEP-PP (A): remove the remaining compatibility code (PP-05..PP-10) and fix the frozen clock (#262) #265 and SWEEP-PP (B): experiment_design.csv is output only, and the pairing card is rebuilt on the draft (PP-02) #266): ruff check and format clean, 5163 passed, 4 skipped, code rules clean.
• 6a2f37d (head) changes only the tests: the faked Drive path is now substituted into the cells in POSIX form. A Windows temporary path inside a Python string literal is a \U… escape error, which made 16 notebook tests fail on Windows CI for f67bea0. After that commit, the notebook tests and code rules were run locally (58 passed). CI on 6a2f37d is green on all 7 jobs (lint, and ubuntu/macos/windows × 3.11/3.13).
• The 4 skips are platform skips that were already there:
  • test_cli_log.py:166, test_folder_rules.py:199 and test_folder_rules.py:230: the file system tells names apart by case;
  • test_discovery.py:665: running as root ignores file modes.
• Headless Chromium screenshots of the three cells' output (JupyterLab and faked Colab), and of cell 3 run alone, were rendered for the owner.

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