Refresh colab snapshot

[bendichter]

Colab's default image has changed several times since the snapshot in .github/colab-preinstalled.txt was last refreshed on 2026-08-22, most recently with the move to Ubuntu 24.04 on 2026-09-04. 88 preinstalled packages now differ, so the install cells were pulling click, cryptography, fsspec, pydantic, and others back to the August versions on every run. In 001172/HigleyLab that was 11 downgrades.

Snapshot Refresh and Re-Lock

The snapshot is refreshed from googlecolab/backend-info and the 44 CI-tested notebooks are re-locked against it. Every pin that changed matches Colab's current version, and no package outside the snapshot moved. Notebooks excluded from CI are left alone because their pins cannot be verified after a re-lock. Two of them (validate_lev6 and the cosyne advanced_asset_search) hold click==8.1.8 for the dandi releases they pin, and re-locking them would have moved dandi to 0.80 and pynwb to 4.2.

Re-Locks Keep Current Pins

lock_notebook.py now hands the notebook's current pins to uv as the previous lock, so a re-lock moves only what the snapshot or requirements.in forces. Before this change a re-lock also floated packages Colab does not ship (dandi 0.77 to 0.80, numcodecs, deno, blessed), which would have turned each snapshot refresh into an untested upgrade. --upgrade restores the old behavior of resolving everything afresh.

Weekly Refresh Job

.github/workflows/refresh-colab-snapshot.yml runs refresh_colab_snapshot.py --relock on Mondays at 05:00 UTC, an hour before the weekly test run, and on manual dispatch. When the snapshot has drifted it pushes to bot/refresh-colab-snapshot and opens or updates one PR that lists the changed packages.

A PR opened with the default GITHUB_TOKEN does not trigger "Test changed notebooks". The workflow uses a COLAB_REFRESH_TOKEN secret when one exists and falls back to the default token. Without the secret, the bot PR needs a close and reopen to get CI.

The workflow has not run yet. I would dispatch it once after merge to confirm it reports no drift.

🤖 Generated with Claude Code

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Executed notebooks

CI executes the notebooks changed in this PR through a Jupyter kernel and publishes each one, with its outputs, as soon as it finishes. Links appear below as notebooks complete; an hourglass means the notebook is still running.

• ✅ 000108/chunglab/demo/2021-09-27_dandi-demo.ipynb
• ✅ 000108/chunglab/demo/dashboard.ipynb
• ✅ 000402/MICrONS/demo/000402_microns_demo.ipynb
• ✅ 000409/IBL/bwm_usage_notebook.ipynb
• ✅ 000458/AllenInstitute/reanalysis.ipynb
• ✅ 000458/FlatironInstitute/000_lindi_vs_fsspec_streaming.ipynb
• ✅ 000458/FlatironInstitute/001_summarize_contents.ipynb
• ✅ 000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure1d.ipynb
• ✅ 000559/dattalab/markowitz_gillis_nature_2023/reproduce_figure_S1.ipynb
• ✅ 000582/Sargolini2006/000582_Sargolini2006_demo.ipynb
• ✅ 000718/CaiLab/zaki_2024/000718_demo.ipynb
• ✅ 000727/clandinin/simple_data_access/reading_data.ipynb
• ✅ 000728/AllenInstitute/visual_coding_ophys_tutorial.ipynb
• ✅ 000947/TurnerLab/public_demo/000947_demo.ipynb
• ✅ 000971/lernerlab/seiler_2024/fiber_photometry_example_notebook.ipynb
• ✅ 000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb
• ✅ 001038/DombeckLab/001038_demo.ipynb
• ✅ 001075/001075_paper_figure_1d.ipynb
• ✅ 001084/HoweLab/001084_demo.ipynb
• ✅ 001170/ReimerLab/public_demo/001170_demo.ipynb
• ✅ 001172/HigleyLab/001172_demo.ipynb
• ✅ 001528/HnaskoLab/Lotfi_2025/001528_demo.ipynb
• ✅ 001538/catalyst_neuro/zhai_2025/figure_1E_dspn_somatic_excitability.ipynb
• ✅ 001538/catalyst_neuro/zhai_2025/figure_2GH_oepsc_analysis.ipynb
• ✅ 001538/catalyst_neuro/zhai_2025/figure_5F_acetylcholine_biosensor.ipynb
• ✅ 001538/catalyst_neuro/zhai_2025/how_to_use_this_dataset.ipynb
• ✅ 001550/PaganLab/01_behavior_demo.ipynb
• ✅ 001550/PaganLab/02_optogenetics_demo.ipynb
• ✅ 001636/TurnerLab/motor_cortex/antidromic_detection_tutorial.ipynb
• ✅ 001636/TurnerLab/motor_cortex/turner_m1_glm.ipynb
• ✅ 001636/TurnerLab/motor_cortex/turner_m1_peth.ipynb
• ✅ 001636/TurnerLab/motor_cortex/turner_m1_usage.ipynb
• ✅ 001687/wanglab/figure2-distance-tuning/figure2_distance_tuning.ipynb
• ✅ 001712/IBL-Widefield/public_demo/raw_widefield.ipynb
• ✅ 001754/CatalystNeuro/001754_demo.ipynb
• ✅ 001933/DombeckLab/001933_demo.ipynb
• ✅ dandi/DANDI User Guide, Part I.ipynb
• ✅ dandi/DANDI User Guide, Part II.ipynb
• ✅ demos/NWBWidget-demo.ipynb
• ✅ tutorials/bcm_2024/analysis-demo.ipynb
• ✅ tutorials/cosyne_2023/simple_dandiset_search.ipynb
• ✅ tutorials/neurodatarehack_2024/advanced_asset_search.ipynb
• ✅ tutorials/neurodatarehack_2024/simple_dandiset_search.ipynb
• ✅ tutorials/open_data_quick_start_2026/Get-to-know-a-Dandiset.ipynb

44 of 44 finished. Commit 2e8dc6c. The executed copies live only in the preview and are removed when the PR closes; nothing is committed to the branch.