001550 PaganLab: Colab-ready behavior + optogenetics notebooks - #175
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The prepended Colab-bootstrap cells stored `source` as a list of lines with the trailing newlines stripped. nbformat concatenates source elements verbatim, so the install cell collapsed onto a single physical line beginning with `#@title …` — turning the whole line (including `!pip install` and `!uv pip install`) into one Python comment. The markdown intro/restart cells were similarly run together. CI never caught this because the test harness extracts pins by regex and runs its own install (it stubs the cell), but a Colab user clicking ▶ would have installed nothing. Regenerate the cells with newline-terminated source lines. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Makes the two Pagan Lab notebooks for DANDI:001550 runnable in Colab and green in CI. This is a cleaned-up version of the work in #136 (original notebooks by @weiglszonja); opening as a fresh PR from a branch in this repo.
Both notebooks pass CI end-to-end and were verified locally with
.github/scripts/run_notebook.py(ok: true).What's included:
#@title display-mode: forminstall cell, restart admonition), per the #149 pattern documented indocs/adding-notebooks.md.uv pip compile, constrained to Colab's preinstalled versions (numpy 2.0.2, matplotlib 3.10.0, networkx 3.6.1, pandas 2.2.2, h5py 3.16.0).dandiresolves to 0.76.4. The DANDI server now rejects clients<0.74.0, andcolab-preinstalled.txtpinsclick==8.3.3, which (via the constraint) was holdingdandiback to 0.68.1 — dandi capsclick<8.2.0(dandi-cli#1631). Relaxed theclickconstraint sodandican be current; the minorclickdowngrade in Colab is covered by the restart admonition.ndx-structured-behaviorto commitb3169248(was@main) in both the install cell andenvironment.yml, for reproducibility.jetTransientoutput keys so the notebooks validate against nbformat.fof(Frontal Orienting Field) andinactivateto the codespell ignore list — both correct neuroscience terms.No headless gotchas: all plotting is matplotlib (
plt.show()/ networkx via Agg), which runs fine in CI.🤖 Generated with Claude Code