tutorial figures (notebook + docs) + PyPI README images + release 0.2.0

[settylab-dotto-bot]

What & why

The tutorial should actually contain its outputs and figures; the red v0.1.0 PyPI deployment and the broken images on the PyPI project page should be fixed; and — since blend (#1), the reuse cache (#2) and smooth-all-once (#3) landed after v0.1.0 — the package should be released as 0.2.0, correctly this time.

A. Tutorial ships executed, with figures (notebook and docs)

Diagnosis. The #3 smooth-all-once merge (9d6ac8c) rebuilt tutorial.ipynb from build_tutorial.py but committed it unexecuted — every output stripped (0 figures; 682501e had 5). The docs ship the notebook pre-executed (nb_execution_mode = "off"), so the live page rendered zero figures and outputs (0 <img>, 0 cell-output containers). The mystnb.unknown_mime_type suppression was a red herring — image/png is standard and renders fine; the sole gap was the missing committed outputs.

Fix. Re-executed on the full 36k-cell section (canonical notebooks/run_tutorial.sh: build → nbconvert --execute → scrub). The committed notebook now carries 7 image/png figures, 0 error outputs, the level-three truncation UserWarning preserved on stderr, and 0 host-path/UUID leaks (scrub exit 0). Local docs build embeds all 7 figures (<img src="_images/…png">). tests/test_tutorial_artifact.py passes 7/7.

Two supporting bug fixes surfaced during re-execution:

• build_tutorial.py — the 10x CloudFront CDN rejects the default Python-urllib User-Agent with HTTP 403, so the dataset download cell failed for everyone. Present a browser User-Agent.
• tests/test_tutorial_artifact.py — the host-path leak test scanned the raw notebook JSON including base64 image data, where /fh/ appears by chance in a big enough figure — a spurious failure. Now scans only the readable surfaces the scrubber cleans (source, stream, text/plain|html|markdown, traceback), never encoded media. Same real intent, no base64 flakiness.

D. Release 0.2.0 (this PR bumps the version; the operator publishes)

blend (#1), the smoothing reuse cache (#2) and smooth-all-once all_genes=True (#3) are new user-facing features since v0.1.0 → a MINOR bump is the correct SemVer step. Bumped pyproject.toml + src/spatial_smooth/__init__.py to 0.2.0 (conf.py tracks __version__, so docs follow); updated the illustrative check_dependencies() output in installation.rst; added a CHANGELOG.md. twine check passes on the 0.2.0 sdist+wheel; full test suite green.

C. Broken images on the PyPI project page

The PyPI long-description is the README (pyproject.toml readme); PyPI resolves image src against nothing, so the two relative figure paths 404 on the project page (and the notebooks/tutorial.ipynb / LICENSE links 404 off-site). Rewrote all four to absolute URLs (raw.githubusercontent.com/.../main/…; github.com/.../blob/main/…). Rendered long-description <img> srcs are absolute and HTTP 200; twine check passes; GitHub still renders everything.

This only becomes visible on the 0.2.0 release. PyPI freezes the long-description per version, so the README image fix does not repair the existing v0.1.0 page — publishing 0.2.0 (below) is what makes the broken-images fix actually show on pypi.org.

B. Why v0.1.0's deployment was red (root cause; fixed by the release procedure, not code)

Run 29120105023 failed at pypa/gh-action-pypi-publish, verbatim:

Trusted publishing exchange failure:
* `invalid-publisher`: valid token, but no corresponding publisher (Publisher with matching claims was not found)
  sub: repo:settylab/spatial-smooth:environment:pypi
  workflow_ref: settylab/spatial-smooth/.github/workflows/release.yml@refs/tags/v0.1.0
  environment: pypi

The OIDC token is valid; PyPI simply has no Trusted Publisher registered for these claims. release.yml is correct (id-token: write, environment pypi, skip-existing: true, @release/v1) — the claims match a TP registration exactly — so no workflow code change. The fix is the one-time TP registration in the release procedure below.

The release procedure — do 0.2.0 correctly this time (operator-owned)

Ordered steps so v0.2.0 publishes green with working images. Steps (a)/(c) need a PyPI project owner and actions:write, which the bot lacks — all operator-owned:

1. (a) Register the pypi.org Trusted Publisher — the missing piece that reddened v0.1.0. On pypi.org → project spatial-smooth → Publishing → add a GitHub Actions publisher: owner settylab, repository spatial-smooth, workflow filename release.yml, environment pypi.
2. (b) Merge this PR (tutorial figures (notebook + docs) + PyPI README images + release 0.2.0 #4) to main.
3. (c) Tag v0.2.0 and publish the GitHub release (Releases → Draft a new release → tag v0.2.0 on main → Publish). Publishing fires release.yml; the OIDC claims now match the TP → it builds and publishes to PyPI. (workflow_dispatch also works, but the release: published trigger is the intended path.)
4. (d) Verify: the pypi deployment is GREEN; pypi.org/project/spatial-smooth/ shows 0.2.0; and the project-page images now render — because 0.2.0's long-description carries the absolute URLs. (The v0.1.0 page stays broken; that's expected — PyPI freezes it per version.)

Do not cut/publish the release from this PR — it is operator + actions:write-gated.

Verification (in this branch)

• notebook: 7 image/png, 0 errors, truncation warning on stderr, 0 readable leaks (scrub exit 0)
• docs: local Sphinx/myst-nb build embeds all 7 figures; title reads spatial-smooth 0.2.0
• version: pyproject.toml + __version__ = 0.2.0; ss.__version__ == "0.2.0"
• pytest full suite → green; twine check dist/* → PASSED on the 0.2.0 sdist+wheel
• long-description <img> srcs absolute + HTTP 200

Notes

• Base main. Please review — do not merge on my behalf (public flagship repo). Nothing published.
• The _static/*.png README assets are unchanged (they already resolve at main).