[solarsys]

Summary

The tutorials page opens the notebook copies in examples/tutorials/series, which predate the 2.1.0 release (they install PyHealth from GitHub and miss the fixes since). This points the page at the maintained 2.1 Colab notebooks, the same ones listed on pyhealth.dev:

• Tutorial series 00–08: links go to the 2.1 Colab notebooks, which install pyhealth==2.1.0. The descriptions for 04 and 07 are updated: 04 compares six models, 07 adds label distributions and baseline checks, and both open on a free T4 GPU.
• New "What's new in PyHealth 2.1" section: the three short notebooks on splits and reproducibility, calibration and confidence intervals, and XGBoost/code mapping.
• Two existing RST errors fixed on the same page:
  • A mis-indented row broke the readmission examples table ("exactly one bullet list expected").
  • The commented-out "Pipeline 5" link swallowed the "Multimodal & Smart Processors" heading.

The notebooks in examples/tutorials/series are unchanged; this PR only changes docs/tutorials.rst.

Testing

• Parsed docs/tutorials.rst with docutils: no errors. The only remaining warning is the pre-existing transition at the end of the file.
• tools/check_pr_rules.py passes.

🤖 Generated with Claude Code

[github-actions]

Test Coverage

Total: 69.05% (17723 / 25668 lines)

Modified file	Coverage	Lines
pyhealth/autoimprove/__init__.py	100.00%	6 / 6
pyhealth/autoimprove/evaluate.py	92.07%	151 / 164
pyhealth/autoimprove/improver.py	95.63%	372 / 389
pyhealth/autoimprove/llm.py	90.62%	29 / 32
pyhealth/autoimprove/proposers.py	93.91%	108 / 115
pyhealth/autoimprove/space.py	95.31%	122 / 128
pyhealth/datasets/omop.py	100.00%	18 / 18
pyhealth/metrics/calibration.py	65.00%	52 / 80
pyhealth/metrics/multiclass.py	25.00%	26 / 104
pyhealth/models/__init__.py	100.00%	52 / 52
pyhealth/models/survival_mdn.py	93.83%	213 / 227
pyhealth/processors/deep_nested_sequence_processor.py	91.37%	180 / 197
pyhealth/processors/nested_sequence_processor.py	92.94%	158 / 170
pyhealth/processors/sequence_processor.py	95.77%	68 / 71
pyhealth/processors/stagenet_processor.py	84.08%	169 / 201

Workflow run · 8986d28

[solarsys]

looks good

[solarsys]

@jhnwu3 could you review and approve this when you get a chance? It only changes docs/tutorials.rst, linking the tutorials page to the PyHealth 2.1 Colab notebooks listed on pyhealth.dev. Checks pass. Auto-merge is not enabled on this repository, so it will be merged by hand once approved.

[solarsys]

/review

[github-actions]

Previous review

AI review: findings

Docs-only change to docs/tutorials.rst. It repoints the 00–08 tutorial links to the 2.1 Colab notebooks, updates the 04 and 07 descriptions, adds a "What's new in PyHealth 2.1" table for three notebooks, and fixes two RST errors (a mis-indented readmission table row and a commented-out Pipeline 5 line that swallowed a heading). I checked the claims against the repo: pyproject.toml is 2.1.0, the local notebooks install pyhealth==2.1.0, notebooks 00, 04 and 07 carry T4 GPU metadata, and PatientSplit, set_pos_weight, CCSR, nested_multihot, XGBoostModel and TreeSHAP all exist, so the feature names on the page are accurate. No code is added, so nothing is redundant with existing components. Blocking (medium): the "What's new" intro says the three notebooks "walk through every 2.1 change", but CHANGELOG.md's 2.1.0 section also lists the Synthea model, the HALO vectorisation and the Trainer best-epoch change, which none of the three notebooks cover. Non-blocking (low): the Colab Drive IDs cannot be checked from the repository, since the local notebooks are the only in-repo copies. Testing is a docutils parse, which is adequate for an RST-only edit. Overall risk is low; the one fix needed is rewording the overclaim.

_{Reviewed commit d4bd9f8}

[github-actions]

Previous review

AI Review

suggestion: need change
decision: need change

Thank you for this PR. Pointing the tutorials page at the maintained 2.1 Colab notebooks, adding the "What's new in PyHealth 2.1" section, and fixing the two RST errors (the mis-indented table row and the swallowed heading) all make the page better. It is close. Coverage isn't a concern for this docs-only change: the whole-repo total is 67.88%, above the 60% bar, and no files under pyhealth/ changed.

To get this merged:

• Reword the intro of the "What's new in PyHealth 2.1" section. It says the three notebooks "walk through every 2.1 change", but the 2.1.0 section of CHANGELOG.md also lists changes that none of the three cover: the Synthea model, the HALO vectorisation and the Trainer best-epoch change. Please either soften the sentence (for example, "walk through the main 2.1 changes on runnable examples") or add coverage of those items. Keeping the link to the release notes for the complete list would help.

Optional suggestions:

• The Colab Drive links can't be checked from the repository. Please open each one once, in a signed-out browser, to confirm it is shared publicly and installs pyhealth==2.1.0.

_{Reviewed commit d4bd9f8}

[solarsys]

Thanks for the review. Fixed in 8986d28: the intro now says the three notebooks "walk through the main 2.1 features on runnable examples", and points to the release notes for the full list of changes.

On the optional point, all twelve Colab links on the page (tutorials 00–08 and the three 2.1 notebooks) open signed-out. Each returns 200 from drive.google.com/file/d/<id>/view, with no redirect to sign-in.

[solarsys]

/review

[github-actions]

AI review: findings

This docs-only PR changes docs/tutorials.rst. It repoints tutorials 00-08 from the GitHub-hosted notebooks in examples/tutorials/series to the maintained 2.1 Colab copies, updates the 04 and 07 descriptions, and adds a "What's new in PyHealth 2.1" table of three notebooks. It also fixes an RST indentation error in the readmission table and a commented-out link that swallowed the "Multimodal & Smart Processors" heading. The Colab IDs for tutorials 00-08 match the cross-links inside the repo's notebooks, and the T4 GPU and model-list claims match examples/tutorials/series/README.md. Every API the new section names exists: PatientSplit with four ratios, BaseModel.set_pos_weight, bootstrap_ci, the calibration metrics listed in CHANGELOG.md, XGBoostModel with TreeSHAP, CCSR mapping, and nested_multihot. Nothing is redundant, since no code is added. There are no code or test changes, and the author reports a docutils parse, which I could not re-run here. Non-blocking: the three "What's new" Colab IDs and the v2.1.0 release-notes URL appear nowhere else in the repo, so someone should open them before merge. Overall risk is low, with no blocking problems found.

_{Reviewed commit 8986d28}

[github-actions]

[low] Three "What's new" Colab links are not verified anywhere in the repo

The Colab IDs for the three new 2.1 notebooks (lines 53, 55, 57) appear only in this file. The tutorial series links are cross-linked from the repo's own notebooks, but the whats_new_*.ipynb files and examples/tutorials/series/README.md do not link to these Colab copies. The README points readers to pyhealth.dev for the maintained copies instead. Before merge, open each link and confirm it goes to the matching 2.1 notebook. Consider adding the same links to the whats_new notebooks or the README so they can be checked in the repo.

[github-actions]

[low] Release-notes URL for v2.1.0 is not referenced elsewhere in the repo

The link to https://github.com/sunlabuiuc/PyHealth/releases/tag/v2.1.0 is not found in the repo; CHANGELOG.md does list the 2.1 features. Confirm that the GitHub release tag exists before merge so the link does not 404.

[github-actions]

AI Review

suggestion: approve
decision: approve

Thank you for this update. Pointing the tutorials page at the maintained PyHealth 2.1 Colab notebooks is useful. The new "What's new in PyHealth 2.1" section and the two RST fixes (the mis-indented readmission table row and the commented-out Pipeline 5 link that swallowed a heading) are welcome too.

The diff only changes docs/tutorials.rst, matching your description, and I found no problems with the edits. The descriptions for 04 and 07 and the API names in the new section look consistent with the library.

Coverage: The whole repository is at 69.05%, above the 60% bar. The coverage report lists some pyhealth/ files, such as metrics/multiclass.py at 25% and metrics/calibration.py at 65%. This PR doesn't touch them, so they don't count against it. A docs-only change needs no new tests.

This looks ready to merge.

Optional suggestions:

• Before merging, open the three new "What's new" Colab links and the v2.1.0 release-notes URL. I can't check from the diff that they are public and load correctly.
• Make sure each Colab notebook is shared as "anyone with the link can view", so readers don't hit a permissions wall.

_{Reviewed commit 8986d28}