DOC: Update docs for new tutorials, issues templates - #131
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Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review. WalkthroughThe pull request adds structured GitHub issue forms and a comprehensive contribution guide. It publishes the guide through Sphinx and updates repository links. It also expands the tutorial documentation from 15 to 18 tutorials and adds preview updates. ChangesContribution and Issue Guidance
Tutorial Documentation Expansion
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: ⚪ Minimal · up to This change adds contribution and issue-intake documentation, updates repository links, and expands tutorial documentation. No current merge-readiness risk is identified. 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
Full details: Title checkExplanation The title accurately identifies the documentation updates, new tutorials, and issue templates. It is concise and directly related to the main changes, although it does not mention the new contributing guide. Full details: Docstring CoverageExplanation No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0 files. (4 skipped: 4 unsupported.) ✨ Finishing Touches🧪 Generate unit tests (beta)
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🟡 Changes recommended
The docs include path currently yields a duplicated “Contributing” top-level title (reST title + Markdown H1), which is likely to produce Sphinx warnings and incorrect document structure.
Once you've addressed the issues Copilot identified, you can request another Copilot review.
Pull request overview
Updates PhysioTwin4D’s contributor-facing documentation by aligning the tutorials index with newly added Tutorial 16–18 content, centralizing the contributing guide into a root-level CONTRIBUTING.md, and adding structured GitHub Issue Forms to improve inbound reporting.
Changes:
- Refresh tutorials landing page counts/cards and expand docs for Tutorials 16–18, including a new preview figure for Tutorial 14.
- Switch documentation and README links to reference a new root
CONTRIBUTING.md, and include it into Sphinx via MyST. - Add GitHub Issue Form templates for bugs, docs issues, and feature requests (and disable blank issues).
File summaries
| File | Description |
|---|---|
| README.md | Updates contributor/discussion/issue entry points and links Contributing to the repo’s CONTRIBUTING.md. |
| docs/tutorials.rst | Adds Tutorial 16–18 cards and detailed sections; adds a preview figure for Tutorial 14 and TODO placeholders for missing preview media. |
| docs/contributing.rst | Replaces the large reST content with an include of the new root CONTRIBUTING.md via myst_parser. |
| docs/assets/tutorial_14_duke_heart_parameter_sweep.png | Adds a Git LFS-tracked preview image used by the Tutorial 14 “Preview” section. |
| CONTRIBUTING.md | Introduces the consolidated contributing guide content in Markdown. |
| .github/ISSUE_TEMPLATE/feature_request.yml | Adds a feature request issue form. |
| .github/ISSUE_TEMPLATE/docs_issue.yml | Adds a documentation issue form. |
| .github/ISSUE_TEMPLATE/config.yml | Disables blank issues and routes questions/ideas to Discussions. |
| .github/ISSUE_TEMPLATE/bug_report.yml | Adds a bug report issue form. |
Review details
- Files reviewed: 9/9 changed files
- Comments generated: 2
- Review effort level: Lite
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Actionable comments posted: 2
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Inline comments:
In `@CONTRIBUTING.md`:
- Around line 40-41: Update the installation instructions to clarify that the
second uv pip install command with --all-extras installs every declared optional
extra, including physicsnemo and all, while the first installs only cuda13,
docs, test, and dev; alternatively, rename the second option if it is not
intended to include all extras.
In `@README.md`:
- Line 33: Update the Contributing and Testing links in README.md to use
absolute repository or hosted-documentation URLs so both remain valid when
rendered on PyPI; apply the same change to the additional occurrence identified
by the review.
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Fix all unresolved CodeRabbit comments on this PR:
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⚙️ Run configuration
Configuration used: Organization UI
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Plan: Team
Run ID: d280e443-27a2-46a1-926c-5b9b2d4f5e48
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docs/assets/tutorial_14_duke_heart_parameter_sweep.pngis excluded by!**/*.png
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.github/ISSUE_TEMPLATE/bug_report.yml.github/ISSUE_TEMPLATE/config.yml.github/ISSUE_TEMPLATE/docs_issue.yml.github/ISSUE_TEMPLATE/feature_request.ymlCONTRIBUTING.mdREADME.mddocs/contributing.rstdocs/tutorials.rst
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #131 +/- ##
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Coverage 48.86% 48.86%
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Files 78 78
Lines 9953 9953
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Hits 4864 4864
Misses 5089 5089
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🟡 Changes recommended
A couple of newly introduced documentation links/examples are hardcoded or inaccurate (e.g., README CONTRIBUTING link and clone snippet), and should be corrected to avoid confusing contributors and breaking forks/tags.
Once you've addressed the issues Copilot identified, you can request another Copilot review.
Review details
Suppressed comments (1)
Previously missed (1) — in code that hasn't changed since the last review.
CONTRIBUTING.md:21
- The clone example uses
PhysioTwin4Das the repository name and directory, but the actual repository isphysiotwin4d. Using the correct name avoids confusion when contributors copy/paste the commands.
- Files reviewed: 9/9 changed files
- Comments generated: 2
- Review effort level: Lite
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🟡 Changes recommended
The new/updated documentation contains at least one broken repo reference (clone URL/path) and README-relative links that won’t work in non-GitHub renderers (e.g., PyPI).
Once you've addressed the issues Copilot identified, you can request another Copilot review.
Review details
Suppressed comments (2)
Previously missed (1) — in code that hasn't changed since the last review.
CONTRIBUTING.md:20
- The clone URL and directory name here don’t match the repository (
Project-MONAI/physiotwin4d). On case-sensitive filesystems thiscd PhysioTwin4Dstep will fail, and the clone URL likely 404s. Update both tophysiotwin4d.
README.md:131
- Same issue as above: the relative
(CONTRIBUTING.md)link won’t resolve on PyPI/docs renderers that only have README.md. Use an absolute GitHub URL (or the hosted-docs URL) so readers can always reach the guide.
See [CONTRIBUTING.md](CONTRIBUTING.md) (also published at [project-monai.github.io/physiotwin4d/contributing.html](https://project-monai.github.io/physiotwin4d/contributing.html)) for code style, testing, IDE setup, and pull request conventions.
- Files reviewed: 9/9 changed files
- Comments generated: 1
- Review effort level: Lite
Summary by CodeRabbit
Documentation
Project Support