ENH: Cleaned up infrastructure and documentation#80
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WalkthroughThis PR reorients repository guidance, package metadata, docs, tutorials, navigation, and reporting toward personalized physiological digital twins from 3D medical images. It also removes the release guide and several local config/document files, updates Git LFS handling for GIF assets, and refreshes project statistics. ChangesDocumentation and guidance rebrand
Estimated code review effort: 3 (Moderate) | ~25 minutes 🚥 Pre-merge checks | ✅ 5✅ Passed checks (5 passed)
✨ Finishing Touches🧪 Generate unit tests (beta)
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Pull request overview
This PR refreshes the project’s “what is PhysioTwin4D” messaging and streamlines repository/docs infrastructure by removing redundant docs pages and consolidating “examples” guidance into the tutorials-centric documentation site.
Changes:
- Updates project description across README, package docstring,
pyproject.toml, and various docs pages to reflect the “physiological digital twins” framing. - Consolidates documentation navigation by removing
docs/examples.rstand re-pointing “examples” references todocs/tutorials.rst. - Cleans up infra/docs artifacts (removes PyPI release guide doc, drops editor-specific configs, adds LFS tracking for tutorial preview GIF placeholders).
Reviewed changes
Copilot reviewed 27 out of 27 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
statistics.md |
Updates project stats and narrative to match current scope and repo layout. |
src/physiotwin4d/__init__.py |
Updates package-level description docstring to new framing. |
README.md |
Replaces long README with a tighter overview pointing to hosted docs. |
pyproject.toml |
Updates project.description to match the new framing. |
MANIFEST.in |
Removes packaging include for the removed PyPI release guide doc. |
docs/tutorials.rst |
Expands tutorial cards with “Inner API usage” and adds preview placeholders. |
docs/README.md |
Updates docs tree description to treat tutorials as canonical examples. |
docs/quickstart.rst |
Repoints “examples” navigation to tutorials. |
docs/PYPI_RELEASE_GUIDE.md |
Removes the PyPI release guide document. |
docs/installation.rst |
Repoints “examples” navigation to tutorials. |
docs/index.rst |
Updates landing page messaging and removes examples/changelog entries. |
docs/faq.rst |
Updates “What is PhysioTwin4D?” answer and repoints examples link to tutorials. |
docs/examples.rst |
Removes the examples page (content now conceptually covered by tutorials/docs). |
docs/developer/extending.rst |
Updates positioning language in developer docs. |
docs/developer/architecture.rst |
Updates architecture overview framing language. |
docs/contributing.rst |
Removes references to the deleted PyPI release guide. |
docs/conf.py |
Removes exclusion of PYPI_RELEASE_GUIDE.md since the doc is deleted. |
docs/cli_scripts/overview.rst |
Updates CLI overview framing language. |
docs/changelog.rst |
Removes the changelog page. |
docs/assets/example.gif |
Adds an LFS-managed placeholder asset referenced by tutorials. |
docs/architecture.rst |
Updates architecture narrative and expands workflow list/relationships. |
CLAUDE.md |
Removes some Claude-specific guidance that duplicates AGENTS.md; updates conventions. |
AGENTS.md |
Updates project description and some environment guidance; clarifies labelmap vs mask terminology. |
.vscode/settings.json |
Removes editor settings file from the repo. |
.gitattributes |
Adds Git LFS tracking for docs/assets/*.gif. |
.cursor/rules/project-standards.mdc |
Removes Cursor rules file from the repo. |
.agents/agents/implementation.md |
Updates the implementation agent’s project description. |
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| Preview | ||
| .. figure:: assets/example.gif | ||
| :alt: Tutorial 1 input preview (placeholder) | ||
| :width: 45% | ||
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| .. figure:: assets/example.gif | ||
| :alt: Tutorial 1 output preview (placeholder) | ||
| :width: 45% | ||
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| version https://git-lfs.github.com/spec/v1 | ||
| oid sha256:8b434d88c3681856ef855b6f9d9b9fc9d3096855e955b543f25494db36f48329 | ||
| size 1196946 |
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| PhysioTwin4D - Methods, workflows, tutorials, and CLI for creating | ||
| personalized physiological digital twins. |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
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Actionable comments posted: 2
🧹 Nitpick comments (1)
CLAUDE.md (1)
71-73: 📐 Maintainability & Code Quality | 🔵 TrivialKeep the data-convention bullets aligned with the canonical contract.
The labelmap and transform wording drifts from
AGENTS.md: labelmaps are integer-label ITK images, and transforms are composite ITK transforms stored in compressed.hdffiles. Mirroring that phrasing here avoids two slightly different instructions for agents.♻️ Proposed wording
- - Labelmaps: ITK images with integer labels defined by anatomy segmenter used. - - Masks: ITK binary images - - Transforms: ITK transforms stored in `.hdf` files with compression + - Labelmaps are ITK images with integer labels; keep anatomy group IDs aligned + across segmenters. + - Masks are binary ITK images. + - Transforms are ITK composite transforms stored in compressed `.hdf` files.🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the rest with a brief reason, keep changes minimal, and validate. In `@CLAUDE.md` around lines 71 - 73, The data-convention bullets in CLAUDE.md should match the canonical wording used in AGENTS.md. Update the Labelmaps and Transforms entries so they describe labelmaps as integer-label ITK images and transforms as composite ITK transforms stored in compressed .hdf files, keeping the wording aligned with the existing contract.
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@docs/tutorials.rst`:
- Around line 341-344: The tutorial paragraph is pointing users to the
lower-level physiotwin4d.vtk_to_usd package instead of the public entry point.
Update the wording in the tutorial to direct readers to ConvertVTKToUSD as the
supported VTK-to-USD interface, and remove or rephrase the mention of advanced
primitives like convert_vtk_file, ConversionSettings, and MaterialData so the
documentation stays focused on the public API.
In `@statistics.md`:
- Line 75: The API reference entry is using the wrong command prefix, so update
the documentation in statistics.md to match repo guidance by replacing the `py
utils/generate_api_map.py` reference with `python utils/generate_api_map.py`.
Make the same correction wherever this API-map command is repeated so readers
are directed to run it from the active venv, and keep the `docs/API_MAP.md`
regeneration guidance aligned with the existing API reference wording.
---
Nitpick comments:
In `@CLAUDE.md`:
- Around line 71-73: The data-convention bullets in CLAUDE.md should match the
canonical wording used in AGENTS.md. Update the Labelmaps and Transforms entries
so they describe labelmaps as integer-label ITK images and transforms as
composite ITK transforms stored in compressed .hdf files, keeping the wording
aligned with the existing contract.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: a127b7d9-dbcb-4c70-bc8d-2c7e4289b815
⛔ Files ignored due to path filters (1)
docs/assets/example.gifis excluded by!**/*.gif
📒 Files selected for processing (26)
.agents/agents/implementation.md.cursor/rules/project-standards.mdc.gitattributes.vscode/settings.jsonAGENTS.mdCLAUDE.mdMANIFEST.inREADME.mddocs/PYPI_RELEASE_GUIDE.mddocs/README.mddocs/architecture.rstdocs/changelog.rstdocs/cli_scripts/overview.rstdocs/conf.pydocs/contributing.rstdocs/developer/architecture.rstdocs/developer/extending.rstdocs/examples.rstdocs/faq.rstdocs/index.rstdocs/installation.rstdocs/quickstart.rstdocs/tutorials.rstpyproject.tomlsrc/physiotwin4d/__init__.pystatistics.md
💤 Files with no reviewable changes (8)
- .cursor/rules/project-standards.mdc
- docs/examples.rst
- docs/contributing.rst
- docs/changelog.rst
- .vscode/settings.json
- docs/PYPI_RELEASE_GUIDE.md
- docs/conf.py
- MANIFEST.in
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