[pratikgx]

Fixes # .

Description

Fixes broken relative links and anchors in README files on main:

• nnunet/README.md: the datalist tutorial link pointed to msd_datalist_generator.ipynb; the notebook in auto3dseg/notebooks/ is msd_crossval_datalist_generator.ipynb.
• bundle/introducing_config/README.md: the plain-text replacement link pointed to ../get_started.md, which does not exist; macro text replacement is covered in ../further_features.md.
• CONTRIBUTING.md: #ci-test-passing-guide did not match the "CI/CD test passing guide" heading, whose anchor is #cicd-test-passing-guide.
• deployment/Triton/README.md: three links used #model-config-file; the heading is "Model Config", so the anchor is #model-config.
• reconstruction/MRI_reconstruction/unet_demo/README.md and varnet_demo/README.md: the table of contents linked #Acknowledgement, but the heading is spelled "Acknowledgment".

Docs-only change, no notebooks touched.

Checks

• Avoid including large-size files in the PR.
• For security purposes, please check the contents and remove any sensitive info such as user names and private key.
• Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder

Summary by CodeRabbit

• Documentation
  • Corrected links and section anchors across the contribution guide, configuration tutorial, deployment instructions, dataset-preparation guide, and MRI reconstruction demos.
  • Updated the Maisi training tutorial link and the Triton Model Config links.
  • Added a reference from the Triton directory-structure guidance to the Model Config section and fixed formatting in the Quick Start example.
  • Removed the link from the “Deepgrow Stats” heading while keeping its description and image unchanged.
  • Standardized heading spacing and corrected the pre/post-processing table-of-contents link.

[coderabbitai]

No actionable comments were generated in the recent review.

Recent review info

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• Run ID: c9b86e35-8f04-4059-9b73-2d760cb03647

Commits

Reviewing files that changed from the base of the PR and between c2db924 and 7badb79.

Files selected for processing: 1

• generation/maisi/maisi_train_controlnet_tutorial.ipynb

Included review availability: This review used your included allowance. Your plan provides up to 8 included reviews per hour; 7 remain after this review.

Walkthrough

This change corrects documentation links and heading anchors, adjusts heading spaces, removes a code fence, and adds a note in the Triton README.

Changes

Documentation updates

Layer / File(s)	Summary
Guide and tutorial links CONTRIBUTING.md, bundle/introducing_config/README.md, nnunet/README.md, generation/maisi/maisi_train_controlnet_tutorial.ipynb	Updated links to the testing guide and three tutorials.
Triton Quick Start and Model Config deployment/Triton/README.md	Corrected Quick Start and Model Config links, removed a closing code fence, and added a note linking the expected directory structure to Model Config.
README anchors and heading text reconstruction/MRI_reconstruction/unet_demo/README.md, reconstruction/MRI_reconstruction/varnet_demo/README.md, deepgrow/ignite/README.md, full_gpu_inference_pipeline/README.md	Updated acknowledgment and pre/post-processing anchors, normalized heading spaces, and changed the “Deepgrow Stats” heading to plain text.

Priority: Low

Estimated code review effort: 1 (Trivial) | ~5 minutes

Change: Bug fix

Suggested reviewers: kumoliu

Merge Risk: Minimal · up to 7badb

No actionable merge-blocking risk remains in the reviewed change.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Description check		The description explains the primary link and anchor fixes and includes relevant checks. However, it is incomplete and inaccurate because the final changes also update the Triton, DeepGrow, and full G…	Update the description to include all final changes, especially the Triton Quick Start and rendering fixes, the removed DeepGrow handler link, the full GPU inference anchor and spacing fixes, and the Maisi notebook link correction. Remove o…

Passed checks: 4 passed

Check name	Status	Explanation
Title check		The title clearly summarizes the main change: fixing broken documentation links and anchors. It is slightly narrower than the full changeset because the PR also updates CONTRIBUTING.md and a notebook.
Docstring Coverage		No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentat…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Docstring Coverage

Explanation

No eligible functions found in the changed files. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff with cyclomatic complexity of at least 2. Documentation-only edits and deletions within surviving functions are included; unchanged diff context and fully deleted functions are excluded. Analyzed 0 functions across 0 files. (1 skipped: 1 unsupported.)

Full details: Description check

Explanation

The description explains the primary link and anchor fixes and includes relevant checks. However, it is incomplete and inaccurate because the final changes also update the Triton, DeepGrow, and full GPU inference READMEs and the Maisi notebook, while the description states that no notebooks were touched.

Resolution

Update the description to include all final changes, especially the Triton Quick Start and rendering fixes, the removed DeepGrow handler link, the full GPU inference anchor and spacing fixes, and the Maisi notebook link correction. Remove or correct the statement that no notebooks were touched. State whether the notebook runner check applies or explain why it was not run.

Finishing Touches

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[ericspod]

@coderabbitai are these link fixes all correct? Are there other broken links elsewhere in the repo?

[coderabbitai]

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🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail
gh pr diff 2085 --repo Project-MONAI/tutorials
printf '\n--- Documentation inventory ---\n'
git ls-files '*.md' '*.ipynb' | awk '/\.md$/ {md++} /\.ipynb$/ {nb++} END {print "Markdown files:",md,"Notebooks:",nb}'
printf '\n--- Changed documents ---\n'
for f in CONTRIBUTING.md bundle/introducing_config/README.md deployment/Triton/README.md nnunet/README.md reconstruction/MRI_reconstruction/unet_demo/README.md reconstruction/MRI_reconstruction/varnet_demo/README.md; do
  printf '\n--- %s ---\n' "$f"
  cat -n "$f"
done
printf '\n--- Target sections ---\n'
rg -n -C3 '^#{1,6} .*|plain text|macro|model-config' bundle/further_features.md
fd -i '.*(contribut|test|model.*config).*' --type f

Length of output: 72911

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail
python -m pip -q install markdown-it-py
python - <<'PY'
import subprocess,json,re,html,unicodedata,collections
from pathlib import Path
from urllib.parse import urlsplit,unquote
from markdown_it import MarkdownIt
md=MarkdownIt('commonmark',{'html':True})
files=subprocess.check_output(['git','ls-files','-z']).decode().split('\0')
docs=[Path(p) for p in files if p.endswith(('.md','.ipynb'))]
data={}
for p in docs:
    if p.suffix=='.md': cells=[(None,p.read_text())]
    else:
        nb=json.loads(p.read_text())
        cells=[(i+1,''.join(c.get('source',[]))) for i,c in enumerate(nb.get('cells',[])) if c.get('cell_type')=='markdown']
    anchors=set(); headings=[]; links=[]; counts=collections.Counter()
    for ci,text in cells:
        toks=md.parse(text)
        for i,t in enumerate(toks):
            line=(t.map[0]+1) if t.map else 1
            loc=f'Line {line}' if ci is None else f'cell {ci}, Markdown line {line}'
            if t.type=='heading_open':
                inline=toks[i+1]
                title=''.join(c.content for c in inline.children or [] if c.type in ('text','code_inline'))
                slug=''.join(c for c in html.unescape(title).lower() if c in (' ','-','_') or unicodedata.category(c)[0] in ('L','N','M')).replace(' ','-')
                base=slug
                while slug in anchors:
                    counts[base]+=1; slug=f'{base}-{counts[base]}'
                anchors.add(slug);headings.append((loc,title,slug))
            if t.type=='inline':
                for c in t.children or []:
                    if c.type in ('link_open','image'):
                        links.append((loc,c.attrGet('href') if c.type=='link_open' else c.attrGet('src')))
            if t.type in ('html_block','inline'):
                content=t.content if t.type=='html_block' else '\n'.join(c.content for c in t.children or [] if c.type=='html_inline')
                for a in re.finditer(r'\b(?:id|name)\s*=\s*["\']([^"\']+)["\']',content): anchors.add(a.group(1))
                for a in re.finditer(r'\b(?:href|src)\s*=\s*["\']([^"\']+)["\']',content):
                    links.append((loc,a.group(1)))
    data[p]=(anchors,headings,links)
missing=[];fragments=[];external=set();checked=0
for p,(_,_,links) in data.items():
    for loc,url in links:
        if not url: continue
        u=urlsplit(html.unescape(url))
        if u.scheme or u.netloc:
            if u.scheme in ('http','https'):external.add(url)
            continue
        if u.path.startswith('/'):continue
        target=Path(__import__('os').path.normpath(str(p.parent/unquote(u.path)))) if u.path else p
        checked+=1
        if not target.exists():
            missing.append((str(p),loc,url,str(target)));continue
        frag=unquote(u.fragment)
        if frag and target in data and frag not in data[target][0]:
            # Uppercase-only fragment differences are listed separately from missing fragments.
            if frag.lower() in {a.lower() for a in data[target][0]}:continue
            fragments.append((str(p),loc,url,str(target)))
print('SUMMARY',json.dumps({'documents':len(docs),'local_link_occurrences_checked':checked,'missing_path_occurrences':len(missing),'unmatched_fragment_candidates':len(fragments),'unique_external_urls_not_checked':len(external)}))
print('\nMISSING PATHS')
for x in missing:print(json.dumps(x))
print('\nUNMATCHED FRAGMENT CANDIDATES')
for x in fragments:print(json.dumps(x))
print('\nTRITON PARSED HEADINGS')
print(json.dumps(data[Path('deployment/Triton/README.md')][1],indent=2))
print('\nMSD TARGET MARKDOWN EXCERPTS')
p=Path('auto3dseg/notebooks/msd_crossval_datalist_generator.ipynb')
nb=json.loads(p.read_text())
for i,c in enumerate(nb['cells']):
    text=''.join(c.get('source',[]))
    if c.get('cell_type')=='markdown' and (i<5 or re.search('spleen|datalist|download',text,re.I)):
        print('cell',i+1,text[:1600])
PY

Length of output: 7560

---

🏁 Script executed:

#!/bin/bash
set -euo pipefail
printf '\n--- Candidate contexts ---\n'
sed -n '125,160p' deepgrow/ignite/README.md
sed -n '115,155p' federated_learning/breast_density_challenge/README.md
cat -n full_gpu_inference_pipeline/README.md
printf '\n--- Possible replacement files ---\n'
fd -i 'handler|predictions|maisi.*tutorial|rxrx1' --type f
printf '\n--- Notebook Markdown context ---\n'
python - <<'PY'
import json
from pathlib import Path
from markdown_it import MarkdownIt
md=MarkdownIt()
for filename,cellnums in [
 ('generation/maisi/maisi_train_controlnet_tutorial.ipynb',[10]),
 ('microscopy/multichannel_microscopy_classification.ipynb',[11]),
 ('3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb',[35])]:
    nb=json.loads(Path(filename).read_text())
    print('\nFILE',filename)
    for i,c in enumerate(nb['cells'],1):
        text=''.join(c.get('source',[]))
        if i in cellnums: print('CELL',i,'\n',text)
        if c.get('cell_type')=='markdown':
            toks=md.parse(text)
            for j,t in enumerate(toks):
                if t.type=='heading_open': print('HEADING cell',i,':',toks[j+1].content)
print('\nMSD DOWNLOAD AND DATALIST CODE (inspection only)')
nb=json.loads(Path('auto3dseg/notebooks/msd_crossval_datalist_generator.ipynb').read_text())
for i,c in enumerate(nb['cells'],1):
    text=''.join(c.get('source',[]))
    if c.get('cell_type')=='code' and any(s in text for s in ['download','datalist','json.dump']):
        print('CELL',i,'\n',text[:2600])
PY
printf '\n--- Replacement and generated-data references ---\n'
rg -n -C2 'handler[s]?\.py|predictions\.json|rxrx1_subset_monai|maisi_diff_unet_training_tutorial|maisi_train_diffusion_model' deepgrow microscopy generation/maisi federated_learning/breast_density_challenge -g '*.md' -g '*.py'

Length of output: 26007

---

@ericspod Yes. All eight link changes in this PR are correct. I checked the target files, target content, and Markdown headings.

Change	Verification
nnunet/README.md	The replacement notebook exists. It downloads the MSD Spleen dataset and writes a cross-validation datalist.
bundle/introducing_config/README.md	bundle/further_features.md contains the macro text replacement example.
CONTRIBUTING.md	#cicd-test-passing-guide matches CI/CD test passing guide.
deployment/Triton/README.md	All three replacement links match Model Config.
Both MRI reconstruction READMEs	#acknowledgment matches the heading in each file.

Other broken links

I scanned 98 Markdown files and the Markdown cells in 173 notebooks. The scan checked 762 local link and image references. I found these additional issues:

Location	Issue	Recommended correction
deepgrow/ignite/README.md, Line 146	./handler.py does not exist.	Replace the link with the current statistics-handler implementation, or remove the obsolete link.
generation/maisi/maisi_train_controlnet_tutorial.ipynb, cell 10	./maisi_diff_unet_training_tutorial.ipynb does not exist.	Use ./maisi_train_diff_unet_tutorial.ipynb.
deployment/Triton/README.md, Line 70	#examples has no rendered target. An extra code fence at Line 109 puts ## Examples: inside a code block.	Remove the extra fence and check the surrounding code blocks. Also fix [Quick Start] (#quick-start) at Line 56 by removing the space before (.
full_gpu_inference_pipeline/README.md, Line 8	The target heading at Line 60 contains a non-breaking space between Setup and python. The generated anchor does not match the link.	Replace the non-breaking space with a normal space.
full_gpu_inference_pipeline/README.md, Line 14	#pre-post-processing-on-gpu-vs-cpu does not match the heading at Line 143. The heading contains / and a trailing non-breaking space.	Remove the trailing non-breaking space and use #prepost-processing-on-gpu-vs-cpu.

Two other missing paths need separate treatment:

• federated_learning/breast_density_challenge/README.md, Line 143 links to downloaded predictions.json. The README explicitly says that the file becomes available after running the download script. This is not a missing committed file, but the link cannot work when browsing GitHub.
• microscopy/multichannel_microscopy_classification.ipynb, cell 11 links to ./rxrx1_subset_monai/README.md#metadata. That path is absent from the checkout. It needs a check against the downloaded dataset before selecting a replacement.

Scope: This was a static local-link check, not a complete external-link audit. I did not request the 569 unique external URLs, execute notebooks, or fully validate renderer-specific notebook anchors. The results do not establish that every other link works.

_{You are interacting with an AI system.}

[ericspod]

Hi @pratikgx thanks for these fixes. I asked coderabbit and there's a few more things that could be addressed, would you be able to do those in this PR as well?

[pratikgx]

@ericspod Thanks! Done in the latest commit: removed the stray code fence in deployment/Triton/README.md (so ## Examples renders and #examples works), fixed the [Quick Start] (#quick-start) link, replaced the non-breaking spaces in the two full_gpu_inference_pipeline/README.md headings and fixed the #prepost-processing-on-gpu-vs-cpu anchor, and removed the link to the deleted deepgrow/ignite/handler.py. I left the maisi_train_controlnet_tutorial.ipynb link out because editing the notebook would trigger the notebook runner in CI. Happy to add it if you prefer. The predictions.json and rxrx1_subset_monai links point to files that only exist after a download, so I left those as they are.

[ericspod]

Hi @pratikgx go ahead and fix the notebook issue, the tests shouldn't take too long to run and it's best to get it done now before we forget. Thanks!

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[pratikgx]

@ericspod Done, the maisi_train_controlnet_tutorial.ipynb link now points to maisi_train_diff_unet_tutorial.ipynb. Thanks!