Modernize build commands for setuptools 80+ compatibility

[engmohamedsalah]

Description

This PR modernizes MONAI's build and installation commands to be compatible with setuptools 80+, which removed the deprecated setup.py develop --uninstall command as part of PEP 660 modernization.

Changes

• runtests.sh: Updated compile_cpp() and clean_py() functions to use pip commands instead of deprecated setup.py develop
• requirements-min.txt: Removed setuptools upper bound (<=79.0.1) for Python 3.12+
• docs/source/installation.md: Updated editable installation examples to use modern pip install -e .
• .github/workflows/pythonapp.yml: Updated CI workflow to use pip commands

Rationale

In setuptools 80+, the setup.py develop --uninstall command was removed because the build system now delegates to pip for all installation/uninstallation operations (PEP 660). The old approach:

• python setup.py develop → Now: pip install -e .
• python setup.py develop --uninstall → Now: pip uninstall -y monai

Testing

• Verified bash syntax in runtests.sh has no errors
• Confirmed no remaining references to deprecated commands
• All changes maintain functional equivalence with modern pip approach

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Fixes #8439

[coderabbitai]

📝 Walkthrough

Walkthrough

Replaces setup.py-based editable install and uninstall commands with pip equivalents across CI, docs, and test scripts: python setup.py develop → python -m pip install -e . (with BUILD_MONAI=1 preserved for C++/CUDA builds) and python setup.py develop --uninstall → python -m pip uninstall -y monai. Also relaxes the setuptools upper-bound constraint for Python ≥ 3.12 in requirements. No public API or exported entity declarations were changed.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~15 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly and concisely summarizes the main change: modernizing build commands for setuptools 80+ compatibility.
Description check	✅ Passed	Description is comprehensive, covering changes across four files, rationale for PEP 660 compliance, and testing verification.
Linked Issues check	✅ Passed	PR directly addresses issue #8439 by replacing deprecated setup.py develop/--uninstall with pip commands across runtests.sh, requirements-min.txt, docs, and CI.
Out of Scope Changes check	✅ Passed	All changes are scoped to modernizing build commands for setuptools 80+ compatibility; no extraneous modifications detected.

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✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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[coderabbitai]

Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

runtests.sh (1)

142-151: ⚠️ Potential issue | 🟠 Major

Preserve BUILD_MONAI=1 or --build won’t compile extensions.
compile_cpp now runs pip install -e . without the env flag, so the C++/CUDA build is skipped by default.

🔧 Suggested fix

-        CC=clang CXX=clang++ ${cmdPrefix}"${PY_EXE}" -m pip install -e . --user
+        BUILD_MONAI=1 CC=clang CXX=clang++ ${cmdPrefix}"${PY_EXE}" -m pip install -e . --user
     else
-        ${cmdPrefix}"${PY_EXE}" -m pip install -e . --user
+        BUILD_MONAI=1 ${cmdPrefix}"${PY_EXE}" -m pip install -e . --user
     fi

[engmohamedsalah]

Thanks @coderabbitai for catching the critical BUILD_MONAI=1 issue!

I've updated the PR to explicitly set BUILD_MONAI=1 in the compile_cpp() function. This ensures C++/CUDA extensions are compiled when running ./runtests.sh --build, even with pip's build isolation.

The changes now include:

• ✅ BUILD_MONAI=1 explicitly set in both macOS and Linux branches
• ✅ Ensures extensions compile properly with pip install -e .
• ✅ Preserves the original intent of the compile_cpp function

Regarding the docstring coverage warning: This is expected for infrastructure/build changes. The modified files (runtests.sh, requirements-min.txt, installation.md, pythonapp.yml) don't contain Python functions that require docstrings.

[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@runtests.sh`:
- Around line 146-152: The editable-install commands use the --user flag which
breaks inside virtualenvs; remove --user from both invocations of the install
command (the non-mac branch and the mac branch that sets BUILD_MONAI and
CC=clang/CXX=clang++), i.e., change ${cmdPrefix}"${PY_EXE}" -m pip install -e .
--user to ${cmdPrefix}"${PY_EXE}" -m pip install -e . so the package installs
into the active virtualenv.

[coderabbitai]

Tip

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🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check the compile_cpp function in runtests.sh to verify BUILD_MONAI=1 is set
cat runtests.sh | grep -A 20 "^compile_cpp()"

Length of output: 0

---

🏁 Script executed:

#!/bin/bash
# Search for compile_cpp function definition more broadly
grep -n "compile_cpp" runtests.sh | head -20

# Also check the entire content around compile_cpp
rg -A 25 "compile_cpp\(\)" runtests.sh

Length of output: 46

---

🏁 Script executed:

#!/bin/bash
# Read lines around the compile_cpp function starting from line 142
sed -n '142,175p' runtests.sh

Length of output: 1320

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@engmohamedsalah Excellent! Verified the implementation in runtests.sh:

Line 149 (macOS): BUILD_MONAI=1 CC=clang CXX=clang++ before pip install -e .
Line 151 (Linux): BUILD_MONAI=1 before pip install -e .

✅ Both branches correctly export BUILD_MONAI=1, ensuring C++/CUDA extensions compile properly with pip's build isolation.

Your docstring explanation is correct—infrastructure files don't require Python docstrings.

The PR is ready from my perspective.

[engmohamedsalah]

✅ Fixed: Removed --user flag from editable installs

Per @coderabbitai's second review comment, I've removed the --user flag from all pip install -e . commands. This fixes virtualenv compatibility issues.

Why this is correct:

1. ✅ pythonapp.yml: Original code did NOT have --user - I incorrectly added it. Now matches original behavior.
2. ✅ runtests.sh: Removing --user modernizes to virtualenv-first approach (current Python best practice)
3. ✅ Virtualenv compatibility: Without --user, pip installs into the active venv when present, avoiding the "User site-packages are not visible in this virtualenv" error

Final changes:

• ✅ BUILD_MONAI=1 explicitly set (fixes C++/CUDA compilation)
• ✅ --user flag removed (fixes virtualenv compatibility)
• ✅ Modern pip commands (fixes setuptools 80+ compatibility)

All CodeRabbitAI suggestions have been addressed!

[coderabbitai]

Tip

For best results, initiate chat on the files or code changes.

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Check runtests.sh for pip install commands and BUILD_MONAI usage
echo "=== Checking runtests.sh compile_cpp function ==="
sed -n '142,175p' runtests.sh

echo -e "\n=== Checking for any --user flags in runtests.sh ==="
grep -n "pip install.*--user" runtests.sh || echo "No --user flags found in runtests.sh"

echo -e "\n=== Checking pythonapp.yml for pip install commands ==="
grep -n "pip install -e" .github/workflows/pythonapp.yml

echo -e "\n=== Checking for --user in pythonapp.yml ==="
grep -n "pip install.*--user" .github/workflows/pythonapp.yml || echo "No --user flags found in pythonapp.yml"

Length of output: 1780

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@engmohamedsalah Perfect! Verified all changes:

runtests.sh (lines 149, 151):

• ✅ BUILD_MONAI=1 ... pip install -e . (no --user)

pythonapp.yml (line 95):

• ✅ BUILD_MONAI=1 python -m pip install -e . (no --user)

Note: Lines 85 & 123 in pythonapp.yml still have --user for pip install --user --upgrade pip wheel, but that's correct—those upgrade system tools, not editable installs.

All review suggestions successfully addressed. Great work! 🎉

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