Modernize build commands for setuptools 80+ compatibility

Replace deprecated setup.py develop commands with modern pip equivalents:
- Replace 'setup.py develop --uninstall' with 'pip uninstall -y monai'
- Replace 'setup.py develop' with 'pip install -e .'
- Remove setuptools upper bound for Python 3.12+ (previously <=79.0.1)
- Add BUILD_MONAI=1 explicitly in compile_cpp to ensure C++/CUDA extensions build
- Remove --user flag from editable installs for virtualenv compatibility

In setuptools 80+, the 'setup.py develop --uninstall' command was removed
as part of PEP 660 modernization. The build system now delegates to pip
for all installation and uninstallation operations.

When using 'pip install -e .', the BUILD_MONAI environment variable must be
set explicitly to trigger C++/CUDA compilation, as it's not automatically
inherited due to pip's build isolation.

The --user flag is removed from editable installs because it breaks inside
virtualenvs (the modern development standard). Without --user, pip installs
into the active virtualenv when present, or prompts for sudo when needed.

Changes made:
- runtests.sh: Updated compile_cpp() and clean_py() to use pip commands,
  set BUILD_MONAI=1 explicitly, and removed --user flag
- requirements-min.txt: Removed setuptools <=79.0.1 upper bound for Python 3.12+
- docs/source/installation.md: Updated editable installation examples
- .github/workflows/pythonapp.yml: Updated CI workflow to use pip commands

Fixes #8439

Signed-off-by: Mohamed Salah <eng.mohamed.tawab@gmail.com>

Author: engmohamedsalah

.github/workflows/pythonapp.yml

@@ -91,8 +91,8 @@ jobs:
       shell: bash
     - name: Run compiled (${{ runner.os }})
       run: |
-        python setup.py develop --uninstall
-        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
+        python -m pip uninstall -y monai
+        BUILD_MONAI=1 python -m pip install -e .  # compile the cpp extensions
       shell: bash
     - name: Run quick tests (CPU ${{ runner.os }})
       run: |

docs/source/installation.md

@@ -135,23 +135,23 @@ You can install it by running:
 
 ```bash
 cd MONAI/
-python setup.py develop
+pip install -e .
 ```
 
 or, to build with MONAI C++/CUDA extensions and install:
 
 ```bash
 cd MONAI/
-BUILD_MONAI=1 python setup.py develop
+BUILD_MONAI=1 pip install -e .
 # for MacOS
-BUILD_MONAI=1 CC=clang CXX=clang++ python setup.py develop
+BUILD_MONAI=1 CC=clang CXX=clang++ pip install -e .
 ```
 
 To uninstall the package please run:
 
 ```bash
 cd MONAI/
-python setup.py develop --uninstall
+pip uninstall -y monai
 
 # to further clean up the MONAI/ folder (Bash script)
 ./runtests.sh --clean

requirements-min.txt

@@ -1,7 +1,7 @@
 # Requirements for minimal tests
 -r requirements.txt
 setuptools>=50.3.0,<66.0.0,!=60.6.0 ; python_version < "3.12"
-setuptools>=70.2.0,<=79.0.1; python_version >= "3.12"
+setuptools>=70.2.0; python_version >= "3.12"
 coverage>=5.5
 parameterized
 packaging

runtests.sh

@@ -73,7 +73,7 @@ function print_usage {
     echo "./runtests.sh -f                      # run coding style and static type checking."
     echo "./runtests.sh --quick --unittests     # run minimal unit tests, for quick verification during code developments."
     echo "./runtests.sh --autofix               # run automatic code formatting using \"isort\" and \"black\"."
-    echo "./runtests.sh --clean                 # clean up temporary files and run \"${PY_EXE} setup.py develop --uninstall\"."
+    echo "./runtests.sh --clean                 # clean up temporary files and uninstall MONAI development package."
     echo "./runtests.sh --formatfix -p /my/code # run automatic code formatting using \"isort\" and \"black\" in specified path."
     echo ""
     echo "Code style check options:"
@@ -143,12 +143,12 @@ function compile_cpp {
     echo "Compiling and installing MONAI cpp extensions..."
     # depends on setup.py behaviour for building
     # currently setup.py uses environment variables: BUILD_MONAI and FORCE_CUDA
-    ${cmdPrefix}"${PY_EXE}" setup.py develop --user --uninstall
+    ${cmdPrefix}"${PY_EXE}" -m pip uninstall -y monai
     if [[ "$OSTYPE" == "darwin"* ]];
     then  # clang for mac os
-        CC=clang CXX=clang++ ${cmdPrefix}"${PY_EXE}" setup.py develop --user
+        BUILD_MONAI=1 CC=clang CXX=clang++ ${cmdPrefix}"${PY_EXE}" -m pip install -e .
     else
-        ${cmdPrefix}"${PY_EXE}" setup.py develop --user
+        BUILD_MONAI=1 ${cmdPrefix}"${PY_EXE}" -m pip install -e .
     fi
 }
 
@@ -179,7 +179,7 @@ function clean_py {
 
     # uninstall the development package
     echo "Uninstalling MONAI development files..."
-    ${cmdPrefix}"${PY_EXE}" setup.py develop --user --uninstall
+    ${cmdPrefix}"${PY_EXE}" -m pip uninstall -y monai
 
     # remove temporary files (in the directory of this script)
     TO_CLEAN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"