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Use expanded pip install tooling #21

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94a6dcc
ENH: Drop Python 3.9 / Slicer 5.8 support
ebrahimebrahim Feb 17, 2026
15710ec
ENH: Use slicer.util pip tools for dependency management
ebrahimebrahim Feb 17, 2026
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260 changes: 27 additions & 233 deletions SlicerNNUnet/SlicerNNUNetLib/InstallLogic.py
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Original file line number Diff line number Diff line change
@@ -1,25 +1,16 @@
import importlib.metadata
import importlib.util
import logging
import sys
from importlib.metadata import version, PackageNotFoundError
from subprocess import CalledProcessError
from typing import Optional, Union, Protocol
from typing import Optional, Protocol

import qt
import slicer
from packaging.requirements import Requirement
from packaging.version import parse, Version

from .Signal import Signal
from packaging.version import Version


class InstallLogicProtocol(Protocol):
"""
Interface definition for the InstallLogic.
Only the methods defined in this interface are stable.
"""
progressInfo: Signal
needsRestart: bool

def setupPythonRequirements(self, nnUNetRequirements: str) -> None:
Expand All @@ -35,12 +26,8 @@ class InstallLogic:
Makes sure that SimpleITK and requests packages are not overwritten during install.
Makes sure that torch is installed separately by PyTorch module.

Copied and adapted from :
https://github.com/lassoan/SlicerTotalSegmentator/blob/main/TotalSegmentator/TotalSegmentator.py

Usage example :
>>> logic = InstallLogic()
>>> logic.progressInfo.connect(print)
>>> logic.getInstalledNNUnetVersion()
None
>>> logic.setupPythonRequirements()
Expand All @@ -49,13 +36,12 @@ class InstallLogic:
"""

def __init__(self, doAskConfirmation=True):
self.progressInfo = Signal("str")
self.doAskConfirmation = doAskConfirmation
self.needsRestart = False

def _log(self, text):
@staticmethod
def _log(text):
logging.info(text)
self.progressInfo(text)

def setupPythonRequirements(self, nnUNetRequirements: str = "nnunetv2") -> bool:
"""
Expand All @@ -65,7 +51,8 @@ def setupPythonRequirements(self, nnUNetRequirements: str = "nnunetv2") -> bool:
Setup may require 3D Slicer to be restarted to fully proceed.
"""
try:
if self.isPackageInstalledAndCompatible(nnUNetRequirements):
req = Requirement(nnUNetRequirements)
if slicer.util.pip_check(req):
self._log(
f"nnUNet is already installed ({self.getInstalledNNUnetVersion()}) "
f"and compatible with requested version ({nnUNetRequirements})."
Expand All @@ -78,161 +65,65 @@ def setupPythonRequirements(self, nnUNetRequirements: str = "nnunetv2") -> bool:
return True

if self.doAskConfirmation:
self._requestPermissionToInstallOrRaise()
if not slicer.util.confirmOkCancelDisplay(
"nnUNet will be installed to 3D Slicer. "
"This install can take a few minutes. "
"Would you like to proceed?",
"nnUNet about to be installed",
):
raise RuntimeError("Install process was manually canceled by user.")

self._log(f"Start nnUNet install with requirements : {nnUNetRequirements}")
torchRequirement = self._installNNUnet(nnUNetRequirements)
self._installPyTorch(torchRequirement)

if sys.version_info < (3, 12):
# Python 3.9 (Slicer-5.8 and earlier) requires several workarounds
self._installACVLUtils() # Since acvl_utils requires pytorch, we need to install acvl_utils after pytorch.
self._downgradeDynamicNetworkArchitecture()
self._log("nnUNet installation completed successfully.")
return True
except Exception as e:
self._log(f"Error occurred during install : {e}")
return False

def getInstalledNNUnetVersion(self) -> Optional[Version]:
return self.getInstalledPackageVersion("nnunetv2")

@classmethod
def isPackageInstalledAndCompatible(cls, req: Union[str, Requirement]) -> bool:
return cls.isPackageInstalled(req) and cls.isInstalledPackageCompatible(req)

@classmethod
def isPackageInstalled(cls, req: Union[str, Requirement]) -> bool:
return cls.getInstalledPackageVersion(req) is not None

@classmethod
def isInstalledPackageCompatible(cls, req: Union[str, Requirement]) -> bool:
"""
Checks if the requirement is installed in this environment and if the installed version is compatible with req.
"""
req = cls.asRequirement(req)
installedVersion = cls.getInstalledPackageVersion(req)
return installedVersion in req.specifier if installedVersion is not None else True

@classmethod
def needsToInstallRequirement(cls, req: Union[str, Requirement]):
"""
Check if the input requirement matches the current environment. Otherwise, return False.
"""
req = cls.asRequirement(req)
if req.marker is not None and not req.marker.evaluate():
return False

# Check if the package is installed and compatible with requirement.
return not cls.isPackageInstalled(req) or not cls.isInstalledPackageCompatible(req)

@classmethod
def getInstalledPackageVersion(cls, req: Union[str, Requirement]) -> Optional[Version]:
req = cls.asRequirement(req)
from importlib.metadata import version, PackageNotFoundError
from packaging.version import parse
try:
return parse(version(req.name))
return parse(version("nnunetv2"))
except PackageNotFoundError:
return None

@classmethod
def asRequirement(cls, req: Union[str, Requirement]) -> Requirement:
"""
Converts input string to Requirement instance.
"""
return req if isinstance(req, Requirement) else Requirement(req)

def _installNNUnet(self, nnunetRequirement: str) -> str:
"""
Installs nnUNet while not installing SimpleITK, torch and requests.

Slicer's SimpleITK uses a special IO class, which should not be replaced.
Torch requires special install using SlicerPyTorch.
Requests would require restart which is unnecessary.
On Python-3.9, acvl-utils has problems with 0.2.1 and 0.2.2 versions, therefore we install it manually separately.
"""
nnUNetPackagesToSkip = [
'SimpleITK',
'torch',
'requests',
]
if sys.version_info < (3, 12):
# Python 3.9 (Slicer-5.8 and earlier)
nnUNetPackagesToSkip.append('acvl-utils')

# Install nnunetv2 with selected dependencies only
self._uninstallNNUnetIfNeeded()
skipped = self.pipInstallSelective('nnunetv2', nnunetRequirement, nnUNetPackagesToSkip)
torchRequirement = next(req for req in skipped if "torch" in req.lower())
return torchRequirement

def _uninstallNNUnetIfNeeded(self):
if not self.isPackageInstalled(Requirement("nnunetv2")):
return
self.pip_uninstall("nnunetv2")
if slicer.util.pip_check(Requirement("nnunetv2")):
slicer.util.pip_uninstall("nnunetv2")

def _downgradeDynamicNetworkArchitecture(self) -> None:
"""
Workaround: fix incompatibility of dynamic_network_architectures==0.4 with totalsegmentator==2.0.5.
Revert to the last working version: dynamic_network_architectures==0.2
"""
if parse(version("dynamic_network_architectures")) == parse("0.4"):
self._log(
f'dynamic_network_architectures package version is incompatible. Installing working version...')
self.pip_install("dynamic_network_architectures==0.2.0")
skipped = slicer.util.pip_install(
nnunetRequirement,
skip_packages=["SimpleITK", "torch", "requests"],
)

def _installACVLUtils(self) -> None:
"""
Workaround: fix incompatibility of acvl-utils 0.2.1 and 0.2.2 with nnunetv2.
Revert to the last working version: acvl-utils==0.2.0
"""
# Recent versions of acvl_utils are broken:
# 0.2.1: https://github.com/MIC-DKFZ/acvl_utils/issues/2
# 0.2.2: https://github.com/MIC-DKFZ/acvl_utils/issues/4
# As a workaround, we install an older version manually. This workaround can be removed after acvl_utils is fixed.
needToInstallAcvlUtils = True
try:
if parse(importlib.metadata.version("acvl_utils")) == parse("0.2"):
# A suitable version is already installed
needToInstallAcvlUtils = False
except Exception as e:
pass
if needToInstallAcvlUtils:
self._log(
f'Installing a working acvl-utils package version...')
slicer.util.pip_install("acvl_utils==0.2")
return next(req for req in skipped if "torch" in req.lower())

def _installPyTorch(self, torchRequirements: str) -> None:
torchLogic = self._getTorchLogic()
torchRequirements = Requirement(torchRequirements)
torchReq = Requirement(torchRequirements)

if self.isPackageInstalled(torchRequirements) and self.isInstalledPackageCompatible(torchRequirements):
if slicer.util.pip_check(torchReq):
return

self._log("PyTorch Python package is required. Installing... (it may take several minutes)")
if torchLogic.installTorch(
askConfirmation=False,
torchVersionRequirement=str(torchRequirements.specifier)
torchVersionRequirement=str(torchReq.specifier)
) is None:
raise RuntimeError(
"Failed to correctly install PyTorch. PyTorch extension needs to be installed to use this module."
)

@classmethod
def _requestPermissionToInstallOrRaise(cls) -> None:
"""
Request user permission to install nnUNet and PyTorch.
"""
ret = qt.QMessageBox.question(
None,
"nnUNet about to be installed",
"nnUNet will be installed to 3D Slicer. "
"This install can take a few minutes. "
"Would you like to proceed?"
)

if ret == qt.QMessageBox.No:
raise RuntimeError("Install process was manually canceled by user.")

def installPyTorchExtensionAndRestartIfNeeded(self):
"""
Install PytorchUtils if not installed and raises RuntimeError if canceled by user or install was unsuccessful.
Expand All @@ -243,6 +134,7 @@ def installPyTorchExtensionAndRestartIfNeeded(self):
if not self.doAskConfirmation:
raise

import qt
ret = qt.QMessageBox.question(
None,
"Pytorch extension not found.",
Expand Down Expand Up @@ -284,101 +176,3 @@ def _getTorchLogic(cls) -> "PyTorchUtilsLogic":
"This module requires PyTorch extension. "
"Install it from the Extensions Manager and restart Slicer to continue."
)

def pipInstallSelective(self, packageToInstall, installCommand, packagesToSkip):
"""
Installs a Python package, skipping a list of packages.
Return the list of skipped requirements (package name with version requirement).
"""
installCommand = self.cleanPyPiRequirement(installCommand)
self.pip_install(f"{installCommand} --no-deps")

# Install all dependencies but the ones listed in packagesToSkip
requirements = importlib.metadata.requires(packageToInstall)
if not requirements:
return []

# Update meta file to remove packages to skip.
# Necessary to avoid having skipped dependencies installed into 3D Slicer during pip updates.
self._removeSkippedPackagesFromMetaDataFile(packageToInstall, packagesToSkip)

skippedRequirements = []
for requirement in requirements:
skipThisPackage = False
for packageToSkip in packagesToSkip:
if requirement.startswith(packageToSkip):
# Do not install
skipThisPackage = True
break

if skipThisPackage:
skippedRequirements.append(requirement)
elif self.needsToInstallRequirement(requirement):
# Install sub dependencies and make sure they enforce requirements not to install
self.pipInstallSelective(Requirement(requirement).name, requirement, packagesToSkip)

return skippedRequirements

@classmethod
def _removeSkippedPackagesFromMetaDataFile(cls, packageToInstall, packagesToSkip):
def doSkipLine(metaLine):
if not metaLine.startswith("Requires-Dist: "):
return False
for packageToSkip in packagesToSkip:
if packageToSkip in metaLine:
return True
return False

# Use Latin-1 encoding to read the file, as it may contain non-ASCII characters and not necessarily in UTF-8 encoding.
with open(cls.packageMetaFilePath(packageToInstall), "r+", encoding="latin1") as file:
filteredLines = "".join([line for line in file if not doSkipLine(line)])
file.seek(0)
file.write(filteredLines)
file.truncate()

@staticmethod
def packageMetaFilePath(packageToInstall):
import importlib.metadata
return [p for p in importlib.metadata.files(packageToInstall) if 'METADATA' in str(p)][0].locate()

@staticmethod
def cleanPyPiRequirement(requirement) -> str:
"""
Returns requirement string compatible with Slicer pip_install call.
"""
import re
req = Requirement(requirement)

# Get any extra pypi to install from the requirements extras
extras = [extra for extra in req.extras]
extras = str(extras) if extras else ""

# Handle special case where extra would be in the marker instead of the extra spec
# Takes into account the ruff ; extra == 'dev' -> ruff[dev] case
extra_pattern = "extra == "
req_marker = str(req.marker)
if not extras and req_marker.startswith(extra_pattern):
req_marker = re.sub(r"\W+", '', req_marker.replace(extra_pattern, ""))
extras = f"[{req_marker}]"

return f"{req.name}{extras}{req.specifier}"

def pip_install(self, package) -> None:
"""
Install and log install of input package.
"""
self._log(f'- Installing {package}...')
try:
slicer.util.pip_install(package)
except CalledProcessError as e:
self._log(f"Install returned non-zero exit status : {e}. Attempting to continue...")

def pip_uninstall(self, package) -> None:
"""
Uninstall and log uninstall of input package.
"""
self._log(f'- Uninstall {package}...')
try:
slicer.util.pip_uninstall(package)
except CalledProcessError as e:
self._log(f"Uninstall returned non-zero exit status : {e}. Attempting to continue...")
1 change: 0 additions & 1 deletion SlicerNNUnet/SlicerNNUNetLib/Widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,6 @@ def __init__(
self.logic.inferenceFinished.connect(self.onInferenceFinished)
self.logic.errorOccurred.connect(self.onInferenceError)
self.logic.progressInfo.connect(self.onProgressInfo)
self.installLogic.progressInfo.connect(self.onProgressInfo)
self.isStopping = False

self.sceneCloseObserver = slicer.mrmlScene.AddObserver(slicer.mrmlScene.EndCloseEvent, self.onSceneChanged)
Expand Down
24 changes: 5 additions & 19 deletions SlicerNNUnet/Testing/InstallLogicTestCase.py
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Original file line number Diff line number Diff line change
@@ -1,24 +1,10 @@
import unittest

from SlicerNNUNetLib import InstallLogic
import slicer
from packaging.requirements import Requirement


class InstallLogicTestCase(unittest.TestCase):
def test_clean_pypi_requirements_rewrites_extra_into_brackets(self):
self.assertEqual(InstallLogic.cleanPyPiRequirement("ruff ; extra == 'dev'"), "ruff[dev]")

def test_clean_pypi_requirements_removes_spaces_from_req_string(self):
self.assertEqual(InstallLogic.cleanPyPiRequirement(" nibabel >=2.3.0 "), "nibabel>=2.3.0")

def test_requirements_for_python_versions_outside_slicer_are_marked_not_needed_to_install(self):
self.assertTrue(InstallLogic.isPackageInstalled("numpy"))
self.assertFalse(InstallLogic.isInstalledPackageCompatible("numpy < 1.0"))
self.assertFalse(InstallLogic.needsToInstallRequirement("numpy < 1.0; python_version<'3.9'"))

def test_requirements_for_unspecified_python_version_are_marked_needed_to_install(self):
self.assertTrue(InstallLogic.isPackageInstalled("numpy"))
self.assertFalse(InstallLogic.isInstalledPackageCompatible("numpy < 1.0"))
self.assertTrue(InstallLogic.needsToInstallRequirement("numpy < 1.0"))

def test_not_installed_package_is_marked_as_not_installed_and_not_compatible(self):
self.assertFalse(InstallLogic.isPackageInstalledAndCompatible("not_package"))
def test_pip_check_nnunetv2_does_not_raise(self):
# Should not raise, regardless of whether nnunetv2 is installed
slicer.util.pip_check(Requirement("nnunetv2"))

@Thibault-Pelletier Thibault-Pelletier Feb 17, 2026

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Test file should be removed altogether (no need to test a Slicer core function in an extension)

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