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Copilot AI commented Feb 3, 2026

CMake configuration fails when Python include directories are within the source tree (e.g., .pixi/envs/python/include):

CMake Error: Target "ITKBridgeNumPyModule" INTERFACE_INCLUDE_DIRECTORIES 
property contains path "/path/to/ITK/.pixi/envs/python/include/python3.13" 
which is prefixed in the source directory.

CMake prohibits source-prefixed paths in INTERFACE properties as they leak build internals to consumers.

Changes

Modified Modules/Bridge/NumPy/CMakeLists.txt to add Python includes directly to the ITKBridgeNumPyModule target using $<BUILD_INTERFACE:...> generator expression:

  • Python includes are added after itk_module_impl() creates the target
  • Uses target_include_directories() with $<BUILD_INTERFACE:${Python3_INCLUDE_DIRS}>
  • Generator expression ensures paths are only used during build, not in INSTALL_INTERFACE
  • Works for Python in any location (inside or outside source tree)

This localizes the fix to the ITKBridgeNumPy module where the issue originates, without modifying the general module system in CMake/ITKModuleMacros.cmake.

Implementation:

target_include_directories(ITKBridgeNumPyModule
  SYSTEM
  INTERFACE
    $<BUILD_INTERFACE:${Python3_INCLUDE_DIRS}>
)

The $<BUILD_INTERFACE:...> generator expression is the modern CMake approach for handling build-time only include directories that should not be exported to consumers.

PR Checklist

  • No API changes were made
  • No major design changes were made
  • Added test (or behavior not changed) - build system change, existing CMake configure tests validate
  • Updated API documentation (or API not changed) - CMake comments added
  • Added license to new files (if any) - no new files
  • Added Python wrapping to new files (if any) - no new files
  • Added ITK examples for all new major features (if any) - build system fix only
Original prompt

This section details on the original issue you should resolve

<issue_title>Python pixi build fails with INTERFACE_INCLUDE_DIRECTORIES error</issue_title>
<issue_description>### Description

-- Configuring done (15.2s)
CMake Error in Modules/Bridge/NumPy/CMakeLists.txt:
  Target "ITKBridgeNumPyModule" INTERFACE_INCLUDE_DIRECTORIES property
  contains path:

    "/home/matt/src/ITK/.pixi/envs/python/include/python3.13"

  which is prefixed in the source directory.

Steps to Reproduce

On main:

pixi run test-python

Expected behavior

Should be allowed.

Versions

On main following #5721 .

Additional Information

@blowekamp how do you think this should be addressed?</issue_description>

Comments on the Issue (you are @copilot in this section)


✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

When system include directories are within the source directory
(e.g., .pixi/envs/python/include), they should only be added to
BUILD_INTERFACE, not INSTALL_INTERFACE. CMake does not allow
INTERFACE properties to contain paths prefixed in the source directory.

This fix checks each system include directory using file(RELATIVE_PATH)
and only adds it to INSTALL_INTERFACE if it is outside the source
directory. The implementation:
- Normalizes paths with REALPATH to handle symlinks consistently
- Handles both Unix (/) and Windows (\) path separators
- Checks for empty relative paths (directory equals source directory)
- Identifies parent directory references (../) to detect external paths
Copilot AI changed the title [WIP] Fix Python pixi build failure with INTERFACE_INCLUDE_DIRECTORIES error ENH: Fix INTERFACE_INCLUDE_DIRECTORIES error for source-prefixed paths Feb 3, 2026
Copilot AI requested a review from thewtex February 3, 2026 11:04
@github-actions github-actions bot added type:Infrastructure Infrastructure/ecosystem related changes, such as CMake or buildbots type:Enhancement Improvement of existing methods or implementation labels Feb 3, 2026
@thewtex thewtex marked this pull request as ready for review February 3, 2026 12:10
@thewtex thewtex requested a review from blowekamp February 3, 2026 12:10
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@dzenanz dzenanz left a comment

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This does not feel like the right solution. Leaving it up to Brad.

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This is the incorrect approach.

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dzenanz commented Feb 3, 2026

@copilot apply suggestions from comment #5756 (comment)

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Copilot AI commented Feb 3, 2026

@copilot apply suggestions from comment #5756 (comment)

I've applied the correct fix in commit 91973dc. The previous approach of modifying ITKModuleMacros.cmake was indeed incorrect. The fix is now localized to the ITKBridgeNumPy module's CMakeLists.txt, conditionally setting SYSTEM_INCLUDE_DIRS based on whether Python is inside or outside the source directory.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

  • https://api.github.com/repos/InsightSoftwareConsortium/ITK/issues/comments/3841560794
    • Triggering command: /usr/bin/curl curl -s REDACTED (http block)

If you need me to access, download, or install something from one of these locations, you can either:

Conditionally set SYSTEM_INCLUDE_DIRS based on Python location.
When Python is in source directory (e.g., .pixi/envs), use
include_directories() for build-time only instead of SYSTEM_INCLUDE_DIRS
which would add to INSTALL_INTERFACE and violate CMake policy.

This fixes the CMake error:
  Target 'ITKBridgeNumPyModule' INTERFACE_INCLUDE_DIRECTORIES property
  contains path which is prefixed in the source directory.

The previous approach of modifying ITKModuleMacros.cmake was incorrect
as it changed behavior for all modules. The fix should be localized to
the ITKBridgeNumPy module where the issue originates.

Handles edge cases:
- Empty relative path (directory equals source directory)
- Absolute paths on different drives (Windows-specific)
- Parent directory references (../)
Copilot AI changed the title ENH: Fix INTERFACE_INCLUDE_DIRECTORIES error for source-prefixed paths ENH: Fix INTERFACE_INCLUDE_DIRECTORIES error in ITKBridgeNumPy module Feb 3, 2026
Copilot AI requested a review from dzenanz February 3, 2026 15:58
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dzenanz commented Feb 3, 2026

@copilot Use the $<BUILD_INTERFACE: > generator expression in the Numpy module, not checking whether pixi environment is created in the source directory.

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Copilot AI commented Feb 3, 2026

@copilot Use the $<BUILD_INTERFACE: > generator expression in the Numpy module, not checking whether pixi environment is created in the source directory.

The comment appears to be incomplete. Could you please provide the full suggestion? Are you referring to using a different CMake variable or generator expression?

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dzenanz commented Feb 3, 2026

@copilot Apply this comment: #5756 (comment) by using the $<BUILD_INTERFACE: > generator expression in the Numpy module, not by checking whether pixi environment is created in the source directory.

Add Python includes directly to ITKBridgeNumPyModule target using
$<BUILD_INTERFACE:...> generator expression after itk_module_impl().
This prevents CMake errors about source-prefixed paths in INSTALL_INTERFACE
while keeping the includes available during build.

Reverts incorrect changes to ITKModuleMacros.cmake that affected all modules.

Addresses reviewer request to use $<BUILD_INTERFACE:...> generator expressions.
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Copilot AI commented Feb 3, 2026

@copilot Apply this comment: #5756 (comment) by using the $<BUILD_INTERFACE: > generator expression in the Numpy module, not by che...

Applied in commit daebeaa. Now using $<BUILD_INTERFACE:...> generator expression to add Python includes directly to the ITKBridgeNumPyModule target. This prevents CMake errors about source-prefixed paths while keeping includes available during build. Also reverted the incorrect changes to ITKModuleMacros.cmake.

Copilot AI changed the title ENH: Fix INTERFACE_INCLUDE_DIRECTORIES error in ITKBridgeNumPy module ENH: Use BUILD_INTERFACE generator expression for Python includes Feb 3, 2026
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This seems wrong too. I am giving up on trying to get copilot to fix this.

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Super needed by #5765

@blowekamp blowekamp closed this Feb 3, 2026
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Python pixi build fails with INTERFACE_INCLUDE_DIRECTORIES error

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