ENH: Add script to install python packages locally by axel-grc · Pull Request #978 · RTKConsortium/RTK

axel-grc · 2026-07-31T20:38:21Z

No description provided.

SimonRit

Nice, just two small questions below

SimonRit · 2026-08-24T14:48:16Z

+#
+# All paths below can be overridden via environment variables.
+
+set -euo pipefail


-eu look good. Why set -o pipefail? There is no pipe here as far as I can tell.
I would also consider adding -x

SimonRit · 2026-08-25T06:45:28Z

+  --config-settings=cmake.define.ITK_USE_PYTHON_LIMITED_API=OFF
+)
+echo "==> Installing RTK Python package (editable)"
+rm -rf "$RTK_PIP_BUILD_DIR"


Should we keep the build directory to avoid recompiling from scratch for C++ changes?

axel-grc · 2026-09-11T10:58:32Z

I made some tests, the script does not do a full rebuild each time a cxx files is changed, so ready to be merged I think

SimonRit

I'd change the script to compile ITK with CudaCommon and RTK ON instead of compiling RTK separately. What do you think?

SimonRit · 2026-09-11T13:16:48Z

+# Prerequisites:
+#   - An ITK build tree with Python wrapping enabled (set ITK_DIR)
+#   - Optionally CUDA (set RTK_USE_CUDA=ON).
+#     When CUDA is enabled, CudaCommon must be findable by ITK.


I'd remove this line, CudaCommon is in ITK as a remote module so it's always findable. CUDA might not be findable but that's beyond the scope of this script.

SimonRit · 2026-09-11T13:19:10Z

+# Verify that ITK Python wrapping is installed in site-packages. RTK wrapping
+# builds on top of the ITK wrapping infrastructure, so ITK's wrapping shared
+# libraries must already be present.
+ITK_PYTHON_DIR=$(python -c "import itk; import os; print(os.path.dirname(itk.__file__))")


If I understand correctly, you must compile ITK first. Why not provide a script that jointly compiles an editable ITK and RTK?

SimonRit · 2026-09-11T13:22:29Z

 * Manually download RTK's source repository from [GitHub](https://github.com/RTKConsortium/RTK) with `git` (recommended) or as a [zip package](https://codeload.github.com/RTKConsortium/RTK/zip/main).
 * Configure the project with CMake pointing to RTK's source directory and setting the CMake option `ITK_DIR` to ITK's compilation directory. All CMake options above can be set except `Module_RTK`.

+A convenience script at `utilities/build_rtk_python.sh` builds and installs RTK as a Python package. It must be run from the RTK source directory. It requires ITK and, when using CUDA, CudaCommon, both built with Python wrapping enabled:


Replace

A convenience script at `utilities/build_rtk_python.sh`

by

The convenience script [build_rtk_python.sh](utilities/build_rtk_python.sh)

please.

axel-grc · 2026-09-14T08:44:03Z

I'd change the script to compile ITK with CudaCommon and RTK ON instead of compiling RTK separately. What do you think?

I'm not sure the joint/editable build is the solution. We can't pip install an ITK source tree, it has no pip build system.
So we can use ITKPythonPackages to build the ITK (and RTK) python packages from a prebuilt ITK. And even then, RTK's hand-written Python (rtkargumentparser.py, init_rtk, rtkExtras, rtkConfig, group/app scripts) has to be copied into the itk python package manually, otherwise the rtk*` applications aren't importable.

SimonRit · 2026-09-14T09:26:13Z

I'd change the script to compile ITK with CudaCommon and RTK ON instead of compiling RTK separately. What do you think?

I'm not sure the joint/editable build is the solution. We can't pip install an ITK source tree, it has no pip build system. So we can use ITKPythonPackages to build the ITK (and RTK) python packages from a prebuilt ITK. And even then, RTK's hand-written Python (rtkargumentparser.py, init_rtk, rtkExtras, rtkConfig, group/app scripts) has to be copied into the itk python package manually, otherwise the rtk*` applications aren't importable.

Ok, I didn't know one couldn't pip install an ITK source tree. So with this script, one needs to

pip install itk (and itk-cudacommon if using CUDA ?)
build ITK with Python wrapping
build RTK according to the script?

It's currently not clear that one needs to pip install itk first, I would clarify this if this is the proposed procedure.

axel-grc · 2026-09-14T12:04:09Z

build RTK ac

We don't need to pip install itk, we just need to build and install itk with python wrapping (and optionally CudaCommon) and give the build path to the script

SimonRit · 2026-09-15T14:45:03Z

build RTK ac

We don't need to pip install itk, we just need to build and install itk with python wrapping (and optionally CudaCommon) and give the build path to the script

I tried to test this (fresh Python env, built ITK, run the script). Here is the result:

(localcomp312) srit@srit-Precision-5480:~/src/rtk/rtk$ ITK_DIR=/home/srit/src/itk/lin64-PythonWrapping-install RTK_PIP_BUILD_DIR=/home/srit/src/rtk/lin64-pip ./utilities/build_rtk_python.sh 
+ RTK_PIP_BUILD_DIR=/home/srit/src/rtk/lin64-pip
+ BUILD_TYPE=Release
+ RTK_USE_CUDA=OFF
+ '[' -z /home/srit/src/itk/lin64-PythonWrapping-install ']'
++ python -c 'import itk; import os; print(os.path.dirname(itk.__file__))'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import itk; import os; print(os.path.dirname(itk.__file__))
    ^^^^^^^^^^
ModuleNotFoundError: No module named 'itk'
+ ITK_PYTHON_DIR=

So pip install itk is required?

SimonRit · 2026-09-15T14:46:42Z

 * Manually download RTK's source repository from [GitHub](https://github.com/RTKConsortium/RTK) with `git` (recommended) or as a [zip package](https://codeload.github.com/RTKConsortium/RTK/zip/main).
 * Configure the project with CMake pointing to RTK's source directory and setting the CMake option `ITK_DIR` to ITK's compilation directory. All CMake options above can be set except `Module_RTK`.

+The convenience script [build_rtk_python.sh](utilities/build_rtk_python.sh) builds and installs RTK as a Python package. It must be run from the RTK source directory. It requires ITK and, when using CUDA, CudaCommon, both built with Python wrapping enabled:


My bad, the link doesn't work. I guess it only works for the .md files copied for readthedocs. Is there a proper way to link to files in the GitHub repository?

SimonRit · 2026-09-16T07:26:45Z

build RTK ac

We don't need to pip install itk, we just need to build and install itk with python wrapping (and optionally CudaCommon) and give the build path to the script

I tried to test this (fresh Python env, built ITK, run the script). Here is the result:
(localcomp312) srit@srit-Precision-5480:~/src/rtk/rtk$ ITK_DIR=/home/srit/src/itk/lin64-PythonWrapping-install RTK_PIP_BUILD_DIR=/home/srit/src/rtk/lin64-pip ./utilities/build_rtk_python.sh 
+ RTK_PIP_BUILD_DIR=/home/srit/src/rtk/lin64-pip
+ BUILD_TYPE=Release
+ RTK_USE_CUDA=OFF
+ '[' -z /home/srit/src/itk/lin64-PythonWrapping-install ']'
++ python -c 'import itk; import os; print(os.path.dirname(itk.__file__))'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import itk; import os; print(os.path.dirname(itk.__file__))
    ^^^^^^^^^^
ModuleNotFoundError: No module named 'itk'
+ ITK_PYTHON_DIR=
So pip install itk is required?

So I progressed by adding the ITK bindings to the PYTHONPATH, as I usually do with my local ITK compilation. Then I had to install scikit_build_core. It's now compiling, I'll let you know if it works...

The error appears when compiling the RTK wrapping independently of ITK with the script utilities/build_rtk_python.sh: In file included from /home/srit/src/itk/lin64-PythonWrapping/Wrapping/castxml_inputs/itkPyBufferRTK.cxx:16: /home/srit/src/itk/itk/Modules/Bridge/NumPy/include/itkPyBuffer.h:30:10: fatal error: 'Python.h' file not found 30 | #include <Python.h> | ^~~~~~~~~~ 1 error generated. gmake[2]: *** [Wrapping/Modules/RTK/CMakeFiles/RTKCastXML.dir/build.make:329: /home/srit/src/itk/lin64-PythonWrapping/Wrapping/castxml_inputs/itkPyBufferRTK.xml] Error 1 gmake[2]: Leaving directory '/home/srit/src/rtk/lin64-toto' gmake[1]: *** [CMakeFiles/Makefile2:2357: Wrapping/Modules/RTK/CMakeFiles/RTKCastXML.dir/all] Error 2 gmake[1]: Leaving directory '/home/srit/src/rtk/lin64-toto' gmake: *** [Makefile:146: all] Error 2

SimonRit · 2026-09-16T11:51:34Z

Ok, it worked with the additional patch I have pushed:
c8c305b
We need to clarify a bit the doc. Should we consider testing the independent compilation of itk-cuda-common?

axel-grc requested a review from SimonRit August 24, 2026 07:59

SimonRit approved these changes Aug 25, 2026

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SimonRit added this to the RTK 3.0 milestone Sep 3, 2026

SimonRit assigned axel-grc Sep 10, 2026

axel-grc force-pushed the PythonInstall branch from 6ed7d44 to 87bf024 Compare September 11, 2026 10:54

axel-grc requested a review from SimonRit September 11, 2026 10:58

SimonRit requested changes Sep 11, 2026

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ENH: Add script to install python packages locally

1291dd9

axel-grc force-pushed the PythonInstall branch from 87bf024 to 1291dd9 Compare September 14, 2026 09:04

SimonRit reviewed Sep 15, 2026

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axel-grc commented Sep 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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axel-grc commented Sep 14, 2026 •

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