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Python requirements need to be updated for latest Slicer python version #55
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jamesfishbaugh
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Apr 4, 2022
…hon 3.9 This commit fixes the following error: Command failed: 1 '/Volumes/D/P/S-0-build/python-install/bin/PythonSlicer' '-m' 'pip' 'install' '--require-hashes' '-r' '/.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-requirements.txt' '--prefix' '/.../ShapeVariationAnalyzer-build/python-packages-install' See also /.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-prefix/src/python-ShapeVariationAnalyzer-requirements-stamp/python-ShapeVariationAnalyzer-requirements-install-*.log This addresses the issue initiated here: DCBIA-OrthoLab#55
jcfr
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Apr 6, 2022
…d of 3.6 This commit fixes the following build error: ``` Command failed: 1 '/Volumes/D/P/S-0-build/python-install/bin/PythonSlicer' '-m' 'pip' 'install' '--require-hashes' '-r' '/.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-requirements.txt' '--prefix' '/.../ShapeVariationAnalyzer-build/python-packages-install' See also /.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-prefix/src/python-ShapeVariationAnalyzer-requirements-stamp/python-ShapeVariationAnalyzer-requirements-install-*.log ``` The updates was performed following these steps using the updated "python_package_updater.py" script assocated with PR Slicer/Slicer#6300: ``` # Set common variables SLICER_SOURCE_DIR=~/Projects/Slicer SLICER_DIR=~/Projects/Slicer-Release/Slicer-build PYTHONSLICER_EXECUTABLE=${SLICER_DIR}/../python-install/bin/PythonSlicer EXTENSION_SOURCE_DIR=/home/jcfr/Projects/ShapeVariationAnalyzer EXTENSION_BINARY_DIR=/home/jcfr/Projects/ShapeVariationAnalyzer-Release # Install packages into the prefix PYTHON_INSTALL_PREFIX=${EXTENSION_BINARY_DIR}/python-packages-install ${PYTHONSLICER_EXECUTABLE} -m pip install --prefix ${PYTHON_INSTALL_PREFIX} scikit_learn # Update extension external projects UPDATER_SCRIPT=${SLICER_SOURCE_DIR}/Utilities/Scripts/python_package_updater.py ${PYTHONSLICER_EXECUTABLE} ${UPDATER_SCRIPT} \ -s ${EXTENSION_SOURCE_DIR}/SuperBuild \ --from-installed-packages --path ${PYTHON_INSTALL_PREFIX}/lib/python3.9/site-packages ``` This addresses the issue initiated here: DCBIA-OrthoLab#55 Co-authored-by: James Fishbaugh <[email protected]>
jcfr
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Apr 6, 2022
…d of 3.6 This commit fixes the following build error: ``` Command failed: 1 '/Volumes/D/P/S-0-build/python-install/bin/PythonSlicer' '-m' 'pip' 'install' '--require-hashes' '-r' '/.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-requirements.txt' '--prefix' '/.../ShapeVariationAnalyzer-build/python-packages-install' See also /.../ShapeVariationAnalyzer-build/python-ShapeVariationAnalyzer-requirements-prefix/src/python-ShapeVariationAnalyzer-requirements-stamp/python-ShapeVariationAnalyzer-requirements-install-*.log ``` The updates was performed following these steps using the updated "python_package_updater.py" script assocated with PR Slicer/Slicer#6300: ``` # Set common variables SLICER_SOURCE_DIR=~/Projects/Slicer SLICER_DIR=~/Projects/Slicer-Release/Slicer-build PYTHONSLICER_EXECUTABLE=${SLICER_DIR}/../python-install/bin/PythonSlicer EXTENSION_SOURCE_DIR=/home/jcfr/Projects/ShapeVariationAnalyzer EXTENSION_BINARY_DIR=/home/jcfr/Projects/ShapeVariationAnalyzer-Release # Install packages into the prefix PYTHON_INSTALL_PREFIX=${EXTENSION_BINARY_DIR}/python-packages-install ${PYTHONSLICER_EXECUTABLE} -m pip install --prefix ${PYTHON_INSTALL_PREFIX} scikit_learn # Update extension external projects UPDATER_SCRIPT=${SLICER_SOURCE_DIR}/Utilities/Scripts/python_package_updater.py ${PYTHONSLICER_EXECUTABLE} ${UPDATER_SCRIPT} \ -s ${EXTENSION_SOURCE_DIR}/SuperBuild \ --from-installed-packages \ --path ${PYTHON_INSTALL_PREFIX}/lib/python3.9/site-packages ``` This addresses the issue initiated here: DCBIA-OrthoLab#55 Co-authored-by: James Fishbaugh <[email protected]>
Closed by 03a9b78. |
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Similar to what is needed at DCBIA-OrthoLab/MFSDA_Python#26
Slicer recently upgraded from Python 3.6.7 to Python 3.9.10 in Slicer/Slicer@34e48e8. There are now observed build errors of the ShapeVariationAnalyzer Slicer extension as seen at https://slicer.cdash.org/viewBuildError.php?buildid=2618477. This is because the python requirements file in the repo is including hashes that are only for Python 3.6 wheels. These need to be updated for Python 3.9 wheels which also means the actual version of packages here will need to be updated as some older versions simply don't have Python 3.9 wheels because that version was released before Python 3.9 was even released. For example
scikit-learn==0.23.1
does not have Python 3.9 wheels available from PyPI (see here).ShapeVariationAnalyzer/SuperBuild/External_python-ShapeVariationAnalyzer-requirements.cmake
Lines 43 to 54 in 9eb7107
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