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This page regroups some problems encountered during the different operations and their fix.
Insatllation of ndlar_flow
ERROR: Failed building wheel for pylandau
Error message
(ndlar_flow.venv) [nsallin@neutrino01 ndlar_flow]$ pip install -e .
Obtaining file:///terabig/nsallin/ndlar_flow
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Preparing editable metadata (pyproject.toml) ... done
Requirement already satisfied: h5py>=2.10 in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from ndlar_flow==1.0.1) (3.13.0)
Requirement already satisfied: pytest in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from ndlar_flow==1.0.1) (8.3.5)
Collecting scipy (from ndlar_flow==1.0.1)
Downloading scipy-1.13.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting scikit-image (from ndlar_flow==1.0.1)
Downloading scikit_image-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
Collecting scikit-learn>=1.3.0 (from ndlar_flow==1.0.1)
Downloading scikit_learn-1.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Requirement already satisfied: h5flow>=0.2.0 in /terabig/nsallin/h5flow (from ndlar_flow==1.0.1) (0.2.4)
Collecting pylandau@ git+https://github.com/cuddandr/pylandau.git#egg=pylandau (from ndlar_flow==1.0.1)
Cloning https://github.com/cuddandr/pylandau.git to /tmp/pip-install-a32r5txi/pylandau_d8f676d31cae45139ef22c068c1411a7
Running command git clone --filter=blob:none --quiet https://github.com/cuddandr/pylandau.git /tmp/pip-install-a32r5txi/pylandau_d8f676d31cae45139ef22c068c1411a7
Resolved https://github.com/cuddandr/pylandau.git to commit a50571d566ec64bd3d6bbc77e9e55eeadfdb830f
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting adc64format@ git+https://github.com/larpix/adc64format.git@v0.1.3#egg=adc64format (from ndlar_flow==1.0.1)
Cloning https://github.com/larpix/adc64format.git (to revision v0.1.3) to /tmp/pip-install-a32r5txi/adc64format_dba4f0ede7d64c018a1266a8728659d2
Running command git clone --filter=blob:none --quiet https://github.com/larpix/adc64format.git /tmp/pip-install-a32r5txi/adc64format_dba4f0ede7d64c018a1266a8728659d2
Resolved https://github.com/larpix/adc64format.git to commit 33f94a60cb654b24723bfeb9dd6f63e097fd4a61
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from adc64format@ git+https://github.com/larpix/adc64format.git@v0.1.3#egg=adc64format->ndlar_flow==1.0.1) (2.0.2)
Requirement already satisfied: tqdm in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from adc64format@ git+https://github.com/larpix/adc64format.git@v0.1.3#egg=adc64format->ndlar_flow==1.0.1) (4.67.1)
Collecting cython==0.29.34 (from pylandau@ git+https://github.com/cuddandr/pylandau.git#egg=pylandau->ndlar_flow==1.0.1)
Using cached Cython-0.29.34-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (3.1 kB)
Requirement already satisfied: PyYAML in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from h5flow>=0.2.0->ndlar_flow==1.0.1) (6.0.2)
Requirement already satisfied: pyyaml-include<2.0 in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from h5flow>=0.2.0->ndlar_flow==1.0.1) (1.4.1)
Collecting joblib>=1.2.0 (from scikit-learn>=1.3.0->ndlar_flow==1.0.1)
Downloading joblib-1.5.0-py3-none-any.whl.metadata (5.6 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn>=1.3.0->ndlar_flow==1.0.1)
Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: exceptiongroup>=1.0.0rc8 in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from pytest->ndlar_flow==1.0.1) (1.2.2)
Requirement already satisfied: iniconfig in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from pytest->ndlar_flow==1.0.1) (2.1.0)
Requirement already satisfied: packaging in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from pytest->ndlar_flow==1.0.1) (25.0)
Requirement already satisfied: pluggy<2,>=1.5 in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from pytest->ndlar_flow==1.0.1) (1.5.0)
Requirement already satisfied: tomli>=1 in /terabig/nsallin/ndlar_flow.venv/lib/python3.9/site-packages (from pytest->ndlar_flow==1.0.1) (2.2.1)
Collecting networkx>=2.8 (from scikit-image->ndlar_flow==1.0.1)
Downloading networkx-3.2.1-py3-none-any.whl.metadata (5.2 kB)
Collecting pillow>=9.1 (from scikit-image->ndlar_flow==1.0.1)
Downloading pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (8.9 kB)
Collecting imageio>=2.33 (from scikit-image->ndlar_flow==1.0.1)
Downloading imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
Collecting tifffile>=2022.8.12 (from scikit-image->ndlar_flow==1.0.1)
Downloading tifffile-2024.8.30-py3-none-any.whl.metadata (31 kB)
Collecting lazy-loader>=0.4 (from scikit-image->ndlar_flow==1.0.1)
Downloading lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
Using cached Cython-0.29.34-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (2.0 MB)
Downloading scikit_learn-1.6.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.5/13.5 MB 50.1 MB/s eta 0:00:00
Downloading joblib-1.5.0-py3-none-any.whl (307 kB)
Downloading scipy-1.13.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.6/38.6 MB 54.3 MB/s eta 0:00:00
Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Downloading scikit_image-0.24.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.9 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.9/14.9 MB 52.0 MB/s eta 0:00:00
Downloading imageio-2.37.0-py3-none-any.whl (315 kB)
Downloading lazy_loader-0.4-py3-none-any.whl (12 kB)
Downloading networkx-3.2.1-py3-none-any.whl (1.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.6/1.6 MB 36.1 MB/s eta 0:00:00
Downloading pillow-11.2.1-cp39-cp39-manylinux_2_28_x86_64.whl (4.6 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 44.9 MB/s eta 0:00:00
Downloading tifffile-2024.8.30-py3-none-any.whl (227 kB)
Building wheels for collected packages: ndlar_flow, adc64format, pylandau
Building editable for ndlar_flow (pyproject.toml) ... done
Created wheel for ndlar_flow: filename=ndlar_flow-1.0.1-0.editable-py3-none-any.whl size=7829 sha256=98929ffdd58bd65a31a73ea604bf68cdc95a17280fc5f1a2c0d27c8076e8349a
Stored in directory: /tmp/pip-ephem-wheel-cache-3aj383d4/wheels/b0/6b/8f/daa407c51bf2b21a3a79bdcd2058ecdac5f0b12434ee962a33
Building wheel for adc64format (pyproject.toml) ... done
Created wheel for adc64format: filename=adc64format-0.1.2-py3-none-any.whl size=10830 sha256=31e47604250a8ae6d6b2e85c549d899c530d3d3bfb8629259aa56b0d5349a808
Stored in directory: /tmp/pip-ephem-wheel-cache-3aj383d4/wheels/21/4d/e6/c1081e07e37fd78e22e5cb71be9cc0a7ee6634010dfc94f915
Building wheel for pylandau (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for pylandau (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [92 lines of output]
/tmp/pip-build-env-hq4fm6bt/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
!!
********************************************************************************
Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).
By 2026-Feb-18, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
********************************************************************************
!!
corresp(dist, value, root_dir)
/tmp/pip-build-env-hq4fm6bt/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsWarning: `install_requires` overwritten in `pyproject.toml` (dependencies)
corresp(dist, value, root_dir)
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-39/pyLandau
copying pyLandau/__init__.py -> build/lib.linux-x86_64-cpython-39/pyLandau
creating build/lib.linux-x86_64-cpython-39/tests
copying tests/__init__.py -> build/lib.linux-x86_64-cpython-39/tests
copying tests/constraints.py -> build/lib.linux-x86_64-cpython-39/tests
copying tests/test_data_types.py -> build/lib.linux-x86_64-cpython-39/tests
copying tests/test_exceptions.py -> build/lib.linux-x86_64-cpython-39/tests
copying tests/test_fuzzing.py -> build/lib.linux-x86_64-cpython-39/tests
copying tests/test_properties.py -> build/lib.linux-x86_64-cpython-39/tests
running egg_info
writing pylandau.egg-info/PKG-INFO
writing dependency_links to pylandau.egg-info/dependency_links.txt
writing requirements to pylandau.egg-info/requires.txt
writing top-level names to pylandau.egg-info/top_level.txt
reading manifest file 'pylandau.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*' under directory 'docs'
adding license file 'LICENSE'
writing manifest file 'pylandau.egg-info/SOURCES.txt'
/tmp/pip-build-env-hq4fm6bt/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:212: _Warning: Package 'pyLandau.cpp' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pyLandau.cpp' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pyLandau.cpp' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pyLandau.cpp' to be distributed and are
already explicitly excluding 'pyLandau.cpp' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
creating build/lib.linux-x86_64-cpython-39/pyLandau/cpp
copying pyLandau/cpp/pylandau.cpp -> build/lib.linux-x86_64-cpython-39/pyLandau/cpp
copying pyLandau/cpp/pylandau.pyx -> build/lib.linux-x86_64-cpython-39/pyLandau/cpp
copying pyLandau/cpp/pylandau_src.cpp -> build/lib.linux-x86_64-cpython-39/pyLandau/cpp
running build_ext
building 'pylandau' extension
creating build/temp.linux-x86_64-cpython-39/pyLandau/cpp
g++ -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DCYTHON_TRACE=1 -IpyLandau/cpp -I/terabig/nsallin/ndlar_flow.venv/include -I/usr/include/python3.9 -I/tmp/pip-build-env-hq4fm6bt/overlay/lib64/python3.9/site-packages/numpy/_core/include -c pyLandau/cpp/pylandau.cpp -o build/temp.linux-x86_64-cpython-39/pyLandau/cpp/pylandau.o
pyLandau/cpp/pylandau.cpp:31:10: fatal error: Python.h: No such file or directory
31 | #include "Python.h"
| ^~~~~~~~~~
compilation terminated.
error: command '/usr/bin/g++' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pylandau
Successfully built ndlar_flow adc64format
Failed to build pylandau
ERROR: Failed to build installable wheels for some pyproject.toml based projects (pylandau)
Solution
The solution was to install pylandau first and then rerun the ndlar_flow install command:
pip install pylandau
and then (in .../ndlar_flow)
pip install -e .