tomotopy
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bab2min
Eigen file not found during pip installation
When running
pip install tomotopy
I get the following output:
Using cached tomotopy-0.12.7.tar.gz (1.3 MB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.11.0 in /Users/path/to/project/venv/lib/python3.12/site-packages (from tomotopy) (1.26.4)
Building wheels for collected packages: tomotopy
^[[A Building wheel for tomotopy (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [92 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-14.0-arm64-cpython-312
creating build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/_version.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/coherence.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/_call_utils.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/_summary.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/utils.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/label.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/_show_progress.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
running egg_info
writing tomotopy.egg-info/PKG-INFO
writing dependency_links to tomotopy.egg-info/dependency_links.txt
writing requirements to tomotopy.egg-info/requires.txt
writing top-level names to tomotopy.egg-info/top_level.txt
reading manifest file 'tomotopy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'src'
warning: no files found matching 'LICENSE.txt'
adding license file 'LICENSE'
writing manifest file 'tomotopy.egg-info/SOURCES.txt'
/Users/path/to/project/venv/lib/python3.12/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'tomotopy.viewer' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'tomotopy.viewer' 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 'tomotopy.viewer' 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 'tomotopy.viewer' to be distributed and are
already explicitly excluding 'tomotopy.viewer' 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)
copying tomotopy/auto_labeling_code.rst -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/auto_labeling_code_with_porter.rst -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/documentation.kr.rst -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
copying tomotopy/documentation.rst -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy
creating build/lib.macosx-14.0-arm64-cpython-312/tomotopy/viewer
copying tomotopy/viewer/__init__.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy/viewer
copying tomotopy/viewer/template.html -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy/viewer
copying tomotopy/viewer/viewer_server.py -> build/lib.macosx-14.0-arm64-cpython-312/tomotopy/viewer
running build_ext
building '_tomotopy' extension
creating build/temp.macosx-14.0-arm64-cpython-312
creating build/temp.macosx-14.0-arm64-cpython-312/src
creating build/temp.macosx-14.0-arm64-cpython-312/src/Labeling
creating build/temp.macosx-14.0-arm64-cpython-312/src/TopicModel
creating build/temp.macosx-14.0-arm64-cpython-312/src/python
clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -DMODULE_NAME=PyInit__tomotopy -Iinclude "-I/Users/path/to/project/venv/lib/python3.12/site-packages/numpy/core/include" "-I/Users/path/to/project/venv/include" -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.12/include/python3.12 -c src/Labeling/FoRelevance.cpp -o build/temp.macosx-14.0-arm64-cpython-312/src/Labeling/FoRelevance.o -std=c++1y -O3 -fpermissive -stdlib=libc++ -Wno-unused-variable -Wno-switch -DTOMOTOPY_ISA=arm64 -arch arm64
In file included from src/Labeling/FoRelevance.cpp:4:
In file included from src/Labeling/FoRelevance.h:4:
In file included from src/Labeling/Labeler.h:4:
In file included from src/Labeling/../TopicModel/TopicModel.hpp:5:
In file included from src/Labeling/../TopicModel/../Utils/Dictionary.h:9:
src/Labeling/../TopicModel/../Utils/serializer.hpp:10:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
^~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' 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 tomotopy
Running setup.py clean for tomotopy
Failed to build tomotopy
ERROR: Could not build wheels for tomotopy, which is required to install pyproject.toml-based projects```
I'm running this on an Apple M3 Pro.
I faced the same error and I went down the route of building from source.
After cloning the repo, run the following commands from within the tomotopy folder:
git clone https://gitlab.com/libeigen/eigen
cd eigen
git checkout tags/3.4.0
cd ..
mkdir include
mv eigen/Eigen/ include/
rm -rf eigen-git-mirror/
git clone https://github.com/bab2min/EigenRand
cd EigenRand
git checkout tags/v0.4.1
cd ..
mv EigenRand/EigenRand include/
git clone https://github.com/mapbox/variant
cd variant
git checkout tags/v1.1.3
cd ..
mv variant/include/mapbox include/
Now, run: python setup.py install.
This took me past the error that this issue talks about. Found these steps in the github workflow files that @bab2min (thanks!) had added. cc: @teresaibarra
(all hail grep!)
