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Installation issues due to newer cython #71

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cthoyt opened this issue Oct 28, 2022 · 2 comments · Fixed by #72
Closed

Installation issues due to newer cython #71

cthoyt opened this issue Oct 28, 2022 · 2 comments · Fixed by #72

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@cthoyt
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cthoyt commented Oct 28, 2022

After running pip install adeft on python 3.11, I'm running into the following error message:

pip install adeft
Collecting adeft
  Using cached adeft-0.11.1.tar.gz (124 kB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: nltk in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from adeft) (3.7)
Requirement already satisfied: scikit-learn>=0.20.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from adeft) (1.1.3)
Requirement already satisfied: boto3 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from adeft) (1.25.3)
Requirement already satisfied: flask in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from adeft) (2.2.2)
Requirement already satisfied: appdirs in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from adeft) (1.4.4)
Requirement already satisfied: numpy>=1.17.3 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from scikit-learn>=0.20.0->adeft) (1.23.4)
Requirement already satisfied: scipy>=1.3.2 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from scikit-learn>=0.20.0->adeft) (1.9.3)
Requirement already satisfied: joblib>=1.0.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from scikit-learn>=0.20.0->adeft) (1.2.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from scikit-learn>=0.20.0->adeft) (3.1.0)
Requirement already satisfied: botocore<1.29.0,>=1.28.3 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from boto3->adeft) (1.28.3)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from boto3->adeft) (1.0.1)
Requirement already satisfied: s3transfer<0.7.0,>=0.6.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from boto3->adeft) (0.6.0)
Requirement already satisfied: Werkzeug>=2.2.2 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from flask->adeft) (2.2.2)
Requirement already satisfied: Jinja2>=3.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from flask->adeft) (3.1.2)
Requirement already satisfied: itsdangerous>=2.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from flask->adeft) (2.1.2)
Requirement already satisfied: click>=8.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from flask->adeft) (8.1.3)
Requirement already satisfied: regex>=2021.8.3 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from nltk->adeft) (2022.9.13)
Requirement already satisfied: tqdm in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from nltk->adeft) (4.64.1)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from botocore<1.29.0,>=1.28.3->boto3->adeft) (2.8.2)
Requirement already satisfied: urllib3<1.27,>=1.25.4 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from botocore<1.29.0,>=1.28.3->boto3->adeft) (1.26.12)
Requirement already satisfied: MarkupSafe>=2.0 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from Jinja2>=3.0->flask->adeft) (2.1.1)
Requirement already satisfied: six>=1.5 in /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.29.0,>=1.28.3->boto3->adeft) (1.16.0)
Building wheels for collected packages: adeft
  Building wheel for adeft (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [50 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-12-x86_64-3.11
      creating build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/util.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/discover.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/disambiguate.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/recognize.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/locations.py -> build/lib.macosx-12-x86_64-3.11/adeft
      creating build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/classify.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/label.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      creating build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/score/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/score/score.py -> build/lib.macosx-12-x86_64-3.11/adeft/score
      creating build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/download.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/__main__.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui
      copying adeft/gui/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui
      creating build/lib.macosx-12-x86_64-3.11/adeft/nlp
      copying adeft/nlp/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      copying adeft/nlp/nlp.py -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      copying adeft/gui/ground/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      copying adeft/gui/ground/ground.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      running egg_info
      writing manifest file 'adeft.egg-info/SOURCES.txt'
      copying adeft/score/_score.c -> build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/nlp/stopwords.json -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      copying adeft/gui/ground/static/ground.css -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      copying adeft/gui/ground/static/scripts.js -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/templates
      copying adeft/gui/ground/templates/input.jinja2 -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/templates
      running build_ext
      creating build/temp.macosx-12-x86_64-3.11
      creating build/temp.macosx-12-x86_64-3.11/adeft
      creating build/temp.macosx-12-x86_64-3.11/adeft/score
      clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/Users/cthoyt/.virtualenvs/indra/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c adeft/score/_score.c -o build/temp.macosx-12-x86_64-3.11/adeft/score/_score.o
      adeft/score/_score.c:209:12: fatal error: 'longintrepr.h' file not found
        #include "longintrepr.h"
                 ^~~~~~~~~~~~~~~
      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 adeft
  Running setup.py clean for adeft
Failed to build adeft
Installing collected packages: adeft
  Running setup.py install for adeft ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for adeft did not run successfully.
  │ exit code: 1
  ╰─> [52 lines of output]
      running install
      /Users/cthoyt/.virtualenvs/indra/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
        warnings.warn(
      running build
      running build_py
      creating build
      creating build/lib.macosx-12-x86_64-3.11
      creating build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/util.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/discover.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/disambiguate.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/recognize.py -> build/lib.macosx-12-x86_64-3.11/adeft
      copying adeft/locations.py -> build/lib.macosx-12-x86_64-3.11/adeft
      creating build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/classify.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      copying adeft/modeling/label.py -> build/lib.macosx-12-x86_64-3.11/adeft/modeling
      creating build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/score/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/score/score.py -> build/lib.macosx-12-x86_64-3.11/adeft/score
      creating build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/download.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      copying adeft/download/__main__.py -> build/lib.macosx-12-x86_64-3.11/adeft/download
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui
      copying adeft/gui/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui
      creating build/lib.macosx-12-x86_64-3.11/adeft/nlp
      copying adeft/nlp/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      copying adeft/nlp/nlp.py -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      copying adeft/gui/ground/__init__.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      copying adeft/gui/ground/ground.py -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground
      running egg_info
      writing manifest file 'adeft.egg-info/SOURCES.txt'
      copying adeft/score/_score.c -> build/lib.macosx-12-x86_64-3.11/adeft/score
      copying adeft/nlp/stopwords.json -> build/lib.macosx-12-x86_64-3.11/adeft/nlp
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      copying adeft/gui/ground/static/ground.css -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      copying adeft/gui/ground/static/scripts.js -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/static
      creating build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/templates
      copying adeft/gui/ground/templates/input.jinja2 -> build/lib.macosx-12-x86_64-3.11/adeft/gui/ground/templates
      running build_ext
      creating build/temp.macosx-12-x86_64-3.11
      creating build/temp.macosx-12-x86_64-3.11/adeft
      creating build/temp.macosx-12-x86_64-3.11/adeft/score
      clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/Users/cthoyt/.virtualenvs/indra/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.11/include/python3.11 -c adeft/score/_score.c -o build/temp.macosx-12-x86_64-3.11/adeft/score/_score.o
      adeft/score/_score.c:209:12: fatal error: 'longintrepr.h' file not found
        #include "longintrepr.h"
                 ^~~~~~~~~~~~~~~
      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: legacy-install-failure

× Encountered error while trying to install package.
╰─> adeft

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

This is a problem because they removed longintrepr.h in python/cpython#28968. It appears that the _score.c file https://github.com/indralab/adeft/blob/e0d882ada0ce81444d5b0a33cfbff33974f5d5c0/adeft/score/_score.c#L1

was generated using an old version of cython (we're on 0.29.32 now) so I think the fix is to regenerate it.
@steppi
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steppi commented Oct 28, 2022

Thanks @cthoyt! Hopefully I’ll have time to recompile tonight.

@cthoyt
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cthoyt commented Oct 28, 2022

Thanks Albert! If it's possible to leave a few notes on how this is done it would be really insightful for the future :)

@steppi steppi mentioned this issue Nov 5, 2022
Merged
@steppi steppi closed this as completed in #72 Nov 5, 2022
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Add Python3.11 support steppi/adeft
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@steppi @cthoyt