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Release a new version #35

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jjacobelli opened this issue Aug 20, 2021 · 1 comment
Closed

Release a new version #35

jjacobelli opened this issue Aug 20, 2021 · 1 comment

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@jjacobelli
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jjacobelli commented Aug 20, 2021 •
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Hi,

I'm currently trying to use forceatlas2 from conda-forge with python3.9 but the build is failing because it's using the version 0.3.5 (recipe and logs). The build from master is working for python3.9. It would be nice if we could have a new release so we can bump the version on conda-forge and so we should be able to publish conda package for python3.9.

Let me know if I can help with anything!

Thank you
@Zethson Zethson mentioned this issue Dec 5, 2021
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@transcriptomics
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I am using the latest M1 macbook pro with python 3.10.3.

For some reason if you clone the repository then compile it works in python 3.9+
I cannot explain why the release tarball has issues. As per some other documentation, it is because tp_print has been removed from type objects for python 3.9+. See below.

So, if you clone the repository using git and then install it works! (I am sure there is an explanation)

test@mac ~/PythonPackages/forceatlas2$ git pull
Already up to date.
test@mac ~/PythonPackages/forceatlas2$ pip3 install . --user
Processing /Users/test/PythonPackages/forceatlas2
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (1.21.5)
Requirement already satisfied: scipy in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (1.8.0)
Requirement already satisfied: tqdm in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (4.63.0)
Building wheels for collected packages: fa2
  Building wheel for fa2 (setup.py) ... done
  Created wheel for fa2: filename=fa2-0.3.5-cp310-cp310-macosx_12_0_x86_64.whl size=155419 sha256=23d907bfec5df0e9d0d522865d1c288b1f8894134bd61b6c5a02467128dfd102
  Stored in directory: /private/var/folders/0s/67yn6b6n3lx4882xx_86ps2m0000gp/T/pip-ephem-wheel-cache-i69s_t3j/wheels/51/1c/a5/5a9ef4f0bc9387d300190bc15adbb98dbda9d90c6da9c2da04
Successfully built fa2
Installing collected packages: fa2
Successfully installed fa2-0.3.5 
test@mac ~/PythonPackages/forceatlas2$

However, if you try to install the release version you get an error:

test@mac ~/PythonPackages$ wget https://github.com/bhargavchippada/forceatlas2/archive/refs/tags/v0.3.5.tar.gz
--2022-03-24 02:54:21--  https://github.com/bhargavchippada/forceatlas2/archive/refs/tags/v0.3.5.tar.gz
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/bhargavchippada/forceatlas2/tar.gz/refs/tags/v0.3.5 [following]
--2022-03-24 02:54:21--  https://codeload.github.com/bhargavchippada/forceatlas2/tar.gz/refs/tags/v0.3.5
Resolving codeload.github.com (codeload.github.com)... 140.82.114.9
Connecting to codeload.github.com (codeload.github.com)|140.82.114.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/x-gzip]
Saving to: ‘v0.3.5.tar.gz’

v0.3.5.tar.gz                                            [  <=>                                                                                                               ] 434.98K  1.03MB/s    in 0.4s    

2022-03-24 02:54:22 (1.03 MB/s) - ‘v0.3.5.tar.gz’ saved [445420]

test@mac ~/PythonPackages$ tar xvf v0.3.5.tar.gz 
x forceatlas2-0.3.5/
x forceatlas2-0.3.5/.gitignore
x forceatlas2-0.3.5/LICENSE
x forceatlas2-0.3.5/MANIFEST.in
x forceatlas2-0.3.5/README.md
x forceatlas2-0.3.5/examples/
x forceatlas2-0.3.5/examples/forceatlas2-layout.ipynb
x forceatlas2-0.3.5/examples/geometric_graph.png
x forceatlas2-0.3.5/examples/grid_graph.png
x forceatlas2-0.3.5/fa2/
x forceatlas2-0.3.5/fa2/__init__.py
x forceatlas2-0.3.5/fa2/fa2util.c
x forceatlas2-0.3.5/fa2/fa2util.pxd
x forceatlas2-0.3.5/fa2/fa2util.py
x forceatlas2-0.3.5/fa2/forceatlas2.py
x forceatlas2-0.3.5/setup.py
test@mac ~/PythonPackages$ cd forceatlas2-0.3.5/
test@mac ~/PythonPackages/forceatlas2-0.3.5$ pip3 install . --user
Processing /Users/test/PythonPackages/forceatlas2-0.3.5
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (1.21.5)
Requirement already satisfied: scipy in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (1.8.0)
Requirement already satisfied: tqdm in /Users/test/.local/lib/python3.10/site-packages (from fa2==0.3.5) (4.63.0)
Building wheels for collected packages: fa2
  Building wheel for fa2 (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [214 lines of output]
      Installing fa2 package (fastest forceatlas2 python implementation)
      
      >>>> Cython is installed?
      Yes
      
      >>>> Starting to install!
      
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-12.3-x86_64-3.10
      creating build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/fa2util.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/__init__.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/forceatlas2.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      running egg_info
      creating fa2.egg-info
      writing fa2.egg-info/PKG-INFO
      writing dependency_links to fa2.egg-info/dependency_links.txt
      writing requirements to fa2.egg-info/requires.txt
      writing top-level names to fa2.egg-info/top_level.txt
      writing manifest file 'fa2.egg-info/SOURCES.txt'
      reading manifest file 'fa2.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      adding license file 'LICENSE'
      writing manifest file 'fa2.egg-info/SOURCES.txt'
      copying fa2/fa2util.c -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/fa2util.pxd -> build/lib.macosx-12.3-x86_64-3.10/fa2
      running build_ext
      skipping 'fa2/fa2util.c' Cython extension (up-to-date)
      building 'fa2.fa2util' extension
      creating build/temp.macosx-12.3-x86_64-3.10
      creating build/temp.macosx-12.3-x86_64-3.10/fa2
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/test/.pyenv/versions/3.10.3/include/python3.10 -c fa2/fa2util.c -o build/temp.macosx-12.3-x86_64-3.10/fa2/fa2util.o
      fa2/fa2util.c:10939:33: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Node.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:10947:33: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Edge.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:10960:35: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Region.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:12133:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:22: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      12 warnings and 3 errors 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 fa2
  Running setup.py clean for fa2
Failed to build fa2
Installing collected packages: fa2
  Attempting uninstall: fa2
    Found existing installation: fa2 0.3.5
    Uninstalling fa2-0.3.5:
      Successfully uninstalled fa2-0.3.5
  Running setup.py install for fa2 ... error
  error: subprocess-exited-with-error
  
  × Running setup.py install for fa2 did not run successfully.
  │ exit code: 1
  ╰─> [212 lines of output]
      Installing fa2 package (fastest forceatlas2 python implementation)
      
      >>>> Cython is installed?
      Yes
      
      >>>> Starting to install!
      
      running install
      running build
      running build_py
      creating build
      creating build/lib.macosx-12.3-x86_64-3.10
      creating build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/fa2util.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/__init__.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/forceatlas2.py -> build/lib.macosx-12.3-x86_64-3.10/fa2
      running egg_info
      writing fa2.egg-info/PKG-INFO
      writing dependency_links to fa2.egg-info/dependency_links.txt
      writing requirements to fa2.egg-info/requires.txt
      writing top-level names to fa2.egg-info/top_level.txt
      reading manifest file 'fa2.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      adding license file 'LICENSE'
      writing manifest file 'fa2.egg-info/SOURCES.txt'
      copying fa2/fa2util.c -> build/lib.macosx-12.3-x86_64-3.10/fa2
      copying fa2/fa2util.pxd -> build/lib.macosx-12.3-x86_64-3.10/fa2
      running build_ext
      skipping 'fa2/fa2util.c' Cython extension (up-to-date)
      building 'fa2.fa2util' extension
      creating build/temp.macosx-12.3-x86_64-3.10
      creating build/temp.macosx-12.3-x86_64-3.10/fa2
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Users/test/.pyenv/versions/3.10.3/include/python3.10 -c fa2/fa2util.c -o build/temp.macosx-12.3-x86_64-3.10/fa2/fa2util.o
      fa2/fa2util.c:10939:33: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Node.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:10947:33: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Edge.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:10960:35: error: no member named 'tp_print' in 'struct _typeobject'
        __pyx_type_3fa2_7fa2util_Region.tp_print = 0;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
      fa2/fa2util.c:12133:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:22: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                           ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12133:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                          (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                         ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                               ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
            PyUnicode_WSTR_LENGTH(op) :                    \
            ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
            ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
                   ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      fa2/fa2util.c:12149:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
                              (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
                                                                ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
             PyUnicode_WSTR_LENGTH(op)))
             ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
      #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                        ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
      Py_DEPRECATED(3.3)
      ^
      /Users/test/.pyenv/versions/3.10.3/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
      #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
                                                           ^
      12 warnings and 3 errors 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.
  WARNING: No metadata found in /Users/test/.local/lib/python3.10/site-packages
  Rolling back uninstall of fa2
  Moving to /Users/test/.local/lib/python3.10/site-packages/fa2-0.3.5.dist-info/
   from /Users/test/.local/lib/python3.10/site-packages/~a2-0.3.5.dist-info
  Moving to /Users/test/.local/lib/python3.10/site-packages/fa2/
   from /Users/test/.local/lib/python3.10/site-packages/~a2
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> fa2

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
test@mac ~/PythonPackages/forceatlas2-0.3.5$

@ojdo ojdo mentioned this issue Apr 19, 2022
Open
@simonvw95 simonvw95 mentioned this issue Jan 18, 2023
Open
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@jjacobelli @transcriptomics