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Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
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Forceatlas2 does not support Python 3.9+ (PAGA implementation) #2067

Closed Zethson closed 1 month ago

Zethson commented 2 years ago

Hi,

didn't see this being tracked here yet. Hope I didn't miss it. Our PAGA implementation uses Forceatlas2, but unfortunately Forceatlas2 is not really maintained anymore and it does not yet support Python 3.9+. Well the latest release at least. The master branch may work.

Sources:

@gokceneraslan I saw that you contributed some code. Do you still have a connection to the maintainer?

ivirshup commented 2 years ago

Trying to figure out how much of a problem this is, how much does PAGA use forceatlas2?

From my skimming of the code: it's optional – the default is to use one of the igraph layout algorithms

Zethson commented 2 years ago

Trying to figure out how much of a problem this is, how much does PAGA use forceatlas2?

From my skimming of the code: it's optional – the default is to use one of the igraph layout algorithms

Options I see:

  1. We fork forceatlas2 and create our own release with its own name. Not a fan of this.
  2. Somebody finds a way to contact the author. I already failed through several channels. No response.
  3. We remove support for forceatlas2 since we have another option.

@ivirshup how comparable are the forceatlas2 and the igraph implementations when it comes to results? Do you have any idea?

ivirshup commented 2 years ago

We remove support for forceatlas2 since we have another option.

I would lean towards this, and just deprecating it.

how comparable are the forceatlas2 and the igraph implementations when it comes to results? Do you have any idea?

I don't know. @falexwolf would probably know better.

falexwolf commented 2 years ago

I think it's fine to remove support for forceatlas!

I don't think differences between these implementations will be dramatic. They're likely not measurable.

Zethson commented 2 years ago

I was eventually able to contact the maintainer and he's looking into making a new release. Will see what happens. Nevertheless, it might not be a bad idea to simplify the code and to only support igraph.

transcriptomics commented 2 years ago

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$
Zethson commented 5 months ago

Someone fixed these issues in https://pypi.org/project/fa2-modified/ but I doubt that we want to move to that.

AminAlam commented 2 months ago

@Zethson Many users have problems with the old fa2 used in Scapy, so I believe it makes sense to move to fa2_modified. I've applied necessary changes to move to fa2_modified In #3220.

flying-sheep commented 2 months ago

It’s on conda-forge, so it’s an option!