Problem installing fa2 on Python3.9

[satrio-yudhoatmojo]

It seems that fa2 is not compatible with Python3.9

`ERROR: Command errored out with exit status 1:
command: /usr/local/opt/python@3.9/bin/python3.9 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-install-345a9yt5/fa2_127e2c475c0344ff93462856df90b805/setup.py'"'"'; file='"'"'/private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-install-345a9yt5/fa2_127e2c475c0344ff93462856df90b805/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-record-tehayj72/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.9/fa2
cwd: /private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-install-345a9yt5/fa2_127e2c475c0344ff93462856df90b805/
Complete output (214 lines):
Installing fa2 package (fastest forceatlas2 python implementation)

>>>> Cython is installed?
Cython is not installed; using pre-generated C files if available
Please install Cython first and try again if you face any installation problems

>>>> Are pre-generated C files available?
Yes

>>>> Starting to install!

running install
running build
running build_py
creating build
creating build/lib.macosx-10.15-x86_64-3.9
creating build/lib.macosx-10.15-x86_64-3.9/fa2
copying fa2/fa2util.py -> build/lib.macosx-10.15-x86_64-3.9/fa2
copying fa2/__init__.py -> build/lib.macosx-10.15-x86_64-3.9/fa2
copying fa2/forceatlas2.py -> build/lib.macosx-10.15-x86_64-3.9/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'
writing manifest file 'fa2.egg-info/SOURCES.txt'
copying fa2/fa2util.c -> build/lib.macosx-10.15-x86_64-3.9/fa2
copying fa2/fa2util.pxd -> build/lib.macosx-10.15-x86_64-3.9/fa2
running build_ext
building 'fa2.fa2util' extension
creating build/temp.macosx-10.15-x86_64-3.9
creating build/temp.macosx-10.15-x86_64-3.9/fa2
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c fa2/fa2util.c -o build/temp.macosx-10.15-x86_64-3.9/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 :
                     ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
      PyUnicode_WSTR_LENGTH(op) :                    \
      ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                     ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
      ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
             ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                     ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
       PyUnicode_WSTR_LENGTH(op)))
       ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                   ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
      PyUnicode_WSTR_LENGTH(op) :                    \
      ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                   ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
      ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
             ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                   ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
       PyUnicode_WSTR_LENGTH(op)))
       ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                         ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
      PyUnicode_WSTR_LENGTH(op) :                    \
      ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                         ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
      ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
             ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                         ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
       PyUnicode_WSTR_LENGTH(op)))
       ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                          ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
      PyUnicode_WSTR_LENGTH(op) :                    \
      ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                          ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
      ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
             ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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 :
                                                          ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
       PyUnicode_WSTR_LENGTH(op)))
       ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
                                  ^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/usr/local/Cellar/python@3.9/3.9.1_3/Frameworks/Python.framework/Versions/3.9/include/python3.9/pyport.h:508:54: 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
----------------------------------------

ERROR: Command errored out with exit status 1: /usr/local/opt/python@3.9/bin/python3.9 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-install-345a9yt5/fa2_127e2c475c0344ff93462856df90b805/setup.py'"'"'; file='"'"'/private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-install-345a9yt5/fa2_127e2c475c0344ff93462856df90b805/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/tb/yb5np6tx5tg852_7ktrz3qy40000gn/T/pip-record-tehayj72/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.9/fa2 Check the logs for full command output.
`

[msalaciak]

I have the same issue with Python 3.9 on Ubuntu 18.04...any luck?

[satrio-yudhoatmojo]

I'm afraid not.

[emigre459]

bump on this, anything anyone has found to correct? I'm afraid the HoloViews/Datashader implementations aren't very fast, so I'm really hoping to use this one

[kruus]

I also had issues, for the same reason.
I hacked around it by avoiding calls to the offending function.
I was able to run examples/forceatlas2-layout.ipynb completely under python 3.9.7
(well after also removing some networkx with_labels argument in one line of the notebook)

I have...

Python version #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021
sys.platform='linux'
3.9.7

My hack prepended this section into fa2util.c and totally guessed how to avoid GET_SIZE completely...

#if PY_VERSION_HEX > 0x03090000 && defined(PyUnicode_KIND)
  #define CYTHON_PEP393_ENABLED 1
  #define __Pyx_PyUnicode_READY(op)       (1)
  #define __Pyx_PyUnicode_GET_LENGTH(u)   PyUnicode_GET_LENGTH(u)
  #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
  #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u)   PyUnicode_MAX_CHAR_VALUE(u)
  #define __Pyx_PyUnicode_KIND(u)         PyUnicode_KIND(u)
  #define __Pyx_PyUnicode_DATA(u)         PyUnicode_DATA(u)
  #define __Pyx_PyUnicode_READ(k, d, i)   PyUnicode_READ(k, d, i)
  #define __Pyx_PyUnicode_WRITE(k, d, i, ch)  PyUnicode_WRITE(k, d, i, ch)
  #define __Pyx_PyUnicode_IS_TRUE(u)      PyUnicode_GET_LENGTH(u)
  #define PyUnicode_GET_SIZE(u)           PyUnicode_GET_LENGTH(u)
#elif ...  as before ... PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)

beefing up code around

forceatlas2/fa2/fa2util.c

Lines 427 to 453 in da3ece0

	#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
	#define CYTHON_PEP393_ENABLED 1
	#define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\
	0 : _PyUnicode_Ready((PyObject *)(op)))
	#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
	#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
	#define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u)
	#define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
	#define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
	#define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
	#define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch)
	#define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u)))
	#else
	#define CYTHON_PEP393_ENABLED 0
	#define PyUnicode_1BYTE_KIND 1
	#define PyUnicode_2BYTE_KIND 2
	#define PyUnicode_4BYTE_KIND 4
	#define __Pyx_PyUnicode_READY(op) (0)
	#define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
	#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
	#define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111)
	#define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
	#define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
	#define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
	#define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch)
	#define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u))
	#endif

[kruus]

Oh. My cython 0.29.26 got it wrong.
(No idea when cython will fully support python 3.9+)

[vasiliy0s]

Have the same issue with python 3.9.1. Fixed with rolling back to 3.8.13 with my virtual env.

[ojdo]

Just in case someone does not stumble over the workaround documented in #35: the current main branch compiles under Python 3.10, so:

git clone https://github.com/bhargavchippada/forceatlas2
cd forceatlas2
# having build dependencies installed
pip install . --user

compiles and installs fine also under current Python environments. It is really just the outdated last release, not a lack of maintenance of the codebase itself.

[dburkhardt]

Bumping this as still being an issue on Python 3.9.15

[Sriharsha-hatwar]

@ojdo what is ther version of Cython you are using and what is the meaining of below line :

# having build dependencies installed

With your steps also, I am not able to install the library. I am getting the below errors :

error: unknown file type '.pxd' (from 'fa2/fa2util.pxd')

Let us know about what needs to be done.

[Sriharsha-hatwar]

Here is the issue to be precise :

Using cached tqdm-4.66.1-py3-none-any.whl (78 kB)
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
  ╰─> [33 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-11.1-arm64-cpython-310
      creating build/lib.macosx-11.1-arm64-cpython-310/fa2
      copying fa2/fa2util.py -> build/lib.macosx-11.1-arm64-cpython-310/fa2
      copying fa2/forceatlas2.py -> build/lib.macosx-11.1-arm64-cpython-310/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'
      warning: no files found matching 'fa2/fa2util.c'
      adding license file 'LICENSE'
      writing manifest file 'fa2.egg-info/SOURCES.txt'
      copying fa2/fa2util.pxd -> build/lib.macosx-11.1-arm64-cpython-310/fa2
      running build_ext
      Compiling fa2/fa2util.py because it changed.
      [1/1] Cythonizing fa2/fa2util.py
      building 'fa2.fa2util' extension
      error: unknown file type '.pxd' (from 'fa2/fa2util.pxd')
      [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
ERROR: Could not build wheels for fa2, which is required to install pyproject.toml-based projects