Problem installing fa2 on Python3.9 #34
Comments
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I have the same issue with Python 3.9 on Ubuntu 18.04...any luck? |
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I'm afraid not. |
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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 |
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I also had issues, for the same reason. I have... My hack prepended this section into fa2util.c and totally guessed how to avoid GET_SIZE completely... beefing up code around Lines 427 to 453 in da3ece0 |
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Oh. My cython 0.29.26 got it wrong. |
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Have the same issue with python 3.9.1. Fixed with rolling back to |
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Just in case someone does not stumble over the workaround documented in #35: the current main branch compiles under Python 3.10, so: 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 It is really just the outdated last release, not a lack of maintenance of the codebase itself. |
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Bumping this as still being an issue on Python 3.9.15 |
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@ojdo what is ther version of Cython you are using and what is the meaining of below line : With your steps also, I am not able to install the library. I am getting the below errors : Let us know about what needs to be done. |
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Here is the issue to be precise : |
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I'm having the same issue of unknonw file type .pxd here with Python 3.10.9 and Cython 3.0.0. |
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Getting the same error too. Not only in Centos 8 but also in Windows 11. Cython 3.0.0 and different versions of python have been tried, including python 3.7.10 and python 3.10.8. All failed. Error messages are shown by the following: × python setup.py bdist_wheel did not run successfully. note: This error originates from a subprocess, and is likely not a problem with pip. × Running setup.py install for fa2 did not run successfully. note: This error originates from a subprocess, and is likely not a problem with pip. × Encountered error while trying to install package. note: This is an issue with the package mentioned above, not pip. |
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I'm getting a similar set of errors on Python 3.10.12 and a bunch of deprecation warnings |
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Same error with Python 3.10 and Cython 3.0. |
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I managed to solve this issue with modifying the setup.py file: |
Switching off fa2/fautil.pxd seems to be a partial solution. This is what I get when run scanpy: Complete solution still needed |
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@eugbrenner You still need to have Cython installed indeed. The modification I made is to make it work with newer versions of Cython |
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@AminAlam. You are right, I did no have cython installed in this venv. Just fixed it. But still have this message |
@eugbrenner This is not happening for me. In general, having Cython should be enough for compiling fa2util.py to fa2util.c. Can you please send the output of the this command |
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Hi, @AminAlam , What I did from the very begining is:
These venvs are:
Although, I managed to install fa2 on all these venvs without errors and warnings, running 'import fa2' results in the same warning in all these venvs. This warning says ' Warning: uncompiled fa2util module. Compile with cython for a 10-100x speed boost.' Is there anything else I can do to speed up fa2 calculations? |
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@eugbrenner Use the setup.py of this commit, and install it using |
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@AminAlam Thanks for your reply. I've done everything that you advised and managed to install fa2_modified into python3.9.17 + cython-3.0.10 and python3.8.13 + cython-3.0.0 virtual environments. Nevertheless, I still get 'Warning: uncompiled fa2util module. Compile with cython for a 10-100x speed boost.' when importing fa2_module at either venv. Furthermore, since I need fa2 to use with scanpy, I get "WARNING: Package 'fa2' is not installed, falling back to layout 'fr'. To use the faster and better ForceAtlas2 layout, install package 'fa2' ( Here is my build directory 'ls -R' output: ./bdist.linux-x86_64: ./lib.linux-x86_64-cpython-38: ./lib.linux-x86_64-cpython-38/fa2_modified: ./lib.linux-x86_64-cpython-39: ./lib.linux-x86_64-cpython-39/fa2_modified: ./temp.linux-x86_64-cpython-38: ./temp.linux-x86_64-cpython-38/fa2_modified: ./temp.linux-x86_64-cpython-39: ./temp.linux-x86_64-cpython-39/fa2_modified: |
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@eugbrenner Please use the codes in |
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@eugbrenner I've changed fa2_modified PyPi setup to ensure it will compile "fa2util.pxd" to "fa2util.c". Please install it using |
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@AminAlam Version 0.3.9 can be installed and run on python3.9.17 + cython-3.0.10 fine! Thank you. Do you have any suggestions to make scanpy use it instead fa2? |
Nice! Happy to hear it's working for you. Regarding your problem: I suggest to change the source code of scapy to make it use fa2_modified instead of fa2. However, I've checked scanpy source code and it seems like they are not using fa2 module. |
It seems that fa2 is not compatible with Python3.9
`ERROR: Command errored out with exit status 1:
command: /usr/local/opt/[email protected]/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)
ERROR: Command errored out with exit status 1: /usr/local/opt/[email protected]/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.
`
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